Introduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" This NASA image is a composite of several satellite-based views of Earth. To make the whole-Earth image, NASA scientists combine observations of different parts of the planet. (credit: NASA/GSFC/NOAA/USGS) 

Viewed from space, Earth offers no clues about the diversity of life it harbors. The first forms of life on Earth are thought be microorganisms that existed for billions of years in the ocean before plants and animals appeared. The mammals, birds, and flowers that we see in modern times are mostly recent species, originating 130 to 200 million years ago. In fact, only in the last 200,000 years have humans started looking like we do today. 

Organisms evolve in response to each other. One of the best examples is disease causing organisms, which have to adapt to overcome the defenses of the organisms they infect. One such organism that has evolved to specialize in infection in humans is Plasmodium , the organism that causes malaria. Biologists use the process of science to learn about the world and the organisms living in it. For example, people have suspected for quite some time that people with blood type O are less likely to die from severe malaria. Now, a team of scientists have been able to explain why. By examining data from several experiments, and by using both inductive and deductive reasoning, the scientists concluded that A and B type blood reacts with a protein excreted by Plasmodium . This reaction causes severe illness. However, type O blood does not react with the protein. You can read more about the response of type A and B blood groups to infection by Plasmodium . 

Introduce the concept of unity and diversity of life. There are so many varieties of organisms and, yet, the cell is the basic unit of life. The fundamental structures and life processes of cells are similar; but, how these cells are utilized in different organisms is hugely varied and reflects adaptation of the organism to its environment. The many differences between species accumulated over long periods of time. Students are often unfamiliar with geological time scales. 

The malaria example was chosen because malaria has been one of the most pervasive and widespread human disease. Therefore, through much of human history, malaria has been a strong force of natural selection on humans. Human genetics has evolved in response to this selection pressure, as with the example of resistance among O-type blood groups described in the introduction. Further examples can also be found here .The Science of Biology The Science of Biology 

In this section, you will explore the following questions: What are the characteristics shared by the natural sciences? What are the steps of the scientific method? Connection for AP courses 

Biology is the science that studies living organisms and their interactions with one another and with their environment. The process of science attempts to describe and understand the nature of the universe by rational means. Science has many fields; those fields related to the physical world, including biology, are considered natural sciences. All of the natural sciences follow the laws of chemistry and physics. For example, when studying biology, you must remember living organisms obey the laws of thermodynamics while using free energy and matter from the environment to carry out life processes that are explored in later chapters, such as metabolism and reproduction. 

Two types of logical reasoning are used in science: inductive reasoning and deductive reasoning. Inductive reasoning uses particular results to produce general scientific principles. Deductive reasoning uses logical thinking to predict results by applying scientific principles or practices. The scientific method is a step-by-step process that consists of: making observations, defining a problem, posing hypotheses, testing these hypotheses by designing and conducting investigations, and drawing conclusions from data and results. Scientists then communicate their results to the scientific community. Scientific theories are subject to revision as new information is collected. 

The content presented in this section supports the Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The Learning Objectives merge Essential Knowledge content with one or more of the seven Science Practices. These objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP Exam questions. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models Learning Objectives 2.3 The student is able to predict how changes in free energy availability affect organisms, populations and ecosystems. 

Illustrate uses of the scientific method in class. Divide students in groups of four or five and ask them to design experiments to test the existence of connections they have wondered about. Help them decide if they have a working hypothesis that can be tested and falsified. Give examples of hypotheses that are not falsifiable because they are based on subjective assessments. They are neither observable nor measurable. For example, birds like classical music is based on a subjective assessment. Ask if this hypothesis can be modified to become a testable hypothesis. Stress the need for controls and provide examples such as the use of placebos in pharmacology. 

Biology is not a collection of facts to be memorized. Biological systems follow the law of physics and chemistry. Give as an example gas laws in chemistry and respiration physiology. Many students come with a 19th century view of natural sciences; each discipline is in its own sphere. Give as an example, bioinformatics which uses organism biology, chemistry, and physics to label DNA with light emitting reporter molecules (Next Generation sequencing). These molecules can then be scanned by light-sensing machinery, allowing huge amounts of information to be gathered on their DNA. Bring to their attention the fact that the analysis of these data is an application of mathematics and computer science. 

For more information about next generation sequencing, check out this informative review . Formerly called blue-green algae, these (a) cyanobacteria, shown here at 300x magnification under a light microscope, are some of Earth s oldest life forms. These (b) stromatolites along the shores of Lake Thetis in Western Australia are ancient structures formed by the layering of cyanobacteria in shallow waters. (credit a: modification of work by NASA; credit b: modification of work by Ruth Ellison; scale-bar data from Matt Russell) 

What is biology? In simple terms, biology is the study of living organisms and their interactions with one another and their environments. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the microscopic or submicroscopic view of a cell to ecosystems and the whole living planet ( [link] ). Listening to the daily news, you will quickly realize how many aspects of biology are discussed every day. For example, recent news topics include Escherichia coli ( [link] ) outbreaks in spinach and Salmonella contamination in peanut butter. Other subjects include efforts toward finding a cure for AIDS, Alzheimer s disease, and cancer. On a global scale, many researchers are committed to finding ways to protect the planet, solve environmental issues, and reduce the effects of climate change. All of these diverse endeavors are related to different facets of the discipline of biology. Escherichia coli ( E. coli ) bacteria, seen in this scanning electron micrograph, are normal residents of our digestive tracts that aid in the absorption of vitamin K and other nutrients. However, virulent strains are sometimes responsible for disease outbreaks. (credit: Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU) The Process of Science 

Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science (from the Latin scientia , meaning knowledge ) can be defined as knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method. It becomes clear from this definition that the application of the scientific method plays a major role in science. The scientific method is a method of research with defined steps that include experiments and careful observation. 

The steps of the scientific method will be examined in detail later, but one of the most important aspects of this method is the testing of hypotheses by means of repeatable experiments. A hypothesis is a suggested explanation for an event, which can be tested. Although using the scientific method is inherent to science, it is inadequate in determining what science is. This is because it is relatively easy to apply the scientific method to disciplines such as physics and chemistry, but when it comes to disciplines like archaeology, psychology, and geology, the scientific method becomes less applicable as it becomes more difficult to repeat experiments. 

These areas of study are still sciences, however. Consider archeology even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, an archeologist can hypothesize that an ancient culture existed based on finding a piece of pottery. Further hypotheses could be made about various characteristics of this culture, and these hypotheses may be found to be correct or false through continued support or contradictions from other findings. A hypothesis may become a verified theory. A theory is a tested and confirmed explanation for observations or phenomena. Science may be better defined as fields of study that attempt to comprehend the nature of the universe. Natural Sciences 

What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Or, maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics ( [link] ). However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences . Thus, a museum of natural sciences might contain any of the items listed above. The diversity of scientific fields includes astronomy, biology, computer science, geology, logic, physics, chemistry, mathematics, and many other fields. (credit: Image Editor /Flickr) 

There is no complete agreement when it comes to defining what the natural sciences include, however. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences , which study living things and include biology, and physical sciences , which study nonliving matter and include astronomy, geology, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on both life and physical sciences and are interdisciplinary. Natural sciences are sometimes referred to as hard science because they rely on the use of quantitative data; social sciences that study society and human behavior are more likely to use qualitative assessments to drive investigations and findings. 

Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology, however, focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things. For example, botanists explore plants, while zoologists specialize in animals. Scientific Reasoning 

One thing is common to all forms of science: an ultimate goal to know. Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical thinking: inductive reasoning and deductive reasoning. 

Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative or quantitative, and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies provide an example. In this type of research, many live brains are observed while people are doing a specific activity, such as viewing images of food. The part of the brain that lights up during this activity is then predicted to be the part controlling the response to the selected stimulus, in this case, images of food. The lighting up of the various areas of the brain is caused by excess absorption of radioactive sugar derivatives by active areas of the brain. The resultant increase in radioactivity is observed by a scanner. Then, researchers can stimulate that part of the brain to see if similar responses result. 

Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reason, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. Studies in climate change can illustrate this type of reasoning. For example, scientists may predict that if the climate becomes warmer in a particular region, then the distribution of plants and animals should change. These predictions have been made and tested, and many such changes have been found, such as the modification of arable areas for agriculture, with change based on temperature averages. 

Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science , which is usually inductive, aims to observe, explore, and discover, while hypothesis-based science , which is usually deductive, begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, and most scientific endeavors combine both approaches. The fuzzy boundary becomes apparent when thinking about how easily observation can lead to specific questions. For example, a gentleman in the 1940s observed that the burr seeds that stuck to his clothes and his dog s fur had a tiny hook structure. On closer inspection, he discovered that the burrs gripping device was more reliable than a zipper. He eventually developed a company and produced the hook-and-loop fastener popularly known today as Velcro. Descriptive science and hypothesis-based science are in continuous dialogue. The Scientific Method 

Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England s Sir Francis Bacon (1561 1626) ( [link] ), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost all fields of study as a logical, rational problem-solving method. Sir Francis Bacon (1561 1626) is credited with being the first to define the scientific method. (credit: Paul van Somer) 

The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: Why is the classroom so warm? Proposing a Hypothesis 

Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, The classroom is warm because no one turned on the air conditioning. But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, The classroom is warm because there is a power failure, and so the air conditioning doesn t work. 

Once a hypothesis has been selected, the student can make a prediction. A prediction is similar to a hypothesis but it typically has the format If . . . then . . . . For example, the prediction for the first hypothesis might be, If the student turns on the air conditioning, then the classroom will no longer be too warm. Testing a Hypothesis 

A valid hypothesis must be testable. It should also be falsifiable , meaning that it can be disproven by experimental results. Importantly, science does not claim to prove anything because scientific understandings are always subject to modification with further information. This step openness to disproving ideas is what distinguishes sciences from non-sciences. The presence of the supernatural, for instance, is neither testable nor falsifiable. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. The control group contains every feature of the experimental group except it is not given the manipulation that is hypothesized about. Therefore, if the results of the experimental group differ from the control group, the difference must be due to the hypothesized manipulation, rather than some outside factor. Look for the variables and controls in the examples that follow. To test the first hypothesis, the student would find out if the air conditioning is on. If the air conditioning is turned on but does not work, there should be another reason, and this hypothesis should be rejected. To test the second hypothesis, the student could check if the lights in the classroom are functional. If so, there is no power failure and this hypothesis should be rejected. Each hypothesis should be tested by carrying out appropriate experiments. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid ( see this figure ). Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected. 

While this warm classroom example is based on observational results, other hypotheses and experiments might have clearer controls. For instance, a student might attend class on Monday and realize she had difficulty concentrating on the lecture. One observation to explain this occurrence might be, When I eat breakfast before class, I am better able to pay attention. The student could then design an experiment with a control to test this hypothesis. 

In hypothesis-based science, specific results are predicted from a general premise. This type of reasoning is called deductive reasoning: deduction proceeds from the general to the particular. But the reverse of the process is also possible: sometimes, scientists reach a general conclusion from a number of specific observations. This type of reasoning is called inductive reasoning, and it proceeds from the particular to the general. Inductive and deductive reasoning are often used in tandem to advance scientific knowledge ( see this figure ) Think About It 

Almost all plants use water, carbon dioxide, and energy from the sun to make sugars. Think about what would happen to plants that don t have sunlight as an energy source or sufficient water. What would happen to organisms that depend on those plants for their own survival? 

Make a prediction about what would happen to the organisms living in a rain forest if 50% of its trees were destroyed. How would you test your prediction? 

Use this example as a model to make predictions. Emphasize there is no rigid scientific method scheme. Active science is a combination of observations and measurement. Offer the example of ecology where the conventional scientific method is not always applicable because researchers cannot always set experiments in a laboratory and control all the variables. Possible answers: Ask students: What happens to plants if light intensity is low or if it is dark? The answer is that plants will soon die if they cannot have a source of energy. Ask students: What happens if plants have no water? The common answers will vary, from Plants dry out to Plants die which is the same end results. Without plants, what will happen to animals that feed on plants? The possible answers are animals will starve or animals will move away What happens to those animals who feed on the animals that feed on those animals? They will either die or migrate following the food trail. This is a good opportunity to show that the ecosystem is interconnected and extend the concepts to producers (the plants that absorb light energy), the primary consumers (herbivores), and secondary consumers (predators). 

Destruction of the rain forest affects the trees, the animals which feed on the vegetation, take shelter on the trees, and large predators which feed on smaller animals. Furthermore, because the trees positively affect rain through massive evaporation and condensation of water vapor, drought follows deforestation. 

Tell students a similar experiment on a grand scale may have happened in the past and introduce the next activity What killed the dinosaurs? 

Some predictions can be made and later observations can support or disprove the prediction. 

Ask, what killed the dinosaurs? Explain many scientists point to a massive asteroid crashing in the Yucatan peninsula in Mexico. One of the effects was the creation of smoke clouds and debris that blocked the Sun, stamped out many plants and, consequently, brought mass extinction. As is common in the scientific community, many other researchers offer divergent explanations. 

Go to this site for a good example of the complexity of scientific method and scientific debate. 

The scientific method consists of a series of well-defined steps. If a hypothesis is not supported by experimental data, a new hypothesis can be proposed. 

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Scientists use two types of reasoning, inductive and deductive reasoning, to advance scientific knowledge. As is the case in this example, the conclusion from inductive reasoning can often become the premise for inductive reasoning. 

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The scientific method may seem too rigid and structured. It is important to keep in mind that, although scientists often follow this sequence, there is flexibility. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests. Notice, too, that the scientific method can be applied to solving problems that aren t necessarily scientific in nature. Two Types of Science: Basic Science and Applied Science 

The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or to bettering our lives? This question focuses on the differences between two types of science: basic science and applied science. 

Basic science or pure science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge s sake, though this does not mean that, in the end, it may not result in a practical application. 

In contrast, applied science or technology, aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster ( [link] ). In applied science, the problem is usually defined for the researcher. After Hurricane Ike struck the Gulf Coast in 2008, the U.S. Fish and Wildlife Service rescued this brown pelican. Thanks to applied science, scientists knew how to rehabilitate the bird. (credit: FEMA) 

Some individuals may perceive applied science as useful and basic science as useless. A question these people might pose to a scientist advocating knowledge acquisition would be, What for? A careful look at the history of science, however, reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the wide knowledge foundation generated through basic science. 

One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, DNA makes new copies of itself, shortly before a cell divides. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science would exist. 

Another example of the link between basic and applied research is the Human Genome Project, a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity; an individual s complete collection of genes is his or her genome.) Other less complex organisms have also been studied as part of this project in order to gain a better understanding of human chromosomes. The Human Genome Project ( [link] ) relied on basic research carried out with simple organisms and, later, with the human genome. An important end goal eventually became using the data for applied research, seeking cures and early diagnoses for genetically related diseases. The Human Genome Project was a 13-year collaborative effort among researchers working in several different fields of science. The project, which sequenced the entire human genome, was completed in 2003. (credit: the U.S. Department of Energy Genome Programs (http://genomics.energy.gov)) 

While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity , that is, by means of a fortunate accident or a lucky surprise. Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew on the dish, killing the bacteria. The mold turned out to be Penicillium , and a new antibiotic was discovered. Even in the highly organized world of science, luck when combined with an observant, curious mind can lead to unexpected breakthroughs. Reporting Scientific Work 

Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists when planning, conducting, and analyzing results are all important for scientific research. For this reason, important aspects of a scientist s work are communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that are reviewed by a scientist s colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists. 

A scientific paper is very different from creative writing. Although creativity is required to design experiments, there are fixed guidelines when it comes to presenting scientific results. First, scientific writing must be brief, concise, and accurate. A scientific paper needs to be succinct but detailed enough to allow peers to reproduce the experiments. 

The scientific paper consists of several specific sections introduction, materials and methods, results, and discussion. This structure is sometimes called the IMRaD format. There are usually acknowledgment and reference sections as well as an abstract (a concise summary) at the beginning of the paper. There might be additional sections depending on the type of paper and the journal where it will be published; for example, some review papers require an outline. 

The introduction starts with brief, but broad, background information about what is known in the field. A good introduction also gives the rationale of the work; it justifies the work carried out and also briefly mentions the end of the paper, where the hypothesis or research question driving the research will be presented. The introduction refers to the published scientific work of others and therefore requires citations following the style of the journal. Using the work or ideas of others without proper citation is considered plagiarism . 

The materials and methods section includes a complete and accurate description of the substances used, and the method and techniques used by the researchers to gather data. The description should be thorough enough to allow another researcher to repeat the experiment and obtain similar results, but it does not have to be verbose. This section will also include information on how measurements were made and what types of calculations and statistical analyses were used to examine raw data. Although the materials and methods section gives an accurate description of the experiments, it does not discuss them. 

Some journals require a results section followed by a discussion section, but it is more common to combine both. If the journal does not allow the combination of both sections, the results section simply narrates the findings without any further interpretation. The results are presented by means of tables or graphs, but no duplicate information should be presented. In the discussion section, the researcher will interpret the results, describe how variables may be related, and attempt to explain the observations. It is indispensable to conduct an extensive literature search to put the results in the context of previously published scientific research. Therefore, proper citations are included in this section as well. 

Finally, the conclusion section summarizes the importance of the experimental findings. While the scientific paper almost certainly answered one or more scientific questions that were stated, any good research should lead to more questions. Therefore, a well-done scientific paper leaves doors open for the researcher and others to continue and expand on the findings. 

Review articles do not follow the IMRAD format because they do not present original scientific findings, or primary literature; instead, they summarize and comment on findings that were published as primary literature and typically include extensive reference sections. Section Summary 

Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part by rational means. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences. 

Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems. 

Two types of logical reasoning are used in science. Inductive reasoning uses particular results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread throughout scientific research is the use of the scientific method, a step-based process that consists of making observations, defining a problem, posing hypotheses, testing these hypotheses, and drawing one or more conclusions. The testing uses proper controls. Scientists present their results in peer-reviewed scientific papers published in scientific journals. A scientific research paper consists of several well-defined sections: introduction, materials and methods, results, and, finally, a concluding discussion. Review papers summarize the research done in a particular field over a period of time. Review Questions 

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[link] Glossary abstract opening section of a scientific paper that summarizes the research and conclusions applied science form of science that aims to solve real-world problems basic science science that seeks to expand knowledge and understanding regardless of the short-term application of that knowledge biology the study of living organisms and their interactions with one another and their environments conclusion section of a scientific paper that summarizes the importance of the experimental findings control part of an experiment that does not change during the experiment deductive reasoning form of logical thinking that uses a general inclusive statement to forecast specific results descriptive science (also, discovery science) form of science that aims to observe, explore, and investigate discussion section of a scientific paper in which the author interprets experimental results, describes how variables may be related, and attempts to explain the phenomenon in question falsifiable able to be disproven by experimental results hypothesis suggested explanation for an observation, which can be tested hypothesis-based science form of science that begins with a specific question and potential testable answers inductive reasoning form of logical thinking that uses related observations to arrive at a general conclusion introduction opening section of a scientific paper, which provides background information about what was known in the field prior to the research reported in the paper life science field of science, such as biology, that studies living things materials and methods section of a scientific paper that includes a complete description of the substances, methods, and techniques used by the researchers to gather data natural science field of science that is related to the physical world and its phenomena and processes peer-reviewed manuscript scientific paper that is reviewed by a scientist s colleagues who are experts in the field of study physical science field of science, such as geology, astronomy, physics, and chemistry, that studies nonliving matter plagiarism using other people s work or ideas without proper citation, creating the false impression that those are the author s original ideas results section of a scientific paper in which the author narrates the experimental findings and presents relevant figures, pictures, diagrams, graphs, and tables, without any further interpretation review article paper that summarizes and comments on findings that were published as primary literature science knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method scientific method method of research with defined steps that include observation, formulation of a hypothesis, testing, and confirming or falsifying the hypothesis serendipity fortunate accident or a lucky surprise theory tested and confirmed explanation for observations or phenomena variable part of an experiment that the experimenter can vary or changeThemes and Concepts of Biology Themes and Concepts of Biology 

By the end of this section, you will be able to: Identify and describe the properties of life Describe the levels of organization among living things Recognize and interpret a phylogenetic tree Connection for AP Courses 

The AP Biology curriculum is organized around four major themes called the Big Ideas that apply to all levels of biological organization from molecules and cells to populations and ecosystems. Each Big Idea identifies key concepts called Enduring Understandings, and Essential Knowledges, along with supporting examples. Simple descriptions define the focus of each Big Idea: Big Idea 1, Evolution; Big Idea 2, Energy and Homeostasis; Big Idea 3, Information and Communication; and Big Idea 4, Systems and Interactions. Evolution explains both the unity and diversity of life, Big Idea 1, and all organisms require energy and molecules to carry out life functions, such as growth and reproduction, Big Idea 2. Living systems also store, transmit, and respond to information, from DNA sequences to nerve impulses and behaviors, Big Idea 3. All biological systems interact, and these interactions result in emergent properties and characteristics unique to life, Big Idea 4. 

The redesigned AP Biology course also emphasizes the investigative practices that students should master. Scientific inquiry usually uses a series of steps to gain new knowledge. The scientific method begins with an observation and follows with a hypothesis to explain the observation; then experiments are conducted to test the hypothesis, gather results, and draw conclusions from data. The AP program has identified seven major categories of Science Practices, which can be described by short phrases: using representations and models to communicate information and solve problems; using mathematics appropriately; engaging in questioning; planning and implementing data collection strategies; analyzing and evaluating data; justifying scientific explanations; and connecting concepts. A Learning Objective merges content with one or more of the seven Science Practices. 

The information presented and the examples highlighted in this section support concepts and Learning Objectives outlined in Big Idea 1 of the AP Biology Curriculum. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 3.1 The student can pose scientific questions. Learning Objective 1.14 The student is able to pose scientific questions that correctly identify essential properties of share, core life processes that provide insights into the history of life on Earth. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 1.18 The student is able to evaluate evidence provided by a data set in conjunction with a phylogenetic tree or simply cladogram to determine evolutionary history and speciation. 

Biology is the science that studies life, but what exactly is life? This may sound like a silly question with an obvious response, but it is not always easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life. Consequently, virologists are not biologists, strictly speaking. Similarly, some biologists study the early molecular evolution that gave rise to life; since the events that preceded life are not biological events, these scientists are also excluded from biology in the strict sense of the term. 

From its earliest beginnings, biology has wrestled with three questions: What are the shared properties that make something alive ? And once we know something is alive, how do we find meaningful levels of organization in its structure? And, finally, when faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? As new organisms are discovered every day, biologists continue to seek answers to these and other questions. Properties of Life 

All living organisms share several key characteristics or functions: order, sensitivity or response to the environment, reproduction, adaptation, growth and development, regulation, homeostasis, energy processing, and evolution. When viewed together, these nine characteristics serve to define life. Order A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems. (credit: Ivengo /Wikimedia Commons) 

Organisms are highly organized, coordinated structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex: inside each cell, atoms make up molecules; these in turn make up cell organelles and other cellular inclusions. In multicellular organisms ( [link] ), similar cells form tissues. Tissues, in turn, collaborate to create organs (body structures with a distinct function). Organs work together to form organ systems. Sensitivity or Response to Stimuli The leaves of this sensitive plant ( Mimosa pudica ) will instantly droop and fold when touched. After a few minutes, the plant returns to normal. (credit: Alex Lomas) 

Organisms respond to diverse stimuli. For example, plants can bend toward a source of light, climb on fences and walls, or respond to touch ( [link] ). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis ) or light ( phototaxis ). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response. 

Watch this video to see how plants respond to a stimulus from opening to light, to wrapping a tendril around a branch, to capturing prey. 

[link] Reproduction 

Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form two new cells. Multicellular organisms often produce specialized reproductive germline cells that will form new individuals. When reproduction occurs, genes containing DNA are passed along to an organism s offspring. These genes ensure that the offspring will belong to the same species and will have similar characteristics, such as size and shape. Growth and Development 

Organisms grow and develop following specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species young ( [link] ) will grow up to exhibit many of the same characteristics as its parents. Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics. (credit: Rocky Mountain Feline Rescue) Regulation 

Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. Two examples of internal functions regulated in an organism are nutrient transport and blood flow. Organs (groups of tissues working together) perform specific functions, such as carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body. Homeostasis Polar bears ( Ursus maritimus ) and other mammals living in ice-covered regions maintain their body temperature by generating heat and reducing heat loss through thick fur and a dense layer of fat under their skin. (credit: longhorndave /Flickr) 

In order to function properly, cells need to have appropriate conditions such as proper temperature, pH, and appropriate concentration of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain internal conditions within a narrow range almost constantly, despite environmental changes, through homeostasis (literally, steady state ) the ability of an organism to maintain constant internal conditions. For example, an organism needs to regulate body temperature through a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear ( [link] ), have body structures that help them withstand low temperatures and conserve body heat. Structures that aid in this type of insulation include fur, feathers, blubber, and fat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat. Energy Processing The California condor ( Gymnogyps californianus ) uses chemical energy derived from food to power flight. California condors are an endangered species; this bird has a wing tag that helps biologists identify the individual. (credit: Pacific Southwest Region U.S. Fish and Wildlife Service) 

All organisms use a source of energy for their metabolic activities. Some organisms capture energy from the sun and convert it into chemical energy in food; others use chemical energy in molecules they take in as food ( [link] ). Activity 

Select an ecosystem of your choice, such as a tropical rainforest, desert, or coral reef, and create a representation to show how several organisms found in the ecosystem interact with each other and the environment. Then, using similarities and differences among the organisms make a hypothesis about their relatedness. 

Consider the levels of organization of the biological world and create a diagram to place these items in order from the smallest level of organization to the most encompassing: skin cell, planet Earth, elephant, tropical rainforest, water molecule, liver, wolf pack, and oxygen atom. Justify the reason why you placed the items in the hierarchy that you did. Think About It 

Homeostasis the ability to stay the same is a feature shared by all living organisms. You go for a long walk on a hot day. Describe how homeostasis keeps your body healthy even though you are sweating profusely. Then describe an example of an adaptation that evolved in a desert plant or animal that allows them to survive in extreme temperatures. 

The first activity is an application of Learning Objective 1.16 and Science Practice 6.1 because the student is justifying the claim that organisms share many features that evolved in the past and are found among organisms today. 

The second activity is an application of Learning Objective 1.16 and Science Practice 6.1 because the student is justifying the claim that life on Earth today is organized into a hierarchy of features, from simple to complex, that evolved in the past. 

The Think about it section is an application of Learning Objective 1.14 and Science Practice 7.2 because students are describing an example of a process that is shared by all living organisms, despite the environment in which they are typically found. 

Ecosystems: Each system must have a common thread of producers fixing sun energy or acquiring energy from chemical reactions, feeding first consumers usually herbivores or decomposers, and second consumers that are predators. The ecosystem must provide shelter, access to food and stable environment. Answers will vary. 

Levels of organization from smallest to largest: Teach students to place the obvious answers first: atom as smallest and planet Earth at the top and then fill the gaps. 

From smallest to largest: 

Oxygen atom 

Water molecule 

Skin cell 

Liver 

Elephant 

Wolf pack 

Tropical rain forest 

Planet Earth 

Adaptation to dry conditions: Stress that animals and plants use general mechanisms to preserve water once the transition to dry land was made. Animals adapted to dry climates have thick skin layers to reduce water loss. Their urinary system is also adapted to concentrate urine, reducing water loss. Animals also respond to extreme heat behaviorally by going out at night or when the sun is low. Plants develop thick waxy layers that cover, leaves in the form of thorns and open stomata (pores) at night. 

Many adaptations are due to convergent evolution. The fins of dolphins are not derived from fins of fish. On the other hand, structures that look very different such as our hands and the wings of bats have the same core structure they are limbs with the same number and arrangement of bones but look different because they are adapted for different functions. Levels of Organization of Living Things 

Living things are highly organized and structured, following a hierarchy that can be examined on a scale from small to large. The atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by one or more chemical bonds. Many molecules that are biologically important are macromolecules , large molecules that are typically formed by polymerization (a polymer is a large molecule that is made by combining smaller units called monomers, which are simpler than macromolecules). An example of a macromolecule is deoxyribonucleic acid (DNA) ( [link] ), which contains the instructions for the structure and functioning of all living organisms. All molecules, including this DNA molecule, are composed of atoms. (credit: brian0918 /Wikimedia Commons) Link to Learning 

Watch this video that animates the three-dimensional structure of the DNA molecule shown in this figure . 

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Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles . Organelles are small structures that exist within cells. Examples of organelles include mitochondria and chloroplasts, which carry out indispensable functions: mitochondria produce energy to power the cell, while chloroplasts enable green plants to utilize the energy in sunlight to make sugars. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack the reproductive mechanism of a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single-celled or colonial organisms that do not have membrane-bound nuclei; in contrast, the cells of eukaryotes do have membrane-bound organelles and a membrane-bound nucleus. 

In larger organisms, cells combine to make tissues , which are groups of similar cells carrying out similar or related functions. Organs are collections of tissues grouped together performing a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. Mammals have many organ systems. For instance, the circulatory system transports blood through the body and to and from the lungs; it includes organs such as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms. 

All the individuals of a species living within a specific area are collectively called a population . For example, a forest may include many pine trees. All of these pine trees represent the population of pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and microbial populations. A community is the sum of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest s community. The forest itself is an ecosystem. An ecosystem consists of all the living things in a particular area together with the abiotic, non-living parts of that environment such as nitrogen in the soil or rain water. At the highest level of organization ( see this figure ), the biosphere is the collection of all ecosystems, and it represents the zones of life on earth. It includes land, water, and even the atmosphere to a certain extent. The biological levels of organization of living things are shown. From a single organelle to the entire biosphere, living organisms are parts of a highly structured hierarchy. (credit organelles : modification of work by Umberto Salvagnin; credit cells : modification of work by Bruce Wetzel, Harry Schaefer/ National Cancer Institute; credit tissues : modification of work by Kilbad; Fama Clamosa; Mikael H ggstr m; credit organs : modification of work by Mariana Ruiz Villareal; credit organisms : modification of work by "Crystal"/Flickr; credit ecosystems : modification of work by US Fish and Wildlife Service Headquarters; credit biosphere : modification of work by NASA) 

[link] The Diversity of Life 

The fact that biology, as a science, has such a broad scope has to do with the tremendous diversity of life on earth. The source of this diversity is evolution , the process of gradual change during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems. 

The evolution of various life forms on Earth can be summarized in a phylogenetic tree ( [link] ). A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of nodes and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch is proportional to the time elapsed since the split. This phylogenetic tree was constructed by microbiologist Carl Woese using data obtained from sequencing ribosomal RNA genes. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotes, single-celled organisms lacking intracellular organelles. (credit: Eric Gaba; NASA Astrobiology Institute) 

Carl Woese and the Phylogenetic Tree In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms together with the four original kingdoms (excluding bacteria). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree ( see this figure ). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape). 

Woese s tree was constructed from comparative sequencing of the genes that are universally distributed, present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese s approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability ( [link] ). The comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea. These images represent different domains. The (a) bacteria in this micrograph belong to Domain Bacteria, while the (b) extremophiles (not visible) living in this hot vent belong to Domain Archaea. Both the (c) sunflower and (d) lion are part of Domain Eukarya. (credit a: modification of work by Drew March; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Leszek Leszcynski) 

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Phylogenetic trees can represent traits that are derived or lost due to evolution. One example is the absence of legs in some sea mammals. For example, Cetaceans are marine mammals that include toothed whales, such as dolphins and killer whales, and baleen whales, such as humpback whales. Cetaceans are descended from even-toed ungulates and share a common ancestry with the hippopotamus, cow, sheep, camel, and pig. 

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Use the diagram to ask the following questions: 

Which animal(s) are most closely related to a duck-billed platypus? Give your reasoning. 

Answer 

the American opossum, least number of common ancestors. 

Circle on one main lineage in the diagram the nodes in red, the tip of the trees in blue and the branches in red. 

Once bats were called flying mice. According to the tree, is this a valid characterization? 

Answer 

No, bats are more closely related to shrew and moles. 

Ask students the question, how did reptiles learn how to fly? 

For an exploration of the evolution of flight visit this site . 

Birds are not modern day dinosaurs. Birds evolved from dinosaurs. Many changes took place over time. Branches of Biological Study 

The scope of biology is broad and therefore contains many branches and subdisciplines. Biologists may pursue one of those subdisciplines and work in a more focused field. For instance, molecular biology and biochemistry study biological processes at the molecular and chemical level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology , the study of microorganisms, is the study of the structure and function of organisms that cannot be seen with the naked eye. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others. Forensic Scientist 

Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace materials associated with crimes. Interest in forensic science has increased in the last few years, possibly because of popular television shows that feature forensic scientists on the job. Also, the development of molecular techniques and the establishment of DNA databases have expanded the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA ( [link] ) found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect larvae or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as well as some intensive math courses. This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory at Fort Gillem, GA. (credit: United States Army CID Command Public Affairs) 

Another field of biological study, neurobiology , studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this subdiscipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches. Researchers work on excavating dinosaur fossils at a site in Castell n, Spain. (credit: Mario Modesto) 

Paleontology , another branch of biology, uses fossils to study life s history ( [link] ). Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. This is just a small sample of the many fields that biologists can pursue. 

Biology is the culmination of the achievements of the natural sciences from their inception to today. Excitingly, it is the cradle of emerging sciences, such as the biology of brain activity, genetic engineering of custom organisms, and the biology of evolution that uses the laboratory tools of molecular biology to retrace the earliest stages of life on earth. A scan of news headlines whether reporting on immunizations, a newly discovered species, sports doping, or a genetically-modified food demonstrates the way biology is active in and important to our everyday world. Section Summary 

Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized parts of a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. The great diversity of life today evolved from less-diverse ancestral organisms over billions of years. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms. 

Biology is very broad and includes many branches and subdisciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others. Review Questions 

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[link] Test Prep for AP Courses 

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[link] Glossary atom smallest and most fundamental unit of matter biochemistry study of the chemistry of biological organisms biosphere collection of all the ecosystems on Earth botany study of plants cell smallest fundamental unit of structure and function in living things community set of populations inhabiting a particular area ecosystem all the living things in a particular area together with the abiotic, nonliving parts of that environment eukaryote organism with cells that have nuclei and membrane-bound organelles evolution process of gradual change during which new species arise from older species and some species become extinct homeostasis ability of an organism to maintain constant internal conditions macromolecule large molecule, typically formed by the joining of smaller molecules microbiology study of the structure and function of microorganisms molecule chemical structure consisting of at least two atoms held together by one or more chemical bonds molecular biology study of biological processes and their regulation at the molecular level, including interactions among molecules such as DNA, RNA, and proteins neurobiology study of the biology of the nervous system organ collection of related tissues grouped together performing a common function organ system level of organization that consists of functionally related interacting organs organelle small structures that exist within cells and carry out cellular functions organism individual living entity paleontology study of life s history by means of fossils phylogenetic tree diagram showing the evolutionary relationships among various biological species based on similarities and differences in genetic or physical traits or both; in essence, a hypothesis concerning evolutionary connections population all of the individuals of a species living within a specific area prokaryote single-celled organism that lacks organelles and does not have nuclei surrounded by a nuclear membrane tissue group of similar cells carrying out related functions zoology study of animalsIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Atoms are the building blocks of molecules found in the universe air, soil, water, rocks . . . and also the cells of all living organisms. In this model of an organic molecule, the atoms of carbon (black), hydrogen (white), nitrogen (blue), oxygen (red), and sulfur (yellow) are shown in proportional atomic size. The silver rods indicate chemical bonds. (credit: modification of work by Christian Guthier) 

All matter, including living things, is made up of various combinations of elements. Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These elements form the major biological molecules nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of living matter. Biologists study these important molecules to understand their unique structures which determine their specialized functions. 

All biological processes follow the laws of physics and chemistry. Therefore, in order to understand how biological systems work, it is important to understand the underlying physics and chemistry. For example, the flow of blood within the circulatory system follows the laws of physics regulating the modes of fluid flow. Chemical laws dictate the breakdown of large, complex food molecules into smaller molecules as well as their conversion to energy stored in adenosine triphosphate (ATP). Polar molecules, the formation of hydrogen bonds, and the resulting properties of water are key to understanding living processes. Recognizing the properties of acids and bases is important to understand various biological processes such as digestion. Therefore, the fundamentals of physics and chemistry are the foundation for gaining insight into biological processes. 

An example of how understanding of chemical processes can give insight to a biological process is recent research on seasonal affective disorder (SAD). This form of depression affects up to 10% of the population in the fall and winter. Symptoms include a tendency to overeat, oversleep, lack of energy, and difficulty concentrating on tasks. Now scientists have found out that not only may SAD be caused by a deficiency in vitamin D, but that it is more common in individuals with darker skin pigmentation. You can read more about it here . 

Before students begin this chapter, it is useful to review these concepts: Atoms consist of protons, neutrons, and electrons; Atoms are most stable when their outermost or valence electron shells contain the maximum number of electrons; Electrons can be transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds. Demonstrate how electrons can be transferred or shared to create bonds using a chemistry model kit or by drawing the atoms and electrons.Atoms, Isotopes, Ions, and Molecules: The Building Blocks Atoms, Isotopes, Ions, and Molecules: The Building Blocks 

In this section, you will explore the following questions: How does atomic structure determine the properties of elements, molecules, and matter? What are the differences among ionic bonds, covalent bonds, polar covalent bonds, and hydrogen bonds? Connection for AP Courses 

Living systems obey the laws of chemistry and physics. Matter is anything that occupies space and mass. The 92 naturally occurring elements have unique properties, and various combinations of them create molecules, which combine to form organelles, cells, tissues, organ system, and organisms. Atoms , which consist of protons, neutrons, and electrons, are the smallest units of matter that retain all their characteristics and are most stable when their outermost or valence electron shells contain the maximum number of electrons. Electrons can be transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van del Waals interactions. Isotopes are different forms of an element that have different numbers of neutrons while retaining the same number of protons; many isotopes, such as carbon-14, are radioactive. 

The information presented and examples highlighted in this section support concepts and Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 2.8 The student is able to justify the selection of data regarding the types of molecules that an animal, plant, or bacterium will take up as necessary building blocks and excrete as waste products. 

At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 92 occur naturally. The remaining elements are synthesized in laboratories and are unstable. 

Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is already taken by another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements chemical symbols derive from their Latin names; for example, the symbol for sodium is Na, referring to natrium , the Latin word for sodium. 

The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). In the non-living world, elements are found in different proportions, and some elements common to living organisms are relatively rare on the earth as a whole, as shown in [link] . For example, the atmosphere is rich in nitrogen and oxygen but contains little carbon and hydrogen, while the earth s crust, although it contains oxygen and a small amount of hydrogen, has little nitrogen and carbon. In spite of their differences in abundance, all elements and the chemical reactions between them obey the same chemical and physical laws regardless of whether they are a part of the living or non-living world. Approximate Percentage of Elements in Living Organisms (Humans) Compared to the Non-living World Element Life (Humans) Atmosphere Earth s Crust Oxygen (O) 65% 21% 46% Carbon (C) 18% trace trace Hydrogen (H) 10% trace 0.1% Nitrogen (N) 3% 78% trace The Structure of the Atom 

To understand how elements come together, we must first discuss the smallest component or building block of an element, the atom. An atom is the smallest unit of matter that retains all of the chemical properties of an element. For example, one gold atom has all of the properties of gold in that it is a solid metal at room temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and containing small amounts of other elements known as impurities. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold. 

An atom is composed of two regions: the nucleus , which is in the center of the atom and contains protons and neutrons, and the outermost region of the atom which holds its electrons in orbit around the nucleus, as illustrated in [link] . Atoms contain protons, electrons, and neutrons, among other subatomic particles. The only exception is hydrogen (H), which is made of one proton and one electron with no neutrons. Elements, such as helium, depicted here, are made up of atoms. Atoms are made up of protons and neutrons located within the nucleus, with electrons in orbitals surrounding the nucleus. 

Protons and neutrons have approximately the same mass, about 1.67 10 -24 grams. Scientists arbitrarily define this amount of mass as one atomic mass unit (amu) or one Dalton, as shown in [link] . Although similar in mass, protons and neutrons differ in their electric charge. A proton is positively charged whereas a neutron is uncharged. Therefore, the number of neutrons in an atom contributes significantly to its mass, but not to its charge. Electrons are much smaller in mass than protons, weighing only 9.11 10 -28 grams, or about 1/1800 of an atomic mass unit. Hence, they do not contribute much to an element s overall atomic mass. Therefore, when considering atomic mass, it is customary to ignore the mass of any electrons and calculate the atom s mass based on the number of protons and neutrons alone. Although not significant contributors to mass, electrons do contribute greatly to the atom s charge, as each electron has a negative charge equal to the positive charge of a proton. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. In these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge. 

Accounting for the sizes of protons, neutrons, and electrons, most of the volume of an atom greater than 99 percent is, in fact, empty space. With all this empty space, one might ask why so-called solid objects do not just pass through one another. The reason they do not is that the electrons that surround all atoms are negatively charged and negative charges repel each other. Protons, Neutrons, and Electrons Charge Mass (amu) Location Proton +1 1 nucleus Neutron 0 1 nucleus Electron 1 0 orbitals Atomic Number and Mass 

Atoms of each element contain a characteristic number of protons and electrons. The number of protons determines an element s atomic number and is used to distinguish one element from another. The number of neutrons is variable, resulting in isotopes, which are different forms of the same atom that vary only in the number of neutrons they possess. Together, the number of protons and the number of neutrons determine an element s mass number , as illustrated in this figure . Note that the small contribution of mass from electrons is disregarded in calculating the mass number. This approximation of mass can be used to easily calculate how many neutrons an element has by simply subtracting the number of protons from the mass number. Since an element s isotopes will have slightly different mass numbers, scientists also determine the atomic mass , which is the calculated mean of the mass number for its naturally occurring isotopes. Often, the resulting number contains a fraction. For example, the atomic mass of chlorine (Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons and 20 neutrons). Carbon has an atomic number of six, and two stable isotopes with mass numbers of twelve and thirteen, respectively. Its atomic mass is 12.11. 

[link] Isotopes 

Isotopes are different forms of an element that have the same number of protons but a different number of neutrons. Some elements such as carbon, potassium, and uranium have naturally occurring isotopes. Carbon-12 contains six protons, six neutrons, and six electrons; therefore, it has a mass number of 12 (six protons and six neutrons). Carbon-14 contains six protons, eight neutrons, and six electrons; its atomic mass is 14 (six protons and eight neutrons). These two alternate forms of carbon are isotopes. Some isotopes may emit neutrons, protons, and electrons, and attain a more stable atomic configuration (lower level of potential energy); these are radioactive isotopes, or radioisotopes. Radioactive decay (carbon-14 losing neutrons to eventually become carbon-12) describes the energy loss that occurs when an unstable atom s nucleus releases radiation. 

Carbon Dating Carbon is normally present in the atmosphere in the form of gaseous compounds like carbon dioxide and methane. Carbon-14 ( 14 C) is a naturally occurring radioisotope that is created in the atmosphere from atmospheric 14 N (nitrogen) by the addition of a neutron and the loss of a proton because of cosmic rays. This is a continuous process, so more 14 C is always being created. As a living organism incorporates 14 C initially as carbon dioxide fixed in the process of photosynthesis, the relative amount of 14 C in its body is equal to the concentration of 14 C in the atmosphere. When an organism dies, it is no longer ingesting 14 C, so the ratio between 14 C and 12 C will decline as 14 C decays gradually to 14 N by a process called beta decay the emission of electrons or positrons. This decay gives off energy in a slow process. 

After approximately 5,730 years, half of the starting concentration of 14 C will have been converted back to 14 N. The time it takes for half of the original concentration of an isotope to decay back to its more stable form is called its half-life. Because the half-life of 14 C is long, it is used to date formerly living objects such as old bones or wood. Comparing the ratio of the 14 C concentration found in an object to the amount of 14 C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. On the basis of this amount, the age of the material, such as the pygmy mammoth shown in [link] , can be calculated with accuracy if it is not much older than about 50,000 years. Other elements have isotopes with different half lives. For example, 40 K (potassium-40) has a half-life of 1.25 billion years, and 235 U (Uranium 235) has a half-life of about 700 million years. Through the use of radiometric dating, scientists can study the age of fossils or other remains of extinct organisms to understand how organisms have evolved from earlier species. The age of carbon-containing remains less than about 50,000 years old, such as this pygmy mammoth, can be determined using carbon dating. (credit: Bill Faulkner, NPS) 

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To learn more about atoms, isotopes, and how to tell one isotope from another, visit this site and run the simulation. 

[link] The Periodic Table 

The different elements are organized and displayed in the periodic table . Devised by Russian chemist Dmitri Mendeleev (1834 1907) in 1869, the table groups elements that, although unique, share certain chemical properties with other elements. The properties of elements are responsible for their physical state at room temperature: they may be gases, solids, or liquids. Elements also have specific chemical reactivity , the ability to combine and to chemically bond with each other. 

In the periodic table, shown in [link] , the elements are organized and displayed according to their atomic number and are arranged in a series of rows and columns based on shared chemical and physical properties. In addition to providing the atomic number for each element, the periodic table also displays the element s atomic mass. Looking at carbon, for example, its symbol (C) and name appear, as well as its atomic number of six (in the upper left-hand corner) and its atomic mass of 12.11. The periodic table shows the atomic mass and atomic number of each element. The atomic number appears above the symbol for the element and the approximate atomic mass appears below it. 

The periodic table groups elements according to chemical properties. The differences in chemical reactivity between the elements are based on the number and spatial distribution of an atom s electrons. Atoms that chemically react and bond to each other form molecules. Molecules are simply two or more atoms chemically bonded together. Logically, when two atoms chemically bond to form a molecule, their electrons, which form the outermost region of each atom, come together first as the atoms form a chemical bond. Electron Shells and the Bohr Model 

It should be stressed that there is a connection between the number of protons in an element, the atomic number that distinguishes one element from another, and the number of electrons it has. In all electrically neutral atoms, the number of electrons is the same as the number of protons. Thus, each element, at least when electrically neutral, has a characteristic number of electrons equal to its atomic number. 

An early model of the atom was developed in 1913 by Danish scientist Niels Bohr (1885 1962). The Bohr model shows the atom as a central nucleus containing protons and neutrons, with the electrons in circular orbitals at specific distances from the nucleus, as illustrated in [link] . These orbits form electron shells or energy levels, which are a way of visualizing the number of electrons in the outermost shells. These energy levels are designated by a number and the symbol n. For example, 1n represents the first energy level located closest to the nucleus. The Bohr model was developed by Niels Bohrs in 1913. In this model, electrons exist within principal shells. An electron normally exists in the lowest energy shell available, which is the one closest to the nucleus. Energy from a photon of light can bump it up to a higher energy shell, but this situation is unstable, and the electron quickly decays back to the ground state. In the process, a photon of light is released. 

Electrons fill orbitals in a consistent order: they first fill the orbitals closest to the nucleus, then they continue to fill orbitals of increasing energy further from the nucleus. If there are multiple orbitals of equal energy, they will be filled with one electron in each energy level before a second electron is added. The electrons of the outermost energy level determine the energetic stability of the atom and its tendency to form chemical bonds with other atoms to form molecules. 

Under standard conditions, atoms fill the inner shells first, often resulting in a variable number of electrons in the outermost shell. The innermost shell has a maximum of two electrons but the next two electron shells can each have a maximum of eight electrons. This is known as the octet rule , which states, with the exception of the innermost shell, that atoms are more stable energetically when they have eight electrons in their valence shell , the outermost electron shell. Examples of some neutral atoms and their electron configurations are shown in this figure . Notice that in this [link] , helium has a complete outer electron shell, with two electrons filling its first and only shell. Similarly, neon has a complete outer 2n shell containing eight electrons. In contrast, chlorine and sodium have seven and one in their outer shells, respectively, but theoretically they would be more energetically stable if they followed the octet rule and had eight. Visual Connections Bohr diagrams indicate how many electrons fill each principal shell. Group 18 elements (helium, neon, and argon are shown) have a full outer, or valence, shell. A full valence shell is the most stable electron configuration. Elements in other groups have partially filled valence shells and gain or lose electrons to achieve a stable electron configuration. 

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Understanding that the organization of the periodic table is based on the total number of protons (and electrons) helps us know how electrons are distributed among the outer shell. The periodic table is arranged in columns and rows based on the number of electrons and where these electrons are located. Take a closer look at the some of the elements in the table s far right column in the periodic table . The group 18 atoms helium (He), neon (Ne), and argon (Ar) all have filled outer electron shells, making it unnecessary for them to share electrons with other atoms to attain stability; they are highly stable as single atoms. Their non-reactivity has resulted in their being named the inert gases (or noble gases ). Compare this to the group 1 elements in the left-hand column. These elements, including hydrogen (H), lithium (Li), and sodium (Na), all have one electron in their outermost shells. That means that they can achieve a stable configuration and a filled outer shell by donating or sharing one electron with another atom or a molecule such as water. Hydrogen will donate or share its electron to achieve this configuration, while lithium and sodium will donate their electron to become stable. As a result of losing a negatively charged electron, they become positively charged ions . Group 17 elements, including fluorine and chlorine, have seven electrons in their outmost shells, so they tend to fill this shell with an electron from other atoms or molecules, making them negatively charged ions. Group 14 elements, of which carbon is the most important to living systems, have four electrons in their outer shell allowing them to make several covalent bonds (discussed below) with other atoms. Thus, the columns of the periodic table represent the potential shared state of these elements outer electron shells that is responsible for their similar chemical characteristics. Electron Orbitals 

Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model of the atom does not accurately reflect how electrons are spatially distributed surrounding the nucleus. They do not circle the nucleus like the earth orbits the sun, but are found in electron orbitals . These relatively complex shapes result from the fact that electrons behave not just like particles, but also like waves. Mathematical equations from quantum mechanics known as wave functions can predict within a certain level of probability where an electron might be at any given time. The area where an electron is most likely to be found is called its orbital. 

Recall that the Bohr model depicts an atom s electron shell configuration. Within each electron shell are subshells, and each subshell has a specified number of orbitals containing electrons. While it is impossible to calculate exactly where an electron is located, scientists know that it is most probably located within its orbital path. Subshells are designated by the letter s, p , d , and f . The s subshell is spherical in shape and has one orbital. Principal shell 1n has only a single s orbital, which can hold two electrons. Principal shell 2n has one s and one p subshell, and can hold a total of eight electrons. The p subshell has three dumbbell-shaped orbitals, as illustrated in [link] . Subshells d and f have more complex shapes and contain five and seven orbitals, respectively. These are not shown in the illustration. Principal shell 3n has s , p , and d subshells and can hold 18 electrons. Principal shell 4n has s , p , d and f orbitals and can hold 32 electrons. Moving away from the nucleus, the number of electrons and orbitals found in the energy levels increases. Progressing from one atom to the next in the periodic table, the electron structure can be worked out by fitting an extra electron into the next available orbital. The s subshells are shaped like spheres. Both the 1n and 2n principal shells have an s orbital, but the size of the sphere is larger in the 2n orbital. Each sphere is a single orbital. p subshells are made up of three dumbbell-shaped orbitals. Principal shell 2n has a p subshell, but shell 1 does not. 

The closest orbital to the nucleus, called the 1s orbital, can hold up to two electrons. This orbital is equivalent to the innermost electron shell of the Bohr model of the atom. It is called the 1 s orbital because it is spherical around the nucleus. The 1 s orbital is the closest orbital to the nucleus, and it is always filled first, before any other orbital can be filled. Hydrogen has one electron; therefore, it has only one spot within the 1 s orbital occupied. This is designated as 1 s 1 , where the superscripted 1 refers to the one electron within the 1 s orbital. Helium has two electrons; therefore, it can completely fill the 1 s orbital with its two electrons. This is designated as 1 s 2 , referring to the two electrons of helium in the 1 s orbital. On the periodic table [link] , hydrogen and helium are the only two elements in the first row (period); this is because they only have electrons in their first shell, the 1 s orbital. Hydrogen and helium are the only two elements that have the 1 s and no other electron orbitals in the electrically neutral state. 

The second electron shell may contain eight electrons. This shell contains another spherical s orbital and three dumbbell shaped p orbitals, each of which can hold two electrons, as shown in [link] . After the 1 s orbital is filled, the second electron shell is filled, first filling its 2 s orbital and then its three p orbitals. When filling the p orbitals, each takes a single electron; once each p orbital has an electron, a second may be added. Lithium (Li) contains three electrons that occupy the first and second shells. Two electrons fill the 1 s orbital, and the third electron then fills the 2 s orbital. Its electron configuration is 1 s 2 2 s 1 . Neon (Ne), on the other hand, has a total of ten electrons: two are in its innermost 1 s orbital and eight fill its second shell (two each in the 2 s and three p orbitals); thus, it is an inert gas and energetically stable as a single atom that will rarely form a chemical bond with other atoms. Larger elements have additional orbitals, making up the third electron shell. While the concepts of electron shells and orbitals are closely related, orbitals provide a more accurate depiction of the electron configuration of an atom because the orbital model specifies the different shapes and special orientations of all the places that electrons may occupy. Link to Learning 

Watch this visual animation to see the spatial arrangement of the p and s orbitals. 

[link] Activity 

Create diagrams to show the placement of protons, neutrons, and electrons in an atom of carbon-12 and carbon-14, respectably. Based on their subatomic difference(s), determine which element is an organism more likely to use to synthesize glucose (C 6 H 12 O 6 ) and give a reason for your choice. 

This activity is an application of Learning Objective 2.8 and Science Practice 4.1 because the student is asked to justify which form of carbon is organism is more likely to take up from the environment and use based on the properties of the element(s). 

Answer 

Carbon-12 is a stable isotope because it contains equal numbers of protons and neutrons. Carbon-14 is less stable and undergoes radioactive decay, losing two neutrons to become the more stable carbon-12. Therefore, organisms are more likely to use carbon-12 to synthesize glucose. Chemical Reactions and Molecules 

All elements are most stable when their outermost shell is filled with electrons according to the octet rule. This is because it is energetically favorable for atoms to be in that configuration and it makes them stable. However, since not all elements have enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms thereby obtaining the electrons they need to attain a stable electron configuration. When two or more atoms chemically bond with each other, the resultant chemical structure is a molecule. The familiar water molecule, H 2 O, consists of two hydrogen atoms and one oxygen atom; these bond together to form water, as illustrated in [link] . Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells. Two or more atoms may bond with each other to form a molecule. When two hydrogens and an oxygen share electrons via covalent bonds, a water molecule is formed. 

Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances used in the beginning of a chemical reaction are called the reactants (usually found on the left side of a chemical equation), and the substances found at the end of the reaction are known as the products (usually found on the right side of a chemical equation). An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction; this direction is not always a one-way street. For the creation of the water molecule shown above, the chemical equation would be: 2 H + O H 2 O 2 H + O H 2 O 

An example of a simple chemical reaction is the breaking down of hydrogen peroxide molecules, each of which consists of two hydrogen atoms bonded to two oxygen atoms (H 2 O 2 ). The reactant hydrogen peroxide is broken down into water, containing one oxygen atom bound to two hydrogen atoms (H 2 O), and oxygen, which consists of two bonded oxygen atoms (O 2 ). In the equation below, the reaction includes two hydrogen peroxide molecules and two water molecules. This is an example of a balanced chemical equation , wherein the number of atoms of each element is the same on each side of the equation. According to the law of conservation of matter, the number of atoms before and after a chemical reaction should be equal, such that no atoms are, under normal circumstances, created or destroyed. 2H 2 O 2 (hydrogen peroxide) 2H 2 O (water) + O 2 (oxygen) 2H 2 O 2 (hydrogen peroxide) 2H 2 O (water) + O 2 (oxygen) 

Even though all of the reactants and products of this reaction are molecules (each atom remains bonded to at least one other atom), in this reaction only hydrogen peroxide and water are representatives of compounds : they contain atoms of more than one type of element. Molecular oxygen, on the other hand, as shown in [link] ,consists of two doubly bonded oxygen atoms and is not classified as a compound but as a mononuclear molecule. The oxygen atoms in an O 2 molecule are joined by a double bond. 

Some chemical reactions, such as the one shown above, can proceed in one direction until the reactants are all used up. The equations that describe these reactions contain a unidirectional arrow and are irreversible . Reversible reactions are those that can go in either direction. In reversible reactions, reactants are turned into products, but when the concentration of product goes beyond a certain threshold (characteristic of the particular reaction), some of these products will be converted back into reactants; at this point, the designations of products and reactants are reversed. This back and forth continues until a certain relative balance between reactants and products occurs a state called equilibrium . These situations of reversible reactions are often denoted by a chemical equation with a double headed arrow pointing towards both the reactants and products. 

For example, in human blood, excess hydrogen ions (H + ) bind to bicarbonate ions (HCO 3 - ) forming an equilibrium state with carbonic acid (H 2 CO 3 ). If carbonic acid were added to this system, some of it would be converted to bicarbonate and hydrogen ions. HCO + H + H 2 CO 3 HCO + H + H 2 CO 3 

In biological reactions, however, equilibrium is rarely obtained because the concentrations of the reactants or products or both are constantly changing, often with a product of one reaction being a reactant for another. To return to the example of excess hydrogen ions in the blood, the formation of carbonic acid will be the major direction of the reaction. However, the carbonic acid can also leave the body as carbon dioxide gas (via exhalation) instead of being converted back to bicarbonate ion, thus driving the reaction to the right by the chemical law known as law of mass action . These reactions are important for maintaining the homeostasis of our blood. HCO + H + H 2 CO 3 CO 2 + H 2 O HCO + H + H 2 CO 3 CO 2 + H 2 O Ions and Ionic Bonds 

Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that are formed by losing electrons. Negative ions are formed by gaining electrons and are called anions. Anions are designated by their elemental name being altered to end in -ide : the anion of chlorine is called chloride, and the anion of sulfur is called sulfide, for example. 

This movement of electrons from one element to another is referred to as electron transfer . As [link] illustrates, sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10 electrons, leaving it with an overall charge of +1. It is now referred to as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net negative ( 1) charge. It is now referred to as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium cation) or 1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom. In the formation of an ionic compound, metals lose electrons and nonmetals gain electrons to achieve an octet. 

Ionic bonds are formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge. 

Certain salts are referred to in physiology as electrolytes (including sodium, potassium, and calcium), ions necessary for nerve impulse conduction, muscle contractions and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise. Covalent Bonds and Other Bonds and Interactions 

Another way the octet rule can be satisfied is by the sharing of electrons between atoms to form covalent bonds . These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. Covalent bonds are commonly found in carbon-based organic molecules, such as our DNA and proteins. Covalent bonds are also found in inorganic molecules like H 2 O, CO 2 , and O 2 . One, two, or three pairs of electrons may be shared, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest. 

The strength of different levels of covalent bonding is one of the main reasons living organisms have a difficult time in acquiring nitrogen for use in constructing their molecules, even though molecular nitrogen, N 2 , is the most abundant gas in the atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, the sharing of these three pairs of electrons between the two nitrogen atoms allows for the filling of their outer electron shells, making the molecule more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of proteins and DNA. 

The formation of water molecules provides an example of covalent bonding. The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds, as shown in [link] . The electron from the hydrogen splits its time between the incomplete outer shell of the hydrogen atoms and the incomplete outer shell of the oxygen atoms. To completely fill the outer shell of oxygen, which has six electrons in its outer shell but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence the well-known formula H 2 O. The electrons are shared between the two elements to fill the outer shell of each, making both elements more stable. Link to Learning 

View this short video to see an animation of ionic and covalent bonding. 

[link] Polar Covalent Bonds 

There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond , shown in this figure , the electrons are unequally shared by the atoms and are attracted more to one nucleus than the other. Because of the unequal distribution of electrons between the atoms of different elements, a slightly positive ( +) or slightly negative ( ) charge develops. This partial charge is an important property of water and accounts for many of its characteristics. 

Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge. This occurs because the nucleus of the oxygen atom is more attractive to the electrons of the hydrogen atoms than the hydrogen nucleus is to the oxygen s electrons. Thus oxygen has a higher electronegativity than hydrogen and the shared electrons spend more time in the vicinity of the oxygen nucleus than they do near the nucleus of the hydrogen atoms, giving the atoms of oxygen and hydrogen slightly negative and positive charges, respectively. Another way of stating this is that the probability of finding a shared electron near an oxygen nucleus is more likely than finding it near a hydrogen nucleus. Either way, the atom s relative electronegativity contributes to the development of partial charges whenever one element is significantly more electronegative than the other, and the charges generated by these polar bonds may then be used for the formation of hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds, which are discussed in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.) Since macromolecules often have atoms within them that differ in electronegativity, polar bonds are often present in organic molecules. Nonpolar Covalent Bonds 

Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O 2 ) is nonpolar because the electrons will be equally distributed between the two oxygen atoms. 

Another example of a nonpolar covalent bond is methane (CH 4 ), also shown in this figure . Carbon has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one, making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same electronegativity but are similar; thus, nonpolar bonds form. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent molecule. Whether a molecule is polar or nonpolar depends both on bond type and molecular shape. Both water and carbon dioxide have polar covalent bonds, but carbon dioxide is linear, so the partial charges on the molecule cancel each other out. Hydrogen Bonds and Van Der Waals Interactions 

Ionic and covalent bonds between elements require energy to break. Ionic bonds are not as strong as covalent, which determines their behavior in biological systems. However, not all bonds are ionic or covalent bonds. Weaker bonds can also form between molecules. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. Without these two types of bonds, life as we know it would not exist. Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells. 

When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a slightly positive charge because hydrogen s electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the + of the hydrogen from one molecule and the charge on the more electronegative atoms of another molecule, usually oxygen or nitrogen, or within the same molecule. This interaction is called a hydrogen bond . This type of bond is common and occurs regularly between water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA double helix. 

Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which are not always symmetrical around an atom. For these attractions to happen, the molecules need to be very close to one another. These bonds along with ionic, covalent, and hydrogen bonds contribute to the three-dimensional structure of the proteins in our cells that is necessary for their proper function. Pharmaceutical Chemist 

Pharmaceutical chemists are responsible for the development of new drugs and trying to determine the mode of action of both old and new drugs. They are involved in every step of the drug development process. Drugs can be found in the natural environment or can be synthesized in the laboratory. In many cases, potential drugs found in nature are changed chemically in the laboratory to make them safer and more effective, and sometimes synthetic versions of drugs substitute for the version found in nature. 

After the initial discovery or synthesis of a drug, the chemist then develops the drug, perhaps chemically altering it, testing it to see if the drug is toxic, and then designing methods for efficient large-scale production. Then, the process of getting the drug approved for human use begins. In the United States, drug approval is handled by the Food and Drug Administration (FDA) and involves a series of large-scale experiments using human subjects to make sure the drug is not harmful and effectively treats the condition it aims to treat. This process often takes several years and requires the participation of physicians and scientists, in addition to chemists, to complete testing and gain approval. 

An example of a drug that was originally discovered in a living organism is Paclitaxel (Taxol), an anti-cancer drug used to treat breast cancer. This drug was discovered in the bark of the pacific yew tree. Another example is aspirin, originally isolated from willow tree bark. Finding drugs often means testing hundreds of samples of plants, fungi, and other forms of life to see if any biologically active compounds are found within them. Sometimes, traditional medicine can give modern medicine clues to where an active compound can be found. For example, the use of willow bark to make medicine has been known for thousands of years, dating back to ancient Egypt. It was not until the late 1800s, however, that the aspirin molecule, known as acetylsalicylic acid, was purified and marketed for human use. 

Occasionally, drugs developed for one use are found to have unforeseen effects that allow these drugs to be used in other, unrelated ways. For example, the drug minoxidil (Rogaine) was originally developed to treat high blood pressure. When tested on humans, it was noticed that individuals taking the drug would grow new hair. Eventually the drug was marketed to men and women with baldness to restore lost hair. 

The career of the pharmaceutical chemist may involve detective work, experimentation, and drug development, all with the goal of making human beings healthier. Bonds Can Be Flexible 

Proteins are mostly made up of carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. The proteins that make up hair contain sulfur bonded to another sulfur, which is called a disulfide bond. These covalent bonds give hair its shape and texture. Heat from a hair straightener breaks the disulfide bonds, which causes the hair to lose its curl. Why do you think this method of hair straightening isn t permanent? 

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Answer 

When hair is straightened the extreme heat causes the disulfide bonds to break. When the hair cools down, the disulfide bonds between the keratin are reformed. Because the keratin molecules are in different positions when the bonds are reformed, the hair stays in the straightened shape. However, these disulfide bonds reform yet again when the hair is exposed to moisture. Section Summary 

Matter is anything that occupies space and has mass. It is made up of elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create molecules, which in turn combine to form cells, tissues, organ systems, and organisms. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions. Review Questions 

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[link] Glossary anion negative ion that is formed by an atom gaining one or more electrons atom the smallest unit of matter that retains all of the chemical properties of an element atomic mass calculated mean of the mass number for an element s isotopes atomic number total number of protons in an atom balanced chemical equation statement of a chemical reaction with the number of each type of atom equalized for both the products and reactants cation positive ion that is formed by an atom losing one or more electrons chemical bond interaction between two or more of the same or different atoms that results in the formation of molecules chemical reaction process leading to the rearrangement of atoms in molecules chemical reactivity the ability to combine and to chemically bond with each other compound substance composed of molecules consisting of atoms of at least two different elements covalent bond type of strong bond formed between two of the same or different elements; forms when electrons are shared between atoms electrolyte ion necessary for nerve impulse conduction, muscle contractions and water balance electron negatively charged subatomic particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a negative charge of 1 unit electron configuration arrangement of electrons in an atom s electron shell (for example, 1s 2 2s 2 2p 6 ) electron orbital how electrons are spatially distributed surrounding the nucleus; the area where an electron is most likely to be found electron transfer movement of electrons from one element to another; important in creation of ionic bonds electronegativity ability of some elements to attract electrons (often of hydrogen atoms), acquiring partial negative charges in molecules and creating partial positive charges on the hydrogen atoms element one of 118 unique substances that cannot be broken down into smaller substances; each element has unique properties and a specified number of protons equilibrium steady state of relative reactant and product concentration in reversible chemical reactions in a closed system hydrogen bond weak bond between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules inert gas (also, noble gas) element with filled outer electron shell that is unreactive with other atoms ion atom or chemical group that does not contain equal numbers of protons and electrons ionic bond chemical bond that forms between ions with opposite charges (cations and anions) irreversible chemical reaction chemical reaction where reactants proceed uni-directionally to form products isotope one or more forms of an element that have different numbers of neutrons law of mass action chemical law stating that the rate of a reaction is proportional to the concentration of the reacting substances mass number total number of protons and neutrons in an atom matter anything that has mass and occupies space molecule two or more atoms chemically bonded together neutron uncharged particle that resides in the nucleus of an atom; has a mass of one amu noble gas see inert gas nonpolar covalent bond type of covalent bond that forms between atoms when electrons are shared equally between them nucleus core of an atom; contains protons and neutrons octet rule rule that atoms are most stable when they hold eight electrons in their outermost shells orbital region surrounding the nucleus; contains electrons periodic table organizational chart of elements indicating the atomic number and atomic mass of each element; provides key information about the properties of the elements polar covalent bond type of covalent bond that forms as a result of unequal sharing of electrons, resulting in the creation of slightly positive and slightly negative charged regions of the molecule product molecule found on the right side of a chemical equation proton positively charged particle that resides in the nucleus of an atom; has a mass of one amu and a charge of +1 radioisotope isotope that emits radiation composed of subatomic particles to form more stable elements reactant molecule found on the left side of a chemical equation reversible chemical reaction chemical reaction that functions bi-directionally, where products may turn into reactants if their concentration is great enough valence shell outermost shell of an atom van der Waals interaction very weak interaction between molecules due to temporary charges attracting atoms that are very close togetherWater Water 

In this section, you will investigate the following questions: How does the molecular structure of water result in unique properties of water that are critical to maintaining life? What are the role of acids, bases, and buffers in dynamic homeostasis? Connection for AP Courses 

Covalent bonds form between atoms when they share electrons to fill their valence electron shells. When the sharing of electrons between atoms is equal, such as O 2 (oxygen) or CH 4 (methane), the covalent bond is said to be nonpolar . However, when electrons are shared, but not equally due to differences in electronegativity (the tendency to attract electrons), the covalent bond is said to be polar . H 2 O (water) is an example of a polar molecule. Because oxygen is more electronegative than hydrogen, the electrons are drawn toward oxygen and away from the hydrogen atoms; consequently, the oxygen atom acquires a slight negative charge and each hydrogen atoms acquires a slightly positive charge. It is important to remember that the electrons are still shared, just not equally. 

Water s polarity allows for the formation of hydrogen bonds between adjacent water molecules, resulting in many unique properties that are critical to maintaining life. For example, water is an excellent solvent because hydrogen bonds allow ions and other polar molecules to dissolve in water. Water s hydrogen bonds also contribute to its high heat capacity and high heat of vaporization, resulting in greater temperature stability. Hydrogen bond formation makes ice less dense as a solid than as a liquid, insulating aquatic environments. Water s cohesive and adhesive properties are seen as it rises inside capillary tubes or travels up a large tree from roots to leaves. The pH or hydrogen ion concentration of a solution is highly regulated to help organisms maintain homeostasis; for example, as will be explored in later chapters, the enzymes that catalyze most chemical reactions in cells are pH specific. Thus, the properties of water are connected to the biochemical and physical processes performed by living organisms. Life on Earth would be very different if these properties were altered if life could exist at all. 

The information presented and the examples highlighted in this section support concepts and Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.3 Organisms must exchange matter with the environment to grow, reproduce and maintain organization. Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question. Learning Objective 2.8 The student is able to justify the selection of data regarding the types of molecules that an animal, plant, or bacterium will take up as necessary building blocks and excrete as waste products. 

Discuss with students why scientists use the criteria of the presence of liquid water to determine if an environment or planet can support life. More information on this topic is available at this site . 

Have students create visual representations with annotations to explain how water s molecular structure and the resulting polarity results in its unique properties. Have the students describe how these properties are vital to life processes. 

Why do scientists spend time looking for water on other planets? Why is water so important? It is because water is essential to life as we know it. Water is one of the more abundant molecules and the one most critical to life on Earth. Approximately 60 70 percent of the human body is made up of water. Without it, life as we know it simply would not exist. 

The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism s cellular chemistry and metabolism occur inside the watery contents of the cell s cytoplasm. Special properties of water are its high heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and adhesive properties, and its dissociation into ions that leads to the generation of pH. Understanding these characteristics of water helps to elucidate its importance in maintaining life. Water s Polarity 

One of water s important properties is that it is composed of polar molecules: the hydrogen and oxygen within water molecules (H 2 O) form polar covalent bonds. While there is no net charge to a water molecule, the polarity of water creates a slightly positive charge on hydrogen and a slightly negative charge on oxygen, contributing to water s properties of attraction. Water s charges are generated because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be found near the oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen. 

As a result of water s polarity, each water molecule attracts other water molecules because of the opposite charges between water molecules, forming hydrogen bonds. Water also attracts or is attracted to other polar molecules and ions. A polar substance that interacts readily with or dissolves in water is referred to as hydrophilic (hydro- = water ; -philic = loving ). In contrast, non-polar molecules such as oils and fats do not interact well with water, as shown in [link] and separate from it rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic water solution). These nonpolar compounds are called hydrophobic (hydro- = water ; -phobic = fearing ). Oil and water do not mix. As this macro image of oil and water shows, oil does not dissolve in water but forms droplets instead. This is due to it being a nonpolar compound. (credit: Gautam Dogra). Water s States: Gas, Liquid, and Solid 

The formation of hydrogen bonds is an important quality of the liquid water that is crucial to life as we know it. As water molecules make hydrogen bonds with each other, water takes on some unique chemical characteristics compared to other liquids and, since living things have a high water content, understanding these chemical features is key to understanding life. In liquid water, hydrogen bonds are constantly formed and broken as the water molecules slide past each other. The breaking of these bonds is caused by the motion (kinetic energy) of the water molecules due to the heat contained in the system. When the heat is raised as water is boiled, the higher kinetic energy of the water molecules causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor). On the other hand, when the temperature of water is reduced and water freezes, the water molecules form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds) that makes ice less dense than liquid water, a phenomenon not seen in the solidification of other liquids. 

Water s lower density in its solid form is due to the way hydrogen bonds are oriented as it freezes: the water molecules are pushed farther apart compared to liquid water. With most other liquids, solidification when the temperature drops includes the lowering of kinetic energy between molecules, allowing them to pack even more tightly than in liquid form and giving the solid a greater density than the liquid. 

The lower density of ice, illustrated and pictured in [link] , an anomaly, causes it to float at the surface of liquid water, such as in an iceberg or in the ice cubes in a glass of ice water. In lakes and ponds, ice will form on the surface of the water creating an insulating barrier that protects the animals and plant life in the pond from freezing. Without this layer of insulating ice, plants and animals living in the pond would freeze in the solid block of ice and could not survive. The detrimental effect of freezing on living organisms is caused by the expansion of ice relative to liquid water. The ice crystals that form upon freezing rupture the delicate membranes essential for the function of living cells, irreversibly damaging them. Cells can only survive freezing if the water in them is temporarily replaced by another liquid like glycerol. Hydrogen bonding makes ice less dense than liquid water. The (a) lattice structure of ice makes it less dense than the freely flowing molecules of liquid water, enabling it to (b) float on water. (credit a: modification of work by Jane Whitney, image created using Visual Molecular Dynamics (VMD) software 1 ; credit b: modification of work by Carlos Ponte) 

Click here to see a 3-D animation of the structure of an ice lattice. (Image credit: Jane Whitney. Image created using Visual Molecular Dynamics VMD software. 2 ) 

[link] Water s High Heat Capacity 

Water s high heat capacity is a property caused by hydrogen bonding among water molecules. Water has the highest specific heat capacity of any liquids. Specific heat is defined as the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius. For water, this amount is one calorie . It therefore takes water a long time to heat and long time to cool. In fact, the specific heat capacity of water is about five times more than that of sand. This explains why the land cools faster than the sea. Due to its high heat capacity, water is used by warm blooded animals to more evenly disperse heat in their bodies: it acts in a similar manner to a car s cooling system, transporting heat from warm places to cool places, causing the body to maintain a more even temperature. Water s Heat of Vaporization 

Water also has a high heat of vaporization , the amount of energy required to change one gram of a liquid substance to a gas. A considerable amount of heat energy (586 cal) is required to accomplish this change in water. This process occurs on the surface of water. As liquid water heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each other, which is required for it to enter its gaseous phase (steam). As a result, water acts as a heat sink or heat reservoir and requires much more heat to boil than does a liquid such as ethanol (grain alcohol), whose hydrogen bonding with other ethanol molecules is weaker than water s hydrogen bonding. Eventually, as water reaches its boiling point of 100 Celsius (212 Fahrenheit), the heat is able to break the hydrogen bonds between the water molecules, and the kinetic energy (motion) between the water molecules allows them to escape from the liquid as a gas. Even when below its boiling point, water s individual molecules acquire enough energy from other water molecules such that some surface water molecules can escape and vaporize: this process is known as evaporation . 

The fact that hydrogen bonds need to be broken for water to evaporate means that a substantial amount of energy is used in the process. As the water evaporates, energy is taken up by the process, cooling the environment where the evaporation is taking place. In many living organisms, including in humans, the evaporation of sweat, which is 90 percent water, allows the organism to cool so that homeostasis of body temperature can be maintained. Water s Solvent Properties 

Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve in it. Therefore, water is referred to as a solvent , a substance capable of dissolving other polar molecules and ionic compounds. The charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules. This is referred to as a sphere of hydration , or a hydration shell, as illustrated in [link] and serves to keep the particles separated or dispersed in the water. 

When ionic compounds are added to water, the individual ions react with the polar regions of the water molecules and their ionic bonds are disrupted in the process of dissociation . Dissociation occurs when atoms or groups of atoms break off from molecules and form ions. Consider table salt (NaCl, or sodium chloride): when NaCl crystals are added to water, the molecules of NaCl dissociate into Na + and Cl ions, and spheres of hydration form around the ions, illustrated in [link] . The positively charged sodium ion is surrounded by the partially negative charge of the water molecule s oxygen. The negatively charged chloride ion is surrounded by the partially positive charge of the hydrogen on the water molecule. When table salt (NaCl) is mixed in water, spheres of hydration are formed around the ions. Water s Cohesive and Adhesive Properties 

Have you ever filled a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion . In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-gas (water-air) interface, although there is no more room in the glass. 

Cohesion allows for the development of surface tension , the capacity of a substance to withstand being ruptured when placed under tension or stress. This is also why water forms droplets when placed on a dry surface rather than being flattened out by gravity. When a small scrap of paper is placed onto the droplet of water, the paper floats on top of the water droplet even though paper is denser (heavier) than the water. Cohesion and surface tension keep the hydrogen bonds of water molecules intact and support the item floating on the top. It s even possible to float a needle on top of a glass of water if it is placed gently without breaking the surface tension, as shown in [link] . The weight of the needle is pulling the surface downward; at the same time, the surface tension is pulling it up, suspending it on the surface of the water and keeping it from sinking. Notice the indentation in the water around the needle. (credit: Cory Zanker) 

These cohesive forces are related to water s property of adhesion , or the attraction between water molecules and other molecules. This attraction is sometimes stronger than water s cohesive forces, especially when the water is exposed to charged surfaces such as those found on the inside of thin glass tubes known as capillary tubes. Adhesion is observed when water climbs up the tube placed in a glass of water: notice that the water appears to be higher on the sides of the tube than in the middle. This is because the water molecules are attracted to the charged glass walls of the capillary more than they are to each other and therefore adhere to it. This type of adhesion is called capillary action , and is illustrated in [link] . Capillary action in a glass tube is caused by the adhesive forces exerted by the internal surface of the glass exceeding the cohesive forces between the water molecules themselves. (credit: modification of work by Pearson-Scott Foresman, donated to the Wikimedia Foundation) 

Why are cohesive and adhesive forces important for life? Cohesive and adhesive forces are important for the transport of water from the roots to the leaves in plants. These forces create a pull on the water column. This pull results from the tendency of water molecules being evaporated on the surface of the plant to stay connected to water molecules below them, and so they are pulled along. Plants use this natural phenomenon to help transport water from their roots to their leaves. Without these properties of water, plants would be unable to receive the water and the dissolved minerals they require. In another example, insects such as the water strider, shown in [link] , use the surface tension of water to stay afloat on the surface layer of water and even mate there. Water s cohesive and adhesive properties allow this water strider ( Gerris sp.) to stay afloat. (credit: Tim Vickers) Activity 

During a process called transpiration, water evaporates through a plant s leaves. Water in the ground travels up from the roots to the leaves. Based on water s molecular properties, create a visual representation (e.g., diagrams or models) with annotations to explain how water travels up a 300-ft. California redwood tree. What other unique properties of water are attributed to its molecular structure, and how are these properties important to life? 

This activity is an application of Learning Objectives 2.8 and Science Practice 4.1 and Learning Objectives 2.9 and Science Practices 1.1 and 1.4 because you are modeling the relationship between water s molecular structure and its unique properties that are essential to maintaining life, including capillary action. pH, Buffers, Acids, and Bases 

The pH of a solution indicates its acidity or alkalinity. H 2 O ( l ) H + ( a q ) + OH - ( a q ) H 2 O ( l ) H + ( a q ) + OH - ( a q ) litmus or pH paper, filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid (acidity) or base (alkalinity) exists in a solution. You might have even used some to test whether the water in a swimming pool is properly treated. In both cases, the pH test measures the concentration of hydrogen ions in a given solution. 

Hydrogen ions are spontaneously generated in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of hydrogen (H + ) ions and hydroxide (OH - ) ions. While the hydroxide ions are kept in solution by their hydrogen bonding with other water molecules, the hydrogen ions, consisting of naked protons, are immediately attracted to un-ionized water molecules, forming hydronium ions (H 3 0 + ). Still, by convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water. 

The concentration of hydrogen ions dissociating from pure water is 1 10 -7 moles H + ions per liter of water. Moles (mol) are a way to express the amount of a substance (which can be atoms, molecules, ions, etc), with one mole being equal to 6.02 x 10 23 particles of the substance. Therefore, 1 mole of water is equal to 6.02 x 10 23 water molecules. The pH is calculated as the negative of the base 10 logarithm of this concentration. The log10 of 1 10 -7 is -7.0, and the negative of this number (indicated by the p of pH ) yields a pH of 7.0, which is also known as neutral pH. The pH inside of human cells and blood are examples of two areas of the body where near-neutral pH is maintained. 

Non-neutral pH readings result from dissolving acids or bases in water. Using the negative logarithm to generate positive integers, high concentrations of hydrogen ions yield a low pH number, whereas low levels of hydrogen ions result in a high pH. An acid is a substance that increases the concentration of hydrogen ions (H + ) in a solution, usually by having one of its hydrogen atoms dissociate. A base provides either hydroxide ions (OH ) or other negatively charged ions that combine with hydrogen ions, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules. 

The stronger the acid, the more readily it donates H + . For example, hydrochloric acid (HCl) completely dissociates into hydrogen and chloride ions and is highly acidic, whereas the acids in tomato juice or vinegar do not completely dissociate and are considered weak acids. Conversely, strong bases are those substances that readily donate OH or take up hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners are highly alkaline and give up OH rapidly when placed in water, thereby raising the pH. An example of a weak basic solution is seawater, which has a pH near 8.0, close enough to neutral pH that marine organisms adapted to this saline environment are able to thrive in it. 

The pH scale is, as previously mentioned, an inverse logarithm and ranges from 0 to 14 ( [link] ). Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in pH in either direction from 7.0 are usually considered inhospitable to life. The pH inside cells (6.8) and the pH in the blood (7.4) are both very close to neutral. However, the environment in the stomach is highly acidic, with a pH of 1 to 2. So how do the cells of the stomach survive in such an acidic environment? How do they homeostatically maintain the near neutral pH inside them? The answer is that they cannot do it and are constantly dying. New stomach cells are constantly produced to replace dead ones, which are digested by the stomach acids. It is estimated that the lining of the human stomach is completely replaced every seven to ten days. The pH scale measures the concentration of hydrogen ions (H + ) in a solution. (credit: modification of work by Edward Stevens) 

Watch this video for a straightforward explanation of pH and its logarithmic scale. 

[link] 

So how can organisms whose bodies require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice, for example) and survive? Buffers are the key. Buffers readily absorb excess H + or OH , keeping the pH of the body carefully maintained in the narrow range required for survival. Maintaining a constant blood pH is critical to a person s well-being. The buffer maintaining the pH of human blood involves carbonic acid (H 2 CO 3 ), bicarbonate ion (HCO 3 ), and carbon dioxide (CO 2 ). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, hydrogen ions are removed, moderating pH changes. Similarly, as shown in [link] , excess carbonic acid can be converted to carbon dioxide gas and exhaled through the lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing the blood s pH. Likewise, if too much OH is introduced into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH. Without this buffer system, the body s pH would fluctuate enough to put survival in jeopardy. This diagram shows the body s buffering of blood pH levels. The blue arrows show the process of raising pH as more CO 2 is made. The purple arrows indicate the reverse process: the lowering of pH as more bicarbonate is created. 

Other examples of buffers are antacids used to combat excess stomach acid. Many of these over-the-counter medications work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating pH, bringing relief to those that suffer heartburn after eating. The unique properties of water that contribute to this capacity to balance pH as well as water s other characteristics are essential to sustaining life on Earth. 

To learn more about water. Visit the U.S. Geological Survey Water Science for Schools All About Water! website. 

[link] Acid Rain When rain water is too acidic, it can greatly damage living organisms, such as this forest in the Czech Republic. 

[link] Section Summary 

Water has many properties that are critical to maintaining life. It is a polar molecule, allowing for the formation of hydrogen bonds. Hydrogen bonds allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules cause the water to have a high heat capacity, meaning it takes a lot of added heat to raise its temperature. As the temperature rises, the hydrogen bonds between water continually break and form anew. This allows for the overall temperature to remain stable, although energy is added to the system. Water also exhibits a high heat of vaporization, which is key to how organisms cool themselves by the evaporation of sweat. Water s cohesive forces allow for the property of surface tension, whereas its adhesive properties are seen as water rises inside capillary tubes. The pH value is a measure of hydrogen ion concentration in a solution and is one of many chemical characteristics that is highly regulated in living organisms through homeostasis. Acids and bases can change pH values, but buffers tend to moderate the changes they cause. These properties of water are intimately connected to the biochemical and physical processes performed by living organisms, and life would be very different if these properties were altered, if it could exist at all. Review Questions 

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[link] Critical Thinking Questions 

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[link] Test Prep for AP Courses 

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[link] Footnotes 1 W. Humphrey W., A. Dalke, and K. Schulten, VMD Visual Molecular Dynamics, Journal of Molecular Graphics 14 (1996): 33-38. 2 W. Humphrey W., A. Dalke, and K. Schulten, VMD Visual Molecular Dynamics, Journal of Molecular Graphics 14 (1996): 33-38. Glossary acid molecule that donates hydrogen ions and increases the concentration of hydrogen ions in a solution adhesion attraction between water molecules and other molecules base molecule that donates hydroxide ions or otherwise binds excess hydrogen ions and decreases the concentration of hydrogen ions in a solution buffer substance that prevents a change in pH by absorbing or releasing hydrogen or hydroxide ions calorie amount of heat required to change the temperature of one gram of water by one degree Celsius capillary action occurs because water molecules are attracted to charges on the inner surfaces of narrow tubular structures such as glass tubes, drawing the water molecules to the sides of the tubes cohesion intermolecular forces between water molecules caused by the polar nature of water; responsible for surface tension dissociation release of an ion from a molecule such that the original molecule now consists of an ion and the charged remains of the original, such as when water dissociates into H + and OH - evaporation separation of individual molecules from the surface of a body of water, leaves of a plant, or the skin of an organism heat of vaporization of water high amount of energy required for liquid water to turn into water vapor hydrophilic describes ions or polar molecules that interact well with other polar molecules such as water hydrophobic describes uncharged non-polar molecules that do not interact well with polar molecules such as water litmus paper (also, pH paper) filter paper that has been treated with a natural water-soluble dye that changes its color as the pH of the environment changes so it can be used as a pH indicator pH paper see litmus paper pH scale scale ranging from zero to 14 that is inversely proportional to the concentration of hydrogen ions in a solution solvent substance capable of dissolving another substance specific heat capacity the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius sphere of hydration when a polar water molecule surrounds charged or polar molecules thus keeping them dissolved and in solution surface tension tension at the surface of a body of liquid that prevents the molecules from separating; created by the attractive cohesive forces between the molecules of the liquidCarbon Carbon 

In this section, you will investigate the following questions: Why is carbon important for life? How do functional groups determine the properties of biological molecules? Connection for AP Courses 

The unique properties of carbon make it a central part of biological molecules. With four valence electrons, carbon can covalently bond to oxygen, hydrogen, and nitrogen to form the many molecules important for cellular function. Carbon and hydrogen can form either hydrocarbon chains or rings. Functional groups , such as CH 3 (methyl) and COOH (carboxyl), are groups of atoms that give specific properties to hydrocarbon chains or rings that define their overall chemical characteristics and function. For example, the attachment of a carboxyl group (-COOH) makes a molecule more acidic, whereas the presence of an amine group (NH 2 ) makes a molecule more basic. (As we will explore in the next chapter, amino acids have both a carboxyl group and an amine group.) Isomers are molecules with the same molecular formula (i.e., same kinds and numbers of atoms), but different molecular structures resulting in different properties or functions. (Don t confuse isomer with isotope !) 

The information presented and examples highlighted in this section support concepts and Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.3 Organisms must exchange matter with the environment to grow, reproduce and maintain organization. Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question. Learning Objective 2.8 The student is able to justify the selection of data regarding the types of molecules that an animal, plant, or bacterium will take up as necessary building blocks and excrete as waste products. 

As a class, discuss how important carbon is in life forms. Include in the discussion how proteins, DNA, carbohydrates, biological molecules that distinguish life from inanimate materials, are composed of carbon. You can challenge students to consider a life form based on silicon instead of carbon, using this article as a catalyst. 

Cells are made of many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or backbone, of the macromolecules. 

Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH 4 . Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell. Hydrocarbons 

Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH 4 ) described above. We often use hydrocarbons in our daily lives as fuels like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which is released when these molecules are burned (oxidized). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms, as illustrated in [link] . The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbons and the four hydrogen atoms form a shape known as a tetrahedron, with four triangular faces; for this reason, methane is described as having tetrahedral geometry. Methane has a tetrahedral geometry, with each of the four hydrogen atoms spaced 109.5 apart. 

As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the geometry of the molecule in a specific way. This three-dimensional shape or conformation of the large molecules of life (macromolecules) is critical to how they function. Hydrocarbon Chains 

Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched or unbranched. Furthermore, the overall geometry of the molecule is altered by the different geometries of single, double, and triple covalent bonds, illustrated in [link] . The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the geometry of the molecule. The names of all three molecules start with the prefix eth-, which is the prefix for two carbon hydrocarbons. The suffixes -ane, -ene, and -yne refer to the presence of single, double, or triple carbon-carbon bonds, respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butane, and butyne for four carbon molecules, and so on. Double and triple bonds change the geometry of the molecule: single bonds allow rotation along the axis of the bond, whereas double bonds lead to a planar configuration and triple bonds to a linear one. These geometries have a significant impact on the shape a particular molecule can assume. When carbon forms single bonds with other atoms, the shape is tetrahedral. When two carbon atoms form a double bond, the shape is planar, or flat. Single bonds, like those found in ethane, are able to rotate. Double bonds, like those found in ethene cannot rotate, so the atoms on either side are locked in place. Hydrocarbon Rings 

So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons , which consist of linear chains of carbon atoms. Another type of hydrocarbon, aromatic hydrocarbons , consists of closed rings of carbon atoms. Ring structures are found in hydrocarbons, sometimes with the presence of double bonds, which can be seen by comparing the structure of cyclohexane to benzene in [link] . Examples of biological molecules that incorporate the benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. The benzene ring is also found in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen. Some hydrocarbons have both aliphatic and aromatic portions; beta-carotene is an example of such a hydrocarbon. Carbon can form five-and six membered rings. Single or double bonds may connect the carbons in the ring, and nitrogen may be substituted for carbon. Isomers 

The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. Molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds are known as isomers. Structural isomers (like butane and isobutene shown in figure a ) differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C 4 H 10 ), but the different arrangement of the atoms within the molecules leads to differences in their chemical properties. For example, due to their different chemical properties, butane is suited for use as a fuel for cigarette lighters and torches, whereas isobutene is suited for use as a refrigerant and a propellant in spray cans. 

Geometric isomers , on the other hand, have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule butene (C 4 H 8 ), the two methyl groups (CH 3 ) can be on either side of the double covalent bond central to the molecule, as illustrated in figure b . When the carbons are bound on the same side of the double bond, this is the cis configuration; if they are on opposite sides of the double bond, it is a trans configuration. In the trans configuration, the carbons form a more or less linear structure, whereas the carbons in the cis configuration make a bend (change in direction) of the carbon backbone. Molecules that have the same number and type of atoms arranged differently are called isomers. (a) Structural isomers have a different covalent arrangement of atoms. (b) Geometric isomers have a different arrangement of atoms around a double bond. (c) Enantiomers are mirror images of each other. 

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In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis or trans configuration, illustrated in [link] . Fats with at least one double bond between carbon atoms are unsaturated fats. When some of these bonds are in the cis configuration, the resulting bend in the carbon backbone of the chain means that triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. On the other hand, triglycerides with trans double bonds (popularly called trans fats), have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats. In the human diet, trans fats are linked to an increased risk of cardiovascular disease, so many food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, triglycerides without double bonds between carbon atoms are called saturated fats, meaning that they contain all the hydrogen atoms available. Saturated fats are a solid at room temperature and usually of animal origin. These space-filling models show a cis (oleic acid) and a trans (eliadic acid) fatty acid. Notice the bend in the molecule cause by the cis configuration. Enantiomers 

Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are mirror images. As shown in [link] , an amino acid alanine example, the two structures are non-superimposable. In nature, only the L-forms of amino acids are used to make proteins. Some D forms of amino acids are seen in the cell walls of bacteria, but never in their proteins. Similarly, the D-form of glucose is the main product of photosynthesis and the L-form of the molecule is rarely seen in nature. D-alanine and L-alanine are examples of enantiomers or mirror images. Only the L-forms of amino acids are used to make proteins. Functional Groups 

Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. They are found along the carbon backbone of macromolecules. This carbon backbone is formed by chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen. Molecules with other elements in their carbon backbone are substituted hydrocarbons . 

The functional groups in a macromolecule are usually attached to the carbon backbone at one or several different places along its chain and/or ring structure. Each of the four types of macromolecules proteins, lipids, carbohydrates, and nucleic acids has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms. 

A functional group can participate in specific chemical reactions. Some of the important functional groups in biological molecules are shown in [link] ; they include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the non-polar methane molecule. Among the hydrophilic functional groups is the carboxyl group found in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H + ) from the COOH group resulting in the negatively charged COO - group; this contributes to the hydrophilic nature of whatever molecule it is found on. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic. The functional groups shown here are found in many different biological molecules. 

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate, as illustrated in [link] . Hydrogen bonds connect two strands of DNA together to create the double-helix structure. Activity 

Carbon forms the backbone of important biological molecules. Create a mini-poster of a simple food chain that shows how carbon enters and exits each organism on the chain. Based on the food chain you created, make a prediction regarding the impact of human activity on the supply of carbon in the food chain. 

This activity is an application of Learning Objectives 2.8 and Science Practice 4.1 because the student is describing the types of molecules that organisms take up as necessary building blocks or excrete as wastes. 

The carbon cycle involves the movement of carbon between the atmosphere, biosphere, and oceans. Human activities have an effect on the carbon cycle, resulting in the rise of carbon dioxide in the atmosphere and acidification of the oceans due to the burning of fossil fuels. Deforestation leads to decreased absorption of carbon dioxide by plants for photosynthesis. Section Summary 

The unique properties of carbon make it a central part of biological molecules. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function. Carbon has four electrons in its outermost shell and can form four bonds. Carbon and hydrogen can form hydrocarbon chains or rings. Functional groups are groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function. Review Questions 

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[link] Glossary aliphatic hydrocarbon hydrocarbon consisting of a linear chain of carbon atoms aromatic hydrocarbon hydrocarbon consisting of closed rings of carbon atoms enantiomers molecules that share overall structure and bonding patterns, but differ in how the atoms are three dimensionally placed such that they are mirror images of each other functional group group of atoms that provides or imparts a specific function to a carbon skeleton geometric isomer isomer with similar bonding patterns differing in the placement of atoms alongside a double covalent bond hydrocarbon molecule that consists only of carbon and hydrogen isomers molecules that differ from one another even though they share the same chemical formula organic molecule any molecule containing carbon (except carbon dioxide) structural isomers molecules that share a chemical formula but differ in the placement of their chemical bonds substituted hydrocarbon hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbonsIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Foods such as bread, fruit, and cheese are rich sources of biological macromolecules. (credit: modification of work by Bengt Nyman) 

Food provides the body with the nutrients it needs to survive. Many of these critical nutrients are biological macromolecules, or large molecules, necessary for and built by living things. For example, the amino acids found in protein are needed to build healthy bone and muscle. The body uses fat molecules to build new cells, store energy, and for proper digestion. Carbohydrates are the primary source of the body s energy. Nucleic acids contain genetic information. 

While all living things, including humans, need macromolecules in their daily diet, an imbalance of any one of them can lead to health problems. For example, eating too much fat can lead to cardiovascular problems, and too much protein can lead to problems with the kidneys. Some people think that removing whole grains, such as wheat, from one s diet can be beneficial. However, scientists have found that to not be true for the majority of people. In fact, just the opposite may be true, because whole wheat contains more dietary fiber than other types of grains. The full research review can be found here . 

Stress from the beginning that most chemicals used by the body that are made up of smaller units strung together for specific functions are termed macromolecules. The same methods of combination and separation are used for all of these molecules.Synthesis of Biological Macromolecules Synthesis of Biological Macromolecules 

In this section, you will explore the following questions: How are complex macromolecule polymers synthesized from monomers? What is the difference between dehydration (or condensation) and hydrolysis reactions? Connection for AP Courses 

Living organisms need food to survive as it contains critical nutrients in the form of biological macromolecules. These large molecules are composed mainly of six elements sulfur, phosphorus, oxygen, nitrogen, carbon, and hydrogen (SPONCH) in different quantities and arrangements. Complex polymers are built from combinations of smaller monomers by dehydration synthesis, a chemical reaction in which a molecule of water is removed between two linking monomers. (Think of a train: each boxcar, including the caboose, represents a monomer, and the entire train is a polymer.) During digestion, polymers can be broken down by hydrolysis, or the addition of water. Both dehydration and hydrolysis reactions in cells are catalyzed by specific enzymes. Dehydration reactions typically require an investment of energy for new bond formation, whereas hydrolysis reactions typically release energy that can be used to power cellular processes. The four categories of macromolecules are carbohydrates, lipids, proteins, and nucleic acids. Evidence supports scientists claim that the organic precursors of these biological molecules were present on primitive Earth. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 1 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A learning objective merges required content with one or more of the seven Science Practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life 

Enduring Understanding 1.D The origin of living systems is explained by natural processes. Essential Knowledge 1.D.1 There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence. Science Practice 1.2 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 1.27 The student is able to describe a scientific hypothesis about the origin of life on Earth. Essential Knowledge 1.D.1 There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence. Science Practice 3.3 The student can evaluate scientific questions. Learning Objective 1.28 The student is able to evaluate scientific questions based on hypotheses about the origin of life on Earth. 

Stress to the class that macromolecules are produced through dehydration synthesis and taken apart through hydrolysis. As the names imply, water is involved in both cases. Dehydration Synthesis 

As you ve learned, biological macromolecules are large molecules, necessary for life, that are built from smaller organic molecules. There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids); each is an important cell component and performs a wide array of functions. Combined, these molecules make up the majority of a cell s dry mass (recall that water makes up the majority of its complete mass). Biological macromolecules are organic, meaning they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, and additional minor elements. 

Most macromolecules are made from single subunits, or building blocks, called monomers . The monomers combine with each other using covalent bonds to form larger molecules known as polymers . In doing so, monomers release water molecules as byproducts. This type of reaction is known as dehydration synthesis , which means to put together while losing water. In the dehydration synthesis reaction depicted above, two molecules of glucose are linked together to form the disaccharide maltose. In the process, a water molecule is formed. 

Explain that when something is dehydrated, water is removed from it. Identify the specific hydrogen and specific hydroxyl group in the models or illustrations that are removed from two monomers to make the water. The remaining oxygen atom is used to link the two monomers together. 

Hydrolysis is the splitting or lysis of a bond between monomers within a polymer, using water. Explain that the two parts of water, the hydrogen atom and hydroxyl group, are added to the monomers after the separation from the polymer, with the result that each has a hydroxyl group where the oxygen molecule linking them was found. 

Ask the students what came first, biological chemicals or intact cells? Then discuss Miller and Urey s experiments. They can attempt to explain how these complex macromolecules could be created in the absence of life. The resulting molecules floated around in the atmosphere and eventually fell into the early oceans, then probably became incorporated into primitive cells. 

In a dehydration synthesis reaction ( [link] ), the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water. At the same time, the monomers share electrons and form covalent bonds. As additional monomers join, this chain of repeating monomers forms a polymer. Different types of monomers can combine in many configurations, giving rise to a diverse group of macromolecules. Even one kind of monomer can combine in a variety of ways to form several different polymers: for example, glucose monomers are the constituents of starch, glycogen, and cellulose. Hydrolysis 

Polymers are broken down into monomers in a process known as hydrolysis, which means to split with water. Hydrolysis is a reaction in which a water molecule is used during the breakdown of another compound ( [link] ). During these reactions, the polymer is broken into two components: one part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH ) from a split water molecule. In the hydrolysis reaction shown here, the disaccharide maltose is broken down to form two glucose monomers with the addition of a water molecule. Note that this reaction is the reverse of the synthesis reaction shown in [link] . 

Dehydration and hydrolysis reactions are catalyzed, or sped up, by specific enzymes; dehydration reactions involve the formation of new bonds, requiring energy, while hydrolysis reactions break bonds and release energy. These reactions are similar for most macromolecules, but each monomer and polymer reaction is specific for its class. For example, in our bodies, food is hydrolyzed, or broken down, into smaller molecules by catalytic enzymes in the digestive system. This allows for easy absorption of nutrients by cells in the intestine. Each macromolecule is broken down by a specific enzyme. For instance, carbohydrates are broken down by amylase, sucrase, lactase, or maltase. Proteins are broken down by the enzymes pepsin and peptidase, and by hydrochloric acid. Lipids are broken down by lipases. Breakdown of these macromolecules provides energy for cellular activities. Link to Learning 

Visit this site to see visual representations of dehydration synthesis and hydrolysis. 

[link] Recreating Primordial Earth 

Many people wonder how life formed on Earth. In 1953, Stanley Miller and Harold Urey developed an apparatus like the one shown in [link] to model early conditions on earth. They wanted to test if organic molecules could form from inorganic precursors believed to exist very early in Earth s history. They used boiling water to mimic early Earth s oceans. Steam from the ocean combined with methane, ammonia, and hydrogen gases from the early Earth s atmosphere and was exposed to electrical sparks to act as lightning. As the gas mixture cooled and condensed, it was found to contain organic compounds, such as amino acids and nucleotides. According to the abiogenesis theory, these organic molecules came together to form the earliest form of life about 3.5 billion years ago. (credit: Yassine Mrabet) Think About It 

How does Stanley Miller s and Harold Urey s model support the claim that organic precursors present on early Earth could have assembled into large, complex molecules necessary for life? What chemical ingredients were present on early Earth? 

This question is an application of Learning Objectives 1.27 and Science Practice 1.2 because students are asked to describe how the organic soup model supports the formation of complex polymers from simple organic precursors. Section Summary 

Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromolecules large molecules necessary for life that are built from smaller organic molecules. Macromolecules are made up of single units known as monomers that are joined by covalent bonds to form larger polymers. The polymer is more than the sum of its parts: it acquires new characteristics, and leads to an osmotic pressure that is much lower than that formed by its ingredients; this is an important advantage in the maintenance of cellular osmotic conditions. A monomer joins with another monomer with the release of a water molecule, leading to the formation of a covalent bond. These types of reactions are known as dehydration or condensation reactions. When polymers are broken down into smaller units (monomers), a molecule of water is used for each bond broken by these reactions; such reactions are known as hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Dehydration reactions typically require an investment of energy for new bond formation, while hydrolysis reactions typically release energy by breaking bonds. Review Questions 

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[link] Glossary biological macromolecule large molecule necessary for life that is built from smaller organic molecules dehydration synthesis (also, condensation) reaction that links monomer molecules together, releasing a molecule of water for each bond formed hydrolysis reaction causes breakdown of larger molecules into smaller molecules with the utilization of water monomer smallest unit of larger molecules called polymers polymer chain of monomer residues that is linked by covalent bonds; polymerization is the process of polymer formation from monomers by condensationCarbohydrates Carbohydrates 

By the end of this section, you will be able to: What is the role of carbohydrates in cells and in the extracellular materials of animals and plants? What are the different classifications of carbohydrates? How are monosaccharide building blocks assembled into disaccharides and complex polysaccharides? Connection for AP Courses 

Carbohydrates provide energy for the cell and structural support to plants, fungi, and arthropods such as insects, spiders, and crustaceans. Consisting of carbon, hydrogen, and oxygen in the ratio CH 2 O or carbon hydrated with water, carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the macromolecule. Monosaccharides are linked by glycosidic bonds that form as a result of dehydration synthesis. Glucose, galactose, and fructose are common isomeric monosaccharides, whereas sucrose or table sugar is a disaccharide. Examples of polysaccharides include cellulose and starch in plants and glycogen in animals. Although storing glucose in the form of polymers like starch or glycogen makes it less accessible for metabolism, this prevents it from leaking out of cells or creating a high osmotic pressure that could cause excessive water uptake by the cell. Insects have a hard outer skeleton made of chitin, a unique nitrogen-containing polysaccharide. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 4 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 4.1 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 1.3 The student can refine representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 6.1 The student can justify claims with evidence. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecules. Molecular Structures 

Most people are familiar with carbohydrates, one type of macromolecule, especially when it comes to what we eat. To lose weight, some individuals adhere to low-carb diets. Athletes, in contrast, often carb-load before important competitions to ensure that they have enough energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. Carbohydrates also have other important functions in humans, animals, and plants. 

Carbohydrates can be represented by the stoichiometric formula (CH 2 O) n , where n is the number of carbons in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This formula also explains the origin of the term carbohydrate : the components are carbon ( carbo ) and the components of water (hence, hydrate ). Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides. Monosaccharides 

Monosaccharides (mono- = one ; sacchar- = sweet ) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbons usually ranges from three to seven. Most monosaccharide names end with the suffix -ose. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is known as an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R'), it is known as a ketose. Depending on the number of carbons in the sugar, they also may be known as trioses (three carbons), pentoses (five carbons), and or hexoses (six carbons). See [link] for an illustration of the monosaccharides. Monosaccharides are classified based on the position of their carbonyl group and the number of carbons in the backbone. Aldoses have a carbonyl group (indicated in green) at the end of the carbon chain, and ketoses have a carbonyl group in the middle of the carbon chain. Trioses, pentoses, and hexoses have three, five, and six carbon backbones, respectively. 

The chemical formula for glucose is C 6 H 12 O 6 . In humans, glucose is an important source of energy. During cellular respiration, energy is released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water, and glucose in turn is used for energy requirements for the plant. Excess glucose is often stored as starch that is catabolized (the breakdown of larger molecules by cells) by humans and other animals that feed on plants. 

Galactose (part of lactose, or milk sugar) and fructose (found in sucrose, in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C 6 H 12 O 6 ), they differ structurally and chemically (and are known as isomers) because of the different arrangement of functional groups around the asymmetric carbon; all of these monosaccharides have more than one asymmetric carbon ( (Figure) ). 

Glucose, galactose, and fructose are all hexoses. They are structural isomers, meaning they have the same chemical formula (C 6 H 12 O 6 ) but a different arrangement of atoms. 

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Glucose, galactose, and fructose are isomeric monosaccharides (hexoses), meaning they have the same chemical formula but have slightly different structures. Glucose and galactose are aldoses, and fructose is a ketose. 

Monosaccharides can exist as a linear chain or as ring-shaped molecules; in aqueous solutions they are usually found in ring forms ( [link] ). Glucose in a ring form can have two different arrangements of the hydroxyl group (OH) around the anomeric carbon (carbon 1 that becomes asymmetric in the process of ring formation). If the hydroxyl group is below carbon number 1 in the sugar, it is said to be in the alpha ( ) position, and if it is above the plane, it is said to be in the beta ( ) position. Five and six carbon monosaccharides exist in equilibrium between linear and ring forms. When the ring forms, the side chain it closes on is locked into an or position. Fructose and ribose also form rings, although they form five-membered rings as opposed to the six-membered ring of glucose. Disaccharides 

Disaccharides (di- = two ) form when two monosaccharides undergo a dehydration reaction (also known as a condensation reaction or dehydration synthesis). During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond formed between a carbohydrate molecule and another molecule (in this case, between two monosaccharides) is known as a glycosidic bond ( [link] ). Glycosidic bonds (also called glycosidic linkages) can be of the alpha or the beta type. Sucrose is formed when a monomer of glucose and a monomer of fructose are joined in a dehydration reaction to form a glycosidic bond. In the process, a water molecule is lost. By convention, the carbon atoms in a monosaccharide are numbered from the terminal carbon closest to the carbonyl group. In sucrose, a glycosidic linkage is formed between carbon 1 in glucose and carbon 2 in fructose. 

Common disaccharides include lactose, maltose, and sucrose ( [link] ). Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose. Common disaccharides include maltose (grain sugar), lactose (milk sugar), and sucrose (table sugar). Polysaccharides 

A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide (poly- = many ). The chain may be branched or unbranched, and it may contain different types of monosaccharides. The molecular weight may be 100,000 daltons or more depending on the number of monomers joined. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides. 

Starch is the stored form of sugars in plants and is made up of a mixture of amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose, and the excess glucose, beyond the plant s immediate energy needs, is stored as starch in different plant parts, including roots and seeds. The starch in the seeds provides food for the embryo as it germinates and can also act as a source of food for humans and animals. The starch that is consumed by humans is broken down by enzymes, such as salivary amylases, into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose. 

Starch is made up of glucose monomers that are joined by 1-4 or 1-6 glycosidic bonds. The numbers 1-4 and 1-6 refer to the carbon number of the two residues that have joined to form the bond. As illustrated in [link] , amylose is starch formed by unbranched chains of glucose monomers (only 1-4 linkages), whereas amylopectin is a branched polysaccharide ( 1-6 linkages at the branch points). Amylose and amylopectin are two different forms of starch. Amylose is composed of unbranched chains of glucose monomers connected by 1,4 glycosidic linkages. Amylopectin is composed of branched chains of glucose monomers connected by 1,4 and 1,6 glycosidic linkages. Because of the way the subunits are joined, the glucose chains have a helical structure. Glycogen (not shown) is similar in structure to amylopectin but more highly branched. Obtain copies of metabolic charts and use them to illustrate to students the connections between carbohydrate metabolism, lipid and amino acid production and breakdown. Have the students trace a molecule of glucose through its metabolism and identify the linkage points between macromolecule pathways. Ask the students what happens when excess sugar is ingested, at the molecular level. Have the class research the dangers of excess carbohydrate intake, including the health hazards that can result. Suggest that they research a condition relevant to their family. Carbohydrates or sugars include more than just table sugar. All have the basic formula CH 2 O. The ratio of carbon, hydrogen, and oxygen is always the same. The number of carbons determines the category of sugar. Biological sugars are usually pentoses (5 carbon or C 5 H 10 O 5 ) or hexoses (6 carbon or C 6 H 12 O 6 ). Monosaccharides are the building blocks of all sugars. If two are combined, they are disaccharides; if more than two are combined, they make up a large molecule called a polysaccharide. The type of linkage between the monomers determines whether animals can digest them. If the oxygen linking the monomers is oriented down relative to both adjacent carbons, it is called an alpha bond and can be digested. If the oxygen atom orients upward relative to one carbon and downward relative to the next, it is called a beta bond and is not able to be digested by animal digestive enzymes. In the United States, people consume large quantities of carbohydrates, often in the form of sugars. Carbohydrates provide an immediate source of energy when broken down. They are also involved in the metabolism of other types of macromolecules. Sugars can be converted into a number of amino acids, nucleic acids, and fats as needed by the body. 

Glycogen is the storage form of glucose in humans and other vertebrates and is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process known as glycogenolysis. 

Cellulose is the most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose; this provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by 1-4 glycosidic bonds ( [link] ). In cellulose, glucose monomers are linked in unbranched chains by 1-4 glycosidic linkages. Because of the way the glucose subunits are joined, every glucose monomer is flipped relative to the next one resulting in a linear, fibrous structure. 

As shown in [link] , every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength which is so important to plant cells. While the 1-4 linkage cannot be broken down by human digestive enzymes, herbivores such as cows, koalas, buffalos, and horses are able, with the help of the specialized flora in their stomach, to digest plant material that is rich in cellulose and use it as a food source. In these animals, certain species of bacteria and protists reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal. Termites are also able to break down cellulose because of the presence of other organisms in their bodies that secrete cellulases. 

Carbohydrates serve various functions in different animals. Arthropods (insects, crustaceans, and others) have an outer skeleton, called the exoskeleton, which protects their internal body parts (as seen in the bee in [link] ). This exoskeleton is made of the biological macromolecule chitin , which is a polysaccharide-containing nitrogen. It is made of repeating units of N-acetyl- -d-glucosamine, a modified sugar. Chitin is also a major component of fungal cell walls; fungi are neither animals nor plants and form a kingdom of their own in the domain Eukarya. Insects have a hard outer exoskeleton made of chitin, a type of polysaccharide. (credit: Louise Docker) Registered Dietitian 

Obesity is a worldwide health concern, and many diseases such as diabetes and heart disease are becoming more prevalent because of obesity. This is one of the reasons why registered dietitians are increasingly sought after for advice. Registered dietitians help plan nutrition programs for individuals in various settings. They often work with patients in health care facilities, designing nutrition plans to treat and prevent diseases. For example, dietitians may teach a patient with diabetes how to manage blood sugar levels by eating the correct types and amounts of carbohydrates. Dietitians may also work in nursing homes, schools, and private practices. 

To become a registered dietitian, one needs to earn at least a bachelor s degree in dietetics, nutrition, food technology, or a related field. In addition, registered dietitians must complete a supervised internship program and pass a national exam. Those who pursue careers in dietetics take courses in nutrition, chemistry, biochemistry, biology, microbiology, and human physiology. Dietitians must become experts in the chemistry and physiology (biological functions) of food (proteins, carbohydrates, and fats). Benefits of Carbohydrates 

Are carbohydrates good for you? People who wish to lose weight are often told that carbohydrates are bad for them and should be avoided. Some diets completely forbid carbohydrate consumption, claiming that a low-carbohydrate diet helps people to lose weight faster. However, carbohydrates have been an important part of the human diet for thousands of years; artifacts from ancient civilizations show the presence of wheat, rice, and corn in our ancestors storage areas. 

Carbohydrates should be supplemented with proteins, vitamins, and fats to be parts of a well-balanced diet. Calorie-wise, a gram of carbohydrate provides 4.3 Kcal. For comparison, fats provide 9 Kcal/g, a less desirable ratio. Carbohydrates contain soluble and insoluble elements; the insoluble part is known as fiber, which is mostly cellulose. Fiber has many uses; it promotes regular bowel movement by adding bulk, and it regulates the rate of consumption of blood glucose. Fiber also helps to remove excess cholesterol from the body: fiber binds to the cholesterol in the small intestine, then attaches to the cholesterol and prevents the cholesterol particles from entering the bloodstream, and then cholesterol exits the body via the feces. Fiber-rich diets also have a protective role in reducing the occurrence of colon cancer. In addition, a meal containing whole grains and vegetables gives a feeling of fullness. As an immediate source of energy, glucose is broken down during the process of cellular respiration, which produces ATP, the energy currency of the cell. Without the consumption of carbohydrates, the availability of instant energy would be reduced. Eliminating carbohydrates from the diet is not the best way to lose weight. A low-calorie diet that is rich in whole grains, fruits, vegetables, and lean meat, together with plenty of exercise and plenty of water, is the more sensible way to lose weight. 

For an additional perspective on carbohydrates, explore Biomolecules: the Carbohydrates through this interactive animation . 

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Use a molecular model kit to construct a polysaccharide from several different monosaccharide monomers. Explain how the structure of the polysaccharide determines its primary function as an energy storage molecule. Then use your model to describe how changes in structure result in changes in function. Think About It Explain why athletes often carb-load before a big game or tournament. Explain why it is difficult for some animals, including humans, to digest cellulose. Describe a structural difference between cellulose and starch, which is easily digested by humans. How are cows and other ruminants able to digest cellulose? 

This activity is an application of Learning Objective 4.1 and Science Practice 7.1 and Learning Objective 4.3 and science practices 6.1 and 6.4 because students first construct a model to show the connection between structure and function at the molecular level and then use the model to predict how changes in structure at the molecular level can affect a molecule s properties and function(s). 

The first Think About It question is an application of Learning Objective 4.1 and Science Practice 7.1 because students are connecting the structure of a molecule to its function. 

The second Think About It question is an application of Learning Objective 4.1 and Science Practice 7.1 and Learning Objective 4.2 and Science Practice 1.3 because students are using representations of the structural features of molecules to explain the relationship between its structure and its properties function(s). Section Summary 

Carbohydrates are a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and all of the arthropods that include lobsters, crabs, shrimp, insects, and spiders. Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the molecule. Monosaccharides are linked by glycosidic bonds that are formed as a result of dehydration reactions, forming disaccharides and polysaccharides with the elimination of a water molecule for each bond formed. Glucose, galactose, and fructose are common monosaccharides, whereas common disaccharides include lactose, maltose, and sucrose. Starch and glycogen, examples of polysaccharides, are the storage forms of glucose in plants and animals, respectively. The long polysaccharide chains may be branched or unbranched. Cellulose is an example of an unbranched polysaccharide, whereas amylopectin, a constituent of starch, is a highly branched molecule. Storage of glucose, in the form of polymers like starch of glycogen, makes it slightly less accessible for metabolism; however, this prevents it from leaking out of the cell or creating a high osmotic pressure that could cause excessive water uptake by the cell. Review Questions 

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[link] Glossary carbohydrate biological macromolecule in which the ratio of carbon to hydrogen and to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells and form the a cellular exoskeleton of arthropods cellulose polysaccharide that makes up the cell wall of plants; provides structural support to the cell chitin type of carbohydrate that forms the outer skeleton of all arthropods that include crustaceans and insects; it also forms the cell walls of fungi disaccharide two sugar monomers that are linked together by a glycosidic bond glycogen storage carbohydrate in animals glycosidic bond bond formed by a dehydration reaction between two monosaccharides with the elimination of a water molecule monosaccharide single unit or monomer of carbohydrates polysaccharide long chain of monosaccharides; may be branched or unbranched starch storage carbohydrate in plantsProteins Proteins 

In this section, you will investigate the following questions: What are functions of proteins in cells and tissues? What is the relationship between amino acids and proteins? What are the four levels of protein organization? What is the relationship between protein shape and function? Connection for AP Courses 

Proteins are long chains of different sequences of the 20 amino acids that each contain an amino group (-NH 2 ), a carboxyl group (-COOH), and a variable group. (Think of how many protein words can be made with 20 amino acid letters ). Each amino acid is linked to its neighbor by a peptide bond formed by a dehydration reaction. A long chain of amino acids is known as a polypeptide. Proteins serve many functions in cells. They act as enzymes that catalyze chemical reactions, provide structural support, regulate the passage of substances across the cell membrane, protect against disease, and coordinate cell signaling pathways. Protein structure is organized at four levels: primary, secondary, tertiary, and quaternary. The primary structure is the unique sequence of amino acids. A change in just one amino acid can change protein structure and function. For example, sickle cell anemia results from just one amino acid substitution in a hemoglobin molecule consisting of 574 amino acids. The secondary structure consists of the local folding of the polypeptide by hydrogen bond formation; leading to the helix and pleated sheet conformations. In the tertiary structure, various interactions, e.g., hydrogen bonds, ionic bonds, disulfide linkages, and hydrophobic interactions between R groups, contribute to the folding of the polypeptide into different three-dimensional configurations. Most enzymes are of tertiary configuration. If a protein is denatured, loses its three-dimensional shape, it may no longer be functional. Environmental conditions such as temperature and pH can denature proteins. Some proteins, such as hemoglobin, are formed from several polypeptides, and the interactions of these subunits form the quaternary structure of proteins. 

Information presented and the examples highlighted in the section, support concepts and Learning Objectives outlined in Big Idea 4 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven science practices. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 1.3 The student can refine representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 6.1 The student can justify claims with evidence. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecules. 

Twenty amino acids can be formed into a nearly limitless number of different proteins. The sequence of the amino acids ultimately determines the final configuration of the protein chain, giving the molecule its specific function. 

Emphasize that proteins have a variety of functions in the body. Table 3.1 contains some examples of these functions. Note that not all enzymes work under the same conditions. Amylase only works in an alkaline medium, such as in saliva, while pepsin works in the acid environment of the stomach. Discuss other materials that can be carried by protein in body fluids in addition to the substances listed for transport in the text. Proteins also carry insoluble lipids in the body and transport charged ions, such as calcium, magnesium, and zinc. Discuss another important structural protein, collagen, as it is found throughout the body, including in most connective tissues. Emphasize that not all hormones are proteins and that steroid based hormones were discussed in the previous section. 

The amino group of an amino acid loses an electron and becomes positively charged. The carboxyl group easily gains an electron, becoming negatively charged. This results in the amphipathic characteristic of amino acids and gives the compounds solubility in water. The presence of both functional groups also allows dehydration synthesis to join the individual amino acids into a peptide chain. 

Protein structure is explained as though it occurs in three to four discrete steps. In reality, the structural changes that result in a functional protein occur on a continuum. As the primary structure is formed off the ribosomes, the polypeptide chain goes through changes until the final configuration is achieved. Have the students imagine a strand of spaghetti as it cooks in a clear pot. Initially, the strand is straight (ignore the stiffness for this example). While it cooks, the strand will bend and twist and (again, for this example), fold itself into a loose ball made up of the strand of pasta. The resulting strand has a particular shape. Ask the students what types of chemical bonds or forces might affect protein structure. These shapes are dictated by the position of amino acids along the strand. Other forces will complete the folding and maintain the structure. Types and Functions of Proteins 

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence. 

Enzymes , which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) it acts on. The enzyme may help in breakdown, rearrangement, or synthesis reactions. Enzymes that break down their substrates are called catabolic enzymes, enzymes that build more complex molecules from their substrates are called anabolic enzymes, and enzymes that affect the rate of reaction are called catalytic enzymes. It should be noted that all enzymes increase the rate of reaction and, therefore, are considered to be organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch. 

Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps to regulate the blood glucose level. The primary types and functions of proteins are listed in [link] . Protein Types and Functions Type Examples Functions Digestive Enzymes Amylase, lipase, pepsin, trypsin Help in digestion of food by catabolizing nutrients into monomeric units Transport Hemoglobin, albumin Carry substances in the blood or lymph throughout the body Structural Actin, tubulin, keratin Construct different structures, like the cytoskeleton Hormones Insulin, thyroxine Coordinate the activity of different body systems Defense Immunoglobulins Protect the body from foreign pathogens Contractile Actin, myosin Effect muscle contraction Storage Legume storage proteins, egg white (albumin) Provide nourishment in early development of the embryo and the seedling 

Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function, and this shape is maintained by many different types of chemical bonds. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to loss of function, known as denaturation . All proteins are made up of different arrangements of the same 20 types of amino acids. Amino Acids 

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha ( ) carbon, bonded to an amino group (NH 2 ), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group ( [link] ). Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached. 

The name "amino acid" is derived from the fact that they contain both amino group and carboxyl-acid-group in their basic structure. As mentioned, there are 20 amino acids present in proteins. Ten of these are considered essential amino acids in humans because the human body cannot produce them and they are obtained from the diet. For each amino acid, the R group (or side chain) is different ( [link] ). 

There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature. 

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The chemical nature of the side chain determines the nature of the amino acid (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also known as basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the standard structure of an animo acid since its amino group is not separate from the side chain ( [link] ). 

Amino acids are represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val. Just as some fatty acids are essential to a diet, some amino acids are necessary as well. They are known as essential amino acids, and in humans they include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary for construction of proteins in the body, although not produced by the body; which amino acids are essential varies from organism to organism. 

The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond , which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water. The resulting bond is the peptide bond ( [link] ). Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the amino group of the incoming amino acid. In the process, a molecule of water is released. 

The products formed by such linkages are called peptides. As more amino acids join to this growing chain, the resulting chain is known as a polypeptide. Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require the addition of other chemical groups. Only after these modifications is the protein completely functional. 

Click through the steps of protein synthesis in this interactive tutorial . 

[link] The Evolutionary Significance of Cytochrome c 

Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally found in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the central ion of the heme gets alternately reduced and oxidized during electron transfer. Because this essential protein s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species; in other words, evolutionary kinship can be assessed by measuring the similarities or differences among various species DNA or protein sequences. 

Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that has been sequenced to date, 37 of these amino acids appear in the same position in all samples of cytochrome c. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, the single difference found was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position. 

[link] Protein Structure 

As discussed earlier, the shape of a protein is critical to its function. For example, an enzyme can bind to a specific substrate at a site known as the active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary. Primary Structure 

The unique sequence of amino acids in a polypeptide chain is its primary structure . For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulfide bonds. The N terminal amino acid of the A chain is glycine, whereas the C terminal amino acid is asparagine ( [link] ). The sequences of amino acids in the A and B chains are unique to insulin. Bovine serum insulin is a protein hormone made of two peptide chains, A (21 amino acids long) and B (30 amino acids long). In each chain, primary structure is indicated by three-letter abbreviations that represent the names of the amino acids in the order they are present. The amino acid cysteine (cys) has a sulfhydryl (SH) group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to form a disulfide (S-S) bond. Two disulfide bonds connect the A and B chains together, and a third helps the A chain fold into the correct shape. Note that all disulfide bonds are the same length, but are drawn different sizes for clarity. 

The unique sequence for every protein is ultimately determined by the gene encoding the protein. A change in nucleotide sequence of the gene s coding region may lead to a different amino acid being added to the growing polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin chain (a small portion of which is shown in [link] ) has a single amino acid substitution, causing a change in protein structure and function. Specifically, the amino acid glutamic acid is substituted by valine in the chain. What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule which dramatically decreases life expectancy is a single amino acid of the 600. What is even more remarkable is that those 600 amino acids are encoded by three nucleotides each, and the mutation is caused by a single base change (point mutation), 1 in 1800 bases. The beta chain of hemoglobin is 147 residues in length, yet a single amino acid substitution leads to sickle cell anemia. In normal hemoglobin, the amino acid at position seven is glutamate. In sickle cell hemoglobin, this glutamate is replaced by a valine. 

Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and assume a crescent or sickle shape, which clogs arteries ( [link] ). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease. In this blood smear, visualized at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped. (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell) Secondary Structure 

The local folding of the polypeptide in some regions gives rise to the secondary structure of the protein. The most common are the -helix and -pleated sheet structures ( [link] ). Both structures are the -helix structure the helix held in shape by hydrogen bonds. The hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain. The -helix and -pleated sheet are secondary structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Certain amino acids have a propensity to form an -helix, while others have a propensity to form a -pleated sheet. 

Every helical turn in an alpha helix has 3.6 amino acid residues. The R groups (the variant groups) of the polypeptide protrude out from the -helix chain. In the -pleated sheet, the pleats are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons and extend above and below the folds of the pleat. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive nitrogen atom in the amino group and the partially negative oxygen atom in the carbonyl group of the peptide backbone. The -helix and -pleated sheet structures are found in most globular and fibrous proteins and they play an important structural role. Tertiary Structure 

The unique three-dimensional structure of a polypeptide is its tertiary structure ( [link] ). This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups creates the complex three-dimensional tertiary structure of a protein. The nature of the R groups found in the amino acids involved can counteract the formation of the hydrogen bonds described for standard secondary structures. For example, R groups with like charges are repelled by each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding. The tertiary structure of proteins is determined by a variety of chemical interactions. These include hydrophobic interactions, ionic bonding, hydrogen bonding and disulfide linkages. 

All of these interactions, weak and strong, determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it may no longer be functional. Quaternary Structure 

In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure . Weak interactions between the subunits help to stabilize the overall structure. For example, insulin (a globular protein) has a combination of hydrogen bonds and disulfide bonds that cause it to be mostly clumped into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after the formation of the disulfide linkages that hold the remaining chains together. Silk (a fibrous protein), however, has a -pleated sheet structure that is the result of hydrogen bonding between different chains. 

The four levels of protein structure (primary, secondary, tertiary, and quaternary) are illustrated in [link] . The four levels of protein structure can be observed in these illustrations. (credit: modification of work by National Human Genome Research Institute) Denaturation and Protein Folding 

Each protein has its own unique sequence and shape that are held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what is known as denaturation. Denaturation is often reversible because the primary structure of the polypeptide is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is when an egg is fried. The albumin protein in the liquid egg white is denatured when placed in a hot pan. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the digestive enzymes of the stomach retain their activity under these conditions. 

Protein folding is critical to its function. It was originally thought that the proteins themselves were responsible for the folding process. Only recently was it found that often they receive assistance in the folding process from protein helpers known as chaperones (or chaperonins) that associate with the target protein during the folding process. They act by preventing aggregation of polypeptides that make up the complete protein structure, and they disassociate from the protein once the target protein is folded. 

For an additional perspective on proteins, view this animation called Biomolecules: The Proteins. 

[link] Think About It Predict what happens if even one amino acid is substituted for another in a polypeptide and provide a specific example. What categories of amino acids would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer of a plasma cell membrane? Activity 

Folding is an important property of proteins, especially enzymes. Proteins have a narrow range of conditions in which they fold properly; outside that range, proteins can unfold (denature) and often cannot refold and become functional again. Investigate one disease that results from improper folding of a protein. Describe causes of the unfolding and consequences to the molecular structure of the polypeptide that result in the disease. 

The first Think About It question is an application of Learning Objective 4.3 and Science Practices 6.1 and 6.4 because students are predicting how a change in the subcomponents of a molecule can affect the properties of the molecule. 

The second Think About It question is an application of Learning Objective 4.2 and Science Practice 1.3 because students are using representations of molecules along with a model of the cell membrane to describe how the molecular structure of amino acids determines their location with a protein or other structure such as the phospholipid bilayer. 

The activity is an application of Learning Objective 4.1 and Science Practice 7.1, Learning Objective 4.2 and Science Practice 1.3, and Learning Objective 4.3 and Science Practices 6.1 and 6.4 because students are asked to explain how environmental factors can alter the molecular structure of a protein and how this change can result in a change in function, i.e., disease. Section Summary 

Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers, or hormones. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that is linked to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. Each amino acid is linked to its neighbors by a peptide bond. A long chain of amino acids is known as a polypeptide. 

Proteins are organized at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the unique sequence of amino acids. The local folding of the polypeptide to form structures such as the helix and -pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is known as the quaternary structure of a protein. Protein shape and function are intricately linked; any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function. Review Questions 

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[link] Glossary alpha-helix structure ( -helix) type of secondary structure of proteins formed by folding of the polypeptide into a helix shape with hydrogen bonds stabilizing the structure amino acid monomer of a protein; has a central carbon or alpha carbon to which an amino group, a carboxyl group, a hydrogen, and an R group or side chain is attached; the R group is different for all 20 amino acids beta-pleated sheet ( -pleated) secondary structure found in proteins in which pleats are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain chaperone (also, chaperonin) protein that helps nascent protein in the folding process denaturation loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals enzyme catalyst in a biochemical reaction that is usually a complex or conjugated protein hormone chemical signaling molecule, usually protein or steroid, secreted by endocrine cells that act to control or regulate specific physiological processes peptide bond bond formed between two amino acids by a dehydration reaction polypeptide long chain of amino acids linked by peptide bonds primary structure linear sequence of amino acids in a protein protein biological macromolecule composed of one or more chains of amino acids quaternary structure association of discrete polypeptide subunits in a protein secondary structure regular structure formed by proteins by intramolecular hydrogen bonding between the oxygen atom of one amino acid residue and the hydrogen attached to the nitrogen atom of another amino acid residue tertiary structure three-dimensional conformation of a protein, including interactions between secondary structural elements; formed from interactions between amino acid side chainsLipids Lipids 

In this section, you will explore the following questions: What are the four major types of lipids? What are functions of fats in living organisms? What is the difference between saturated and unsaturated fatty acids? What is the molecular structure of phospholipids, and what is the role of phospholipids in cells? What is the basic structure of a steroid, and what are examples of their functions? How does cholesterol help maintain the fluid nature of the plasma membrane of cells? Connection for AP Courses 

Lipids also are sources of energy that power cellular processes. Like carbohydrates, lipids are composed of carbon, hydrogen, and oxygen, but these atoms are arranged differently. Most lipids are nonpolar and hydrophobic. Major types include fats and oils, waxes, phospholipids, and steroids. A typical fat consists of three fatty acids bonded to one molecule of glycerol, forming triglycerides or triacylglycerols. The fatty acids may be saturated or unsaturated, depending on the presence or absence of double bonds in the hydrocarbon chain; a saturated fatty acid has the maximum number of hydrogen atoms bonded to carbon and, thus, only single bonds. In general, fats that are liquid at room temperature (e.g., canola oil) tend to be more unsaturated than fats that are solid at room temperature. In the food industry, oils are artificially hydrogenated to make them chemically more appropriate for use in processed foods. During this hydrogenation process, double bonds in the cis- conformation in the hydrocarbon chain may be converted to double bonds in the trans- conformation; unfortunately, trans fats have been shown to contribute to heart disease. Phospholipids are a special type of lipid associated with cell membranes and typically have a glycerol (or sphingosine) backbone to which two fatty acid chains and a phosphate-containing group are attached. As a result, phospholipids are considered amphipathic because they have both hydrophobic and hydrophilic components. (In Chapters 4 and 5 we will explore in more detail how the amphipathic nature of phospholipids in plasma cell membranes helps regulate the passage of substances into and out of the cell.) Although the molecular structures of steroids differ from that of triglycerides and phospholipids, steroids are classified as lipids based on their hydrophobic properties. Cholesterol is a type of steroid in animal cells plasma membrane. Cholesterol is also the precursor of steroid hormones such as testosterone. 

Information presented and the examples highlighted in the section, support concepts outlined in Big Idea 4 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 1.3 The student can refine representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 6.1 The student can justify claims with evidence. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecules. 

An important misconception to overcome for students is that lipids are not bad for the body. They are absolutely essential to the body s functions, including for growth and survival. 

Another concept to discuss is the insolubility of lipids in water. It is obvious in salad dressing, but why does it occur? If other functional groups are attached to lipids, they may contain some charges and give a degree of solubility to the lipid, but most lipids do not have any charges on the surface of the molecules and are not soluble in water, therefore, lipids are usually described as being hydrophobic. 

Insoluble lipids must be attached to proteins in the body to become soluble in body fluids. Have the class research the proteins that transport and carry lipids. Identify their contributions to health or sickness. Fats and Oils 

Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon carbon or carbon hydrogen bonds. Non-polar molecules are hydrophobic ( water fearing ), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals ( [link] ). For example, their water-repellant hydrophobic nature can help keep aquatic birds and mammals dry by forming a protective layer over fur or feathers. Lipids are also the building blocks of many hormones and an important constituent of all cellular membranes. Lipids include fats, waxes, phospholipids, and steroids. 

The difference between a fat and an oil is the state of the compound at room temperature (68 F). A fat is a solid or semisolid material and an oil is a liquid at this temperature. Both fats and oils are made up of glycerol and two or three fatty acid chains attached to its carbons by way of dehydration synthesis. A fatty acid is a chain of carbon atoms with hydrogen atoms attached at the open bonding sites. If the chain is fully saturated with hydrogen atoms, it is termed a saturated fat. This tends to give the compound a relatively stiff configuration and helps it to be a solid. If any of the hydrogen atoms are missing, it is called an unsaturated fat or oil. The absence of hydrogen atoms along the chain causes double bonds to form between adjacent carbon atoms, which results in a bend in the chain. This causes the molecules to push away other molecules near it, preventing the packing of fatty acid chains, and resulting in a liquid at room temperature. Fats tend to contain a high concentration of saturated fatty acids and oils tend to contain more unsaturated fatty acid chains. Both types have an effect on health; a high amount of saturated fats is significantly less healthy than a higher amount of unsaturated lipids. An exception trans fat, an unsaturated fat found in processed foods. Trans fats behave like a saturated lipid. 

Divide the class into three sections: section 1: dairy department; section 2: salad dressings, and section 3: potato chips.. Each section will visit the supermarket and identify which fats or oils are in five items in their category. Then, each section will prepare a chart listing their findings and share it with the class. Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them from the elements. (credit: Ken Bosma) 

A fat molecule consists of two main components glycerol and fatty acids. Glycerol is an organic compound (alcohol) with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons to which a carboxyl group is attached, hence the name fatty acid. The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12 18 carbons. In a fat molecule, the fatty acids are attached to each of the three carbons of the glycerol molecule with an ester bond through an oxygen atom ( [link] ). Triacylglycerol is formed by the joining of three fatty acids to a glycerol backbone in a dehydration reaction. Three molecules of water are released in the process. 

During this ester bond formation, three water molecules are released. The three fatty acids in the triacylglycerol may be similar or dissimilar. Fats are also called triacylglycerols or triglycerides because of their chemical structure. Some fatty acids have common names that specify their origin. For example, palmitic acid, a saturated fatty acid , is derived from the palm tree. Arachidic acid is derived from Arachis hypogea, the scientific name for groundnuts or peanuts. 

Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is said to be saturated. Saturated fatty acids are saturated with hydrogen; in other words, the number of hydrogen atoms attached to the carbon skeleton is maximized. Stearic acid is an example of a saturated fatty acid ( [link] ) Stearic acid is a common saturated fatty acid. 

When the hydrocarbon chain contains a double bond, the fatty acid is said to be unsaturated . Oleic acid is an example of an unsaturated fatty acid ( [link] ). Oleic acid is a common unsaturated fatty acid. 

Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil). 

When a fatty acid has no double bonds, it is known as a saturated fatty acid because no more hydrogen may be added to the carbon atoms of the chain. A fat may contain similar or different fatty acids attached to glycerol. Long straight fatty acids with single bonds tend to get packed tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid (common in meat) and the fat with butyric acid (common in butter) are examples of saturated fats. Mammals store fats in specialized cells called adipocytes, where globules of fat occupy most of the cell s volume. In plants, fat or oil is stored in many seeds and is used as a source of energy during seedling development. Unsaturated fats or oils are usually of plant origin and contain cis unsaturated fatty acids. Cis and trans indicate the configuration of the molecule around the double bond. If hydrogens are present in the same plane, it is referred to as a cis fat; if the hydrogen atoms are on two different planes, it is referred to as a trans fat . The cis double bond causes a bend or a kink that prevents the fatty acids from packing tightly, keeping them liquid at room temperature ( [link] ). Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated fats help to lower blood cholesterol levels whereas saturated fats contribute to plaque formation in the arteries. Saturated fatty acids have hydrocarbon chains connected by single bonds only. Unsaturated fatty acids have one or more double bonds. Each double bond may be in a cis or trans configuration. In the cis configuration, both hydrogens are on the same side of the hydrocarbon chain. In the trans configuration, the hydrogens are on opposite sides. A cis double bond causes a kink in the chain. Trans Fats 

In the food industry, oils are artificially hydrogenated to make them semi-solid and of a consistency desirable for many processed food products. Simply speaking, hydrogen gas is bubbled through oils to solidify them. During this hydrogenation process, double bonds of the cis - conformation in the hydrocarbon chain may be converted to double bonds in the trans- conformation. 

Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans fats. Recent studies have shown that an increase in trans fats in the human diet may lead to an increase in levels of low-density lipoproteins (LDL), or bad cholesterol, which in turn may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently banned the use of trans fats, and food labels are required to display the trans fat content. Omega Fatty Acids 

Essential fatty acids are fatty acids required but not synthesized by the human body. Consequently, they have to be supplemented through ingestion via the diet. Omega -3 fatty acids (like that shown in [link] ) fall into this category and are one of only two known for humans (the other being omega-6 fatty acid). These are polyunsaturated fatty acids and are called omega-3 because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by a double bond. Alpha-linolenic acid is an example of an omega-3 fatty acid. It has three cis double bonds and, as a result, a curved shape. For clarity, the carbons are not shown. Each singly bonded carbon has two hydrogens associated with it, also not shown. 

The farthest carbon away from the carboxyl group is numbered as the omega ( ) carbon, and if the double bond is between the third and fourth carbon from that end, it is known as an omega-3 fatty acid. Nutritionally important because the body does not make them, omega-3 fatty acids include alpha-linoleic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), all of which are polyunsaturated. Salmon, trout, and tuna are good sources of omega-3 fatty acids. Research indicates that omega-3 fatty acids reduce the risk of sudden death from heart attacks, reduce triglycerides in the blood, lower blood pressure, and prevent thrombosis by inhibiting blood clotting. They also reduce inflammation, and may help reduce the risk of some cancers in animals. 

Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of fried foods and other fatty foods leads to weight gain. However, fats do have important functions. Many vitamins are fat soluble, and fats serve as a long-term storage form of fatty acids: a source of energy. They also provide insulation for the body. Therefore, healthy fats in moderate amounts should be consumed on a regular basis. 

This question is an application Learning Objective 4.3 and Science Practices 6.1 and 6.4 because students are predicting how a change in the subcomponents of a molecule can affect the properties of the molecule. 

A phospholipid is made of a phosphate group bonded to a glycerol that is linked to two fatty acid chains. One of the fatty acid chains is saturated and the other unsaturated. The saturated one is straight, while the unsaturated chain contains a bend. Phospholipids make up lipid bilayers, the main component of most plasma membranes and give it a fluid like property, a result of the fatty acid tails creating space between phospholipid molecules. 

The concept of a bent fatty acid tail contributing to the fluidity of a cell membrane can be difficult to visualize. Obtain some old fashioned, wooden clothes-pins. The knob at the top becomes a phosphate molecule. The two prongs of the pins become fatty acids. Both prongs are stiff, so they are saturated fatty acids. There are no unsaturated fatty acids in this demonstration. Hold a number of the pins tightly in your hand and ask a student to remove a pin in the center. They shouldn t be able to, as you are pressing the prongs of all of the pins together. This would be in a cell membrane without any unsaturated fatty acids pushing adjacent chains away, creating spaces that allow the membrane to behave like a fluid. Think About It 

Explain why trans fats have been banned from some restaurants. How are trans fats made, and what effect does a simple chemical change have on the properties of the lipid? Waxes 

Wax covers the feathers of some aquatic birds and the leaf surfaces of some plants. Because of the hydrophobic nature of waxes, they prevent water from sticking on the surface ( [link] ). Waxes are made up of long fatty acid chains esterified to long-chain alcohols. Waxy coverings on some leaves are made of lipids. (credit: Roger Griffith) Phospholipids 

Phospholipids are major constituents of the plasma membrane, the outermost layer of animal cells. Like fats, they are composed of fatty acid chains attached to a glycerol or sphingosine backbone. Instead of three fatty acids attached as in triglycerides, however, there are two fatty acids forming diacylglycerol, and the third carbon of the glycerol backbone is occupied by a modified phosphate group ( [link] ). A phosphate group alone attached to a diaglycerol does not qualify as a phospholipid; it is phosphatidate (diacylglycerol 3-phosphate), the precursor of phospholipids. The phosphate group is modified by an alcohol. Phosphatidylcholine and phosphatidylserine are two important phospholipids that are found in plasma membranes. A phospholipid is a molecule with two fatty acids and a modified phosphate group attached to a glycerol backbone. The phosphate may be modified by the addition of charged or polar chemical groups. Two chemical groups that may modify the phosphate, choline and serine, are shown here. Both choline and serine attach to the phosphate group at the position labeled R via the hydroxyl group indicated in green. 

A phospholipid is an amphipathic molecule, meaning it has a hydrophobic and a hydrophilic part. The fatty acid chains are hydrophobic and cannot interact with water, whereas the phosphate-containing group is hydrophilic and interacts with water ( [link] ). The phospholipid bilayer is the major component of all cellular membranes. The hydrophilic head groups of the phospholipids face the aqueous solution. The hydrophobic tails are sequestered in the middle of the bilayer. 

The head is the hydrophilic part, and the tail contains the hydrophobic fatty acids. In a membrane, a bilayer of phospholipids forms the matrix of the structure, the fatty acid tails of phospholipids face inside, away from water, whereas the phosphate group faces the outside, aqueous side ( [link] ). 

Phospholipids are responsible for the dynamic nature of the plasma membrane. If a drop of phospholipids is placed in water, it spontaneously forms a structure known as a micelle, where the hydrophilic phosphate heads face the outside and the fatty acids face the interior of this structure. 

Fats are amphiphilic molecules. In other words, the long hydrocarbon tail is hydrophobic, and the glycerol part of the molecule is hydrophilic. When in water, fats will arrange themselves into a ball called a micelle so that the hydrophilic heads are on the outer surface, and the hydrophobic tails are on the inside where they are protected from the surrounding water. 

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The predominant steroid found in the body is cholesterol, which is used variously by the body to form steroidal hormones and give flexibility to cells, such as red blood cells, which must change their shape to get through blood vessels and tissues. Steroids 

Unlike the phospholipids and fats discussed earlier, steroids have a fused ring structure. Although they do not resemble the other lipids, they are grouped with them because they are also hydrophobicand insoluble in water. All steroids have four linked carbon rings and several of them, like cholesterol, have a short tail ( [link] ). Many steroids also have the OH functional group, which puts them in the alcohol classification (sterols). Steroids such as cholesterol and cortisol are composed of four fused hydrocarbon rings. 

Cholesterol is the most common steroid. Cholesterol is mainly synthesized in the liver and is the precursor to many steroid hormones such as testosterone and estradiol, which are secreted by the gonads and endocrine glands. It is also the precursor to Vitamin D. Cholesterol is also the precursor of bile salts, which help in the emulsification of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms by lay people, it is necessary for proper functioning of the body. It is a component of the plasma membrane of animal cells and is found within the phospholipid bilayer. Being the outermost structure in animal cells, the plasma membrane is responsible for the transport of materials and cellular recognition and it is involved in cell-to-cell communication. 

For an additional perspective on lipids, explore the interactive animation Biomolecules: The Lipids . 

[link] Section Summary 

Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats are a stored form of energy and are also known as triacylglycerols or triglycerides. Fats are made up of fatty acids and either glycerol or sphingosine. Fatty acids may be unsaturated or saturated, depending on the presence or absence of double bonds in the hydrocarbon chain. If only single bonds are present, they are known as saturated fatty acids. Unsaturated fatty acids may have one or more double bonds in the hydrocarbon chain. Phospholipids make up the matrix of membranes. They have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-containing group are attached. Steroids are another class of lipids. Their basic structure has four fused carbon rings. Cholesterol is a type of steroid and is an important constituent of the plasma membrane, where it helps to maintain the fluid nature of the membrane. It is also the precursor of steroid hormones such as testosterone. Review Questions 

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[link] Glossary lipid macromolecule that is nonpolar and insoluble in water omega fat type of polyunsaturated fat that is required by the body; the numbering of the carbon omega starts from the methyl end or the end that is farthest from the carboxylic end phospholipid major constituent of the membranes; composed of two fatty acids and a phosphate-containing group attached to a glycerol backbone saturated fatty acid long-chain of hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized steroid type of lipid composed of four fused hydrocarbon rings forming a planar structure trans fat fat formed artificially by hydrogenating oils, leading to a different arrangement of double bond(s) than those found in naturally occurring lipids triacylglycerol (also, triglyceride) fat molecule; consists of three fatty acids linked to a glycerol molecule unsaturated fatty acid long-chain hydrocarbon that has one or more double bonds in the hydrocarbon chain wax lipid made of a long-chain fatty acid that is esterified to a long-chain alcohol; serves as a protective coating on some feathers, aquatic mammal fur, and leavesNucleic Acids Nucleic Acids 

In this section, you will investigate the following questions: What are the two types of nucleic acid? What is the structure and role of DNA? What is the structure and roles of RNA? Connection for AP Courses 

Nucleic acids (DNA and RNA) comprise the fourth group of biological macromolecules and contain phosphorus (P) in addition to carbon, hydrogen, oxygen, and nitrogen. Conserved through evolution in all organisms, nucleic acids store and transmit hereditary information. As will be explored in more detail in Chapters 14-17, DNA contains the instructions for the synthesis of proteins by dictating the sequences of amino acids in polypeptides through processes known as transcription and translation. Nucleic acids are made up of nucleotides; in turn, each nucleotide consists of a pentose sugar (deoxyribose in DNA and ribose in RNA), a nitrogenous base (adenine, cytosine, guanine, and thymine or uracil), and a phosphate group. DNA carries the genetic blueprint of the cell that is passed from parent to offspring via cell division. DNA has a double-helical structure with the two strands running in opposite directions (antiparallel), connected by hydrogen bonds and complementary to each other. In DNA, purines pair with pyrimidines: adenine pairs with thymine (A-T), and cytosine pairs with guanine (C-G). In RNA, uracil replaces thymine to pair with adenine (U-A). RNA also differs from DNA in that it is single-stranded and has many forms, such as messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA) that all participate in the synthesis of proteins. MicroRNAs (miRNAs) regulate the use of mRNA. The flow of genetic information is usually DNA RNA protein, also known as the Central Dogma of Life. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 3 and Big Idea 4 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 1.3 The student can refine representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 6.1 The student can justify claims with evidence. 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecules. 

Use Table 3.2 to illustrate the major differences between DNA and RNA. 

A polynucleotide is not formed through a traditional dehydration synthesis reaction. Instead of removing the components of water from the monomers, a phosphate group is removed from each to form the linkage. 

The primary functions of nucleic acids is to store genetic information needed to produce proteins and to facilitate the appropriate linkages between amino acids. Another function of nucleic acids is in energy transfer, discussed in a later chapter. 

The concept of the double helix of DNA can be challenging to understand. Ask the students to imagine a rope ladder with the top of the right side labeled 3 and the other end of that side labeled 5. The top of the left side is labeled 5 and the other end 3, so the numbers are going in opposite directions on opposite sides of the ladder, giving the sides of the structure an antiparallel orientation. Now imagine grabbing the ladder from the top and twisting. That is a double helix. It is double because there are two sides to it. You might try to draw a ladder, with its labels; then, ask the students to imagine it twisting. Another possibility is to have students use pipe cleaners to build the double helix. 

RNA usually exists as a single strand. Messenger RNA (mRNA) can be found in the nucleus, where it mirrors the sequence of nucleotides found in DNA, and in the cytoplasm, where it delivers its message to ribosomes for protein assembly. Ribosomes are made of ribosomal RNA (rRNA) and protein. Transfer RNA (tRNA) carries amino acids to the ribosomes for attachment to a developing protein. MicroRNA (miRNA) are the smallest RNA molecules and their role involves the regulation of gene expression by interfering with the expression of certain mRNA. 

Some viruses contain double stranded RNA, but plants and animals do not. DNA and RNA 

Nucleic acids are the most important macromolecules for the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell. 

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) . DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope. 

The entire genetic content of a cell is known as its genome, and the study of genomes is genomics. In eukaryotic cells but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products; other genes code for RNA products. DNA controls all of the cellular activities by turning the genes on or off. 

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA) . Other types of RNA like rRNA, tRNA, and microRNA are involved in protein synthesis and its regulation. 

DNA and RNA are made up of monomers known as nucleotides . The nucleotides combine with each other to form a polynucleotide , DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group ( [link] ). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups. A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1 through 5 (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the 1 position of the ribose, and the phosphate is attached to the 5 position. When a polynucleotide is formed, the 5 phosphate of the incoming nucleotide attaches to the 3 hydroxyl group at the end of the growing chain. Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2 position. Bases can be divided into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring. 

The nitrogenous bases, important components of nucleotides, are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus, decreases the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T). 

Adenine and guanine are classified as purines . The primary structure of a purine is two carbon-nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure ( [link] ). Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases are simply known by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas RNA contains A, U, G, and C. 

The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose ( [link] ). The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar molecule are numbered as 1 , 2 , 3 , 4 , and 5 (1 is read as one prime ). The phosphate residue is attached to the hydroxyl group of the 5 carbon of one sugar and the hydroxyl group of the 3 carbon of the sugar of the next nucleotide, which forms a 5 3 phosphodiester linkage. The phosphodiester linkage is not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules: its formation involves the removal of two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages. DNA Double-Helix Structure 

DNA has a double-helix structure ( [link] ). The sugar and phosphate lie on the outside of the helix, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, in pairs; the pairs are bound to each other by hydrogen bonds. Every base pair in the double helivx is separated from the next base pair by 0.34 nm. The two strands of the helix run in opposite directions, meaning that the 5 carbon end of one strand will face the 3 carbon end of its matching strand. (This is referred to as antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.) Native DNA is an antiparallel double helix. The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand. (credit: Jerome Walker/Dennis Myts) 

Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain pyrimidine. This means A can pair with T, and G can pair with C, as shown in [link] . This is known as the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand. 

In a double stranded DNA molecule, the two strands run antiparallel to one another so that one strand runs 5 to 3 and the other 3 to 5 . The phosphate backbone is located on the outside, and the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine base pairs with cytosine. 

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Ribonucleic acid, or RNA, is mainly involved in the process of protein synthesis under the direction of DNA. RNA is usually single-stranded and is made of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and the phosphate group. 

There are four major types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and microRNA (miRNA). The first, mRNA, carries the message from DNA, which controls all of the cellular activities in a cell. If a cell requires a certain protein to be synthesized, the gene for this product is turned on and the messenger RNA is synthesized in the nucleus. The RNA base sequence is complementary to the coding sequence of the DNA from which it has been copied. However, in RNA, the base T is absent and U is present instead. If the DNA strand has a sequence AATTGCGC, the sequence of the complementary RNA is UUAACGCG. In the cytoplasm, the mRNA interacts with ribosomes and other cellular machinery ( [link] ). A ribosome has two parts: a large subunit and a small subunit. The mRNA sits in between the two subunits. A tRNA molecule recognizes a codon on the mRNA, binds to it by complementary base pairing, and adds the correct amino acid to the growing peptide chain. 

The mRNA is read in sets of three bases known as codons. Each codon codes for a single amino acid. In this way, the mRNA is read and the protein product is made. Ribosomal RNA (rRNA) is a major constituent of ribosomes on which the mRNA binds. The rRNA ensures the proper alignment of the mRNA and the ribosomes; the rRNA of the ribosome also has an enzymatic activity (peptidyl transferase) and catalyzes the formation of the peptide bonds between two aligned amino acids. Transfer RNA (tRNA) is one of the smallest of the four types of RNA, usually 70 90 nucleotides long. It carries the correct amino acid to the site of protein synthesis. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain. microRNAs are the smallest RNA molecules and their role involves the regulation of gene expression by interfering with the expression of certain mRNA messages. [link] summarizes features of DNA and RNA. Features of DNA and RNA DNA RNA Function Carries genetic information Involved in protein synthesis Location Remains in the nucleus Leaves the nucleus Structure Double helix Usually single-stranded Sugar Deoxyribose Ribose Pyrimidines Cytosine, thymine Cytosine, uracil Purines Adenine, guanine Adenine, guanine 

Even though the RNA is single stranded, most RNA types show extensive intramolecular base pairing between complementary sequences, creating a predictable three-dimensional structure essential for their function. 

As you have learned, information flow in an organism takes place from DNA to RNA to protein. DNA dictates the structure of mRNA in a process known as transcription , and RNA dictates the structure of protein in a process known as translation . This is known as the Central Dogma of Life, which holds true for all organisms; however, exceptions to the rule occur in connection with viral infections. 

To learn more about DNA, explore the Howard Hughes Medical Institute BioInteractive animations on the topic of DNA. 

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Using construction paper, markers, and scissors, construct a model of DNA with at least 8 nucleotides. Then, use the model to distinguish between DNA and RNA and hypothesize how the DNA molecule is replicated during cell division. (Keep your molecule to model the processes of transcription and translation that you will explore in Chapter 15.) Think About It 

A mutation occurs, and cytosine is replaced with adenine. Explain how this affects how the changed strand will base pair with its complimentary strand of DNA. 

This activity is an application of Learning Objective 3.1 and Science Practice 6.5, Learning Objective 4.1 and Science Practice 7.1, and Learning Objective 4.2 and Science Practice 1.3 because students are constructing a model to explain how DNA stores genetic information, to distinguish between DNA and RNA, and to propose a method how DNA is replicated in cell division. 

The Think About It question is an application of Learning Objective 3.6 and Science Practice 6.4 and Learning Objective 4.3 and Science Practices 6.1 and 6.4 because students are predicting how a change in a DNA sequence can affect the genetic information it carries. Section Summary 

Nucleic acids are molecules made up of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA. DNA carries the genetic blueprint of the cell and is passed on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is single-stranded and is made of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) is copied from the DNA, is exported from the nucleus to the cytoplasm, and contains information for the construction of proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis, whereas transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. microRNA regulates the use of mRNA for protein synthesis. Review Questions 

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[link] Glossary deoxyribonucleic acid (DNA) double-helical molecule that carries the hereditary information of the cell messenger RNA (mRNA) RNA that carries information from DNA to ribosomes during protein synthesis nucleic acid biological macromolecule that carries the genetic blueprint of a cell and carries instructions for the functioning of the cell nucleotide monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous base phosphodiester linkage covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking two pentose sugars of neighboring nucleotides polynucleotide long chain of nucleotides purine type of nitrogenous base in DNA and RNA; adenine and guanine are purines pyrimidine type of nitrogenous base in DNA and RNA; cytosine, thymine, and uracil are pyrimidines ribonucleic acid (RNA) single-stranded, often internally base paired, molecule that is involved in protein synthesis ribosomal RNA (rRNA) RNA that ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes the formation of the peptide linkage transcription process through which messenger RNA forms on a template of DNA transfer RNA (tRNA) RNA that carries activated amino acids to the site of protein synthesis on the ribosome translation process through which RNA directs the formation of proteinIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" (a) Nasal sinus cells (viewed with a light microscope), (b) onion cells (viewed with a light microscope), and (c) Vibrio tasmaniensis bacterial cells (seen through a scanning electron microscope) are from very different organisms, yet all share certain characteristics of basic cell structure. (credit a: modification of work by Ed Uthman, MD; credit b: modification of work by Umberto Salvagnin; credit c: modification of work by Anthony D'Onofrio, William H. Fowle, Eric J. Stewart, and Kim Lewis of the Lewis Lab at Northeastern University; scale-bar data from Matt Russell) 

Close your eyes and picture a brick wall. What is the basic building block of that wall? A single brick, of course. Like a brick wall, your body is composed of basic building blocks called cells. 

Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone cells help to support and protect the body. Immune system cells fight invading pathogens. Additionally, blood cells carry nutrients and oxygen throughout the body while removing carbon dioxide and other waste. Each of these cell types plays a vital role during the growth, development, and ongoing maintenance of the body. In spite of their enormous variety, however, cells from all organisms even organisms as diverse as bacteria, onion, and human share certain fundamental characteristics. 

In humans, before a cell develops into its specialized type, it is called a stem cell. A stem cell is a cell that has not undergone the changes involved in specialization. In this state, it may differentiate to become one of many different specialized cells, and it may divide to produce more stem cells. Under normal circumstances, once a cell becomes specialized, it remains that way. However, scientists have been working on coaxing stem cells in the laboratory to become a particular specialization. For example, scientists at the Cincinnati Children s Hospital Medical Center have learned how to use stem cells to grow stomach tissue in plastic cell and tissue culture dishes. This accomplishment will enable researchers to study gastric human diseases, such as stomach cancer. You can read more about it here . 

Stem cells retain the potential to become many different types of cell. Totipotent stem cells such as the zygote and the cells in the very early stages of the dividing embryo can become any cell in the body. By the time the zygote has undergone sufficient division the 16-cell stage, some cells are committed to a particular path and are called pluripotent. Each pluripotent cell has a large potential and can differentiate into many of the types of cells that ultimately make up the adult organism. Multipotent cells are still present in numerous adult tissues such as the bone marrow and the brain and can differentiate into a number of different cell types, albeit within a narrow range. The classic example is seen in the formation of blood cells in the bone marrow. An unspecialized cell in the blood lineage may become a red blood cell or a white blood cell, but not a muscle cell. Further down the path of differentiation, the precursor of a white blood cell lineage has lost the capability to develop into a red blood cell; however, it can still differentiate into one of the several kinds of white blood cells. 

For the most part, differentiated cells retain all of their genetic material, making it a possibility to reverse the differentiation process and turn specialized adult cells into pluripotent stem cells. This is the key to the experiment described in the warm up. 

Ask students what would happen if they chose a career in the future and were never allowed to change their decision (e.g., Once an accountant, always an accountant. ) 

Compare totipotent cells to students in middle school with all possibilities wide open. In high school, some differentiation has taken place by choosing AP classes. As they progress through their studies, some paths may be closing. Ask students to compare differentiation to academic paths. At which stage of their education, are students totipotent? (Possible answers: elementary, middle or high school) When do students become pluripotent? (Possible answers: choice of secondary education, vocational school, college) When do they become multipotent? (Possible answers: choice of major, graduate school) Emphasize that it is easier for a student in one natural science to switch to a different natural science, for example, go from physics to geology. Can you change drastically career at a later stage in life? This is comparable to developing pluripotent adult stem cells. The DNA is still there. 

Embryonic cells cannot become any cell in the body. They are multipotent, not totipotent. Explain that the ability to differentiate pluripotent adult stem cells in organoids is a major breakthrough because it is an alternative to using embryonic tissue.Studying Cells Studying Cells 

In this section, you will explore the following questions: What is the role of cells in organisms? What is the difference between light microscopy and electron microscopy? What is the cell theory? 

An introduction to the principle of microscopy will facilitate the discussion of the various types of instruments. Explain to students the concepts of magnification, resolution, and contrast, which together contribute to the quality of microscopy. In particular, explain that resolution is determined by the smallest wavelength in visible light in the light microscope and the distance separating two atoms in solid material in a transmission electron microscope. 

Review with students the tenets of the cell theory, because the cell, as the fundamental unit of life, is at the foundation of all biological classes. Life cannot be divided into pieces smaller than the cell and still be considered independent life. Therefore, viruses are considered particles, not cells, because viruses, for one, cannot replicate on their own. All living organisms are made of one or more cells. Those cells are similar in size. Why are cells so similar in size, no matter how large the organism itself grows? The main answer lies in how surface area and volume scale with cell radius and how these parameters affect exchange with the environment. This is covered in the next module. 

Beginners consider magnification the most important quality of a microscope. Magnification without resolution yields a very large but blurry image which does not inform the viewer on the nature of the specimen. Illustrate the point by referring to the resolution of a photographic image or a YouTube video with which many students are familiar. Emphasize the importance of contrast. A cell is transparent unless it contains colored components or dense structures. Ask students for examples of such structures. Answers may include chloroplasts, chromoplasts, nuclei or other dense structures. Connection for AP Courses 

A cell is the smallest unit of a living thing. A living thing, whether made of one cell (like bacteria) or many cells (like a human), is called an organism. Thus, cells are the basic building blocks of all organisms. 

Several cells of one kind that interconnect with each other and perform a shared function form tissues, several tissues combine to form an organ (your stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being). Here, we will examine the structure and function of cells. 

There are many types of cells, all grouped into one of two broad categories: prokaryotic and eukaryotic. For example, both animal and plant cells are classified as eukaryotic cells, whereas bacterial cells are classified as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, let s first examine how biologists study cells. Microscopy 

Cells vary in size. With few exceptions, individual cells cannot be seen with the naked eye, so scientists use microscopes (micro- = small ; -scope = to look at ) to study them. A microscope is an instrument that magnifies an object. Most photographs of cells are taken with a microscope, and these images can also be called micrographs. 

The optics of a microscope s lenses change the orientation of the image that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Because of the manner by which light travels through the lenses, this system of two lenses produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). Light Microscopes 

To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight m) in diameter; the head of a pin of is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on the head of a pin. 

Most student microscopes are classified as light microscopes ( [link] a ). Visible light passes and is bent through the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells. 

Light microscopes commonly used in the undergraduate college laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the ability of a microscope to distinguish two adjacent structures as separate: the higher the resolution, the better the clarity and detail of the image. When oil immersion lenses are used for the study of small objects, magnification is usually increased to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes. (a) Most light microscopes used in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers. (b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers. (credit a: modification of work by "GcG"/Wikimedia Commons; credit b: modification of work by Evan Bench) Electron Microscopes 

In contrast to light microscopes, electron microscopes ( [link] b ) use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail ( [link] ), it also provides higher resolving power. The method used to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so living cells cannot be viewed with an electron microscope. 

In a scanning electron microscope, a beam of electrons moves back and forth across a cell s surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. (a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope. (b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. (credit a: modification of work by CDC/Armed Forces Institute of Pathology, Charles N. Farmer, Rocky Mountain Laboratories; credit b: modification of work by NIAID, NIH; scale-bar data from Matt Russell) 

For another perspective on cell size, try the HowBig interactive at this site . 

[link] Cell Theory 

The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protista (a type of single-celled organism) and sperm, which he collectively termed animalcules. 

In a 1665 publication called Micrographia , experimental scientist Robert Hooke coined the term cell for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. 

By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory , which states that all living things are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory. Cytotechnologist 

Have you ever heard of a medical test called a Pap smear ( [link] )? In this test, a doctor takes a small sample of cells from the uterine cervix of a patient and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection. 

Cytotechnologists (cyto- = cell ) are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells; they study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, who is a medical doctor who can make a clinical diagnosis. 

Cytotechnologists play a vital role in saving people s lives. When abnormalities are discovered early, a patient s treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, were obtained from a Pap smear. Normal cells are on the left. The cells on the right are infected with human papillomavirus (HPV). Notice that the infected cells are larger; also, two of these cells each have two nuclei instead of one, the normal number. (credit: modification of work by Ed Uthman, MD; scale-bar data from Matt Russell) Section Summary 

A cell is the smallest unit of life. Most cells are so tiny that they cannot be seen with the naked eye. Therefore, scientists use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells. Review Questions 

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[link] Glossary cell theory see unified cell theory electron microscope an instrument that magnifies an object using a beam of electrons passed and bent through a lens system to visualize a specimen light microscope an instrument that magnifies an object using a beam visible light passed and bent through a lens system to visualize a specimen microscope an instrument that magnifies an object unified cell theory a biological concept that states that all organisms are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cellsProkaryotic Cells Prokaryotic Cells 

In this section, you will explore the following questions: What are the major structures of prokaryotic cells? What limits the size of a cell? Connection for AP Courses 

According to the cell theory, all living organisms, from bacteria to humans, are composed of cells, the smallest units of living matter. Often too small to be seen without a microscope, cells come in all sizes and shapes, and their small size allows for a large surface area-to-volume ratio that enables a more efficient exchange of nutrients and wastes with the environment. 

There are three basic types of cells: archaea, bacteria, and eukaryotes. Both archaea and bacteria are classified as prokaryotes, whereas cells of animals, plants, fungi, and protists are eukaryotes. Archaea are a unique group of organisms and likely evolved in the harsh conditions of early Earth and are still prevalent today in extreme environments, such as hot springs and polar regions. All cells share features that reflect their evolution from a common ancestor; these features are 1) a plasma membrane that separates the cell from its environment; 2) cytoplasm comprising the jelly-like cytosol inside the cell; 3) ribosomes that are important for the synthesis of proteins, and 4) DNA to store and transmit hereditary information. 

Prokaryotes may also have a cell wall that acts as an extra layer of protection against the external environment. The term prokaryote means before nucleus, and prokaryotes do not have nuclei. Rather, their DNA exists as a single circular chromosome in the central part of the cell called the nucleoid. Some bacterial cells also have circular DNA plasmids that often carry genes for resistance to antibiotics (Chapter 17). Other common prokaryotic cell features include flagella and pili. 

The content presented in this section supports the learning objectives outlined in Big Idea 1 and Big Idea 2 of the AP Biology Curriculum Framework. The AP Learning Objectives merge essential knowledge content with one or more of the seven Science Practices. These objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP exam questions. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.D The origin of living systems is explained by natural processes. Essential Knowledge 1.D.2 Scientific evidence from many different disciplines supports models of the origin of life. Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question. Learning Objective 1.32 The student is able to justify the selection of geological, physical, chemical, and biological data that reveal early Earth conditions. Essential Knowledge 2.A.3 Organisms must exchange matter with the environment to grow, reproduce and maintain organization. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Learning Objective 2.6 The student is able to use calculated surface area-to-volume ratios to predict which cell(s) might eliminate wastes or procure nutrients faster by diffusion. Essential Knowledge 2.A.3 Organisms must exchange matter with the environment to grow, reproduce and maintain organization. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.7 The student will be able to explain how cell sizes and shapes affect the overall rate of nutrient intake and the rate of waste elimination. 

The major structures common to all bacteria are depicted in Figure 4.5. The cell wall contains a complex structural component, the peptidoglycan layer, which has yet to be observed in any eukaryotic cell. This peptidoglycan layer is made of a network of alternating modified complex sugar units, the glycans, joined by peptide cross-bridges. This rigid structure contributes to the shape of bacterial cells and protects them against changes in osmotic pressure in the environment. Antibiotics such as penicillin interfere with the synthesis of the peptidoglycan layers and cause bacterial cells to lyse without affecting the human host. 

Many bacterial cells contain plasmids: small, extrachromosomal rings of double-stranded DNA which can replicate independently of the bacterial chromosome and often carry genes which confer resistance to antibiotics. Bacteria readily transfer plasmids to other bacterial cells by a mechanism called horizontal gene transfer, thereby spreading antibiotic resistance. 

Cells at the lower end of the size spectrum are limited on just how small they can be. To illustrate, compare a bacterial cell to a bag packed for camping in the wilderness. In order to make the camping trip possible, the bag must contain a minimum amount of supplies and equipment. Here, introduce the concept of prokaryotes, bacteria and archaea. Prokaryotes are the most successful organisms on the planet. They probably appeared first during evolution and occupy every possible environment. 

Surface area-to-volume ratio limits the maximum size of a cell. Nutrients and intermediates enter the cell by diffusion. As the cell increases in size, the volume increase outpaces the surface area increase, and the cell size exceeds the capacity of the surface area to adequately exchange nutrients and waste with the external environment. 

All bacteria cause disease. This misconception started with the germ theory of disease when it became clear that some of the most feared diseases were caused by microorganisms. In fact, very few microorganisms are actually pathogens. The balance between control of infectious diseases and reasonable sanitary standards is often misunderstood. Excess hygiene is thought to have caused an increase in asthma and other immune system imbalances between a human host and the human microbiome. Ask students if one can be too clean. The notion that improved hygiene has led to increases in the prevalence of allergies and asthma is called the hygiene hypothesis. 

Until recently, surface area-to-volume ratio was considered the main factor in determining the limits of cell sizes. New research opened the possibility that other factors such as avoiding predators, cell division mechanics and environment also contribute to size and shape determination. The topic is reviewed in the following article: 

Young, K. D. (2006). The Selective Value of Bacterial Shape. Microbiology and Molecular Biology Reviews , 70 (3), 660 703. doi:10.1128 /MMBR.00001-06 

Show in class, if possible, the following video from HHMI on the discovery of microbial life by Leeuwenhoek. 

Use the video to discuss what set apart the single lens microscope of Leeuwenhoek. Challenge students by asking them why the rapid development of microbiology, the so-called golden age, happened in the nineteenth century, close to 200 years after the discovery of microbial life. One of the main reasons is the germ theory of disease. Once the connection was made between devastating diseases and microbes, the interest in microorganisms soared. 

Ask students if they can think of ways in which bacteria are beneficial and write them on the board. Include the obvious ones such as probiotics; food and fermentation; and the less obvious ones such as to stimulate the immune system, biofuels, bioremediation (here mention cleaning oil spills), and synthesis of useful products (antibiotics). 

Ask students if a cell in a 30-meter long blue whale is considerably larger than a cell in a tiny water flea at 3 mm long. Record answers on the board. Cells are similar in size because there are constraints on how large and how small they can be and still be functionally independent entities. 

Cells fall into one of two broad categories: prokaryotic and eukaryotic. Only the predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro- = before ; -kary- = nucleus ). Cells of animals, plants, fungi, and protists are all eukaryotes (ceu- = true ) and are made up of eukaryotic cells. Components of Prokaryotic Cells 

All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like cytosol within the cell in which other cellular components are found; 3) DNA, the genetic material of the cell; and 4) ribosomes, which synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways. 

A prokaryote is a simple, mostly single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle. We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is found in a central part of the cell: the nucleoid ( [link] ). This figure shows the generalized structure of a prokaryotic cell. All prokaryotes have chromosomal DNA localized in a nucleoid, ribosomes, a cell membrane, and a cell wall. The other structures shown are present in some, but not all, bacteria. 

While the Earth is approximately 4.6 billion years old, the earliest fossil evidence for life are of microbial mats that date back to 3.5 billion years. 

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Most prokaryotes have a peptidoglycan cell wall and many have a polysaccharide capsule ( [link] ). The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for locomotion. Pili are used to exchange genetic material during a type of reproduction called conjugation. Fimbriae are used by bacteria to attach to a host cell. Career Connection 

Microbiologist The most effective action anyone can take to prevent the spread of contagious illnesses is to wash his or her hands. Why? Because microbes (organisms so tiny that they can only be seen with microscopes) are ubiquitous. They live on doorknobs, money, your hands, and many other surfaces. If someone sneezes into his hand and touches a doorknob, and afterwards you touch that same doorknob, the microbes from the sneezer s mucus are now on your hands. If you touch your hands to your mouth, nose, or eyes, those microbes can enter your body and could make you sick. 

However, not all microbes (also called microorganisms) cause disease; most are actually beneficial. You have microbes in your gut that make vitamin K. Other microorganisms are used to ferment beer and wine. 

Microbiologists are scientists who study microbes. Microbiologists can pursue a number of careers. Not only do they work in the food industry, they are also employed in the veterinary and medical fields. They can work in the pharmaceutical sector, serving key roles in research and development by identifying new sources of antibiotics that could be used to treat bacterial infections. 

Environmental microbiologists may look for new ways to use specially selected or genetically engineered microbes for the removal of pollutants from soil or groundwater, as well as hazardous elements from contaminated sites. These uses of microbes are called bioremediation technologies. Microbiologists can also work in the field of bioinformatics, providing specialized knowledge and insight for the design, development, and specificity of computer models of, for example, bacterial epidemics. Cell Size 

At 0.1 to 5.0 m in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10 to 100 m ( [link] ). The small size of prokaryotes allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly diffuse out. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport. This figure shows relative sizes of microbes on a logarithmic scale (recall that each unit of increase in a logarithmic scale represents a 10-fold increase in the quantity being measured). 

Small size, in general, is necessary for all cells, whether prokaryotic or eukaryotic. Let s examine why that is so. First, we ll consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. You may remember from your high school geometry course that the formula for the surface area of a sphere is 4 r 2 , while the formula for its volume is 4 r 3 /3. Thus, as the radius of a cell increases, its surface area increases as the square of its radius, but its volume increases as the cube of its radius (much more rapidly). Therefore, as a cell increases in size, its surface area-to-volume ratio decreases. This same principle would apply if the cell had the shape of a cube ( see this figure ). If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. In other words, as a cell grows, it becomes less efficient. One way to become more efficient is to divide; another way is to develop organelles that perform specific tasks. These adaptations lead to the development of more sophisticated cells called eukaryotic cells. Visual Connections 

Notice that as a cell increases in size, its surface area-to-volume ratio decreases. When there is insufficient surface area to support a cell s increasing volume, a cell will either divide or die. The cell on the left has a volume of 1 mm 3 and a surface area of 6 mm 2 , with a surface area-to-volume ratio of 6 to 1, whereas the cell on the right has a volume of 8 mm 3 and a surface area of 24 mm 2 , with a surface area-to-volume ratio of 3 to 1. 

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Create an annotated diagram to explain how approximately 300 million alveoli in a human lung increases surface area for gas exchange to the size of a tennis court. Use the diagram to explain how the cellular structures of alveoli, capillaries, and red blood cells allow for rapid diffusion of O 2 and CO 2 among them. Think About It 

Which of the following cells would likely exchange nutrients and wastes with its environment more efficiently: a spherical cell with a diameter of 5 m or a cubed-shaped cell with a side length of 7 m? Provide a quantitative justification for your answer based on surface area-to-volume ratios. 

This activity is an application of Learning Objective 2.6 and Science Practice 6.2 because students are creating a diagram to explain diffusion rates across membranes. 

The Think about it question is an application of Learning Objective 2.6 and Science Practice 2.2 and Learning Objective 2.7 and Science Practice 2.2 because they need to calculate surface area-to-volume ratios for two different shapes and sizes of cells to predict which one procures nutrients or eliminates wastes more efficiently. 

Cell sizes and shapes can vary. The longest cells are neurons that start at the brain and reach the limbs. Other examples of large cells include bird eggs, skeletal muscle cells, and the marine algae Caulerpa and Acetabularia . These are exceptional cells and have unusual solutions to the surface area-to-volume challenge. 

The main point is that the alveoli cover a large surface because they are essentially very small beads packed in two large bags, the lungs. The sum of the individual surface areas of these microscopic beads is equivalent to the surface of a tennis court (roughly 200 m 2 for singles). The surface area of a sphere is 4 r 2 . If the average diameter of an alveolus is 300 m, which is equal to 0.3mm, the average surface area of an alveolus is 4 ( 0.3 mm 2 ) 2 0 . 3 mm 2 4 ( 0.3 mm 2 ) 2 0 . 3 mm 2 

1mm=10 -3 m 

1mm 2 =1mm*1mm=10 -3 m*10 -3 m=10 -6 m 2 

The surface area of an alveolus in square meters is equal to 0.3 10 -6 m 2 . If there are 300 million (300 10 6 ) alveoli in one lung, the total surface is equal to about 90m 2 which is almost half the area of a tennis court! 

Demonstration 

Take a piece of paper and crumple it to show how a large surface area can fit in a small volume. 

The alveoli are squamous cells, thin and flat; the capillaries have the diameter of a hair (from the Latin capellus , meaning hair ). Oxygen diffuses through very thin barriers only two cell membranes thick. 

Calculate: 

The dimension of the sphere given is the diameter. It must be divided by 2 to obtain the value for the radius. 

D=5 m and r=D/2=2.5 m 

Surface area of sphere: 4 r 2 =78.54 m 2 

Volume: 4/3 r 3 = 65.45 m 3 

Surface area-to-volume ratio=1.2 m -1 

Cube 

Surface area: 6s 2 =294 m 2 

Volume: s 3 = 343 m 3 

Surface area to volume: 294/343 =0.86 m -1 

The sphere has a larger surface area to volume ratio and would exchange chemicals with the environment more efficiently to support its volume, even though the cube has a larger surface area. 

Desai B.V., Harmon, R. M. and Green K. J. (2009). Desmosomes at a glance Journal of Cell Science 122, 4401-4407 Section Summary 

Prokaryotes are predominantly single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, and DNA that is not membrane-bound. Most have peptidoglycan cell walls and many have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1 to 5.0 m. 

As a cell increases in size, its surface area-to-volume ratio decreases. If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. Review Questions 

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[link] Glossary nucleoid central part of a prokaryotic cell in which the chromosome is found prokaryote unicellular organism that lacks a nucleus or any other membrane-bound organelleEukaryotic Cells Eukaryotic Cells 

In this section, you will explore the following questions: How does the structure of the eukaryotic cell resemble as well as differ from the structure of the prokaryotic cell? What are structural differences between animal and plant cells? What are the functions of the major cell structures? Connection for AP Courses 

Eukaryotic cells possess many features that prokaryotic cells lack, including a nucleus with a double membrane that encloses DNA. In addition, eukaryotic cells tend to be larger and have a variety of membrane-bound organelles that perform specific, compartmentalized functions. Evidence supports the hypothesis that eukaryotic cells likely evolved from prokaryotic ancestors; for example, mitochondria and chloroplasts feature characteristics of independently-living prokaryotes. Eukaryotic cells come in all shapes, sizes, and types (e.g. animal cells, plant cells, and different types of cells in the body). (Hint: This a rare instance where you should create a list of organelles and their respective functions because later you will focus on how various organelles work together, similar to how your body s organs work together to keep you healthy.) Like prokaryotes, all eukaryotic cells have a plasma membrane, cytoplasm, ribosomes, and DNA. Many organelles are bound by membranes composed of phospholipid bilayers embedded with proteins to compartmentalize functions such as the storage of hydrolytic enzymes and the synthesis of proteins. The nucleus houses DNA, and the nucleolus within the nucleus is the site of ribosome assembly. Functional ribosomes are found either free in the cytoplasm or attached to the rough endoplasmic reticulum where they perform protein synthesis. The Golgi apparatus receives, modifies, and packages small molecules like lipids and proteins for distribution. Mitochondria and chloroplasts participate in free energy capture and transfer through the processes of cellular respiration and photosynthesis, respectively. Peroxisomes oxidize fatty acids and amino acids, and they are equipped to break down hydrogen peroxide formed from these reactions without letting it into the cytoplasm where it can cause damage. Vesicles and vacuoles store substances, and in plant cells, the central vacuole stores pigments, salts, minerals, nutrients, proteins, and degradation enzymes and helps maintain rigidity. In contrast, animal cells have centrosomes and lysosomes but lack cell walls. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 1, Big Idea 2, and Big Idea 4 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 7.2 The student can connect concepts in and across domains to generalize or extrapolate in and/or across enduring understandings Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments. Essential Knowledge 2.B.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.13 The student is able to explain how internal membranes and organelles contribute to cell functions. Essential Knowledge 2.B.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 2.14 The student is able to use representations and models to describe differences in prokaryotic and eukaryotic cells. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.2 The structure and function of subcellular components, and their interactions, provide essential cellular processes. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 4.5 The student is able to construct explanations based on scientific evidence as to how interactions of subcellular structures provide essential functions. 

Divide students into groups of 4 5 and assign each group either a bacterial, plant or animal cell and ask each group to draw the cell and its components on a large sheet of paper. Groups will use a separate sheet of paper to list all the structures and their respective functions. Ask each group to present its cell model to the rest of the class. Post the drawings on the wall of the class. Update the models with corrections as needed. 

Many students reason that plant cells do not need mitochondria because the chloroplasts within plant cells convert light energy into chemical energy, and, therefore, mitochondria are not needed. Stress that all eukaryotic cells (with only few exceptions) contain mitochondria. 

Emphasize that the diagrams in the textbook represent generalizations. Cells vary enormously in shapes and functions. Some internal structures may be predominant according to the type of cell. For instance, liver cells that detoxify chemicals and synthesize lipids have an extensive smooth endoplasmic reticulum. 

Have you ever heard the phrase form follows function? It s a philosophy practiced in many industries. In architecture, this means that buildings should be constructed to support the activities that will be carried out inside them. For example, a skyscraper should be built with several elevator banks; a hospital should be built so that its emergency room is easily accessible. 

Our natural world also utilizes the principle of form following function, especially in cell biology, and this will become clear as we explore eukaryotic cells ( [link] ). Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus; 2) numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others; and 3) several, rod-shaped chromosomes. Because a eukaryotic cell s nucleus is surrounded by a membrane, it is often said to have a true nucleus. The word organelle means little organ, and, as already mentioned, organelles have specialized cellular functions, just as the organs of your body have specialized functions. 

At this point, it should be clear to you that eukaryotic cells have a more complex structure than prokaryotic cells. Organelles allow different functions to be compartmentalized in different areas of the cell. Before turning to organelles, let s first examine two important components of the cell: the plasma membrane and the cytoplasm. 

These figures show the major organelles and other cell components of (a) a typical animal cell and (b) a typical eukaryotic plant cell. The plant cell has a cell wall, chloroplasts, plastids, and a central vacuole structures not found in animal cells. Plant cells do not have lysosomes or centrosomes. 

[link] The Plasma Membrane 

Like prokaryotes, eukaryotic cells have a plasma membrane ( [link] ), a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule with two fatty acid chains and a phosphate-containing group. The plasma membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane. The eukaryotic plasma membrane is a phospholipid bilayer with proteins and cholesterol embedded in it. 

The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular = microvillus); ( [link] ). Such cells are typically found lining the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form following function. People with celiac disease have an immune response to gluten, which is a protein found in wheat, barley, and rye. The immune response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and diarrhea. Patients suffering from celiac disease must follow a gluten-free diet. Microvilli, shown here as they appear on cells lining the small intestine, increase the surface area available for absorption. These microvilli are only found on the area of the plasma membrane that faces the cavity from which substances will be absorbed. (credit "micrograph": modification of work by Louisa Howard) The Cytoplasm 

The cytoplasm is the entire region of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up of organelles suspended in the gel-like cytosol , the cytoskeleton, and various chemicals ( [link] ). Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there, too. Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm. The Nucleus 

Typically, the nucleus is the most prominent organelle in a cell ( [link] ). The nucleus (plural = nuclei) houses the cell s DNA and directs the synthesis of ribosomes and proteins. Let s look at it in more detail ( [link] ). The nucleus stores chromatin (DNA plus proteins) in a gel-like substance called the nucleoplasm. The nucleolus is a condensed region of chromatin where ribosome synthesis occurs. The boundary of the nucleus is called the nuclear envelope. It consists of two phospholipid bilayers: an outer membrane and an inner membrane. The nuclear membrane is continuous with the endoplasmic reticulum. Nuclear pores allow substances to enter and exit the nucleus. The Nuclear Envelope 

The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus ( [link] ). Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers. 

The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semi-solid fluid inside the nucleus, where we find the chromatin and the nucleolus. Chromatin and Chromosomes 

To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material. You may remember that in prokaryotes, DNA is organized into a single circular chromosome. In eukaryotes, chromosomes are linear structures. Every eukaryotic species has a specific number of chromosomes in the nuclei of its body s cells. For example, in humans, the chromosome number is 46, while in fruit flies, it is eight. Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, proteins are attached to chromosomes, and they resemble an unwound, jumbled bunch of threads. These unwound protein-chromosome complexes are called chromatin ( [link] ); chromatin describes the material that makes up the chromosomes both when condensed and decondensed. (a) This image shows various levels of the organization of chromatin (DNA and protein). (b) This image shows paired chromosomes. (credit b: modification of work by NIH; scale-bar data from Matt Russell) The Nucleolus 

We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus called the nucleolus (plural = nucleoli) aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported out through the pores in the nuclear envelope to the cytoplasm. Ribosomes 

Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. They may be attached to the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum and the outer membrane of the nuclear envelope ( [link] ). Electron microscopy has shown us that ribosomes, which are large complexes of protein and RNA, consist of two subunits, aptly called large and small ( [link] ). Ribosomes receive their orders for protein synthesis from the nucleus where the DNA is transcribed into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. Amino acids are the building blocks of proteins. Ribosomes are made up of a large subunit (top) and a small subunit (bottom). During protein synthesis, ribosomes assemble amino acids into proteins. 

Because proteins synthesis is an essential function of all cells (including enzymes, hormones, antibodies, pigments, structural components, and surface receptors), ribosomes are found in practically every cell. Ribosomes are particularly abundant in cells that synthesize large amounts of protein. For example, the pancreas is responsible for creating several digestive enzymes and the cells that produce these enzymes contain many ribosomes. Thus, we see another example of form following function. Mitochondria 

Mitochondria (singular = mitochondrion) are often called the powerhouses or energy factories of a cell because they are responsible for making adenosine triphosphate (ATP), the cell s main energy-carrying molecule. ATP represents the short-term stored energy of the cell. Cellular respiration is the process of making ATP using the chemical energy found in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a byproduct. 

In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria that produce ATP. Your muscle cells need a lot of energy to keep your body moving. When your cells don t get enough oxygen, they do not make a lot of ATP. Instead, the small amount of ATP they make in the absence of oxygen is accompanied by the production of lactic acid. 

Mitochondria are oval-shaped, double membrane organelles ( [link] ) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration. This electron micrograph shows a mitochondrion as viewed with a transmission electron microscope. This organelle has an outer membrane and an inner membrane. The inner membrane contains folds, called cristae, which increase its surface area. The space between the two membranes is called the intermembrane space, and the space inside the inner membrane is called the mitochondrial matrix. ATP synthesis takes place on the inner membrane. (credit: modification of work by Matthew Britton; scale-bar data from Matt Russell) Peroxisomes 

Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. (Many of these oxidation reactions release hydrogen peroxide, H 2 O 2 , which would be damaging to cells; however, when these reactions are confined to peroxisomes, enzymes safely break down the H 2 O 2 into oxygen and water.) For example, alcohol is detoxified by peroxisomes in liver cells. Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars. Vesicles and Vacuoles 

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Other than the fact that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them: The membranes of vesicles can fuse with either the plasma membrane or other membrane systems within the cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The membrane of a vacuole does not fuse with the membranes of other cellular components. Animal Cells versus Plant Cells 

At this point, you know that each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles, but there are some striking differences between animal and plant cells. While both animal and plant cells have microtubule organizing centers (MTOCs), animal cells also have centrioles associated with the MTOC: a complex called the centrosome. Animal cells each have a centrosome and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, whereas animal cells do not. The Centrosome 

The centrosome is a microtubule-organizing center found near the nuclei of animal cells. It contains a pair of centrioles, two structures that lie perpendicular to each other ( [link] ). Each centriole is a cylinder of nine triplets of microtubules. The centrosome consists of two centrioles that lie at right angles to each other. Each centriole is a cylinder made up of nine triplets of microtubules. Nontubulin proteins (indicated by the green lines) hold the microtubule triplets together. 

The centrosome (the organelle where all microtubules originate) replicates itself before a cell divides, and the centrioles appear to have some role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division isn t clear, because cells that have had the centrosome removed can still divide, and plant cells, which lack centrosomes, are capable of cell division. Lysosomes 

Animal cells have another set of organelles not found in plant cells: lysosomes. The lysosomes are the cell s garbage disposal. In plant cells, the digestive processes take place in vacuoles. Enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. These enzymes are active at a much lower pH than that of the cytoplasm. Therefore, the pH within lysosomes is more acidic than the pH of the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, so again, the advantage of compartmentalizing the eukaryotic cell into organelles is apparent. The Cell Wall 

If you examine [link] b , the diagram of a plant cell, you will see a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protistan cells also have cell walls. While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose ( [link] ), a polysaccharide made up of glucose units. Have you ever noticed that when you bite into a raw vegetable, like celery, it crunches? That s because you are tearing the rigid cell walls of the celery cells with your teeth. Cellulose is a long chain of -glucose molecules connected by a 1-4 linkage. The dashed lines at each end of the figure indicate a series of many more glucose units. The size of the page makes it impossible to portray an entire cellulose molecule. Chloroplasts 

Like the mitochondria, chloroplasts have their own DNA and ribosomes, but chloroplasts have an entirely different function. Chloroplasts are plant cell organelles that carry out photosynthesis. Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. This is a major difference between plants and animals; plants (autotrophs) are able to make their own food, like sugars, while animals (heterotrophs) must ingest their food. 

Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast s inner membrane is a set of interconnected and stacked fluid-filled membrane sacs called thylakoids ( [link] ). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane that surrounds the grana is called the stroma. The chloroplast has an outer membrane, an inner membrane, and membrane structures called thylakoids that are stacked into grana. The space inside the thylakoid membranes is called the thylakoid space. The light harvesting reactions take place in the thylakoid membranes, and the synthesis of sugar takes place in the fluid inside the inner membrane, which is called the stroma. Chloroplasts also have their own genome, which is contained on a single circular chromosome. 

The chloroplasts contain a green pigment called chlorophyll , which captures the light energy that drives the reactions of photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria perform photosynthesis, but their chlorophyll is not relegated to an organelle. 

Endosymbiosis We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation. 

Symbiosis is a relationship in which organisms from two separate species depend on each other for their survival. Endosymbiosis (endo- = within ) is a mutually beneficial relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. We have already mentioned that microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and from drying out, and they receive abundant food from the environment of the large intestine. 

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that bacteria have DNA and ribosomes, just as mitochondria and chloroplasts do. Scientists believe that host cells and bacteria formed an endosymbiotic relationship when the host cells ingested both aerobic and autotrophic bacteria (cyanobacteria) but did not destroy them. Through many millions of years of evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the autotrophic bacteria becoming chloroplasts. 

[link] The Central Vacuole 

Previously, we mentioned vacuoles as essential components of plant cells. If you look at [link] b , you will see that plant cells each have a large central vacuole that occupies most of the area of the cell. The central vacuole plays a key role in regulating the cell s concentration of water in changing environmental conditions. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That s because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of plant cells results in the wilted appearance of the plant. 

The central vacuole also supports the expansion of the cell. When the central vacuole holds more water, the cell gets larger without having to invest a lot of energy in synthesizing new cytoplasm. Activity Construct a concept map or Venn diagram to describe the relationships that exist among the three domains of life (Archaea, Bacteria, and Eukarya) based on cellular features. Share your diagram with other students in the class for review and revision. Mystery Cell ID. Using a microscope, identify several types of cells, e.g., prokaryote/eukaryote, plant/animal, based on general features and justify your identification. Ten-Minute Debate. Working in small teams, create a visual representation to support the claim that eukaryotes evolved from symbiotic relationships among groups of prokaryotes. Think About It If the nucleolus were not able to carry out its function, what other cellular organelles would be affected? Would a human liver cell that lacked endoplasmic reticulum be able to metabolize toxins? Antibiotics are medicines that are used to fight bacterial infections. These medicines kill prokaryotic cells without harming human cells. What part(s) of the bacterial cell do antibiotics target and provide reasoning for your answer. 

The first activity is an application of Learning Objectives 1.15 and Science Practice 7.2 because students are describing features common to all cells that suggest common ancestry. 

The second activity is an application of Learning Objectives 2.14 and Science Practice 1.4 because the students are describing features that typify various cell types based on models presented in the textbook. 

The third activity is an application of Learning Objectives 1.16 and Science Practice 6.1 because the students are describing evidence that supports the claim that eukaryotes evolved from prokaryotes. and following with a question that could be investigated to provide additional support for this claim. 

The first question is an application of Learning Objectives 4.4 and Science Practice 6.4 because the students are asked to make predictions about the functions of cellular organelles. 

The second question is an application of Learning Objectives 2.14 and Science Practice 1.4 because the students are describing differences between prokaryotic and eukaryotic cells based on models of the cell(s). 

Although ribosomes are well-conserved, there are enough differences between prokaryotic and eukaryotic ribosomes that many antibiotics target the prokaryotic ribosomes without affecting the eukaryotic ribosomes. Mention that ribosomes in mitochondria and chloroplasts are very similar to the prokaryotic ribosomes. This is a strong point in support of the endosymbiotic theory. 

Choose a light or electron microscope or set of micrographs to extend the activity. This enables the students to take size into consideration. Use table 4.1 as a guide. Point out that eventually all organelles would be affected by a loss of ribosome function, as protein synthesis shuts down. A human liver cell that lacked the smooth endoplasmic reticulum (SER) would not breakdown toxins, as that is one of the functions of the SER. This is an opportunity to differentiate between RER and SER. All antibiotics inhibit growth either by killing (bactericidal) or by interfering with growth (bacteriostatic). Penicillin and derivatives inhibit the synthesis of peptidoglycans in the cell wall. Without a cell wall, bacterial cells lyse. Section Summary 

Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleus s nucleolus is the site of ribosome assembly. Ribosomes are either found in the cytoplasm or attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria participate in cellular respiration; they are responsible for the majority of ATP produced in the cell. Peroxisomes hydrolyze fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules. 

Animal cells also have a centrosome and lysosomes. The centrosome has two bodies perpendicular to each other, the centrioles, and has an unknown purpose in cell division. Lysosomes are the digestive organelles of animal cells. 

Plant cells and plant-like cells each have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole can expand without having to produce more cytoplasm. Review Questions 

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[link] Glossary cell wall rigid cell covering made of cellulose that protects the cell, provides structural support, and gives shape to the cell central vacuole large plant cell organelle that regulates the cell s storage compartment, holds water, and plays a significant role in cell growth as the site of macromolecule degradation centrosome region in animal cells made of two centrioles chlorophyll green pigment that captures the light energy that drives the light reactions of photosynthesis chloroplast plant cell organelle that carries out photosynthesis chromatin protein-DNA complex that serves as the building material of chromosomes chromosome structure within the nucleus that is made up of chromatin that contains DNA, the hereditary material cytoplasm entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals cytosol gel-like material of the cytoplasm in which cell structures are suspended eukaryotic cell cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs lysosome organelle in an animal cell that functions as the cell s digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles mitochondria (singular = mitochondrion) cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cell s main energy-carrying molecule nuclear envelope double-membrane structure that constitutes the outermost portion of the nucleus nucleolus darkly staining body within the nucleus that is responsible for assembling the subunits of the ribosomes nucleoplasm semi-solid fluid inside the nucleus that contains the chromatin and nucleolus nucleus cell organelle that houses the cell s DNA and directs the synthesis of ribosomes and proteins organelle compartment or sac within a cell peroxisome small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons plasma membrane phospholipid bilayer with embedded (integral) or attached (peripheral) proteins, and separates the internal content of the cell from its surrounding environment ribosome cellular structure that carries out protein synthesis vacuole membrane-bound sac, somewhat larger than a vesicle, which functions in cellular storage and transport vesicle small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatusThe Endomembrane System and Proteins The Endomembrane System and Proteins 

In this section, you will explore the following questions: What is the relationship between the structure and function of the components of the endomembrane system, especially with regard to the synthesis of proteins? Connection for AP Courses 

In addition to the presence of nuclei, eukaryotic cells are distinguished by an endomembrane system that includes the plasma membrane, nuclear envelope, lysosomes, vesicles, endoplasmic reticulum, and Golgi apparatus. These subcellular components work together to modify, tag, package, and transport proteins and lipids. The rough endoplasmic reticulum (RER) with its attached ribosomes is the site of protein synthesis and modification. The smooth endoplasmic reticulum (SER) synthesizes carbohydrates, lipids including phospholipids and cholesterol, and steroid hormones; engages in the detoxification of medications and poisons; and stores calcium ions. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens. Just like your body uses different organs that work together, cells use these organelles interact to perform specific functions. For example, proteins that are synthesized in the RER then travel to the Golgi apparatus for modification and packaging for either storage or transport. If these proteins are hydrolytic enzymes, they can be stored in lysosomes. Mitochondria produce the energy needed for these processes. This functional flow through several organelles, a process which is dependent on energy produced by yet another organelle, serves as a hallmark illustration of the cell s complex, interconnected dependence on its organelles. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 2 and Big Idea 4 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. 

Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments. Essential Knowledge 2.B.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.13 The student is able to explain how internal membranes and organelles contribute to cell functions. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.2 The structure and function of subcellular components, and their interactions, provide essential cellular processes. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 4.5 The student is able to construct explanations based on scientific evidence as to how interactions of subcellular structures provide essential functions. 

Students will need help in visualizing the endomembrane system. For example, explain how the interior membrane surface of a vesicle will face the outside of the cell, once the vesicle fuses with the plasma membrane. Use rubber bands to simulate vesicles and mark the inside with a sharpie or a pen. Follow the ink marks as the vesicle rubber band fuses with the cell membrane (cut the rubber band to facilitate the fusion being modeled.) 

Students may think that all ribosomes are attached to the rough endoplasmic reticulum. Stress that there are free ribosomes as well. They are found in the cytosol where they are involved in the synthesis of cytosolic proteins, which remain within the cytosol. Free and bound ribosomes are identical in structure . Individual ribosomes cycle between free and membrane-bound positions as needed. 

Mitochondria and chloroplasts also contain ribosomes which resemble those of prokaryotes. This observation is one of the arguments in favor of the endosymbiotic theory. 

Smooth endoplasmic reticulum is not as important as the rough endoplasmic reticulum. No, both endomembrane networks play important roles in the life of a cell. The Endoplasmic Reticulum 

The endomembrane system (endo = within ) is a group of membranes and organelles ( [link] ) in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, which we ve already mentioned, and the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles. The endomembrane system does not include the membranes of either mitochondria or chloroplasts. 

"Membrane and secretory proteins are synthesized in the rough endoplasmic reticulum (RER). The RER also sometimes modifies proteins. In this illustration, a (green) integral membrane protein in the ER is modified by attachment of a (purple) carbohydrate. Vesicles with the integral protein bud from the ER and fuse with the cis face of the Golgi apparatus. As the protein passes along the Golgi s cisternae, it is further modified by the addition of more carbohydrates. After its synthesis is complete, it exits as integral membrane protein of the vesicle that bud from the Golgi s trans face and when the vesicle fuses with the cell membrane the protein becomes integral portion of that cell membrane. (credit: modification of work by Magnus Manske) 

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The endoplasmic reticulum (ER) ( [link] ) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions are performed in separate areas of the ER: the rough ER and the smooth ER, respectively. 

The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope. Rough ER 

The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope ( [link] ). This transmission electron micrograph shows the rough endoplasmic reticulum and other organelles in a pancreatic cell. (credit: modification of work by Louisa Howard) 

Ribosomes transfer their newly synthesized proteins into the lumen of the RER where they undergo structural modifications, such as folding or the acquisition of side chains. These modified proteins will be incorporated into cellular membranes the membrane of the ER or those of other organelles or secreted from the cell (such as protein hormones, enzymes). The RER also makes phospholipids for cellular membranes. 

If the phospholipids or modified proteins are not destined to stay in the RER, they will reach their destinations via transport vesicles that bud from the RER s membrane ( [link] ). 

Since the RER is engaged in modifying proteins (such as enzymes, for example) that will be secreted from the cell, you would be correct in assuming that the RER is abundant in cells that secrete proteins. This is the case with cells of the liver, for example. Smooth ER 

The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface ( [link] ). Functions of the SER include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storage of calcium ions. 

In muscle cells, a specialized SER called the sarcoplasmic reticulum is responsible for storage of the calcium ions that are needed to trigger the coordinated contractions of the muscle cells. 

You can watch an excellent animation of the endomembrane system here . At the end of the animation, there is a short self-assessment. 

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Cardiologist Heart disease is the leading cause of death in the United States. This is primarily due to our sedentary lifestyle and our high trans-fat diets. 

Heart failure is just one of many disabling heart conditions. Heart failure does not mean that the heart has stopped working. Rather, it means that the heart can t pump with sufficient force to transport oxygenated blood to all the vital organs. Left untreated, heart failure can lead to kidney failure and failure of other organs. 

The wall of the heart is composed of cardiac muscle tissue. Heart failure occurs when the endoplasmic reticula of cardiac muscle cells do not function properly. As a result, an insufficient number of calcium ions are available to trigger a sufficient contractile force. 

Cardiologists (cardi- = heart ; -ologist = one who studies ) are doctors who specialize in treating heart diseases, including heart failure. Cardiologists can make a diagnosis of heart failure via physical examination, results from an electrocardiogram (ECG, a test that measures the electrical activity of the heart), a chest X-ray to see whether the heart is enlarged, and other tests. If heart failure is diagnosed, the cardiologist will typically prescribe appropriate medications and recommend a reduction in table salt intake and a supervised exercise program. The Golgi Apparatus 

We have already mentioned that vesicles can bud from the ER and transport their contents elsewhere, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles still need to be sorted, packaged, and tagged so that they wind up in the right place. Sorting, tagging, packaging, and distribution of lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranes ( [link] ). The Golgi apparatus in this white blood cell is visible as a stack of semicircular, flattened rings in the lower portion of the image. Several vesicles can be seen near the Golgi apparatus. (credit: modification of work by Louisa Howard) 

The receiving side of the Golgi apparatus is called the cis face. The opposite side is called the trans face. The transport vesicles that formed from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is the addition of short chains of sugar molecules. These newly modified proteins and lipids are then tagged with phosphate groups or other small molecules so that they can be routed to their proper destinations. 

Finally, the modified and tagged proteins are packaged into secretory vesicles that bud from the trans face of the Golgi. While some of these vesicles deposit their contents into other parts of the cell where they will be used, other secretory vesicles fuse with the plasma membrane and release their contents outside the cell. 

In another example of form following function, cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundance of Golgi. 

In plant cells, the Golgi apparatus has the additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell. Career Connection 

Geneticist Many diseases arise from genetic mutations that prevent the synthesis of critical proteins. One such disease is Lowe disease (also called oculocerebrorenal syndrome, because it affects the eyes, brain, and kidneys). In Lowe disease, there is a deficiency in an enzyme localized to the Golgi apparatus. Children with Lowe disease are born with cataracts, typically develop kidney disease after the first year of life, and may have impaired mental abilities. 

Lowe disease is a genetic disease caused by a mutation on the X chromosome. The X chromosome is one of the two human sex chromosome, as these chromosomes determine a person's sex. Females possess two X chromosomes while males possess one X and one Y chromosome. In females, the genes on only one of the two X chromosomes are expressed. Therefore, females who carry the Lowe disease gene on one of their X chromosomes have a 50/50 chance of having the disease. However, males only have one X chromosome and the genes on this chromosome are always expressed. Therefore, males will always have Lowe disease if their X chromosome carries the Lowe disease gene. The location of the mutated gene, as well as the locations of many other mutations that cause genetic diseases, has now been identified. Through prenatal testing, a woman can find out if the fetus she is carrying may be afflicted with one of several genetic diseases. 

Geneticists analyze the results of prenatal genetic tests and may counsel pregnant women on available options. They may also conduct genetic research that leads to new drugs or foods, or perform DNA analyses that are used in forensic investigations. Lysosomes 

In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are considered to be parts of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body s immune system. In a process known as phagocytosis or endocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome s hydrolytic enzymes then destroy the pathogen ( [link] ). A macrophage has engulfed (phagocytized) a potentially pathogenic bacterium and then fuses with a lysosomes within the cell to destroy the pathogen. Other organelles are present in the cell but for simplicity are not shown. Activity 

Homemade Cell Project. Using inexpensive and common household items, create a model of a specific eukaryotic cell (e.g., neuron, white blood cell, plant root cell, or Paramecium ) that demonstrates how at least three organelles work together to perform a specific function. Think About It 

A certain cell type functions primarily to synthesize proteins for export. What is the most likely route the newly made protein takes through the cell? Justify your prediction. 

The activity is an application of Learning Objective 2.13 and Science Practice 6.2 and Learning Objective 4.6 and Science Practice 1.4 because students are asked to create a model that describes various organelles in a specific cell type and then describe how organelles work together to perform a characteristic function of the cell. 

The Think About It question is an application of Learning Objective 4.4 and Science Practice 6.4 because students are making a prediction about the interactions of subcellular organelles in performing a specific function. 

The path is ribosomes rough ER vesicle Golgi apparatus vesicle and release. Use information in the text. Section Summary 

The endomembrane system includes the nuclear envelope, lysosomes, vesicles, the ER, and Golgi apparatus, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport proteins and lipids that form the membranes. 

The RER modifies proteins and synthesizes phospholipids used in cell membranes. The SER synthesizes carbohydrates, lipids, and steroid hormones; engages in the detoxification of medications and poisons; and stores calcium ions. Sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus. Lysosomes are created by the budding of the membranes of the RER and Golgi. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens. Review Questions 

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[link] Glossary endomembrane system group of organelles and membranes in eukaryotic cells that work together modifying, packaging, and transporting lipids and proteins endoplasmic reticulum (ER) series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids Golgi apparatus eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution rough endoplasmic reticulum (RER) region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification and phospholipid synthesis smooth endoplasmic reticulum (SER) region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies certain chemicals (like pesticides, preservatives, medications, and environmental pollutants), and stores calcium ionsThe Cytoskeleton The Cytoskeleton 

In this section, you will explore the following questions: How do the various components of the cytoskeleton perform their functions? Connection for AP Courses 

All cells, from simple bacteria to complex eukaryotes, possess a cytoskeleton composed of different types of protein elements, including microfilaments, intermediate filaments, and microtubules. The cytoskeleton serves a variety of purposes: provides rigidity and shape to the cell, facilitates cellular movement, anchors the nucleus and other organelles in place, moves vesicles through the cell, and pulls replicated chromosomes to the poles of a dividing cell. These protein elements are also integral to the movement of centrioles, flagella, and cilia. 

The information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 1 of the AP Biology Curriculum Framework, as shown in the table below. 

The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. 

Describe the cytoskeleton both as a skeleton because it provides the cell with shape and as muscles because it allows cells to move. The subunits of the cytoskeleton assemble and disassemble constantly, which is hard to imagine. Stress the concept of dynamic equilibrium. A vivid animation may illustrate the point better. Another way to demonstrate this is to have a few students stand in a line and then have a pool of students stand nearby. Then, on by one, ask students from the pool to exchange places with a student standing in the line. The line itself can grow and shrink by adding or taking away students in the line, respectively. 

Both prokaryotic and eukaryotic cells possess cytoskeletons involved in cell division and shape maintenance. Although the molecular structures of cytoskeleton proteins are similar between two types of cells, the actual amino acid sequences of these proteins show very low levels of homology between the cytoskeleton proteins in prokaryotes and eukaryotes. 

The two systems are not closely related. 

Although the cytoskeleton of prokaryotes was discovered in the mid 90 s, the misconception that prokaryotes do not have a cytoskeleton is still widespread. Microfilaments 

If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that help maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable cells within multicellular organisms to move. Collectively, this network of protein fibers is known as the cytoskeleton . There are three types of fibers within the cytoskeleton: microfilaments, intermediate filaments, and microtubules ( [link] ). Here, we will examine each. Microfilaments thicken the cortex around the inner edge of a cell; like rubber bands, they resist tension. Microtubules are found in the interior of the cell where they maintain cell shape by resisting compressive forces. Intermediate filaments are found throughout the cell and hold organelles in place. 

Of the three types of protein fibers in the cytoskeleton, microfilaments are the narrowest. They function in cellular movement, have a diameter of about 7 nm, and are made of two intertwined strands of a globular protein called actin ( [link] ). For this reason, microfilaments are also known as actin filaments. Microfilaments are made of two intertwined strands of actin. 

Actin is powered by ATP to assemble its filamentous form, which serves as a track for the movement of a motor protein called myosin. This enables actin to engage in cellular events requiring motion, such as cell division in animal cells and cytoplasmic streaming, which is the circular movement of the cell cytoplasm in plant cells. Actin and myosin are plentiful in muscle cells. When your actin and myosin filaments slide past each other, your muscles contract. 

Microfilaments also provide some rigidity and shape to the cell. They can depolymerize (disassemble) and reform quickly, thus enabling a cell to change its shape and move. White blood cells (your body s infection-fighting cells) make good use of this ability. They can move to the site of an infection and phagocytize the pathogen. 

To see an example of a white blood cell in action, click here and watch a short time-lapse video of the cell capturing two bacteria. It engulfs one and then moves on to the other. 

[link] Intermediate Filaments 

Intermediate filaments are made of several strands of fibrous proteins that are wound together ( [link] ). These elements of the cytoskeleton get their name from the fact that their diameter, 8 to 10 nm, is between those of microfilaments and microtubules. Intermediate filaments consist of several intertwined strands of fibrous proteins. 

Intermediate filaments have no role in cell movement. Their function is purely structural. They bear tension, thus maintaining the shape of the cell, and anchor the nucleus and other organelles in place. [link] shows how intermediate filaments create a supportive scaffolding inside the cell. 

The intermediate filaments are the most diverse group of cytoskeletal elements. Several types of fibrous proteins are found in the intermediate filaments. You are probably most familiar with keratin, the fibrous protein that strengthens your hair, nails, and the epidermis of the skin. Microtubules 

As their name implies, microtubules are small hollow tubes. The walls of the microtubule are made of polymerized dimers of -tubulin and -tubulin, two globular proteins ( [link] ). With a diameter of about 25 nm, microtubules are the widest components of the cytoskeleton. They help the cell resist compression, provide a track along which vesicles move through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. Like microfilaments, microtubules can dissolve and reform quickly. Microtubules are hollow. Their walls consist of 13 polymerized dimers of -tubulin and -tubulin (right image). The left image shows the molecular structure of the tube. 

Microtubules are also the structural elements of flagella, cilia, and centrioles (the latter are the two perpendicular bodies of the centrosome). In fact, in animal cells, the centrosome is the microtubule-organizing center. In eukaryotic cells, flagella and cilia are quite different structurally from their counterparts in prokaryotes, as discussed below. Flagella and Cilia 

To refresh your memory, flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell (for example, sperm, Euglena ). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, many of them extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecia) or substances along the outer surface of the cell (for example, the cilia of cells lining the Fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that trap particulate matter and move it toward your nostrils.) 

Despite their differences in length and number, flagella and cilia share a common structural arrangement of microtubules called a 9 + 2 array. This is an appropriate name because a single flagellum or cilium is made of a ring of nine microtubule doublets, surrounding a single microtubule doublet in the center ( [link] ). This transmission electron micrograph of two flagella shows the 9 + 2 array of microtubules: nine microtubule doublets surround a single microtubule doublet. (credit: modification of work by Dartmouth Electron Microscope Facility, Dartmouth College; scale-bar data from Matt Russell) Think About It 

The ribosomes in bacterial cells and in human cells are made up of proteins and ribosomal RNA, suggesting that both kinds of cells share a common ancestor cell type. What are examples of other features of cells that provide evidence for common ancestry? 

This question is an application of Learning Objectives 1.15 and Science Practice 7.2 because shared conserved core biological processes and features support the concept of common ancestry for all organisms on Earth. 

In both prokaryotes and eukaryotes, DNA is the hereditary material and has the same structure. 

The cytosol is made of an aqueous gel. The membrane is a fluid bilayer in which proteins are embedded. Do not use the flagellum as an example. It is convergent evolution. 

You have now completed a broad survey of the components of prokaryotic and eukaryotic cells. For a summary of cellular components in prokaryotic and eukaryotic cells, see [link] . Components of Prokaryotic and Eukaryotic Cells Cell Component Function Present in Prokaryotes? Present in Animal Cells? Present in Plant Cells? Plasma membrane Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of cell Yes Yes Yes Cytoplasm Provides turgor pressure to plant cells as fluid inside the central vacuole; site of many metabolic reactions; medium in which organelles are found Yes Yes Yes Nucleolus Darkened area within the nucleus where ribosomal subunits are synthesized. No Yes Yes Nucleus Cell organelle that houses DNA and directs synthesis of ribosomes and proteins No Yes Yes Ribosomes Protein synthesis Yes Yes Yes Mitochondria ATP production/cellular respiration No Yes Yes Peroxisomes Oxidizes and thus breaks down fatty acids and amino acids, and detoxifies poisons No Yes Yes Vesicles and vacuoles Storage and transport; digestive function in plant cells No Yes Yes Centrosome Unspecified role in cell division in animal cells; source of microtubules in animal cells No Yes No Lysosomes Digestion of macromolecules; recycling of worn-out organelles No Yes No Cell wall Protection, structural support and maintenance of cell shape Yes, primarily peptidoglycan No Yes, primarily cellulose Chloroplasts Photosynthesis No No Yes Endoplasmic reticulum Modifies proteins and synthesizes lipids No Yes Yes Golgi apparatus Modifies, sorts, tags, packages, and distributes lipids and proteins No Yes Yes Cytoskeleton Maintains cell s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within cell, and enables unicellular organisms to move independently Yes Yes Yes Flagella Cellular locomotion Some Some No, except for some plant sperm cells. Cilia Cellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtration Some Some No Section Summary 

The cytoskeleton has three different types of protein elements. From narrowest to widest, they are the microfilaments (actin filaments), intermediate filaments, and microtubules. Microfilaments are often associated with myosin. They provide rigidity and shape to the cell and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural element of centrioles, flagella, and cilia. Review Questions 

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[link] Glossary cilium (plural = cilia) short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell cytoskeleton network of protein fibers that collectively maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable unicellular organisms to move independently flagellum (plural = flagella) long, hair-like structure that extends from the plasma membrane and is used to move the cell intermediate filament cytoskeletal component, composed of several intertwined strands of fibrous protein, that bears tension, supports cell-cell junctions, and anchors cells to extracellular structures microfilament narrowest element of the cytoskeleton system; it provides rigidity and shape to the cell and enables cellular movements microtubule widest element of the cytoskeleton system; it helps the cell resist compression, provides a track along which vesicles move through the cell, pulls replicated chromosomes to opposite ends of a dividing cell, and is the structural element of centrioles, flagella, and ciliaConnections between Cells and Cellular Activities Connections between Cells and Cellular Activities 

In this section, you will explore the following questions: What are the components of the extracellular matrix? What are the roles of tight junctions, gap junctions, and plasmodesmata in allowing cells to exchange materials with the environment and communicate with other cells? Connection for AP Courses 

With the exception of gap junctions between animal cells and plasmodesmata between plant cells that facilitate the exchange of substances, the information presented in Section 4.6| Connections between Cells and Cellular Activities is not required for AP . Concepts about cell communication and signaling processes that are required for AP , including the features of cells that make communication possible, are covered in Chapter 9. 

You already know that a group of similar cells working together is called a tissue. As you might expect that, if cells are to work together, they must communicate with one another, just as you need to communicate with others when you work on a group project. Let s take a look at how cells communicate with one another. 

Review the role of the extracellular matrix by comparing it to a scaffold outside of a building that buttresses and supports the main structure. It is an extension of the cell in animal tissues and provides essential functions in mechanical support, cell-cell communication, wound healing, and organism development. 

Cell junctions can be compared to the piecing together of fabric. Pieces of fabric are tightly joined by a seam. Tight junctions similarly glue cells together. Rivets and snaps bind fabric tightly in specific spots as desmosomes form close associations in specific areas. Gap junctions are almost like pins and allow trafficking between the cytoplasm of adjacent cells. 

Cells in tissues are usually inadequately visualized as puzzle pieces that interlock but that are functionally independent. Dispel this notion by stressing the importance of cell junctions. In multicellular organisms, cells interact with their neighboring cells. 

You already know that a group of similar cells working together is called a tissue. As you might expect, if cells are to work together, they must communicate with each other, just as you need to communicate with others if you work on a group project. Let s take a look at how cells communicate with each other. Extracellular Matrix of Animal Cells 

Most animal cells release materials into the extracellular space. The primary components of these materials are proteins, and the most abundant protein is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. Collectively, these materials are called the extracellular matrix ( [link] ). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other. How can this happen? The extracellular matrix consists of a network of proteins and carbohydrates. 

Cells have protein receptors on the extracellular surfaces of their plasma membranes. When a molecule within the matrix binds to the receptor, it changes the molecular structure of the receptor. The receptor, in turn, changes the conformation of the microfilaments positioned just inside the plasma membrane. These conformational changes induce chemical signals inside the cell that reach the nucleus and turn on or off the transcription of specific sections of DNA, which affects the production of associated proteins, thus changing the activities within the cell. 

Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, stimulates the adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to produce clotting factors. Intercellular Junctions 

Cells can also communicate with each other via direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata are junctions between plant cells, whereas animal cell contacts include tight junctions, gap junctions, and desmosomes. Plasmodesmata 

In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated by the cell wall that surrounds each cell ( see this figure b ). How then, can a plant transfer water and other soil nutrients from its roots, through its stems, and to its leaves? Such transport uses the vascular tissues (xylem and phloem) primarily. There also exist structural modifications called plasmodesmata (singular = plasmodesma), numerous channels that pass between cell walls of adjacent plant cells, connect their cytoplasm, and enable materials to be transported from cell to cell, and thus throughout the plant ( [link] ). A plasmodesma is a channel between the cell walls of two adjacent plant cells. Plasmodesmata allow materials to pass from the cytoplasm of one plant cell to the cytoplasm of an adjacent cell. Tight Junctions 

A tight junction is a watertight seal between two adjacent animal cells ( [link] ). The cells are held tightly against each other by proteins (predominantly two proteins called claudins and occludins). Tight junctions form watertight connections between adjacent animal cells. Proteins create tight junction adherence. (credit: modification of work by Mariana Ruiz Villareal) 

This tight adherence prevents materials from leaking between the cells; tight junctions are typically found in epithelial tissues that line internal organs and cavities, and comprise most of the skin. For example, the tight junctions of the epithelial cells lining your urinary bladder prevent urine from leaking out into the extracellular space. Desmosomes 

Also found only in animal cells are desmosomes , which act like spot welds between adjacent epithelial cells ( [link] ). Short proteins called cadherins in the plasma membrane connect to intermediate filaments to create desmosomes. The cadherins join two adjacent cells together and maintain the cells in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles. A desmosome forms a very strong spot weld between cells. It is created by the linkage of cadherins and intermediate filaments. (credit: modification of work by Mariana Ruiz Villareal) Gap Junctions 

Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate ( [link] ). Structurally, however, gap junctions and plasmodesmata differ. A gap junction is a protein-lined pore that allows water and small molecules to pass between adjacent animal cells. (credit: modification of work by Mariana Ruiz Villareal) 

Gap junctions develop when a set of six proteins (called connexins) in the plasma membrane arrange themselves in an elongated donut-like configuration called a connexon. When the pores ( doughnut holes ) of connexons in adjacent animal cells align, a channel between the two cells forms. Gap junctions are particularly important in cardiac muscle: The electrical signal for the muscle to contract is passed efficiently through gap junctions, allowing the heart muscle cells to contract in tandem. Link to Learning 

To conduct a virtual microscopy lab and review the parts of a cell, work through the steps of this interactive assignment . 

[link] Section Summary 

Animal cells communicate via their extracellular matrices and are connected to each other via tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other via plasmodesmata. 

When protein receptors on the surface of the plasma membrane of an animal cell bind to a substance in the extracellular matrix, a chain of reactions begins that changes activities taking place within the cell. Plasmodesmata are channels between adjacent plant cells, while gap junctions are channels between adjacent animal cells. However, their structures are quite different. A tight junction is a watertight seal between two adjacent cells, while a desmosome acts like a spot weld. Review Questions 

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[link] Glossary desmosome linkages between adjacent epithelial cells that form when cadherins in the plasma membrane attach to intermediate filaments extracellular matrix material (primarily collagen, glycoproteins, and proteoglycans) secreted from animal cells that provides mechanical protection and anchoring for the cells in the tissue gap junction channel between two adjacent animal cells that allows ions, nutrients, and low molecular weight substances to pass between cells, enabling the cells to communicate plasmodesma (plural = plasmodesmata) channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell tight junction firm seal between two adjacent animal cells created by protein adherenceIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Despite its seeming hustle and bustle, Grand Central Station functions with a high level of organization: People and objects move from one location to another, they cross or are contained within certain boundaries, and they provide a constant flow as part of larger activity. Analogously, a plasma membrane s functions involve movement within the cell and across boundaries in the process of intracellular and intercellular activities. (credit: modification of work by Randy Le Moine) 

The plasma membrane, which is also called the cell membrane, has many functions; but, the most basic one is to define the borders and act as gatekeeper for the cell. The plasma membrane is selectively permeable, meaning some molecules can freely enter or leave the cell. Others require help from specialized structures, other molecules, or require energy in order to cross. One example of a molecule that assists other molecules across the plasma membrane is a protein called NPC1. This protein is involved in moving cholesterol and other types of fats across the plasma membrane. Some people have a genetic condition resulting in improperly functioning NPC1. As a result, excessive cholesterol accumulates within cells causing a condition called NPC Disease. 

Scientists from the Albert Einstein College of Medicine, Harvard Medical School, and the Whitehead Institute for Biomedical Research discovered that the Ebola virus also uses NPC1 to hitch a ride into cells and replicate. The scientists used mice that lacked the NPC1 protein to test this hypothesis. When the scientists tried to infect these mice with Ebola, none of the mice got sick. Then they tried to infect mice with partially functioning NPC1 and found that they got sick, but did not die. In other words, without properly functioning NPC1, the Ebola virus cannot infect a mouse. If this pattern also exists in humans, it means that anyone with NPC Disease and its subsequent problem with high cholesterol may also be protected from Ebola. 

The complete research report can be found here . 

Show students a wilted plant and ask them why the plant has wilted. What is happening on a cellular level regarding movement of molecules? Can the wilting can be reversed? 

Plants have cell walls that surround the plasma membrane and prevent cell lysis in a hypotonic solution. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic to the cellular environment and water will always enter a cell if water is available. This inflow of water produces turgor pressure, which stiffens the cell walls of the plant. In non-woody plants, turgor pressure supports the plant. Conversely, if the plant is not watered, the extracellular fluid will become hypertonic, causing water to leave the cell. In this condition, the cell does not shrink because the cell wall is not flexible. However, the cell membrane detaches from the wall and constricts the cytoplasm. This is called plasmolysis. Plants in this condition lose turgor pressure and wilt. 

Before students begin this chapter, it is useful to review these concepts: Plasma membranes are the membrane boundary of all cells. Eukaryotic cells have a plasma membrane and intracellular membranes: including: a nuclear membrane and membrane-bound organelles (such as mitochondria). In contrast, prokaryotic cells only have a plasma membrane. 

Also, review definitions: intracellular, extracellular, cytosol, and extracellular fluid; cell surface to area rations and rates of diffusion.Components and Structure Components and Structure 

In this section, you will explore the following questions: How does the fluid mosaic model describe the structure and components of the plasma cell membrane? How do the molecular components of the membrane provide fluidity? Connection for AP Courses 

Like an art mosaic, the plasma membrane consists of several different components. Phospholipids (which we studied in previously) form a bilayer; the hydrophobic, fatty acid tails are in contact with each other and hydrophilic portions of the phospholipids are oriented toward the aqueous internal and external environments. Several types of proteins with different functions stud the membrane. Integral proteins often span the membrane and can transport materials into or out of the cells; these embedded proteins can be hydrophilic or hydrophobic, depending on their placement within the membrane. Peripheral proteins found on the exterior and interior surfaces of membranes can serve as enzymes, structural attachments for fibers of the cytoskeleton, and part of a cell s recognition sites. These cell-specific proteins play a vital role in immune function; enable cells of a certain type (e.g., liver cells) to identify each other when forming a tissue; and allow hormones and other molecules to recognize target cells. These proteins float throughout the membrane, constantly in flux. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The learning objectives provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments. Essential Knowledge 2.B.1 Cell membranes are selectively permeable due to their structure. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.10 The student is able to use representations and models to pose scientific questions about the properties of cell membranes and selective permeability based on molecular structure. Essential Knowledge 2.B.1 Cell membranes are selectively permeable due to their structure. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize and extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 2.11 The student is able to construct models that connect the movement of molecules across membrane with membrane structure and function. 

Educreations is a free iPad app that allows students to build electronic slides with narration. If student have access to an iPad, have students use the app to construct a model of the plasma membrane and its molecular components complete with an audio narrative. For more information, go here . 

Students may think that all cell membranes are identical. Discuss with students not all membranes are identical, and different membranes differ in composition. While all membranes consist of phospholipid bilayers, different membranes will contain unique, proteins that relate to the function of the cell or organelle. In addition, membrane composition can differ depending on how fluid the membrane needs to be. Membranes can differ in saturated fatty acid content (increasing rigidity) versus unsaturated fatty acid content, as well as cholesterol content, which protects the fluidity of the membrane from temperature change. 

The cell membrane has different lipid and protein compositions in distinct types of cells and may have therefore specific names for certain cell types, such as: Sarcolemma in myocytes, Oolemma in oocytes, and Axolemma in neuronal processes axons. 

A cell s plasma membrane defines the cell, outlines its borders, and determines the nature of its interaction with its environment (see [link] for a summary). Cells exclude some substances, take in others, and excrete still others, all in controlled quantities. The plasma membrane must be very flexible to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious functions of a plasma membrane. In addition, the surface of the plasma membrane carries markers that allow cells to recognize one another, which is vital for tissue and organ formation during early development, and which later plays a role in the self versus non-self distinction of the immune response. 

Among the most sophisticated functions of the plasma membrane is the ability to transmit signals by means of complex, integral proteins known as receptors. These proteins act both as receivers of extracellular inputs and as activators of intracellular processes. These membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors, and they activate intracellular response cascades when their effectors are bound. Occasionally, receptors are hijacked by viruses (HIV, human immunodeficiency virus, is one example) that use them to gain entry into cells, and at times, the genes encoding receptors become mutated, causing the process of signal transduction to malfunction with disastrous consequences. Fluid Mosaic Model 

The existence of the plasma membrane was identified in the 1890s, and its chemical components were identified in 1915. The principal components identified at that time were lipids and proteins. The first widely accepted model of the plasma membrane s structure was proposed in 1935 by Hugh Davson and James Danielli; it was based on the railroad track appearance of the plasma membrane in early electron micrographs. They theorized that the structure of the plasma membrane resembles a sandwich, with protein being analogous to the bread, and lipids being analogous to the filling. In the 1950s, advances in microscopy, notably transmission electron microscopy (TEM), allowed researchers to see that the core of the plasma membrane consisted of a double, rather than a single, layer. A new model that better explains both the microscopic observations and the function of that plasma membrane was proposed by S.J. Singer and Garth L. Nicolson in 1972. 

The explanation proposed by Singer and Nicolson is called the fluid mosaic model . The model has evolved somewhat over time, but it still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components including phospholipids, cholesterol, proteins, and carbohydrates that gives the membrane a fluid character. Plasma membranes range from 5 to 10 nm in thickness. For comparison, human red blood cells, visible via light microscopy, are approximately 8 m wide, or approximately 1,000 times wider than a plasma membrane. The membrane does look a bit like a sandwich ( [link] ). The fluid mosaic model of the plasma membrane describes the plasma membrane as a fluid combination of phospholipids, cholesterol, and proteins. Carbohydrates attached to lipids (glycolipids) and to proteins (glycoproteins) extend from the outward-facing surface of the membrane. 

The principal components of a plasma membrane are lipids (phospholipids and cholesterol), proteins, and carbohydrates attached to some of the lipids and some of the proteins. A phospholipid is a molecule consisting of glycerol, two fatty acids, and a phosphate-linked head group. Cholesterol, another lipid composed of four fused carbon rings, is found alongside the phospholipids in the core of the membrane. The proportions of proteins, lipids, and carbohydrates in the plasma membrane vary with cell type, but for a typical human cell, protein accounts for about 50 percent of the composition by mass, lipids (of all types) account for about 40 percent of the composition by mass, with the remaining 10 percent of the composition by mass being carbohydrates. However, the concentration of proteins and lipids varies with different cell membranes. For example, myelin, an outgrowth of the membrane of specialized cells that insulates the axons of the peripheral nerves, contains only 18 percent protein and 76 percent lipid. The mitochondrial inner membrane contains 76 percent protein and only 24 percent lipid. The plasma membrane of human red blood cells is 30 percent lipid. Carbohydrates are present only on the exterior surface of the plasma membrane and are attached to proteins, forming glycoproteins , or attached to lipids, forming glycolipids . Phospholipids 

The main fabric of the membrane is composed of amphiphilic, phospholipid molecules. The hydrophilic or water-loving areas of these molecules (which look like a collection of balls in an artist s rendition of the model) ( [link] ) are in contact with the aqueous fluid both inside and outside the cell. Hydrophobic , or water-hating molecules, tend to be non-polar. They interact with other non-polar molecules in chemical reactions, but generally do not interact with polar molecules. When placed in water, hydrophobic molecules tend to form a ball or cluster. The hydrophilic regions of the phospholipids tend to form hydrogen bonds with water and other polar molecules on both the exterior and interior of the cell. Thus, the membrane surfaces that face the interior and exterior of the cell are hydrophilic. In contrast, the interior of the cell membrane is hydrophobic and will not interact with water. Therefore, phospholipids form an excellent two-layer cell membrane that separates fluid within the cell from the fluid outside of the cell. 

A phospholipid molecule ( [link] ) consists of a three-carbon glycerol backbone with two fatty acid molecules attached to carbons 1 and 2, and a phosphate-containing group attached to the third carbon. This arrangement gives the overall molecule an area described as its head (the phosphate-containing group), which has a polar character or negative charge, and an area called the tail (the fatty acids), which has no charge. The head can form hydrogen bonds, but the tail cannot. A molecule with this arrangement of a positively or negatively charged area and an uncharged, or non-polar, area is referred to as amphiphilic or dual-loving. This phospholipid molecule is composed of a hydrophilic head and two hydrophobic tails. The hydrophilic head group consists of a phosphate-containing group attached to a glycerol molecule. The hydrophobic tails, each containing either a saturated or an unsaturated fatty acid, are long hydrocarbon chains. 

This characteristic is vital to the structure of a plasma membrane because, in water, phospholipids tend to become arranged with their hydrophobic tails facing each other and their hydrophilic heads facing out. In this way, they form a lipid bilayer a barrier composed of a double layer of phospholipids that separates the water and other materials on one side of the barrier from the water and other materials on the other side. In fact, phospholipids heated in an aqueous solution tend to spontaneously form small spheres or droplets (called micelles or liposomes), with their hydrophilic heads forming the exterior and their hydrophobic tails on the inside ( [link] ). In an aqueous solution, phospholipids tend to arrange themselves with their polar heads facing outward and their hydrophobic tails facing inward. (credit: modification of work by Mariana Ruiz Villareal) Proteins 

Proteins make up the second major component of plasma membranes. Integral proteins (some specialized types are called integrins) are, as their name suggests, integrated completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the hydrophobic region of the the phospholipid bilayer ( [link] ). Single-pass integral membrane proteins usually have a hydrophobic transmembrane segment that consists of 20 25 amino acids. Some span only part of the membrane associating with a single layer while others stretch from one side of the membrane to the other, and are exposed on either side. Some complex proteins are composed of up to 12 segments of a single protein, which are extensively folded and embedded in the membrane ( [link] ). This type of protein has a hydrophilic region or regions, and one or several mildly hydrophobic regions. This arrangement of regions of the protein tends to orient the protein alongside the phospholipids, with the hydrophobic region of the protein adjacent to the tails of the phospholipids and the hydrophilic region or regions of the protein protruding from the membrane and in contact with the cytosol or extracellular fluid. Integral membranes proteins may have one or more alpha-helices that span the membrane (examples 1 and 2), or they may have beta-sheets that span the membrane (example 3). (credit: Foobar /Wikimedia Commons) 

Peripheral proteins are found on the exterior and interior surfaces of membranes, attached either to integral proteins or to phospholipids. Peripheral proteins, along with integral proteins, may serve as enzymes, as structural attachments for the fibers of the cytoskeleton, or as part of the cell s recognition sites. These are sometimes referred to as cell-specific proteins. The body recognizes its own proteins and attacks foreign proteins associated with invasive pathogens. Carbohydrates 

Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids) ( [link] ). These carbohydrate chains may consist of 2 60 monosaccharide units and can be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other. These sites have unique patterns that allow the cell to be recognized, much the way that the facial features unique to each person allow him or her to be recognized. This recognition function is very important to cells, as it allows the immune system to differentiate between body cells (called self ) and foreign cells or tissues (called non-self ). Similar types of glycoproteins and glycolipids are found on the surfaces of viruses and may change frequently, preventing immune cells from recognizing and attacking them. 

These carbohydrates on the exterior surface of the cell the carbohydrate components of both glycoproteins and glycolipids are collectively referred to as the glycocalyx (meaning sugar coating ). The glycocalyx is highly hydrophilic and attracts large amounts of water to the surface of the cell. This aids in the interaction of the cell with its watery environment and in the cell s ability to obtain substances dissolved in the water. As discussed above, the glycocalyx is also important for cell identification, self/non-self determination, and embryonic development, and is used in cell-cell attachments to form tissues. 

How Viruses Infect Specific Organs Glycoprotein and glycolipid patterns on the surfaces of cells give many viruses an opportunity for infection. HIV and hepatitis viruses infect only specific organs or cells in the human body. HIV is able to penetrate the plasma membranes of a subtype of lymphocytes called T-helper cells, as well as some monocytes and central nervous system cells. The hepatitis virus attacks liver cells. 

These viruses are able to invade these cells, because the cells have binding sites on their surfaces that are specific to and compatible with certain viruses ( [link] ). Other recognition sites on the virus s surface interact with the human immune system, prompting the body to produce antibodies. Antibodies are made in response to the antigens or proteins associated with invasive pathogens, or in response to foreign cells, such as might occur with an organ transplant. These same sites serve as places for antibodies to attach and either destroy or inhibit the activity of the virus. Unfortunately, these recognition sites on HIV change at a rapid rate because of mutations, making the production of an effective vaccine against the virus very difficult, as the virus evolves and adapts. A person infected with HIV will quickly develop different populations, or variants, of the virus that are distinguished by differences in these recognition sites. This rapid change of surface markers decreases the effectiveness of the person s immune system in attacking the virus, because the antibodies will not recognize the new variations of the surface patterns. In the case of HIV, the problem is compounded by the fact that the virus specifically infects and destroys cells involved in the immune response, further incapacitating the host. HIV binds to the CD4 receptor, a glycoprotein on the surfaces of T cells. (credit: modification of work by NIH, NIAID) 

[link] Membrane Fluidity 

The mosaic characteristic of the membrane, described in the fluid mosaic model, helps to illustrate its nature. The integral proteins and lipids exist in the membrane as separate but loosely attached molecules. These resemble the separate, multicolored tiles of a mosaic picture, and they float, moving somewhat with respect to one another. The membrane is not like a balloon, however, that can expand and contract; rather, it is fairly rigid and can burst if penetrated or if a cell takes in too much water. However, because of its mosaic nature, a very fine needle can easily penetrate a plasma membrane without causing it to burst, and the membrane will flow and self-seal when the needle is extracted. 

The mosaic characteristics of the membrane explain some but not all of its fluidity. There are two other factors that help maintain this fluid characteristic. One factor is the nature of the phospholipids themselves. In their saturated form, the fatty acids in phospholipid tails are saturated with bound hydrogen atoms. There are no double bonds between adjacent carbon atoms. This results in tails that are relatively straight. In contrast, unsaturated fatty acids do not contain a maximal number of hydrogen atoms, but they do contain some double bonds between adjacent carbon atoms; a double bond results in a bend in the string of carbons of approximately 30 degrees ( [link] ). 

Thus, if saturated fatty acids, with their straight tails, are compressed by decreasing temperatures, they press in on each other, making a dense and fairly rigid membrane. If unsaturated fatty acids are compressed, the kinks in their tails elbow adjacent phospholipid molecules away, maintaining some space between the phospholipid molecules. This elbow room helps to maintain fluidity in the membrane at temperatures at which membranes with saturated fatty acid tails in their phospholipids would freeze or solidify. The relative fluidity of the membrane is particularly important in a cold environment. A cold environment tends to compress membranes composed largely of saturated fatty acids, making them less fluid and more susceptible to rupturing. Many organisms (fish are one example) are capable of adapting to cold environments by changing the proportion of unsaturated fatty acids in their membranes in response to the lowering of the temperature. 

Visit this site to see animations of the fluidity and mosaic quality of membranes. 

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Animals have an additional membrane constituent that assists in maintaining fluidity. Cholesterol, which lies alongside the phospholipids in the membrane, tends to dampen the effects of temperature on the membrane. Thus, this lipid functions as a buffer, preventing lower temperatures from inhibiting fluidity and preventing increased temperatures from increasing fluidity too much. Thus, cholesterol extends, in both directions, the range of temperature in which the membrane is appropriately fluid and consequently functional. Cholesterol also serves other functions, such as organizing clusters of transmembrane proteins into lipid rafts. The Components and Functions of the Plasma Membrane Component Location Phospholipid Main fabric of the membrane Cholesterol Attached between phospholipids and between the two phospholipid layers Integral proteins (for example, integrins) Embedded within the phospholipid layer(s). May or may not penetrate through both layers Peripheral proteins On the inner or outer surface of the phospholipid bilayer; not embedded within the phospholipids Carbohydrates (components of glycoproteins and glycolipids) Generally attached to proteins on the outside membrane layer 

Immunologist The variations in peripheral proteins and carbohydrates that affect a cell s recognition sites are of prime interest in immunology. These changes are taken into consideration in vaccine development. Many infectious diseases, such as smallpox, polio, diphtheria, and tetanus, were conquered by the use of vaccines. 

Immunologists are the physicians and scientists who research and develop vaccines, as well as treat and study allergies or other immune problems. Some immunologists study and treat autoimmune problems (diseases in which a person s immune system attacks his or her own cells or tissues, such as lupus) and immunodeficiencies, whether acquired (such as acquired immunodeficiency syndrome, or AIDS) or hereditary (such as severe combined immunodeficiency, or SCID). Immunologists are called in to help treat organ transplantation patients, who must have their immune systems suppressed so that their bodies will not reject a transplanted organ. Some immunologists work to understand natural immunity and the effects of a person s environment on it. Others work on questions about how the immune system affects diseases such as cancer. In the past, the importance of having a healthy immune system in preventing cancer was not at all understood. 

To work as an immunologist, a PhD or MD is required. In addition, immunologists undertake at least 2 3 years of training in an accredited program and must pass an examination given by the American Board of Allergy and Immunology. Immunologists must possess knowledge of the functions of the human body as they relate to issues beyond immunization, and knowledge of pharmacology and medical technology, such as medications, therapies, test materials, and surgical procedures. Activity 

Using appropriate media, construct a model of the plasma membrane and its molecular components. In the next section, you will use the model to demonstrate the movement of different substances across the membrane. Think About It 

What research questions can be asked about plasma membranes? State three questions relating to plasma membranes along with possible solutions to the questions. 

Students can use construction paper, colored pencils or markers, scissors, glue, and other media to construct a model of the plasma cell membrane and its molecular components. 

The model should include a depiction of the phospholipids of the bilayer, as well as carbohydrates, glycoproteins, cholesterol, integral proteins, and peripheral proteins. 

Questions that students may list about plasma membranes are: Why do phospholipids spontaneously form bilayers in aqueous solution? How do phospholipids and proteins contribute to the fluidity of plasma membranes? How does cholesterol affect the fluidity of the phospholipids and proteins? Why is it advantageous for membranes to be fluid? 

Possible solutions to these questions posed by students are: 

Phospholipids spontaneously form various structures in aqueous solution, including lipid bilayers. These are formed because the phospholipid tails are hydrophobic and the head is hydrophilic. This promotes the formation of structures that remove the hydrophobic tail from contact with the aqueous solution. The mosaic characteristic of the membrane helps the plasma membrane remain fluid. The integral proteins and lipids exist in the membrane as separate, but loosely attached molecules. The plasma membrane must be very flexible to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow capillaries. Membrane-dependent functions, such as phagocytosis and cell signaling, can be regulated by the fluidity of the cell membrane. Section Summary 

The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane, forming complexes that function to identify the cell to other cells. The fluid nature of the membrane is due to temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of cholesterol embedded in the membrane, and the mosaic nature of the proteins and protein-carbohydrate combinations, which are not firmly fixed in place. Plasma membranes enclose and define the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux. Review Questions 

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[link] Glossary amphiphilic molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments fluid mosaic model describes the structure of the plasma membrane as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity) glycolipid combination of carbohydrates and lipids glycoprotein combination of carbohydrates and proteins hydrophilic molecule with the ability to bond with water; water-loving hydrophobic molecule that does not have the ability to bond with water; water-hating integral protein protein integrated into the membrane structure that interacts extensively with the hydrocarbon chains of membrane lipids and often spans the membrane; these proteins can be removed only by the disruption of the membrane by detergents peripheral protein protein found at the surface of a plasma membrane either on its exterior or interior side; these proteins can be removed (washed off of the membrane) by a high-salt washPassive Transport Passive Transport 

By the end of this section, you will be able to: Identify and describe the properties of life. Why and how does passive transport occur across membranes? What is tonicity, and how is it relevant to passive transport? Connection for AP Courses 

Preventing dehydration is important for both plants and animals. Water moves across plasma membranes by a specific type of diffusion called osmosis. The concentration gradient of water across a membrane is inversely proportional to the concentration of solutes; that is, water moves through channel proteins called aquaporins from higher water concentration to lower water concentration. Solute concentration outside and inside the cell influences the rate of osmosis. Tonicity describes how the extracellular concentration of solutes can change the volume of a cell by affecting osmosis, often correlating with the osmolarity of the solution, i.e., the total solute concentration of the solution. In a hypotonic situation, because the extracellular fluid has a lower concentration of solutes (lower osmolarity) than the fluid inside the cell, water enters the cell, causing it to swell and possibly burst. The cell walls of plants prevent them from bursting, but animal cells, such as red blood cells, can lyse. When a cell is placed in a hypertonic solution, water leaves the cell because the cell has a higher water potential than the extracellular solution. When the concentrations of solute are equal on both sides of the membrane (isotonic), no net movement of water into or out of the cell occurs. Living organisms have evolved a variety of ways to maintain osmotic balance; for example, marine fish secrete excess salt through the gills to maintain dynamic homeostasis. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments. Essential Knowledge 2.B.2 Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.11 The student is able to construct models that connect the movement of molecules across membranes with membrane structure and function. Essential Knowledge 2.B.2 Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.12 The student is able to use representations and models to analyze situation or solve problems qualitatively and quantitatively to investigate whether dynamic homeostasis is maintained by the active movement of molecules across membranes. 

Discuss with students what semi permeable membranes are and how artificial membranes can be used to purify water using reverse osmosis. For more information, go here . 

Students may think that diffusion and osmosis are identical and the terms are interchangeable. Discuss with students the difference between diffusion and osmosis. Diffusion is the movement of solutes from an area of high concentration to an area of lower concentration. Osmosis is the movement of water molecules across a semipermeable membrane in a direction to balance the solute concentration. In diffusion, the solutes move. In osmosis, the water moves. In both, the goal is the same: to balance out the solute concentration. 

Plasma membranes must allow certain substances to enter and leave a cell, and prevent some harmful materials from entering and some essential materials from leaving. In other words, plasma membranes are selectively permeable they allow some substances to pass through, but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed. Some cells require larger amounts of specific substances than do other cells; they must have a way of obtaining these materials from extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special mechanisms that facilitate transport. Some materials are so important to a cell that it spends some of its energy, hydrolyzing adenosine triphosphate (ATP), to obtain these materials. Red blood cells use some of their energy doing just that. All cells spend the majority of their energy to maintain an imbalance of sodium and potassium ions between the interior and exterior of the cell. 

The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to exert any of its energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration. A physical space in which there is a range of concentrations of a single substance is said to have a concentration gradient . Selective Permeability 

Plasma membranes are asymmetric: the interior of the membrane is not identical to the exterior of the membrane. In fact, there is a considerable difference between the array of phospholipids and proteins between the two leaflets that form a membrane. On the interior of the membrane, some proteins serve to anchor the membrane to fibers of the cytoskeleton. There are peripheral proteins on the exterior of the membrane that bind elements of the extracellular matrix. Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature of plasma membranes ( [link] ). The exterior surface of the plasma membrane is not identical to the interior surface of the same membrane. 

Recall that plasma membranes are amphiphilic: They have hydrophilic and hydrophobic regions. This characteristic helps the movement of some materials through the membrane and hinders the movement of others. Lipid-soluble material with a low molecular weight can easily slip through the hydrophobic lipid core of the membrane. Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the plasma membranes in the digestive tract and other tissues. Fat-soluble drugs and hormones also gain easy entry into cells and are readily transported into the body s tissues and organs. Molecules of oxygen and carbon dioxide have no charge and so pass through membranes by simple diffusion. 

Polar substances present problems for the membrane. While some polar molecules connect easily with the outside of a cell, they cannot readily pass through the lipid core of the plasma membrane. Additionally, while small ions could easily slip through the spaces in the mosaic of the membrane, their charge prevents them from doing so. Ions such as sodium, potassium, calcium, and chloride must have special means of penetrating plasma membranes. Simple sugars and amino acids also need help with transport across plasma membranes, achieved by various transmembrane proteins (channels). Diffusion 

Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across a space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of ammonia in a room filled with people. The ammonia gas is at its highest concentration in the bottle; its lowest concentration is at the edges of the room. The ammonia vapor will diffuse, or spread away, from the bottle, and gradually, more and more people will smell the ammonia as it spreads. Materials move within the cell s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion ( [link] ). Diffusion expends no energy. On the contrary, concentration gradients are a form of potential energy, dissipated as the gradient is eliminated. Diffusion through a permeable membrane moves a substance from an area of high concentration (extracellular fluid, in this case) down its concentration gradient (into the cytoplasm). (credit: modification of work by Mariana Ruiz Villareal) 

Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the concentration gradients of other materials. In addition, each substance will diffuse according to that gradient. Within a system, there will be different rates of diffusion of the different substances in the medium. Factors That Affect Diffusion 

Molecules move constantly in a random manner, at a rate that depends on their mass, their environment, and the amount of thermal energy they possess, which in turn is a function of temperature. This movement accounts for the diffusion of molecules through whatever medium in which they are localized. A substance will tend to move into any space available to it until it is evenly distributed throughout it. After a substance has diffused completely through a space, removing its concentration gradient, molecules will still move around in the space, but there will be no net movement of the number of molecules from one area to another. This lack of a concentration gradient in which there is no net movement of a substance is known as dynamic equilibrium. While diffusion will go forward in the presence of a concentration gradient of a substance, several factors affect the rate of diffusion. Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes. Mass of the molecules diffusing: Heavier molecules move more slowly; therefore, they diffuse more slowly. The reverse is true for lighter molecules. Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of diffusion. Lower temperatures decrease the energy of the molecules, thus decreasing the rate of diffusion. Solvent density: As the density of a solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting through the denser medium. If the medium is less dense, diffusion increases. Because cells primarily use diffusion to move materials within the cytoplasm, any increase in the cytoplasm s density will inhibit the movement of the materials. An example of this is a person experiencing dehydration. As the body s cells lose water, the rate of diffusion decreases in the cytoplasm, and the cells functions deteriorate. Neurons tend to be very sensitive to this effect. Dehydration frequently leads to unconsciousness and possibly coma because of the decrease in diffusion rate within the cells. Solubility: As discussed earlier, nonpolar or lipid-soluble materials pass through plasma membranes more easily than polar materials, allowing a faster rate of diffusion. Surface area and thickness of the plasma membrane: Increased surface area increases the rate of diffusion, whereas a thicker membrane reduces it. Distance travelled: The greater the distance that a substance must travel, the slower the rate of diffusion. This places an upper limitation on cell size. A large, spherical cell will die because nutrients or waste cannot reach or leave the center of the cell, respectively. Therefore, cells must either be small in size, as in the case of many prokaryotes, or be flattened, as with many single-celled eukaryotes. 

A variation of diffusion is the process of filtration. In filtration, material moves according to its concentration gradient through a membrane; sometimes the rate of diffusion is enhanced by pressure, causing the substances to filter more rapidly. This occurs in the kidney, where blood pressure forces large amounts of water and accompanying dissolved substances, or solutes , out of the blood and into the renal tubules. The rate of diffusion in this instance is almost totally dependent on pressure. One of the effects of high blood pressure is the appearance of protein in the urine, which is squeezed through by the abnormally high pressure. Facilitated transport 

In facilitated transport , also called facilitated diffusion, materials diffuse across the plasma membrane with the help of membrane proteins. A concentration gradient exists that would allow these materials to diffuse into the cell without expending cellular energy. However, these materials are ions are polar molecules that are repelled by the hydrophobic parts of the cell membrane. Facilitated transport proteins shield these materials from the repulsive force of the membrane, allowing them to diffuse into the cell. 

The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed to specific integral proteins that facilitate their passage. Some of these integral proteins are collections of beta pleated sheets that form a pore or channel through the phospholipid bilayer. Others are carrier proteins which bind with the substance and aid its diffusion through the membrane. Channels 

The integral proteins involved in facilitated transport are collectively referred to as transport proteins , and they function as either channels for the material or carriers. In both cases, they are transmembrane proteins. Channels are specific for the substance that is being transported. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids; they additionally have a hydrophilic channel through their core that provides a hydrated opening through the membrane layers ( [link] ). Passage through the channel allows polar compounds to avoid the nonpolar central layer of the plasma membrane that would otherwise slow or prevent their entry into the cell. Aquaporins are channel proteins that allow water to pass through the membrane at a very high rate. Facilitated transport moves substances down their concentration gradients. They may cross the plasma membrane with the aid of channel proteins. (credit: modification of work by Mariana Ruiz Villareal) 

Channel proteins are either open at all times or they are gated, which controls the opening of the channel. The attachment of a particular ion to the channel protein may control the opening, or other mechanisms or substances may be involved. In some tissues, sodium and chloride ions pass freely through open channels, whereas in other tissues a gate must be opened to allow passage. An example of this occurs in the kidney, where both forms of channels are found in different parts of the renal tubules. Cells involved in the transmission of electrical impulses, such as nerve and muscle cells, have gated channels for sodium, potassium, and calcium in their membranes. Opening and closing of these channels changes the relative concentrations on opposing sides of the membrane of these ions, resulting in the facilitation of electrical transmission along membranes (in the case of nerve cells) or in muscle contraction (in the case of muscle cells). Carrier Proteins 

Another type of protein embedded in the plasma membrane is a carrier protein . This aptly named protein binds a substance and, in doing so, triggers a change of its own shape, moving the bound molecule from the outside of the cell to its interior ( [link] ); depending on the gradient, the material may move in the opposite direction. Carrier proteins are typically specific for a single substance. This selectivity adds to the overall selectivity of the plasma membrane. The exact mechanism for the change of shape is poorly understood. Proteins can change shape when their hydrogen bonds are affected, but this may not fully explain this mechanism. Each carrier protein is specific to one substance, and there are a finite number of these proteins in any membrane. This can cause problems in transporting enough of the material for the cell to function properly. When all of the proteins are bound to their ligands, they are saturated and the rate of transport is at its maximum. Increasing the concentration gradient at this point will not result in an increased rate of transport. Some substances are able to move down their concentration gradient across the plasma membrane with the aid of carrier proteins. Carrier proteins change shape as they move molecules across the membrane. (credit: modification of work by Mariana Ruiz Villareal) 

An example of this process occurs in the kidney. Glucose, water, salts, ions, and amino acids needed by the body are filtered in one part of the kidney. This filtrate, which includes glucose, is then reabsorbed in another part of the kidney. Because there are only a finite number of carrier proteins for glucose, if more glucose is present than the proteins can handle, the excess is not transported and it is excreted from the body in the urine. In a diabetic individual, this is described as spilling glucose into the urine. A different group of carrier proteins called glucose transport proteins, or GLUTs, are involved in transporting glucose and other hexose sugars through plasma membranes within the body. 

Channel and carrier proteins transport material at different rates. Channel proteins transport much more quickly than do carrier proteins. Channel proteins facilitate diffusion at a rate of tens of millions of molecules per second, whereas carrier proteins work at a rate of a thousand to a million molecules per second. Osmosis 

Osmosis is the movement of water through a semipermeable membrane according to the concentration gradient of water across the membrane, which is inversely proportional to the concentration of solutes. While diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the diffusion of solutes in the water. Not surprisingly, the aquaporins that facilitate water movement play a large role in osmosis, most prominently in red blood cells and the membranes of kidney tubules. Mechanism 

Osmosis is a special case of diffusion. Water, like other substances, moves from an area of high concentration to one of low concentration. An obvious question is what makes water move at all? Imagine a beaker with a semipermeable membrane separating the two sides or halves ( [link] ). On both sides of the membrane the water level is the same, but there are different concentrations of a dissolved substance, or solute , that cannot cross the membrane (otherwise the concentrations on each side would be balanced by the solute crossing the membrane). If the volume of the solution on both sides of the membrane is the same, but the concentrations of solute are different, then there are different amounts of water, the solvent, on either side of the membrane. In osmosis, water always moves from an area of higher water concentration to one of lower concentration. In the diagram shown, the solute cannot pass through the selectively permeable membrane, but the water can. 

To illustrate this, imagine two full glasses of water. One has a single teaspoon of sugar in it, whereas the second one contains one-quarter cup of sugar. If the total volume of the solutions in both cups is the same, which cup contains more water? Because the large amount of sugar in the second cup takes up much more space than the teaspoon of sugar in the first cup, the first cup has more water in it. 

Returning to the beaker example, recall that it has a mixture of solutes on either side of the membrane. A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Thus, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane osmosis will continue until the concentration gradient of water goes to zero or until the hydrostatic pressure of the water balances the osmotic pressure. Osmosis proceeds constantly in living systems. Tonicity 

Tonicity describes how an extracellular solution can change the volume of a cell by affecting osmosis. A solution's tonicity often directly correlates with the osmolarity of the solution. Osmolarity describes the total solute concentration of the solution. A solution with low osmolarity has a greater number of water molecules relative to the number of solute particles; a solution with high osmolarity has fewer water molecules with respect to solute particles. In a situation in which solutions of two different osmolarities are separated by a membrane permeable to water, though not to the solute, water will move from the side of the membrane with lower osmolarity (and more water) to the side with higher osmolarity (and less water). This effect makes sense if you remember that the solute cannot move across the membrane, and thus the only component in the system that can move the water moves along its own concentration gradient. An important distinction that concerns living systems is that osmolarity measures the number of particles (which may be molecules) in a solution. Therefore, a solution that is cloudy with cells may have a lower osmolarity than a solution that is clear, if the second solution contains more dissolved molecules than there are cells. Hypotonic Solutions 

Three terms hypotonic, isotonic, and hypertonic are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic situation, the extracellular fluid has lower osmolarity than the fluid inside the cell, and water enters the cell. (In living systems, the point of reference is always the cytoplasm, so the prefix hypo - means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher concentration of water in the solution than does the cell. In this situation, water will follow its concentration gradient and enter the cell. Hypertonic Solutions 

As for a hypertonic solution, the prefix hyper - refers to the extracellular fluid having a higher osmolarity than the cell s cytoplasm; therefore, the fluid contains less water than the cell does. Because the cell has a relatively higher concentration of water, water will leave the cell. Isotonic Solutions 

In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the osmolarity of the cell matches that of the extracellular fluid, there will be no net movement of water into or out of the cell, although water will still move in and out. Blood cells and plant cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances ( [link] ). 

Osmotic pressure changes the shape of red blood cells in hypertonic, isotonic, and hypotonic solutions (credit: Mariana Ruiz Villareal) 

For a video illustrating the process of diffusion in solutions, visit this site . 

[link] Tonicity in Living Systems 

In a hypotonic environment, water enters a cell, and the cell swells. In an isotonic condition, the relative concentrations of solute and solvent are equal on both sides of the membrane. There is no net water movement; therefore, there is no change in the size of the cell. In a hypertonic solution, water leaves a cell and the cell shrinks. If either the hypo- or hyper- condition goes to excess, the cell s functions become compromised, and the cell may be destroyed. 

A red blood cell will burst, or lyse, when it swells beyond the plasma membrane s capability to expand. Remember, the membrane resembles a mosaic, with discrete spaces between the molecules composing it. If the cell swells, and the spaces between the lipids and proteins become too large, the cell will break apart. 

In contrast, when excessive amounts of water leave a red blood cell, the cell shrinks, or crenates. This has the effect of concentrating the solutes left in the cell, making the cytosol denser and interfering with diffusion within the cell. The cell s ability to function will be compromised and may also result in the death of the cell. 

Various living things have ways of controlling the effects of osmosis a mechanism called osmoregulation. Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis in a hypotonic solution. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic to the cellular environment, and water will always enter a cell if water is available. This inflow of water produces turgor pressure, which stiffens the cell walls of the plant ( [link] ). In nonwoody plants, turgor pressure supports the plant. Conversly, if the plant is not watered, the extracellular fluid will become hypertonic, causing water to leave the cell. In this condition, the cell does not shrink because the cell wall is not flexible. However, the cell membrane detaches from the wall and constricts the cytoplasm. This is called plasmolysis . Plants lose turgor pressure in this condition and wilt ( [link] ). The turgor pressure within a plant cell depends on the tonicity of the solution that it is bathed in. (credit: modification of work by Mariana Ruiz Villareal) Without adequate water, the plant on the left has lost turgor pressure, visible in its wilting; the turgor pressure is restored by watering it (right). (credit: Victor M. Vicente Selvas) 

Tonicity is a concern for all living things. For example, paramecia and amoebas, which are protists that lack cell walls, have contractile vacuoles. This vesicle collects excess water from the cell and pumps it out, keeping the cell from lysing as it takes on water from its environment ( [link] ). A paramecium s contractile vacuole, here visualized using bright field light microscopy at 480x magnification, continuously pumps water out of the organism s body to keep it from bursting in a hypotonic medium. (credit: modification of work by NIH; scale-bar data from Matt Russell) 

Many marine invertebrates have internal salt levels matched to their environments, making them isotonic with the water in which they live. Fish, however, must spend approximately five percent of their metabolic energy maintaining osmotic homeostasis. Freshwater fish live in an environment that is hypotonic to their cells. These fish actively take in salt through their gills and excrete diluted urine to rid themselves of excess water. Saltwater fish live in the reverse environment, which is hypertonic to their cells, and they secrete salt through their gills and excrete highly concentrated urine. 

In vertebrates, the kidneys regulate the amount of water in the body. Osmoreceptors are specialized cells in the brain that monitor the concentration of solutes in the blood. If the levels of solutes increase beyond a certain range, a hormone is released that retards water loss through the kidney and dilutes the blood to safer levels. Animals also have high concentrations of albumin, which is produced by the liver, in their blood. This protein is too large to pass easily through plasma membranes and is a major factor in controlling the osmotic pressures applied to tissues. Activity 

Use the model of the plasma cell membrane you constructed to demonstrate how O 2 and CO 2 , H 2 O, Na + and K + , and glucose are transported across the membrane. Think About It 

Why should farmers consider the salinity of the soil in which they grow crops? 

Answer: Farmers need to consider the salinity of soil, because the movement of water into and out of plant cells depends on the solute concentration of their environment. In soil high in saline, water will be drawn out of root cells causing the cells to shrivel, and the plant to die. Student demonstrations should include the transport of different molecules across plasma membranes, which is shown in the illustration. Molecules of oxygen, carbon dioxide, and water have no charge and so pass through membranes by simple diffusion. Na+ and K+ have a charge and require a transport protein (the sodium potassium pump) in order to move across the plasma membrane via active transport. The College Board presents an expanded diffusion/osmosis activity on which this lab investigation is based. Please see Investigation 4 in the AP Biology Investigative Labs: An Inquiry-Based Approach. 

Observing Osmosis in Model Cells 

Materials: 

3 dialysis bags 

3 medium-sized beakers 

Stock starch solution 

Distilled water 

Iodine dropper bottle 

Thread 

Balance or scale 

Preparation: 

To prepare the percent starch solutions, determine the volume of the solution you wish to use (e.g., 100 ml) and add the mass of solute, in grams, equivalent to the desired percent concentration: 

Percent solution = [Mass of solute (g) / Volume of solution (ml)] 100 Label each dialysis bag with one of the three concentrations: 1%, 25%, and 60%. Then, moisten the dialysis tubing to make it easier to open. Fill each tube with the corresponding solution about three-quarters of the way fill in order to leave space to tie off the top of the bag. Tie the tops of the bags tightly with standard thread. Do not place the bags in the iodine solution yet, as they will first be weighed in front of the students. 

With students present, explain to them the details of the setup and show them how iodine is used as an indicator for the presence of starch. Also explain that dialysis tubing is semipermeable, as it contains pores that permit the passage of small ions and molecules, like water; but will not permit the passage of larger molecules, like proteins. In this way, the dialysis bag models a semipermeable cell membrane. Fill each beaker about three-quarters of the way with distilled water. Add 3 8 drops of iodine, based on the strength of your iodine, and stir so that the solution is yellow in color. Weigh each dialysis bag and record the weights on a chart visible to the class. Ask students: If each dialysis bag were a cell, would it be hypertonic, hypotonic, or isotonic relative to the distilled water? How quickly will water flow into or out of the dialysis bag by osmosis? What will happen if the starch solution comes in contact with the iodine solution? Immerse the dialysis bags in the iodine solution for 45 min to 1 hour. While waiting, ask students to predict how osmosis will affect the weight of the three dialysis bags. Will the weight of the bags increase, decrease, or remain the same? Remove the bags and carefully rinse them under a gentle tap. Pat the bags dry to remove excess water. Weigh each bag and place the results on the board. Ask students: Was both water and starch able to pass through the dialysis tubing? How do you know, based on your results? Did the concentration of the starch solutions affect the rate of osmosis? Why would this occur? 

Results: 

Starch molecules cannot pass through the dialysis tubing. However, the iodine solution can pass from the beaker into the dialysis bag. This turns the starch solution from colorless to purple. The amount of iodine that diffuses into the bag is related to the concentration of each solution. As the starch concentration increases, more iodine solution will diffuse into the bag, causing the bag to increase in weight. 

This lab is an application of Learning Objective 2.4 and Science Practices 1.4 and 3.1 and Learning Objective 2.5 and Science Practice 6.2 because as students collect and analyze data in addition, as part of their experimental design, students draw conclusions from the data. Section Summary 

The passive forms of transport, diffusion and osmosis, move materials of small molecular weight across membranes. Substances diffuse from areas of high concentration to areas of lower concentration, and this process continues until the substance is evenly distributed in a system. In solutions containing more than one substance, each type of molecule diffuses according to its own concentration gradient, independent of the diffusion of other substances. Many factors can affect the rate of diffusion, including concentration gradient, size of the particles that are diffusing, temperature of the system, and so on. 

In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is made possible by specialized proteins, such as channels and transporters. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins that facilitate transport. Review Questions 

[link] 

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[link] Critical Thinking Questions 

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[link] Test Prep for AP Courses 

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[link] Glossary aquaporin channel protein that allows water through the membrane at a very high rate carrier protein membrane protein that moves a substance across the plasma membrane by changing its own shape channel protein membrane protein that allows a substance to pass through its hollow core across the plasma membrane concentration gradient area of high concentration adjacent to an area of low concentration diffusion passive process of transport of low-molecular weight material according to its concentration gradient facilitated transport process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins hypertonic situation in which extracellular fluid has a higher osmolarity than the fluid inside the cell, resulting in water moving out of the cell hypotonic situation in which extracellular fluid has a lower osmolarity than the fluid inside the cell, resulting in water moving into the cell isotonic situation in which the extracellular fluid has the same osmolarity as the fluid inside the cell, resulting in no net movement of water into or out of the cell osmolarity total amount of substances dissolved in a specific amount of solution osmosis transport of water through a semipermeable membrane according to the concentration gradient of water across the membrane that results from the presence of solute that cannot pass through the membrane passive transport method of transporting material through a membrane that does not require energy plasmolysis detaching of the cell membrane from the cell wall and constriction of the cell membrane when a plant cell is in a hypertonic solution selectively permeable characteristic of a membrane that allows some substances through but not others solute substance dissolved in a liquid to form a solution tonicity amount of solute in a solution transport protein membrane protein that facilitates passage of a substance across a membrane by binding itActive Transport Active Transport 

By the end of this section, you will be able to: How do electrochemical gradients affect the active transport of ions and molecules across membranes? Connection for AP Courses 

If a substance must move into the cell against its concentration gradient, the cell must use free energy, often provided by ATP, and carrier proteins acting as pumps to move the substance. Substances that move across membranes by this mechanism, a process called active transport, include ions, such as Na + and K + . The combined gradients that affect movement of an ion are its concentration gradient and its electrical gradient (the difference in charge across the membrane); together these gradients are called the electrochemical gradient. To move substances against an electrochemical gradient requires free energy. The sodium-potassium pump, which maintains electrochemical gradients across the membranes of nerve cells in animals, is an example of primary active transport. The formation of H + gradients by secondary active transport (co-transport) is important in cellular respiration and photosynthesis and moving glucose into cells. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices (SP). 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments. Essential Knowledge 2.B.2 Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 2.12 The student is able to use representations and models to analyze situations or solve problems qualitatively and quantitatively to investigate whether dynamic homeostasis is maintained by the active movement of molecules across membranes. 

Discuss with students the differences between passive and active transport using visuals such as this video . 

Active transport mechanisms require the use of the cell s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient that is, if the concentration of the substance inside the cell is greater than its concentration in the extracellular fluid (and vice versa) the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight materials, such as ions, through the membrane. Other mechanisms transport much larger molecules. Electrochemical Gradient 

We have discussed simple concentration gradients differential concentrations of a substance across a space or a membrane but in living systems, gradients are more complex. Because ions move into and out of cells and because cells contain proteins that do not move across the membrane and are mostly negatively charged, there is also an electrical gradient, a difference of charge, across the plasma membrane. The interior of living cells is electrically negative with respect to the extracellular fluid in which they are bathed, and at the same time, cells have higher concentrations of potassium (K + ) and lower concentrations of sodium (Na + ) than does the extracellular fluid. So in a living cell, the concentration gradient of Na + tends to drive it into the cell, and the electrical gradient of Na + (a positive ion) also tends to drive it inward to the negatively charged interior. The situation is more complex, however, for other elements such as potassium. The electrical gradient of K + , a positive ion, also tends to drive it into the cell, but the concentration gradient of K + tends to drive K + out of the cell ( [link] ). The combined gradient of concentration and electrical charge that affects an ion is called its electrochemical gradient . 

Electrochemical gradients arise from the combined effects of concentration gradients and electrical gradients. (credit: Synaptitude /Wikimedia Commons) 

[link] Moving Against a Gradient 

To move substances against a concentration or electrochemical gradient, the cell must use energy. This energy is harvested from ATP generated through the cell s metabolism. Active transport mechanisms, collectively called pumps , work against electrochemical gradients. Small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive movements. Much of a cell s supply of metabolic energy may be spent maintaining these processes. (Most of a red blood cell s metabolic energy is used to maintain the imbalance between exterior and interior sodium and potassium levels required by the cell.) Because active transport mechanisms depend on a cell s metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP. 

Two mechanisms exist for the transport of small-molecular weight material and small molecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane, which is directly dependent on ATP. Secondary active transport describes the movement of material that is due to the electrochemical gradient established by primary active transport that does not directly require ATP. Carrier Proteins for Active Transport 

An important membrane adaption for active transport is the presence of specific carrier proteins or pumps to facilitate movement: there are three types of these proteins or transporters ( [link] ). A uniporter carries one specific ion or molecule. A symporter carries two different ions or molecules, both in the same direction. An antiporter also carries two different ions or molecules, but in different directions. All of these transporters can also transport small, uncharged organic molecules like glucose. These three types of carrier proteins are also found in facilitated diffusion, but they do not require ATP to work in that process. Some examples of pumps for active transport are Na + -K + ATPase, which carries sodium and potassium ions, and H + -K + ATPase, which carries hydrogen and potassium ions. Both of these are antiporter carrier proteins. Two other carrier proteins are Ca 2+ ATPase and H + ATPase, which carry only calcium and only hydrogen ions, respectively. Both are pumps. A uniporter carries one molecule or ion. A symporter carries two different molecules or ions, both in the same direction. An antiporter also carries two different molecules or ions, but in different directions. (credit: modification of work by Lupask /Wikimedia Commons) 

The primary active transport that functions with the active transport of sodium and potassium allows secondary active transport to occur. The second transport method is still considered active because it depends on the use of energy as does primary transport (illustrative example). Primary active transport moves ions across a membrane, creating an electrochemical gradient (electrogenic transport). (credit: modification of work by Mariana Ruiz Villareal) 

One of the most important pumps in animal cells is the sodium-potassium pump (Na + -K + ATPase), which maintains the electrochemical gradient (and the correct concentrations of Na + and K + ) in living cells. The sodium-potassium pump moves K + into the cell while moving Na + out at the same time, at a ratio of three Na + for every two K + ions moved in. The Na + -K + ATPase exists in two forms, depending on its orientation to the interior or exterior of the cell and its affinity for either sodium or potassium ions. The process consists of the following six steps: With the enzyme oriented towards the interior of the cell, the carrier has a high affinity for sodium ions. Three ions bind to the protein. The protein carrier hydrolyzes ATP and a low-energy phosphate group attaches to it. As a result, the carrier changes shape and re-orients itself towards the exterior of the membrane. The protein s affinity for sodium decreases and the three sodium ions leave the carrier. The shape change increases the carrier s affinity for potassium ions, and two such ions attach to the protein. Subsequently, the low-energy phosphate group detaches from the carrier. With the phosphate group removed and potassium ions attached, the carrier protein repositions itself towards the interior of the cell. The carrier protein, in its new configuration, has a decreased affinity for potassium, and the two ions are released into the cytoplasm. The protein now has a higher affinity for sodium ions, and the process starts again. 

Several things have happened as a result of this process. At this point, there are more sodium ions outside of the cell than inside and more potassium ions inside than out. For every three ions of sodium that move out, two ions of potassium move in. This results in the interior being slightly more negative relative to the exterior. This difference in charge is important to creating the conditions necessary for the secondary process. Therefore, the sodium-potassium pump is an electrogenic pump (a pump that creates a charge imbalance) contributing to the membrane potential. 

[link] 

Visit the site to see a simulation of active transport in a sodium-potassium ATPase. 

[link] Activity 

Create a representation/diagram (or use the model you constructed of the plasma cell membrane) to explain how the sodium-potassium pump contributes to the net negative change of the interior of an animal nerve cell. Think About It 

If the pH outside the cell decreases, would you expect the amount of amino acids and glucose transported into the cell to increase or decrease? Justify your reasoning. The Na + -K + ATPase pump uses energy to move 3 Na + ions out of a neuron for every 2 K + ions moved into a neuron, which contributes to the net negative change of the interior of an animal nerve cell. Student models of the sodium-potassium pump in nerve cells should look similar to this illustration . Answer to Think About It question: A decrease in pH means an increase in positively charged H+ ions, and an increase in the electrical gradient across the membrane. The transport of amino acids into the cell will increase. Secondary Active Transport (Co-transport) 

Secondary active transport brings sodium ions, and possibly other compounds, into the cell. As sodium ion concentrations build outside of the plasma membrane because of the action of the primary active transport process, an electrochemical gradient is created. If a channel protein exists and is open, the sodium ions will be pulled through the membrane. This movement is used to transport other substances that can attach themselves to the transport protein through the membrane ( [link] ). Many amino acids, as well as glucose, enter a cell this way. This secondary process is also used to store high-energy hydrogen ions in the mitochondria of plant and animal cells for the production of ATP. The potential energy that accumulates in the stored hydrogen ions is translated into kinetic energy as the ions surge through the channel protein ATP synthase, and that energy is used to convert ADP into ATP. Visual Connections 

An electrochemical gradient, created by primary active transport, can move other substances against their concentration gradients, a process called co-transport or secondary active transport. (credit: modification of work by Mariana Ruiz Villareal) 

[link] Section Summary 

The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. A positive ion, for example, might tend to diffuse into a new area, down its concentration gradient, but if it is diffusing into an area of net positive charge, its diffusion will be hampered by its electrical gradient. When dealing with ions in aqueous solutions, a combination of the electrochemical and concentration gradients, rather than just the concentration gradient alone, must be considered. Living cells need certain substances that exist inside the cell in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel this transport. Active transport of small molecular-sized materials uses integral proteins in the cell membrane to move the materials: These proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In co-transport (or secondary active transport), energy from primary transport can be used to move another substance into the cell and up its concentration gradient. Review Questions 

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[link] Critical Thinking Questions 

[link] Glossary active transport method of transporting material that requires energy antiporter transporter that carries two ions or small molecules in different directions electrochemical gradient gradient produced by the combined forces of an electrical gradient and a chemical gradient electrogenic pump pump that creates a charge imbalance primary active transport active transport that moves ions or small molecules across a membrane and may create a difference in charge across that membrane pump active transport mechanism that works against electrochemical gradients secondary active transport movement of material that is due to the electrochemical gradient established by primary active transport symporter transporter that carries two different ions or small molecules, both in the same direction transporter specific carrier proteins or pumps that facilitate movement uniporter transporter that carries one specific ion or moleculeBulk Transport Bulk Transport 

By the end of this section, you will be able to: What are the differences among the different types of endocytosis: (phagocytosis, pinocytosis, and receptor-mediated endocytosis) and exocytosis? Connection for AP Courses 

Diffusion, osmosis, and active transport are used to transport fairly small molecules across plasma cell membranes. However, sometimes large particles, such as macromolecules, parts of cells, or even unicellular microorganisms, can be engulfed by other cells in a process called phagocytosis or cell eating. In this form of endocytosis, the cell membrane surrounds the particle, pinches off, and brings the particle into the cell. For example, when bacteria invade the human body, a type of white blood cell called a neutrophil will remove the invaders by this process. Similarly, in pinocytosis or cell drinking, the cell takes in droplets of liquid. In receptor-mediated endocytosis, uptake of substances by the cell is targeted to a single type of substance that binds to a specific receptor protein on the external surface of the cell membrane (e.g., hormones and their target cells) before under going endocytosis. Some human diseases, such as familial hypercholesterolemia, are caused by the failure of receptor-mediated endocytosis. Exocytosis is the process of exporting material out of the cell; vesicles containing substances fuse with the plasma membrane and the contents are released to the exterior of the cell. The secretion of neurotransmitters at synapses between neurons is an example of exocytosis. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. 

Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments. Essential Knowledge 2.B.2 Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 2.12 The student is able to use representations and models to analyze situations or solve problems qualitatively and quantitatively to investigate whether dynamic homeostasis is maintained by the active movement of molecules across membranes. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. 

Enduring Understanding 2.D Growth and dynamic homeostasis of a biological system are influenced by changes in the system s environment. Essential Knowledge 2.D.4 Plants and animals have a variety of chemical defenses against infections that affect dynamic homeostasis. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 2.30 The student can create representations or models to describe nonspecific immune defenses in plants and animals. 

Ask students to consider how large polar molecules required by cells, such as proteins and polysaccharides, can enter cells when they are unable to cross cell membranes. These molecules enter cells through the active transport mechanism of endocytosis. This video on endocytosis and exocytosis can be used to demonstrate this information. 

In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles (see [link] for examples). Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell. Endocytosis 

Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created intracellular vesicle formed from the plasma membrane. Phagocytosis 

Phagocytosis (the condition of cell eating ) is the process by which large particles, such as cells or relatively large particles, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil will remove the invaders through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil ( [link] ). In phagocytosis, the cell membrane surrounds the particle and engulfs it. (credit: Mariana Ruiz Villareal) 

In preparation for phagocytosis, a portion of the inward-facing surface of the plasma membrane becomes coated with a protein called clathrin , which stabilizes this section of the membrane. The coated portion of the membrane then extends from the body of the cell and surrounds the particle, eventually enclosing it. Once the vesicle containing the particle is enclosed within the cell, the clathrin disengages from the membrane and the vesicle merges with a lysosome for the breakdown of the material in the newly formed compartment (endosome). When accessible nutrients from the degradation of the vesicular contents have been extracted, the newly formed endosome merges with the plasma membrane and releases its contents into the extracellular fluid. The endosomal membrane again becomes part of the plasma membrane. Activity 

Create a representation/diagram to describe how a neutrophil, a type of human white blood cell, attacks and destroys an invading bacterium. What cellular organelles are involved in this process? 

Student diagrams should show receptors in the neutrophil that bind to the bacteria and the plasma membrane of the neutrophil surrounding the bacteria. The diagram should also show a lysosome merging with vesicle containing the bacteria, and breakdown of the bacteria by the lysosome. Pinocytosis 

A variation of endocytosis is called pinocytosis . This literally means cell drinking and was named at a time when the assumption was that the cell was purposefully taking in extracellular fluid. In reality, this is a process that takes in molecules, including water, which the cell needs from the extracellular fluid. Pinocytosis results in a much smaller vesicle than does phagocytosis, and the vesicle does not need to merge with a lysosome ( [link] ). In pinocytosis, the cell membrane invaginates, surrounds a small volume of fluid, and pinches off. (credit: Mariana Ruiz Villareal) 

A variation of pinocytosis is called potocytosis . This process uses a coating protein, called caveolin , on the cytoplasmic side of the plasma membrane, which performs a similar function to clathrin. The cavities in the plasma membrane that form the vacuoles have membrane receptors and lipid rafts in addition to caveolin. The vacuoles or vesicles formed in caveolae (singular caveola) are smaller than those in pinocytosis. Potocytosis is used to bring small molecules into the cell and to transport these molecules through the cell for their release on the other side of the cell, a process called transcytosis. Receptor-mediated Endocytosis 

A targeted variation of endocytosis employs receptor proteins in the plasma membrane that have a specific binding affinity for certain substances ( [link] ). In receptor-mediated endocytosis, uptake of substances by the cell is targeted to a single type of substance that binds to the receptor on the external surface of the cell membrane. (credit: modification of work by Mariana Ruiz Villareal) 

In receptor-mediated endocytosis , as in phagocytosis, clathrin is attached to the cytoplasmic side of the plasma membrane. If uptake of a compound is dependent on receptor-mediated endocytosis and the process is ineffective, the material will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused by the failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as bad cholesterol) is removed from the blood by receptor-mediated endocytosis. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear LDL particles from their blood. 

Although receptor-mediated endocytosis is designed to bring specific substances that are normally found in the extracellular fluid into the cell, other substances may gain entry into the cell at the same site. Flu viruses, diphtheria, and cholera toxin all have sites that cross-react with normal receptor-binding sites and gain entry into cells. 

See receptor-mediated endocytosis in action, and click on different parts for a focused animation. 

[link] Exocytosis 

The reverse process of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes discussed above in that its purpose is to expel material from the cell into the extracellular fluid. Waste material is enveloped in a membrane and fuses with the interior of the plasma membrane. This fusion opens the membranous envelope on the exterior of the cell, and the waste material is expelled into the extracellular space ( [link] ). Other examples of cells releasing molecules via exocytosis include the secretion of proteins of the extracellular matrix and secretion of neurotransmitters into the synaptic cleft by synaptic vesicles. In exocytosis, vesicles containing substances fuse with the plasma membrane. The contents are then released to the exterior of the cell. (credit: modification of work by Mariana Ruiz Villareal) Methods of Transport, Energy Requirements, and Types of Material Transported Transport Method Active/Passive Material Transported Diffusion Passive Small-molecular weight material Osmosis Passive Water Facilitated transport/diffusion Passive Sodium, potassium, calcium, glucose Primary active transport Active Sodium, potassium, calcium Secondary active transport Active Amino acids, lactose Phagocytosis Active Large macromolecules, whole cells, or cellular structures Pinocytosis and potocytosis Active Small molecules (liquids/water) Receptor-mediated endocytosis Active Large quantities of macromolecules Section Summary 

Active transport methods require the direct use of ATP to fuel the transport. Large particles, such as macromolecules, parts of cells, or whole cells, can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by an envelope of plasma membrane. Vesicle contents are broken down by the cell, with the particles either used as food or dispatched. Pinocytosis is a similar process on a smaller scale. The plasma membrane invaginates and pinches off, producing a small envelope of fluid from outside the cell. Pinocytosis imports substances that the cell needs from the extracellular fluid. The cell expels waste in a similar but reverse manner: it pushes a membranous vacuole to the plasma membrane, allowing the vacuole to fuse with the membrane and incorporate itself into the membrane structure, releasing its contents to the exterior. Review Questions 

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[link] Critical Thinking Questions 

[link] Test Prep for AP Courses 

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[link] Glossary caveolin protein that coats the cytoplasmic side of the plasma membrane and participates in the process of liquid update by potocytosis clathrin protein that coats the inward-facing surface of the plasma membrane and assists in the formation of specialized structures, like coated pits, for phagocytosis endocytosis type of active transport that moves substances, including fluids and particles, into a cell exocytosis process of passing bulk material out of a cell pinocytosis a variation of endocytosis that imports macromolecules that the cell needs from the extracellular fluid potocytosis variation of pinocytosis that uses a different coating protein (caveolin) on the cytoplasmic side of the plasma membrane receptor-mediated endocytosis variation of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesiclesIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" A hummingbird needs energy to maintain prolonged periods of flight. The bird obtains its energy from taking in food and transforming the nutrients into energy through a series of biochemical reactions. The flight muscles in birds are extremely efficient in energy production. (credit: modification of work by Cory Zanker) 

Virtually every task performed by living organisms requires energy. Energy is needed to perform heavy labor and exercise. Humans also use a great deal of energy while thinking and even during sleep. In fact, the living cells of every organism constantly use energy. Nutrients and other molecules are imported, metabolized (broken down), synthesized into new molecules, modified if needed, transported around the cell, and, in some cases, distributed to the entire organism. For example, the large proteins that make up muscles are actively built from smaller molecules. Complex carbohydrates are broken down into simple sugars that the cell uses for energy. Just as energy is required to both build and demolish a building, energy is required for both the synthesis and breakdown of molecules. Additionally, signaling molecules such as hormones and neurotransmitters are actively transported between cells. Pathogenic bacteria and viruses are ingested and broken down by cells. Cells must also export waste and toxins to stay healthy. Many cells swim or move surrounding materials via the beating motion of cellular appendages such as cilia and flagella. 

All of the cellular processes listed above require a steady supply of energy. From where, and in what form, does this energy come? How do living cells obtain energy and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. 

How enzymes lower the activation energy required to begin a chemical reaction in the body will also be discussed in this chapter. Enzymes are crucial for life; without them the chemical reactions required to survive would not happen fast enough for an organism to survive. For example, in an individual who lacks one of the enzymes needed to break down a type of carbohydrate known as a mucopolysaccharide, waste products accumulate in the cells and cause progressive brain damage. This deadly genetic disease is called Sanfilippo Syndrome type B or Mucopolysaccharidosis III. Previously incurable, scientists have now discovered a way to replace the missing enzyme in the brain of mice. Read more about the scientists research here . 

Metabolism encompasses a wide range of cellular activities, including the need for energy and the elimination of wastes from cells, tissues, and organs.Energy and Metabolism Energy and Metabolism 

In this section, you will explore the following questions: What are metabolic pathways? What are the differences between anabolic and catabolic pathways? How do chemical reactions play a role in energy transfer? Connection for AP Courses 

All living systems, from simple cells to complex ecosystems, require free energy to conduct cell processes such as growth and reproduction. 

Organisms have evolved various strategies to capture, store, transform, and transfer free energy. A cell s metabolism refers to the chemical reactions that occur within it. Some metabolic reactions involve the breaking down of complex molecules into simpler ones with a release of energy (catabolism), whereas other metabolic reactions require energy to build complex molecules (anabolism). A central example of these pathways is the synthesis and breakdown of glucose. 

The content presented in this section supports the Learning Objectives outlined in Big Idea 1 and Big Idea 2 of the AP Biology Curriculum Framework listed below. The AP Learning Objectives merge Essential Knowledge content with one or more of the seven Science Practices. These objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP exam questions. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 3.1 The student can pose scientific questions. Learning Objective 1.14 The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insight into the history of life on Earth. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 6.1 The student can justify claims with evidence. Learning Objective 1.16 The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction, and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.1 All living systems require a constant input of free energy. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.1 The student is able to explain how biological systems use free energy based on empirical data that all organisms require constant energy input to maintain organization, to grow and to reproduce. 

Starting with the definition of metabolism as the total chemical activity of an organism, ask students for examples of processes that fit. Tally the examples on a board or screen and expand on them as appropriate. 

The concepts of anabolism and catabolism may be difficult to keep straight. Use the example of anabolic steroids as a way (inappropriate and dangerous) to build up the body, therefore, any anabolic process builds macromolecules and the opposite, catabolic, breaks them down. 

Scientists use the term bioenergetics to discuss the concept of energy flow ( [link] ) through living systems, such as cells. Cellular processes such as the building and breaking down of complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Just as living things must continually consume food to replenish what has been used, cells must continually produce more energy to replenish that used by the many energy-requiring chemical reactions that constantly take place. All of the chemical reactions that take place inside cells, including those that use energy and those that release energy, are the cell s metabolism . Most life forms on earth get their energy from the sun. Plants use photosynthesis to capture sunlight, and herbivores eat those plants to obtain energy. Carnivores eat the herbivores, and decomposers digest plant and animal matter. Metabolism of Carbohydrates 

The metabolism of sugar (a simple carbohydrate) is a classic example of the many cellular processes that use and produce energy. Living things consume sugar as a major energy source, because sugar molecules have a great deal of energy stored within their bonds. The breakdown of glucose, a simple sugar, is described by the equation: C 6 H 12 O 6 + 6O 2 6 CO 2 + 6H 2 O + energy C 6 H 12 O 6 + 6O 2 6 CO 2 + 6H 2 O + energy size 12{C rSub { size 8{6} } H rSub { size 8{12} } O rSub { size 8{2} } } {} 

Carbohydrates that are consumed have their origins in photosynthesizing organisms like plants ( [link] ). During photosynthesis, plants use the energy of sunlight to convert carbon dioxide gas (CO 2 ) into sugar molecules, like glucose (C 6 H 12 O 6 ). Because this process involves synthesizing a larger, energy-storing molecule, it requires an input of energy to proceed. The synthesis of glucose is described by this equation (notice that it is the reverse of the previous equation): 6CO 2 + 6H 2 O + energy C 6 H 12 O 6 + 6O 2 6CO 2 + 6H 2 O + energy C 6 H 12 O 6 + 6O 2 size 12{C rSub { size 8{6} } H rSub { size 8{12} } O rSub { size 8{2} } } {} 

During the chemical reactions of photosynthesis, energy is provided in the form of a very high-energy molecule called ATP, or adenosine triphosphate, which is the primary energy currency of all cells. Just as the dollar is used as currency to buy goods, cells use molecules of ATP as energy currency to perform immediate work. The sugar (glucose) is stored as starch or glycogen. Energy-storing polymers like these are broken down into glucose to supply molecules of ATP. 

Solar energy is required to synthesize a molecule of glucose during the reactions of photosynthesis. In photosynthesis, light energy from the sun is initially transformed into chemical energy that is temporally stored in the energy carrier molecules ATP and NADPH (nicotinamide adenine dinucleotide phosphate). The stored energy in ATP and NADPH is then used later in photosynthesis to build one molecule of glucose from six molecules of CO 2 . This process is analogous to eating breakfast in the morning to acquire energy for your body that can be used later in the day. Under ideal conditions, energy from 18 molecules of ATP is required to synthesize one molecule of glucose during the reactions of photosynthesis. Glucose molecules can also be combined with and converted into other types of sugars. When sugars are consumed, molecules of glucose eventually make their way into each living cell of the organism. Inside the cell, each sugar molecule is broken down through a complex series of chemical reactions. The goal of these reactions is to harvest the energy stored inside the sugar molecules. The harvested energy is used to make high-energy ATP molecules, which can be used to perform work, powering many chemical reactions in the cell. The amount of energy needed to make one molecule of glucose from six molecules of carbon dioxide is 18 molecules of ATP and 12 molecules of NADPH (each one of which is energetically equivalent to three molecules of ATP), or a total of 54 ATP molecule equivalents required for the synthesis of one molecule of glucose. This process is a fundamental and efficient way for cells to generate the molecular energy that they require. Plants, like this oak tree, use energy from sunlight to make sugar and other organic molecules. Both plants and animals, like this squirrel, use cellular respiration to derive energy from the organic molecules originally produced by plants. 

Ask the students where the energy used for metabolism comes from. Have them trace the energy back to the plants and light energy that the plants convert to sugars. Begin to introduce the interactions between carbohydrate metabolism, lipids, and proteins. Ask them what the ultimate end of the energy is (heat). Metabolic Pathways 

The processes of making and breaking down sugar molecules illustrate two types of metabolic pathways. A metabolic pathway is a series of interconnected biochemical reactions that convert a substrate molecule or molecules, step-by-step, through a series of metabolic intermediates, eventually yielding a final product or products. In the case of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. These two opposite processes the first requiring energy and the second producing energy are referred to as anabolic (building) and catabolic (breaking down) pathways, respectively. Consequently, metabolism is composed of building (anabolism) and degradation (catabolism). 

Discuss the evolution of metabolic pathways as they probably developed on Earth. Using the Miller Urey experiment discussed in Chapter 3, ask why there was no free oxygen in an early atmosphere. What pathways could develop under these conditions? How did this limit the development of organisms? What pathway created free oxygen as a waste that could permeate the atmosphere? Is this really a good idea for the organisms that existed? Why? 

This tree shows the evolution of the various branches of life. The vertical dimension is time. Early life forms, in blue, used anaerobic metabolism to obtain energy from their surroundings. 

Evolution of Metabolic Pathways There is more to the complexity of metabolism than understanding the metabolic pathways alone. Metabolic complexity varies from organism to organism. Photosynthesis is the primary pathway in which photosynthetic organisms like plants (the majority of global synthesis is done by planktonic algae) harvest the sun s energy and convert it into carbohydrates. The by-product of photosynthesis is oxygen, required by some cells to carry out cellular respiration. During cellular respiration, oxygen aids in the catabolic breakdown of carbon compounds, like carbohydrates. Among the products of this catabolism are CO 2 and ATP. In addition, some eukaryotes perform catabolic processes without oxygen (fermentation); that is, they perform or use anaerobic metabolism. 

Organisms probably evolved anaerobic metabolism to survive (living organisms came into existence about 3.8 billion years ago, when the atmosphere lacked oxygen). Despite the differences between organisms and the complexity of metabolism, researchers have found that all branches of life share some of the same metabolic pathways, suggesting that all organisms evolved from the same ancient common ancestor ( [link] ). Evidence indicates that over time, the pathways diverged, adding specialized enzymes to allow organisms to better adapt to their environment, thus increasing their chance to survive. However, the underlying principle remains that all organisms must harvest energy from their environment and convert it to ATP to carry out cellular functions. 

[link] Anabolic and Catabolic Pathways 

Anabolic pathways require an input of energy to synthesize complex molecules from simpler ones. Synthesizing sugar from CO 2 is one example. Other examples are the synthesis of large proteins from amino acid building blocks, and the synthesis of new DNA strands from nucleic acid building blocks. These biosynthetic processes are critical to the life of the cell, take place constantly, and demand energy provided by ATP and other high-energy molecules like NADH (nicotinamide adenine dinucleotide) and NADPH ( [link] ). 

ATP is an important molecule for cells to have in sufficient supply at all times. The breakdown of sugars illustrates how a single molecule of glucose can store enough energy to make a great deal of ATP, 36 to 38 molecules. This is a catabolic pathway. Catabolic pathways involve the degradation (or breakdown) of complex molecules into simpler ones. Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce ATP. Other energy-storing molecules, such as fats, are also broken down through similar catabolic reactions to release energy and make ATP ( [link] ). 

It is important to know that the chemical reactions of metabolic pathways don t take place spontaneously. Each reaction step is facilitated, or catalyzed, by a protein called an enzyme. Enzymes are important for catalyzing all types of biological reactions those that require energy as well as those that release energy. Anabolic pathways are those that require energy to synthesize larger molecules. Catabolic pathways are those that generate energy by breaking down larger molecules. Both types of pathways are required for maintaining the cell s energy balance. Think About It 

Describe two different cellular functions in different organisms that require energy that parallel human energy-requiring functions such as physical exercise. 

This question is an application of Learning Objectives1.15 and Science Practice 7.2 because the student is describing how similar energy pathways among different organisms reflect common ancestry. Possible answer: 

Muscles contain the contractile proteins actin and myosin. When these proteins shorten, movement occurs. The same proteins are found in unicellular amoebas that cause the movement of the organism. 

The active transport of sodium and potassium across cell membranes occurs in all multi-celled organisms, including all of the precursors to humans on the evolutionary ladder. Section Summary 

Cells perform the functions of life through various chemical reactions. A cell s metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve the breaking down of complex chemicals into simpler ones, such as the breakdown of large macromolecules. This process is referred to as catabolism, and such reactions are associated with a release of energy. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as the synthesis of macromolecules. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively. Review Questions 

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[link] Glossary anabolic (also, anabolism) pathways that require an input of energy to synthesize complex molecules from simpler ones bioenergetics study of energy flowing through living systems catabolic (also, catabolism) pathways in which complex molecules are broken down into simpler ones metabolism all the chemical reactions that take place inside cells, including anabolism and catabolismPotential, Kinetic, Free, and Activation Energy Potential, Kinetic, Free, and Activation Energy 

In this section, you will explore the following questions: What is energy ? What is the difference between kinetic and potential energy? What is free energy, and how does free energy related to activation energy? What is the difference between endergonic and exergonic reactions? Connection for AP Courses 

Although cells and organisms require free energy to survive, they cannot spontaneously create energy, as stated in the Law of Conservation of Energy. Energy is available in different forms. For example, objects in motion possess kinetic energy, whereas objects that are not in motion possess potential energy. The chemical energy in molecules, such as glucose, is potential energy because when bonds break in chemical reactions, free energy is released. Free energy is a measure of energy that is available to do work. The free energy of a system changes during energy transfers such as chemical reactions, and this change is referred to as G or Gibbs free energy. The G of a reaction can be negative or positive, depending on whether the reaction releases energy (exergonic) or requires energy input (endergonic). All reactions require an input of energy called activation energy in order to reach the transition state at which they will proceed. (In another section, we will explore how enzymes speed up chemical reactions by lowering activation energy barriers.) 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A All living systems require constant input of free energy. Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.1 The student is able to explain how biological systems use free energy based on empirical data that all organisms require constant energy input to maintain organization, to grow, and to reproduce. Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 6.2 The student can justify claims with evidence. Learning Objective 2.2 The student is able to justify a scientific claim that free energy is required for living systems to maintain organization, to grow or to reproduce, but that multiple strategies exist in different living systems. 

Energy is defined as the ability to do work. As you ve learned, energy exists in different forms. For example, electrical energy, light energy, and heat energy are all different types of energy. While these are all familiar types of energy that one can see or feel, there is another type of energy that is much less tangible. This energy is associated with something as simple as an object held above the ground. In order to appreciate the way energy flows into and out of biological systems, it is important to understand more about the different types of energy that exist in the physical world. Types of Energy 

When an object is in motion, there is energy associated with that object. In the example of an airplane in flight, there is a great deal of energy associated with the motion of the airplane. This is because moving objects are capable of enacting a change, or doing work. Think of a wrecking ball. Even a slow-moving wrecking ball can do a great deal of damage to other objects. However, a wrecking ball that is not in motion is incapable of performing work. Energy associated with objects in motion is called kinetic energy . A speeding bullet, a walking person, the rapid movement of molecules in the air (which produces heat), and electromagnetic radiation like light all have kinetic energy. 

Now what if that same motionless wrecking ball is lifted two stories above a car with a crane? If the suspended wrecking ball is unmoving, is there energy associated with it? The answer is yes. The suspended wrecking ball has energy associated with it that is fundamentally different from the kinetic energy of objects in motion. This form of energy results from the fact that there is the potential for the wrecking ball to do work. If it is released, indeed it would do work. Because this type of energy refers to the potential to do work, it is called potential energy . Objects transfer their energy between kinetic and potential in the following way: As the wrecking ball hangs motionless, it has 0 kinetic and 100 percent potential energy. Once it is released, its kinetic energy begins to increase because it builds speed due to gravity. At the same time, as it nears the ground, it loses potential energy. Somewhere mid-fall it has 50 percent kinetic and 50 percent potential energy. Just before it hits the ground, the ball has nearly lost its potential energy and has near-maximal kinetic energy. Other examples of potential energy include the energy of water held behind a dam ( [link] ), or a person about to skydive out of an airplane. Water behind a dam has potential energy. Moving water, such as in a waterfall or a rapidly flowing river, has kinetic energy. (credit dam : modification of work by "Pascal"/Flickr; credit waterfall : modification of work by Frank Gualtieri) 

Potential energy is not only associated with the location of matter (such as a child sitting on a tree branch), but also with the structure of matter. A spring on the ground has potential energy if it is compressed; so does a rubber band that is pulled taut. The very existence of living cells relies heavily on structural potential energy. On a chemical level, the bonds that hold the atoms of molecules together have potential energy. Remember that anabolic cellular pathways require energy to synthesize complex molecules from simpler ones, and catabolic pathways release energy when complex molecules are broken down. The fact that energy can be released by the breakdown of certain chemical bonds implies that those bonds have potential energy. In fact, there is potential energy stored within the bonds of all the food molecules we eat, which is eventually harnessed for use. This is because these bonds can release energy when broken. The type of potential energy that exists within chemical bonds, and is released when those bonds are broken, is called chemical energy ( [link] ). Chemical energy is responsible for providing living cells with energy from food. The release of energy is brought about by breaking the molecular bonds within fuel molecules. The molecules in gasoline (octane, the chemical formula shown) contain chemical energy within the chemical bonds. This energy is transformed into kinetic energy that allows a car to race on a racetrack. (credit car : modification of work by Russell Trow) 

Draw examples from the class of potential vs. kinetic energy. Have several prepared before hand. If there are only a few examples given, ask the students which category your examples fall into. Include examples of chemical energy, such as the hand warmers that depend on chemical release of heat, gasoline, and gunpowder. End with the chemical energy in ATP, emphasizing it is a type of potential energy, and its role in metabolism. 

Visit this site and select A simple pendulum on the menu (under Harmonic Motion ) to see the shifting kinetic (K) and potential energy (U) of a pendulum in motion. 

[link] Free Energy 

After learning that chemical reactions release energy when energy-storing bonds are broken, an important next question is how is the energy associated with chemical reactions quantified and expressed? How can the energy released from one reaction be compared to that of another reaction? A measurement of free energy is used to quantitate these energy transfers. Free energy is called Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. Recall that according to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an unusable form such as heat, resulting in entropy. Gibbs free energy specifically refers to the energy associated with a chemical reaction that is available after entropy is accounted for. In other words, Gibbs free energy is usable energy, or energy that is available to do work. 

Every chemical reaction involves a change in free energy, called delta G ( G). The change in free energy can be calculated for any system that undergoes such a change, such as a chemical reaction. To calculate G, subtract the amount of energy lost to entropy (denoted as S) from the total energy change of the system. This total energy change in the system is called enthalpy and is denoted as H . The formula for calculating G is as follows, where the symbol T refers to absolute temperature in Kelvin (degrees Celsius + 273): G = H T S G = H T S 

The standard free energy change of a chemical reaction is expressed as an amount of energy per mole of the reaction product (either in kilojoules or kilocalories, kJ/mol or kcal/mol; 1 kJ = 0.239 kcal) under standard pH, temperature, and pressure conditions. Standard pH, temperature, and pressure conditions are generally calculated at pH 7.0 in biological systems, 25 degrees Celsius, and 100 kilopascals (1 atm pressure), respectively. It is important to note that cellular conditions vary considerably from these standard conditions, and so standard calculated G values for biological reactions will be different inside the cell. Endergonic Reactions and Exergonic Reactions 

If energy is released during a chemical reaction, then the resulting value from the above equation will be a negative number. In other words, reactions that release energy have a G 0. A negative G also means that the products of the reaction have less free energy than the reactants, because they gave off some free energy during the reaction. Reactions that have a negative G and consequently release free energy are called exergonic reactions . Think: ex ergonic means energy is ex iting the system. These reactions are also referred to as spontaneous reactions, because they can occur without the addition of energy into the system. Understanding which chemical reactions are spontaneous and release free energy is extremely useful for biologists, because these reactions can be harnessed to perform work inside the cell. An important distinction must be drawn between the term spontaneous and the idea of a chemical reaction that occurs immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time. 

If a chemical reaction requires an input of energy rather than releasing energy, then the G for that reaction will be a positive value. In this case, the products have more free energy than the reactants. Thus, the products of these reactions can be thought of as energy-storing molecules. These chemical reactions are called endergonic reactions , and they are non-spontaneous. An endergonic reaction will not take place on its own without the addition of free energy. 

Let s revisit the example of the synthesis and breakdown of the food molecule, glucose. Remember that the building of complex molecules, such as sugars, from simpler ones is an anabolic process and requires energy. Therefore, the chemical reactions involved in anabolic processes are endergonic reactions. On the other hand, the catabolic process of breaking sugar down into simpler molecules releases energy in a series of exergonic reactions. Like the example of rust above, the breakdown of sugar involves spontaneous reactions, but these reactions don t occur instantaneously. [link] shows some other examples of endergonic and exergonic reactions. Later sections will provide more information about what else is required to make even spontaneous reactions happen more efficiently. 

Shown are some examples of endergonic processes (ones that require energy) and exergonic processes (ones that release energy). These include (a) a compost pile decomposing, (b) a chick hatching from a fertilized egg, (c) sand art being destroyed, and (d) a ball rolling down a hill. (credit a: modification of work by Natalie Maynor; credit b: modification of work by USDA; credit c: modification of work by Athlex /Flickr; credit d: modification of work by Harry Malsch) 

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An important concept in the study of metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction ( [link] ). The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system will undergo chemical reactions in both directions until a state of equilibrium is reached. This state of equilibrium is one of the lowest possible free energy and a state of maximal entropy. Energy must be put into the system to push the reactants and products away from a state of equilibrium. Either reactants or products must be added, removed, or changed. If a cell were a closed system, its chemical reactions would reach equilibrium, and it would die because there would be insufficient free energy left to perform the work needed to maintain life. In a living cell, chemical reactions are constantly moving towards equilibrium, but never reach it. This is because a living cell is an open system. Materials pass in and out, the cell recycles the products of certain chemical reactions into other reactions, and chemical equilibrium is never reached. In this way, living organisms are in a constant energy-requiring, uphill battle against equilibrium and entropy. This constant supply of energy ultimately comes from sunlight, which is used to produce nutrients in the process of photosynthesis. Exergonic and endergonic reactions result in changes in Gibbs free energy. Exergonic reactions release energy; endergonic reactions require energy to proceed. 

The concept or entropy can be difficult. Have the students survey their neighborhood for houses, sheds, store fronts, any structures that are deteriorating due to lack of maintenance. Also have them identify older homes, buildings that are in good shape and are actively maintained. Activation Energy 

There is another important concept that must be considered regarding endergonic and exergonic reactions. Even exergonic reactions require a small amount of energy input to get going before they can proceed with their energy-releasing steps. These reactions have a net release of energy, but still require some energy in the beginning. This small amount of energy input necessary for all chemical reactions to occur is called the activation energy (or free energy of activation) and is abbreviated E A ( [link] ). 

Why would an energy-releasing, negative G reaction actually require some energy to proceed? The reason lies in the steps that take place during a chemical reaction. During chemical reactions, certain chemical bonds are broken and new ones are formed. For example, when a glucose molecule is broken down, bonds between the carbon atoms of the molecule are broken. Since these are energy-storing bonds, they release energy when broken. However, to get them into a state that allows the bonds to break, the molecule must be somewhat contorted. A small energy input is required to achieve this contorted state. This contorted state is called the transition state , and it is a high-energy, unstable state. For this reason, reactant molecules don t last long in their transition state, but very quickly proceed to the next steps of the chemical reaction. Free energy diagrams illustrate the energy profiles for a given reaction. Whether the reaction is exergonic or endergonic determines whether the products in the diagram will exist at a lower or higher energy state than both the reactants and the products. However, regardless of this measure, the transition state of the reaction exists at a higher energy state than the reactants, and thus, E A is always positive. 

Watch an animation of the move from free energy to transition state at this site. 

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Where does the activation energy required by chemical reactants come from? The source of the activation energy needed to push reactions forward is typically heat energy from the surroundings. Heat energy (the total bond energy of reactants or products in a chemical reaction) speeds up the motion of molecules, increasing the frequency and force with which they collide; it also moves atoms and bonds within the molecule slightly, helping them reach their transition state. For this reason, heating up a system will cause chemical reactants within that system to react more frequently. Increasing the pressure on a system has the same effect. Once reactants have absorbed enough heat energy from their surroundings to reach the transition state, the reaction will proceed. 

The activation energy of a particular reaction determines the rate at which it will proceed. The higher the activation energy, the slower the chemical reaction will be. The example of iron rusting illustrates an inherently slow reaction. This reaction occurs slowly over time because of its high E A . Additionally, the burning of many fuels, which is strongly exergonic, will take place at a negligible rate unless their activation energy is overcome by sufficient heat from a spark. Once they begin to burn, however, the chemical reactions release enough heat to continue the burning process, supplying the activation energy for surrounding fuel molecules. Like these reactions outside of cells, the activation energy for most cellular reactions is too high for heat energy to overcome at efficient rates. In other words, in order for important cellular reactions to occur at appreciable rates (number of reactions per unit time), their activation energies must be lowered ( [link] ); this is referred to as catalysis. This is a very good thing as far as living cells are concerned. Important macromolecules, such as proteins, DNA, and RNA, store considerable energy, and their breakdown is exergonic. If cellular temperatures alone provided enough heat energy for these exergonic reactions to overcome their activation barriers, the essential components of a cell would disintegrate. 

Clearly explain the significance of the activation energy needed for chemical reactions, even with exergonic reactions. Use the figure of exergonic reactions with a delta G less than zero to show that though the change in energy is negative, there still is a need for activation energy. Include examples of ways that enzymes lower the activation energy needed. Emphasize that this is the way enzymes speed up reactions, they make it easier for the reactions to occur. 

Activation energy is the energy required for a reaction to proceed, and it is lower if the reaction is catalyzed. The horizontal axis of this diagram describes the sequence of events in time. 

[link] Think About It 

All plants use water, carbon dioxide, and energy from the sun to make sugars. Think about what would happen to plants that do not have sunlight as an energy source or sufficient water. What would happen to organisms that depend on those plants for their own survival? How does depletion or destruction of forests by human activity affect free energy availability to organisms living in the rain forest? What measures can be taken to try and restore the free energy to an acceptable level? 

This is an application of LO 2.3 and Science Practice 6.4 because students are asked to make a prediction about how a change in free energy availability can affect organisms, populations, and ecosystems. Possible answer: Initially, the loss of trees increases the amount of sunlight available to plants at the ground level. This would increase the amount of free energy available at ground level. The rates of growth of plants would increase due to the increase in free energy available. The increased metabolic rates of plants would eventually deplete soil nutrients leading to a decrease in the number and quality of plants in the area. This would lead to a decrease in free energy as vegetation decreased in both quantity and quality. Section Summary 

Energy comes in many different forms. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Objects that are not in motion may have the potential to do work, and thus, have potential energy. Molecules also have potential energy because the breaking of molecular bonds has the potential to release energy. Living cells depend on the harvesting of potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. The free energy of a system changes during energy transfers such as chemical reactions, and this change is referred to as G. 

The G of a reaction can be negative or positive, meaning that the reaction releases energy or consumes energy, respectively. A reaction with a negative G that gives off energy is called an exergonic reaction. One with a positive G that requires energy input is called an endergonic reaction. Exergonic reactions are said to be spontaneous, because their products have less energy than their reactants. The products of endergonic reactions have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous G reactions) require an initial input of energy in order to reach the transition state, at which they ll proceed. This initial input of energy is called the activation energy. Review Questions 

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[link] Glossary activation energy energy necessary for reactions to occur chemical energy potential energy in chemical bonds that is released when those bonds are broken endergonic describes chemical reactions that require energy input enthalpy total energy of a system exergonic describes chemical reactions that release free energy free energy Gibbs free energy is the usable energy, or energy that is available to do work. heat energy total bond energy of reactants or products in a chemical reaction kinetic energy type of energy associated with objects or particles in motion potential energy type of energy that has the potential to do work; stored energy transition state high-energy, unstable state (an intermediate form between the substrate and the product) occurring during a chemical reactionThe Laws of Thermodynamics The Laws of Thermodynamics 

In this section, you will explore the following questions: What is entropy? What is the difference between the first and second laws of thermodynamics? Connection for AP Courses 

In studying energy, scientists use the term system to refer to the matter and its environment involved in energy transfers, such as an ecosystem. Even single cells are biological systems and all systems require energy to maintain order. The more ordered a system is, the lower its entropy. Entropy is a measure of the disorder of the system. (Think of your bedroom as a system. On Sunday evening, you throw dirty clothes in the laundry basket, put books back on the shelves, and return dirty dishes to the kitchen. Cleaning your room requires an input of energy. What gradually happens as the week progresses? You guessed it: entropy.) All biological systems obey the laws of chemistry and physics, including the laws of thermodynamics that describe the properties and processes of energy transfer in systems. The first law states that the total amount of energy in the universe is constant; energy cannot be created or destroyed, but it can be transformed and transferred. The second law states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system (e.g., your bedroom over the course of a week). Thus, no energy transfer is completely efficient. (We will explore how free energy is stored, transferred, and used in more detail when we study photosynthesis and cellular respiration.) 

Information presented and the examples highlighted in the section, support concepts and Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.1 The student is able to explain how biological systems use free energy based on empirical data that all organisms require constant energy input to maintain organization, to grow, and to reproduce. 

Use the survey that the students conducted previously of their neighborhoods, or town and have them determine the amount of energy (expressed as cost) it would take to repair one example, or bring it back to order . The money is the energy going into the repairs, the materials are what will go directly into the repair and the overhead can be analogous to money that is lost in the process. In a chemical reaction with energy transfer, this overhead is the lost energy expressed as heat. 

Thermodynamics refers to the study of energy and energy transfer involving physical matter. The matter and its environment relevant to a particular case of energy transfer are classified as a system, and everything outside of that system is called the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy is transferred within the system (between the stove, pot, and water). There are two types of systems: open and closed. An open system is one in which energy can be transferred between the system and its surroundings. The stovetop system is open because heat can be lost into the air. A closed system is one that cannot transfer energy to its surroundings. 

Biological organisms are open systems. Energy is exchanged between them and their surroundings, as they consume energy-storing molecules and release energy to the environment by doing work. Like all things in the physical world, energy is subject to the laws of physics. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe. The First Law of Thermodynamics 

The first law of thermodynamics deals with the total amount of energy in the universe. It states that this total amount of energy is constant. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may be transferred from place to place or transformed into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting the energy of sunlight into the chemical energy stored within organic molecules, as shown in this figure . Some examples of energy transformations are shown in [link] . 

The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work. Living cells have evolved to meet this challenge very well. Chemical energy stored within organic molecules such as sugars and fats is transformed through a series of cellular chemical reactions into energy within molecules of ATP. Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building complex molecules, transporting materials, powering the beating motion of cilia or flagella, contracting muscle fibers to create movement, and reproduction. Shown are two examples of energy being transferred from one system to another and transformed from one form to another. Humans can convert the chemical energy in food, like this ice cream cone, into kinetic energy (the energy of movement to ride a bicycle). Plants can convert electromagnetic radiation (light energy) from the sun into chemical energy. (credit ice cream : modification of work by D. Sharon Pruitt; credit kids on bikes : modification of work by Michelle Riggen-Ransom; credit leaf : modification of work by Cory Zanker) The Second Law of Thermodynamics 

A living cell s primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. None of the energy transfers we ve discussed, along with all energy transfers and transformations in the universe, is completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, heat energy is defined as the energy transferred from one system to another that is not doing work. For example, when an airplane flies through the air, some of the energy of the flying plane is lost as heat energy due to friction with the surrounding air. This friction actually heats the air by temporarily increasing the speed of air molecules. Likewise, some energy is lost as heat energy during cellular metabolic reactions. This is good for warm-blooded creatures like us, because heat energy helps to maintain our body temperature. Strictly speaking, no energy transfer is completely efficient, because some energy is lost in an unusable form. 

An important concept in physical systems is that of order and disorder (also known as randomness). The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. Scientists refer to the measure of randomness or disorder within a system as entropy . High entropy means high disorder and low energy ( [link] ). To better understand entropy, think of a student s bedroom. If no energy or work were put into it, the room would quickly become messy. It would exist in a very disordered state, one of high entropy. Energy must be put into the system, in the form of the student doing work and putting everything away, in order to bring the room back to a state of cleanliness and order. This state is one of low entropy. Similarly, a car or house must be constantly maintained with work in order to keep it in an ordered state. Left alone, the entropy of the house or car gradually increases through rust and degradation. Molecules and chemical reactions have varying amounts of entropy as well. For example, as chemical reactions reach a state of equilibrium, entropy increases, and as molecules at a high concentration in one place diffuse and spread out, entropy also increases. Scientific Connection Transfer of Energy and the Resulting Entropy 

Set up a simple experiment to understand how energy is transferred and how a change in entropy results. Take a block of ice. This is water in solid form, so it has a high structural order. This means that the molecules cannot move very much and are in a fixed position. The temperature of the ice is 0 C. As a result, the entropy of the system is low. Allow the ice to melt at room temperature. What is the state of molecules in the liquid water now? How did the energy transfer take place? Is the entropy of the system higher or lower? Why? Heat the water to its boiling point. What happens to the entropy of the system when the water is heated? 

All physical systems can be thought of in this way: Living things are highly ordered, requiring constant energy input to be maintained in a state of low entropy. As living systems take in energy-storing molecules and transform them through chemical reactions, they lose some amount of usable energy in the process, because no reaction is completely efficient. They also produce waste and by-products that aren t useful energy sources. This process increases the entropy of the system s surroundings. Since all energy transfers result in the loss of some usable energy, the second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe. Even though living things are highly ordered and maintain a state of low entropy, the entropy of the universe in total is constantly increasing due to the loss of usable energy with each energy transfer that occurs. Essentially, living things are in a continuous uphill battle against this constant increase in universal entropy. Entropy is a measure of randomness or disorder in a system. Gases have higher entropy than liquids, and liquids have higher entropy than solids. Think About It Imagine a large ant colony with an elaborate nest, containing many tunnels and passageways. Now imagine that an earthquake shakes the ground and demolishes the nest. Did the ant nest have higher entropy before or after the earthquake? What can the ants do to restore their nest to close to its original amount of entropy? Explain your answers. Energy transfers take place constantly in everyday activities. Think of two scenarios: cooking on a stove and driving a car. Explain how the second law of thermodynamics applies to these two scenarios. 

Both questions below are an application of Learning Objectives 2.1 and science practice 6.2 because students are explaining how systems use free energy and how entropy reduces the amount of energy available to the system. Possible answers: 

The ant farm is in a state of higher entropy or disorder after the earthquake. The tunnels have been destroyed and energy must be spent to rebuild them. 

Energy transfers take place constantly in everyday activities. Think of two scenarios: cooking on a stove and driving a car. Explain how the second law of thermodynamics applies to these two scenarios. 

In both examples there is an input of energy that results in work being done, cooking and moving the car, and the loss of heat as a result. The heat loss travels into the room on cooking and into the metal of the engine on gasoline combustion. Energy must be continuously put into the systems in order to maintain the activities. Run out of natural gas or propane and the cooking stops. Run out of gasoline and the car stops. Section Summary 

In studying energy, scientists use the term system to refer to the matter and its environment involved in energy transfers. Everything outside of the system is called the surroundings. Single cells are biological systems. Systems can be thought of as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system is, the lower its entropy. Entropy is a measure of the disorder of a system. As a system becomes more disordered, the lower its energy and the higher its entropy become. 

A series of laws, called the laws of thermodynamics, describe the properties and processes of energy transfer. The first law states that the total amount of energy in the universe is constant. This means that energy can t be created or destroyed, only transferred or transformed. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system. In other words, no energy transfer is completely efficient and tends toward disorder. Review Questions 

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[link] Glossary entropy (S) measure of randomness or disorder within a system heat energy energy transferred from one system to another that is not work (energy of the motion of molecules or particles) thermodynamics study of energy and energy transfer involving physical matterATP: Adenosine Triphosphate ATP: Adenosine Triphosphate 

In this section, you will explore the following questions: Why is ATP considered the energy currency of the cell? How is energy released through the hydrolysis of ATP? Connection for AP Courses 

Adenosine triphosphate or ATP is the energy currency or carrier of the cell. When cells require an input of energy, they use ATP. An ATP nucleotide molecule consists of a five-carbon sugar, the nitrogenous base adenine, and three phosphate groups. (Do not confuse ATP with the nucleotides of DNA and RNA, although they have structural similarities.) The bonds that connect the phosphate have high-energy content, and the energy released from the hydrolysis of ATP to ADP + P i (Adenosine Diphosphate + Pyrophosphate) is used to perform cellular work, such as contracting a muscle or pumping a solute across a cell membrane in active transport. Cells use ATP by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions, with ATP donating its phosphate group to another molecule via a process called phosphorylation. The phosphorylated molecule is at a higher energy state and is less stable than its unphosphorylated form and free energy is released to substrates to perform work during this process. Phosphorylation is an example of energy transfer between molecules. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of living systems require free energy and matter. Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.1 The student is able to explain how biological systems use free energy based on empirical data that all organisms require constant energy input to maintain organization, to grow, and to reproduce. 

It is easy to say that ATP carries energy and transfers it to chemicals to fuel reactions. The hard part is in answering the question, how? All three phosphates are negatively charged and naturally repel each other. Energy is needed to keep them together. Line them up and the repelling forces increase and makes it difficult to get the third phosphate attached. This requires much more energy and creates an unstable bond. Energy is stored in this easily broken bond and can be passed on when the third phosphate is used to phosphorylate another compound. It brings the energy with it and losses some in the transfer, creating wasted energy as heat. 

Even exergonic, energy-releasing reactions require a small amount of activation energy in order to proceed. However, consider endergonic reactions, which require much more energy input, because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate , or ATP . ATP is a small, relatively simple molecule ( [link] ), but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in much the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions. ATP is the primary energy currency of the cell. It has an adenosine backbone with three phosphate groups attached. 

[link] is useful in illustrating the structure of ATP and why it is easy to detach the gamma phosphate that is hanging out at the end of the structure. [link] is useful in illustrating the use of ATP in the sodium-potassium pump that is in every cell membrane. 

As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups ( [link] ). Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. However, not all bonds within this molecule exist in a particularly high-energy state. Both bonds that link the phosphates are equally high-energy bonds ( phosphoanhydride bonds ) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. These high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups. The reason that these bonds are considered high-energy is because the products of such bond breaking adenosine diphosphate (ADP) and one inorganic phosphate group (P i ) have considerably lower free energy than the reactants: ATP and a water molecule. Because this reaction takes place with the use of a water molecule, it is considered a hydrolysis reaction. In other words, ATP is hydrolyzed into ADP in the following reaction: ATP + H 2 O ADP + P i + free energy ATP + H 2 O ADP + P i + free energy size 12{{ATP} + H rSub { size 8{2} } O ADP + P rSub { size 8{i}} + {free energy} } {} 

Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction regenerates ATP from ADP + P i . Indeed, cells rely on the regeneration of ATP just as people rely on the regeneration of spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. The formation of ATP is expressed in this equation: ADP + P i + free energy ATP + H 2 O ADP + P i + free energy ATP + H 2 O size 12{{ATP} + H rSub { size 8{2} } O ADP + P rSub { size 8{i}} + {free energy} } {} 

Two prominent questions remain with regard to the use of ATP as an energy source. Exactly how much free energy is released with the hydrolysis of ATP, and how is that free energy used to do cellular work? The calculated G for the hydrolysis of one mole of ATP into ADP and P i is 7.3 kcal/mole ( 30.5 kJ/mol). Since this calculation is true under standard conditions, it would be expected that a different value exists under cellular conditions. In fact, the G for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: 14 kcal/mol ( 57 kJ/mol). 

ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + P i , and the free energy released during this process is lost as heat. The second question posed above, that is, how the energy released by ATP hydrolysis is used to perform work inside the cell, depends on a strategy called energy coupling. Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions, allowing them to proceed. One example of energy coupling using ATP involves a transmembrane ion pump that is extremely important for cellular function. This sodium-potassium pump (Na + /K + pump) drives sodium out of the cell and potassium into the cell ( [link] ). A large percentage of a cell s ATP is spent powering this pump, because cellular processes bring a great deal of sodium into the cell and potassium out of the cell. The pump works constantly to stabilize cellular concentrations of sodium and potassium. In order for the pump to turn one cycle (exporting three Na+ ions and importing two K + ions), one molecule of ATP must be hydrolyzed. When ATP is hydrolyzed, its gamma phosphate doesn t simply float away, but is actually transferred onto the pump protein. This process of a phosphate group binding to a molecule is called phosphorylation. As with most cases of ATP hydrolysis, a phosphate from ATP is transferred onto another molecule. In a phosphorylated state, the Na + /K + pump has more free energy and is triggered to undergo a conformational change. This change allows it to release Na + to the outside of the cell. It then binds extracellular K + , which, through another conformational change, causes the phosphate to detach from the pump. This release of phosphate triggers the K + to be released to the inside of the cell. Essentially, the energy released from the hydrolysis of ATP is coupled with the energy required to power the pump and transport Na + and K + ions. ATP performs cellular work using this basic form of energy coupling through phosphorylation. 

The sodium-potassium pump is an example of energy coupling. The energy derived from exergonic ATP hydrolysis is used to pump sodium and potassium ions across the cell membrane. 

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Often during cellular metabolic reactions, such as the synthesis and breakdown of nutrients, certain molecules must be altered slightly in their conformation to become substrates for the next step in the reaction series. One example is during the very first steps of cellular respiration, when a molecule of the sugar glucose is broken down in the process of glycolysis. In the first step of this process, ATP is required for the phosphorylation of glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction powers a conformational change that allows the phosphorylated glucose molecule to be converted to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. Here, the exergonic reaction of ATP hydrolysis is coupled with the endergonic reaction of converting glucose into a phosphorylated intermediate in the pathway. Once again, the energy released by breaking a phosphate bond within ATP was used for the phosphorylation of another molecule, creating an unstable intermediate and powering an important conformational change. 

See an interactive animation of the ATP-producing glycolysis process at this site . 

[link] Think About It 

The hydrolysis of one ATP molecules releases 7.3 kcal/mol of energy ( G = 7.3 kcal/mol energy). If it takes 2.1 kcal/mol of energy to move one Na + across the membrane ( G = +2.1 kcal/mol of energy), how many sodium ions could be moved by the hydrolysis of one ATP molecule? 

This question is an application of Learning Objective 2.1 and Science Practice 6.2 because students are explaining how a biological system uses free energy. The question also allows you to apply quantitative skills. Possible answer: 7.3 divided by 2.1 equals 3.476, so three sodium ions can be moved across the membrane with a loss of 0.476 kcal/mol of energy. Section Summary 

ATP is the primary energy-supplying molecule for living cells. ATP is made up of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from the hydrolysis of ATP into ADP + P i is used to perform cellular work. Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to another molecule via a process known as phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from the addition of the phosphate allows the molecule to undergo its endergonic reaction. Review Questions 

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[link] Glossary ATP adenosine triphosphate, the cell s energy currency phosphoanhydride bond bond that connects phosphates in an ATP moleculeEnzymes Enzymes 

In this section, you will explore the following questions: What is the role of enzymes in metabolic pathways? How do enzymes function as molecular catalysts? Connection for AP Courses 

Many chemical reactions in cells occur spontaneously, but happen too slowly to meet the needs of a cell. For example, a teaspoon of sucrose (table sugar), a disaccharide, in a glass of iced tea will take time to break down into two monosaccharides, glucose and fructose; however, if you add a small amount of the enzyme sucrase to the tea, sucrose breaks down almost immediately. Sucrase is an example of an enzyme, a type of biological catalyst. Enzymes are macromolecules most often proteins that speed up chemical reactions by lowering activation energy barriers. Enzymes are very specific for the reactions they catalyze; because they are polypeptides, enzymes can have a variety of shapes attributed to interactions among amino acid R-groups. One part of the enzyme, the active site, interacts with the substrate via the induced fit model of interaction. Substrate binding alters the shape of the enzyme to facilitate the chemical reaction in several different ways, including bringing substrates together in an optimal orientation. After the reaction finishes, the product(s) are released, and the active site returns to its original shape. 

Enzyme activity, and thus the rate of an enzyme-catalyzed reaction, is regulated by environmental conditions, including the amount of substrate, temperature, pH, and the presence of coenzymes, cofactors, activators, and inhibitors. Inhibitors, coenzymes, and cofactors can act competitively by binding to the enzyme s active site, or noncompetitively by binding to the enzyme s allosteric site. An allosteric site is an alternate part of the enzyme that can bind to non substrate molecules. Enzymes work most efficiently under optimal conditions that are specific to the enzyme. For example, trypsin, an enzyme in the human small intestine, works most efficiently at pH 8, whereas pepsin in the stomach works best under acidic conditions. Sometimes environmental factors, especially low pH and high temperatures, alter the shape of the active site; if the shape cannot be restored, the enzyme denatures. The most common method of enzyme regulation in metabolic pathways is via feedback inhibition. 

How can various factors, such as feedback inhibition, regulate enzyme activity? 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 4 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven science practices. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.B Competition and cooperation are important aspects of biological systems. Essential Knowledge 4.B.1 Interactions between molecules affect their structure and function. Science Practice 5.1 The student can analyze data to identify patterns or relationships. Learning Objective 4.17 The student is able to analyze data to identify how molecular interactions affect structure and function. 

The idea that enzymes help chemical reactions to occur, but do not take part in the chemical reaction and are not changed by it can be confusing. Stress that an enzyme and substrate do not covalently bind to each other and the association is temporary. [link] is useful in illustrating enzyme function. If two compounds are to be joined into one during the reaction, and they would anyway if left alone long enough, the enzyme molecule brings them close enough for the reaction to occur faster. If a large molecule is to be split into smaller units, the enzyme stresses the molecule and makes it easier for the covalent bonds holding the molecule to break. In both cases, the enzyme molecule subtlety changes its shape after attaching to the substrate (s). This creates an intermediate phase of the reaction and an enzyme-substrate complex. When the reaction is complete and the product(s) disassociate, the enzyme returns to its original shape. 

A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are called enzymes. Almost all enzymes are proteins, made up of chains of amino acids, and they perform the critical task of lowering the activation energies of chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily. It is important to remember that enzymes don t change the G of a reaction. In other words, they don t change whether a reaction is exergonic (spontaneous) or endergonic. This is because they don t change the free energy of the reactants or products. They only reduce the activation energy required to reach the transition state ( [link] ). Enzymes lower the activation energy of the reaction but do not change the free energy of the reaction. Enzyme Active Site and Substrate Specificity 

The chemical reactants to which an enzyme binds are the enzyme s substrates . There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is called the enzyme s active site . The active site is where the action happens, so to speak. Since enzymes are proteins, there is a unique combination of amino acid residues (also called side chains, or R groups) within the active site. Each residue is characterized by different properties. Residues can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of amino acid residues, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind, albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), enzymes are known for their specificity. The best fit results from the shape and the amino acid functional group s attraction to the substrate. There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is flexibility as well. 

The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to influences by the local environment. It is true that increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature , a process that changes the natural properties of a substance. Likewise, the pH of the local environment can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties that are optimal for catalysis. These residues are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) of the environment can cause enzymes to denature. Induced Fit and Enzyme Function 

For many years, scientists thought that enzyme-substrate binding took place in a simple lock-and-key fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view called induced fit ( [link] ). The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme s structure that confirms an ideal binding arrangement between the enzyme and the transition state of the substrate. This ideal binding maximizes the enzyme s ability to catalyze its reaction. 

View an animation of induced fit at this website . 

[link] 

When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex lowers the activation energy of the reaction and promotes its rapid progression in one of many ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation. The appropriate region (atoms and bonds) of one molecule is juxtaposed to the appropriate region of the other molecule with which it must react. Another way in which enzymes promote the reaction of their substrates is by creating an optimal environment within the active site for the reaction to occur. Certain chemical reactions might proceed best in a slightly acidic or non-polar environment. The chemical properties that emerge from the particular arrangement of amino acid residues within an active site create the perfect environment for an enzyme s specific substrates to react. 

You ve learned that the activation energy required for many reactions includes the energy involved in manipulating or slightly contorting chemical bonds so that they can easily break and allow others to reform. Enzymatic action can aid this process. The enzyme-substrate complex can lower the activation energy by contorting substrate molecules in such a way as to facilitate bond-breaking, helping to reach the transition state. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. The amino acid residues can provide certain ions or chemical groups that actually form covalent bonds with substrate molecules as a necessary step of the reaction process. In these cases, it is important to remember that the enzyme will always return to its original state at the completion of the reaction. One of the hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done catalyzing a reaction, it releases its product(s). According to the induced-fit model, both enzyme and substrate undergo dynamic conformational changes upon binding. The enzyme contorts the substrate into its transition state, thereby increasing the rate of the reaction. Activity 

AP Biology Investigation 13: Enzyme Activity. This investigation allows you to design and conduct experiments to explore the effects of environmental variables, such as temperature and pH, on the rates of enzymatic reactions. 

This lab investigation is an application of LO 4.17 and Science Practice 5.1 because you will analyze experimental data to determine how various environment conditions affect enzyme structure and function and, thus, the rate of enzyme-catalyzed reactions. 

An expanded lab investigation for enzymes, involving determining the effect of pH on the action of turnip peroxidase, is available from the College Board s AP Biology Investigative Labs: An Inquiry-Based Approach , Investigation 13 . Control of Metabolism Through Enzyme Regulation 

It would seem ideal to have a scenario in which all of the enzymes encoded in an organism s genome existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. In reality, this is far from the case. A variety of mechanisms ensure that this does not happen. Cellular needs and conditions vary from cell to cell, and change within individual cells over time. The required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and functionality of different enzymes. 

Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which reactions will proceed and at which rates. This determination is tightly controlled. In certain cellular environments, enzyme activity is partly controlled by environmental factors, like pH and temperature. There are other mechanisms through which cells control the activity of enzymes and determine the rates at which various biochemical reactions will occur. Regulation of Enzymes by Molecules 

Enzymes can be regulated in ways that either promote or reduce their activity. There are many different kinds of molecules that inhibit or promote enzyme function, and various mechanisms exist for doing so. In some cases of enzyme inhibition, for example, an inhibitor molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this happens, the enzyme is inhibited through competitive inhibition , because an inhibitor molecule competes with the substrate for active site binding ( [link] ). On the other hand, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than an allosteric site and still manages to block substrate binding to the active site. Competitive and noncompetitive inhibition affect the rate of reaction differently. Competitive inhibitors affect the initial rate but do not affect the maximal rate, whereas noncompetitive inhibitors affect the maximal rate. 

Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the affinity of the enzyme for its substrate. This type of inhibition is called allosteric inhibition ( [link] ). Most allosterically regulated enzymes are made up of more than one polypeptide, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits are changed slightly such that they bind their substrates with less efficiency. There are allosteric activators as well as inhibitors. Allosteric activators bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme s active site(s) for its substrate(s). Allosteric inhibitors modify the active site of the enzyme so that substrate binding is reduced or prevented. In contrast, allosteric activators modify the active site of the enzyme so that the affinity for the substrate increases. Have you ever wondered how pharmaceutical drugs are developed? (credit: Deborah Austin) 

Drug Discovery by Looking for Inhibitors of Key Enzymes in Specific Pathways Enzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated is a key principle behind the development of many of the pharmaceutical drugs ( [link] ) on the market today. Biologists working in this field collaborate with other scientists, usually chemists, to design drugs. 

Consider statins for example which is the name given to the class of drugs that reduces cholesterol levels. These compounds are essentially inhibitors of the enzyme HMG-CoA reductase. HMG-CoA reductase is the enzyme that synthesizes cholesterol from lipids in the body. By inhibiting this enzyme, the levels of cholesterol synthesized in the body can be reduced. Similarly, acetaminophen, popularly marketed under the brand name Tylenol, is an inhibitor of the enzyme cyclooxygenase. While it is effective in providing relief from fever and inflammation (pain), its mechanism of action is still not completely understood. 

How are drugs developed? One of the first challenges in drug development is identifying the specific molecule that the drug is intended to target. In the case of statins, HMG-CoA reductase is the drug target. Drug targets are identified through painstaking research in the laboratory. Identifying the target alone is not sufficient; scientists also need to know how the target acts inside the cell and which reactions go awry in the case of disease. Once the target and the pathway are identified, then the actual process of drug design begins. During this stage, chemists and biologists work together to design and synthesize molecules that can either block or activate a particular reaction. However, this is only the beginning: both if and when a drug prototype is successful in performing its function, then it must undergo many tests from in vitro experiments to clinical trials before it can get FDA approval to be on the market. 

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Many enzymes don t work optimally, or even at all, unless bound to other specific non-protein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Two types of helper molecules are cofactors and coenzymes . Binding to these molecules promotes optimal conformation and function for their respective enzymes. Cofactors are inorganic ions such as iron (Fe++) and magnesium (Mg++). One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires bound zinc ion (Zn++) to function. Coenzymes are organic helper molecules, with a basic atomic structure made up of carbon and hydrogen, which are required for enzyme action. The most common sources of coenzymes are dietary vitamins ( [link] ). Some vitamins are precursors to coenzymes and others act directly as coenzymes. Vitamin C is a coenzyme for multiple enzymes that take part in building the important connective tissue component, collagen. An important step in the breakdown of glucose to yield energy is catalysis by a multi-enzyme complex called pyruvate dehydrogenase. Pyruvate dehydrogenase is a complex of several enzymes that actually requires one cofactor (a magnesium ion) and five different organic coenzymes to catalyze its specific chemical reaction. Therefore, enzyme function is, in part, regulated by an abundance of various cofactors and coenzymes, which are supplied primarily by the diets of most organisms. Vitamins are important coenzymes or precursors of coenzymes, and are required for enzymes to function properly. Multivitamin capsules usually contain mixtures of all the vitamins at different percentages. Enzyme Compartmentalization 

In eukaryotic cells, molecules such as enzymes are usually compartmentalized into different organelles. This allows for yet another level of regulation of enzyme activity. Enzymes required only for certain cellular processes can be housed separately along with their substrates, allowing for more efficient chemical reactions. Examples of this sort of enzyme regulation based on location and proximity include the enzymes involved in the latter stages of cellular respiration, which take place exclusively in the mitochondria, and the enzymes involved in the digestion of cellular debris and foreign materials, located within lysosomes. Feedback Inhibition in Metabolic Pathways 

Molecules can regulate enzyme function in many ways. A major question remains, however: What are these molecules and where do they come from? Some are cofactors and coenzymes, ions, and organic molecules, as you ve learned. What other molecules in the cell provide enzymatic regulation, such as allosteric modulation, and competitive and noncompetitive inhibition? The answer is that a wide variety of molecules can perform these roles. Some of these molecules include pharmaceutical and non-pharmaceutical drugs, toxins, and poisons from the environment. Perhaps the most relevant sources of enzyme regulatory molecules, with respect to cellular metabolism, are the products of the cellular metabolic reactions themselves. In a most efficient and elegant way, cells have evolved to use the products of their own reactions for feedback inhibition of enzyme activity. Feedback inhibition involves the use of a reaction product to regulate its own further production ( [link] ). The cell responds to the abundance of specific products by slowing down production during anabolic or catabolic reactions. Such reaction products may inhibit the enzymes that catalyzed their production through the mechanisms described above. Metabolic pathways are a series of reactions catalyzed by multiple enzymes. Feedback inhibition, where the end product of the pathway inhibits an upstream step, is an important regulatory mechanism in cells. 

The production of both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in the catabolic breakdown of sugar, the process that produces ATP. In this way, when ATP is abundant, the cell can prevent its further production. Remember that ATP is an unstable molecule that can spontaneously dissociate into ADP. If too much ATP were present in a cell, much of it would go to waste. On the other hand, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that are inhibited by ATP. Thus, when relative levels of ADP are high compared to ATP, the cell is triggered to produce more ATP through the catabolism of sugar. 

Ask students which inhibition is more effective at slowing or limiting the reaction? Relate this to the examples available and discuss why these would be used in specific instances. 

Have the class research antimicrobial treatments that are based on enzyme inhibition, not on the administration of traditional antibiotics. 

Enzymes are not changed by the chemicals they facilitate; therefore, they can be used repeatedly. Yet, how do you keep them from catalyzing reactions when you do not need or want them to react anymore? If enzymes could not be controlled, the reactions would continue until the substrates were depleted, which is not a good situation for a living organism. Competitive and noncompetitive inhibition explains the control of enzyme activity. Research several examples of both in living organisms and explain why they are necessary. Amino acid production is one useful example. Amino acids are required for protein production, but too high a level of any amino acid is toxic, so the pathways must be controlled. Use the feedback inhibition of several pathways as examples. Section Summary 

Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, made up of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can be more easily broken, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates. 

Enzyme action must be regulated so that in a given cell at a given time, the desired reactions are being catalyzed and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes being compartmentalized so that they can only catalyze reactions under certain circumstances. Inhibition and activation of enzymes via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically; noncompetitive inhibitors are usually allosteric. Activators can also enhance the function of enzymes allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, the products of a metabolic pathway serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them. Review Questions 

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[link] Glossary active site specific region of the enzyme to which the substrate binds allosteric inhibition inhibition by a binding event at a site different from the active site, which induces a conformational change and reduces the affinity of the enzyme for its substrate coenzyme small organic molecule, such as a vitamin or its derivative, which is required to enhance the activity of an enzyme cofactor inorganic ion, such as iron and magnesium ions, required for optimal regulation of enzyme activity competitive inhibition type of inhibition in which the inhibitor competes with the substrate molecule by binding to the active site of the enzyme denature process that changes the natural properties of a substance feedback inhibition effect of a product of a reaction sequence to decrease its further production by inhibiting the activity of the first enzyme in the pathway that produces it induced fit dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding substrate molecule on which the enzyme actsIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" This geothermal energy plant transforms thermal energy from deep in the ground into electrical energy, which can be easily used. (credit: modification of work by the U.S. Department of Defense) 

The electrical energy plant in [link] converts energy from one form to another form that can be more easily used. This type of generating plant starts with underground thermal energy (heat) and transforms it into electrical energy that will be transported to homes and factories. Like a generating plant, plants and animals also must take in energy from the environment and convert it into a form that their cells can use. Energy enters an organism s body in one form and is converted into another form that can fuel the organism s life functions. In the process of photosynthesis, plants and other photosynthetic producers take in energy in the form of light (solar energy) and convert it into chemical energy, glucose, which stores this energy in its chemical bonds. Then, a series of metabolic pathways, collectively called cellular respiration, extract the energy from the carbon carbon bonds of glucose and convert it into a form that all living things can use both producers, such as plants, and consumers, such as animals. 

Nearly all organisms perform glycolysis, the first part of both aerobic and anaerobic respiration. One of the key enzymes of glycolysis is pyruvate kinase. Without this enzyme, an organism will die because it is unable to convert nutrients into the energy it needs for survival. Scientists have taken advantage of that fact by blocking pyruvate kinase in some deadly parasites, such as the ones that cause African Sleeping Sickness and Chagas disease. Read more about this research here . 

Before students begin this chapter, it is useful to review these concepts: Cell structure including mitochondria structure; structure of macromolecules including glucose, lipids, and proteins; transport of molecules across membranes including diffusion and facilitated transport.Energy in Living Systems Energy in Living Systems 

In this section, you will explore the following questions: What is the importance of electrons for the transfer of energy in living systems? How is ATP used by the cell as an energy source? Connection for AP Courses 

As we learned in previous chapters, living organisms require free energy to power life processes such as growth, reproduction, movement, and active transport. ATP (adenosine triphosphate) functions as the energy currency for cells. It allows the cells to store energy and transfer it within the cells to provide energy for cellular processes such as growth, movement and active transport. The ATP molecule consists of a ribose sugar and an adenine base with three phosphates attached. In the hydrolysis of ATP, free energy is supplied when a phosphate group or two are detached, and either ADP (adenosine diphosphate) or AMP (adenosine monophosphate) is produced. Energy derived from the metabolism of glucose is used to convert ADP to ATP during cellular respiration. As we explore cellular respiration, we ll learn that the two ways ATP is regenerated by the cell are called substrate-level phosphorylation and oxidative phosphorylation. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 2 and Big Idea 4 of the AP Biology Curriculum Framework, as shown in the table. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.2 Organisms capture and store free energy for use in biological processes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy. Essential Knowledge 2.A.2 Organisms capture and store free energy for use in biological processes. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy. 

Ask students what happens when they eat a candy bar. How is the energy extracted? What do we mean when we say our bodies burn the sugar in food for energy? How are cellular respiration and combustion alike? They are both redox reactions that generate energy from the reaction of fuel (glucose in cellular respiration) with oxygen. However, our bodies need to control the release of this energy, so that cells can capture the free energy released to do useful work. 

Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions. Oxidation and reduction occur in tandem. An oxidation reaction strips an electron from an atom in a compound, and the addition of this electron to another compound is a reduction reaction. Because oxidation and reduction usually occur together, these pairs of reactions are called oxidation reduction reactions, or redox reactions . Electrons and Energy 

The removal of an electron from a molecule, oxidizing it, results in a decrease in potential energy in the oxidized compound. The electron (sometimes as part of a hydrogen atom), does not remain unbonded, however, in the cytoplasm of a cell. Rather, the electron is shifted to a second compound, reducing the second compound. The shift of an electron from one compound to another removes some potential energy from the first compound (the oxidized compound) and increases the potential energy of the second compound (the reduced compound). The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy in an incremental fashion in small packages rather than in a single, destructive burst. This chapter focuses on the extraction of energy from food; you will see that as you track the path of the transfers, you are tracking the path of electrons moving through metabolic pathways. Electron Carriers 

In living systems, a small class of compounds functions as electron shuttles: They bind and carry high-energy electrons between compounds in pathways. The principal electron carriers we will consider are derived from the B vitamin group and are derivatives of nucleotides. These compounds can be easily reduced (that is, they accept electrons) or oxidized (they lose electrons). Nicotinamide adenine dinucleotide (NAD) ( [link] ) is derived from vitamin B3, niacin. NAD + is the oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two electrons and a proton (which together are the equivalent of a hydrogen atom with an extra electron). 

NAD + can accept electrons from an organic molecule according to the general equation: RH Reducing agent + NAD + Oxidizing agent NADH Reduced + R Oxidized RH Reducing agent + NAD + Oxidizing agent NADH Reduced + R Oxidized 

When electrons are added to a compound, they are reduced. A compound that reduces another is called a reducing agent. In the above equation, RH is a reducing agent, and NAD + is reduced to NADH. When electrons are removed from compound, it is oxidized. A compound that oxidizes another is called an oxidizing agent. In the above equation, NAD + is an oxidizing agent, and RH is oxidized to R. 

Similarly, flavin adenine dinucleotide (FAD + ) is derived from vitamin B 2 , also called riboflavin. Its reduced form is FADH 2 . A second variation of NAD, NADP, contains an extra phosphate group. Both NAD + and FAD + are extensively used in energy extraction from sugars, and NADP plays an important role in anabolic reactions and photosynthesis. The oxidized form of the electron carrier (NAD + ) is shown on the left and the reduced form (NADH) is shown on the right. The nitrogenous base in NADH has one more hydrogen ion and two more electrons than in NAD + . ATP in Living Systems 

A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the energy currency of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery. 

When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The energy is used to do work by the cell, usually by the released phosphate binding to another molecule, activating it. For example, in the mechanical work of muscle contraction, ATP supplies the energy to move the contractile muscle proteins. Recall the active transport work of the sodium-potassium pump in cell membranes. ATP alters the structure of the integral protein that functions as the pump, changing its affinity for sodium and potassium. In this way, the cell performs work, pumping ions against their electrochemical gradients. ATP Structure and Function 

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and to a single phosphate group ( [link] ). Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine di phosphate (ADP); the addition of a third phosphate group forms adenosine tri phosphate (ATP). ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate).The negative charges on the phosphate group naturally repel each other, requiring energy to bond them together and releasing energy when these bonds are broken. 

The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called dephosphorylation , releases energy. Energy from ATP 

Hydrolysis is the process of breaking complex macromolecules apart. During hydrolysis, water is split, or lysed, and the resulting hydrogen atom (H + ) and a hydroxyl group (OH - ) are added to the larger molecule. The hydrolysis of ATP produces ADP, together with an inorganic phosphate ion (P i ), and the release of free energy. To carry out life processes, ATP is continuously broken down into ADP, and like a rechargeable battery, ADP is continuously regenerated into ATP by the reattachment of a third phosphate group. Water, which was broken down into its hydrogen atom and hydroxyl group during ATP hydrolysis, is regenerated when a third phosphate is added to the ADP molecule, reforming ATP. 

Obviously, energy must be infused into the system to regenerate ATP. Where does this energy come from? In nearly every living thing on earth, the energy comes from the metabolism of glucose. In this way, ATP is a direct link between the limited set of exergonic pathways of glucose catabolism and the multitude of endergonic pathways that power living cells. Phosphorylation 

Recall that, in some chemical reactions, enzymes may bind to several substrates that react with each other on the enzyme, forming an intermediate complex. An intermediate complex is a temporary structure, and it allows one of the substrates (such as ATP) and reactants to more readily react with each other; in reactions involving ATP, ATP is one of the substrates and ADP is a product. During an endergonic chemical reaction, ATP forms an intermediate complex with the substrate and enzyme in the reaction. This intermediate complex allows the ATP to transfer its third phosphate group, with its energy, to the substrate, a process called phosphorylation. Phosphorylation refers to the addition of the phosphate (~P). This is illustrated by the following generic reaction: A + enzyme + ATP [ A enzyme P ] B + enzyme + ADP + phosphate ion A + enzyme + ATP [ A enzyme P ] B + enzyme + ADP + phosphate ion 

When the intermediate complex breaks apart, the energy is used to modify the substrate and convert it into a product of the reaction. The ADP molecule and a free phosphate ion are released into the medium and are available for recycling through cell metabolism. Substrate Phosphorylation 

ATP is generated through two mechanisms during the breakdown of glucose. A few ATP molecules are generated (that is, regenerated from ADP) as a direct result of the chemical reactions that occur in the catabolic pathways. A phosphate group is removed from an intermediate reactant in the pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP molecule, producing ATP ( [link] ). This very direct method of phosphorylation is called substrate-level phosphorylation . In phosphorylation reactions, the gamma phosphate of ATP is attached to a protein. Oxidative Phosphorylation 

Most of the ATP generated during glucose catabolism, however, is derived from a much more complex process, chemiosmosis, which takes place in mitochondria ( [link] ) within a eukaryotic cell or the plasma membrane of a prokaryotic cell. Chemiosmosis , a process of ATP production in cellular metabolism, is used to generate 90 percent of the ATP made during glucose catabolism and is also the method used in the light reactions of photosynthesis to harness the energy of sunlight. The production of ATP using the process of chemiosmosis is called oxidative phosphorylation because of the involvement of oxygen in the process. In eukaryotes, oxidative phosphorylation takes place in mitochondria. In prokaryotes, this process takes place in the plasma membrane. (Credit: modification of work by Mariana Ruiz Villareal) Think About It 

Explain why it is more metabolically efficient for cells to extract energy from ATP rather than from the bonds of carbohydrates directly. 

This question is an application of Learning Objective 2.5 and Science Practice 6.2 because students are asked to explain why ATP is considered the energy currency of the cell. Possible answer : The catabolism of carbohydrates or other molecules produces free energy which cannot be stored. Excess free energy would result in an increase of heat in the cell, which would destroy it. Free energy can be stored in the phosphate bonds of ATP, which releases the energy when needed through the removal of a phosphate group. Mitochondrial Disease Physician 

What happens when the critical reactions of cellular respiration do not proceed correctly? Mitochondrial diseases are genetic disorders of metabolism. Mitochondrial disorders can arise from mutations in nuclear or mitochondrial DNA, and they result in the production of less energy than is normal in body cells. In type 2 diabetes, for instance, the oxidation efficiency of NADH is reduced, impacting oxidative phosphorylation but not the other steps of respiration. Symptoms of mitochondrial diseases can include muscle weakness, lack of coordination, stroke-like episodes, and loss of vision and hearing. Most affected people are diagnosed in childhood, although there are some adult-onset diseases. Identifying and treating mitochondrial disorders is a specialized medical field. The educational preparation for this profession requires a college education, followed by medical school with a specialization in medical genetics. Medical geneticists can be board certified by the American Board of Medical Genetics and go on to become associated with professional organizations devoted to the study of mitochondrial diseases, such as the Mitochondrial Medicine Society and the Society for Inherited Metabolic Disease. Section Summary 

ATP functions as the energy currency for cells. It allows the cell to store energy briefly and transport it within the cell to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphates attached. As ATP is used for energy, a phosphate group or two are detached, and either ADP or AMP is produced. Energy derived from glucose catabolism is used to convert ADP into ATP. When ATP is used in a reaction, the third phosphate is temporarily attached to a substrate in a process called phosphorylation. The two processes of ATP regeneration that are used in conjunction with glucose catabolism are substrate-level phosphorylation and oxidative phosphorylation through the process of chemiosmosis. Review Questions 

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[link] Glossary chemiosmosis process in which there is a production of adenosine triphosphate (ATP) in cellular metabolism by the involvement of a proton gradient across a membrane dephosphorylation removal of a phosphate group from a molecule oxidative phosphorylation production of ATP using the process of chemiosmosis and oxygen phosphorylation addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP redox reaction chemical reaction that consists of the coupling of an oxidation reaction and a reduction reaction substrate-level phosphorylation production of ATP from ADP using the excess energy from a chemical reaction and a phosphate group from a reactantGlycolysis Glycolysis 

In this section, you will explore the following question: What is the overall result, in terms of molecules produced, in the breakdown of glucose by glycolysis? Connection for AP Courses 

All organisms, from simple bacteria and yeast to complex plants and animals, carry out some form of cellular respiration to capture and supply free energy for cellular processes. Although cellular respiration and photosynthesis evolved as independent processes, today they are interdependent. The products of photosynthesis, carbohydrates and oxygen gas, are used during cellular respiration. Likewise, the byproduct of cellular respiration, CO 2 gas, is used during photosynthesis. Glycolysis is the first pathway used in the breakdown of glucose to extract free energy. Used by nearly all organisms on earth today, glycolysis likely evolved as one of the first metabolic pathways. It is important to note that glycolysis occurs in the cytoplasm of both prokaryotic and eukaryotic cells. (Remember that only eukaryotic cells have mitochondria.) 

Like all metabolic pathways, glycolysis occurs in steps or stages. In the first stage, the six-carbon ring of glucose is prepared for cleavage ( splitting ) into two three-carbon molecules by investing two molecules of ATP to energize the separation. (Don t worry; the cell will get the investment of ATP back. It s like the stock market: You have to invest money to, hopefully, make money!) As glucose is metabolized further, bonds are rearranged through a series of enzyme-catalyzed steps, and free energy is released to form ATP from ADP and free phosphate molecules. The availability of enzymes can affect the rate of glucose metabolism. Two molecules of pyruvate are ultimately produced. High-energy electrons and hydrogen atoms pass to NAD + , reducing it to NADH. Although two molecules of ATP were invested to destabilize glucose at the beginning of the process, four molecules of ATP are formed by substrate-level phosphorylation, resulting in a net gain of two ATP and two NADH molecules for the cell. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 1 and Big Idea 2 of the AP Biology Curriculum Framework, as shown in the table. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A All living systems require constant input of free energy. Essential Knowledge 2.A.2 Organisms capture and store free energy for use in biological processes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy. Essential Knowledge 2.A.2 Organisms capture and store free energy for use in biological processes. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy. 

Discuss with students how glycolysis is considered to be the oldest and most conserved metabolic pathway. Discuss with students how this process is found in all domains of life. Glycolysis is an anaerobic process, and the early atmosphere of Earth had very little oxygen. This means that glycolysis could have taken place in early prokaryotes because it does not require oxygen. Glycolysis takes place in the cell cytosol, and not the mitochondrial membrane. Prokaryotes, which don t have membrane bound organelles, can carry out glycolysis. 

Introduce the process of glycolysis using visuals such as this video . 

You have read that nearly all of the energy used by living cells comes to them in the bonds of the sugar, glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cellular metabolism. Nearly all living organisms carry out glycolysis as part of their metabolism. The process does not use oxygen and is therefore anaerobic . Glycolysis takes place in the cytoplasm of both prokaryotic and eukaryotic cells. Glucose enters heterotrophic cells in two ways. One method is through secondary active transport in which the transport takes place against the glucose concentration gradient. The other mechanism uses a group of integral proteins called GLUT proteins, also known as glucose transporter proteins. These transporters assist in the facilitated diffusion of glucose. 

Glycolysis begins with the six carbon ring-shaped structure of a single glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate . Glycolysis consists of two distinct phases. The first part of the glycolysis pathway traps the glucose molecule in the cell and uses energy to modify it so that the six-carbon sugar molecule can be split evenly into the two three-carbon molecules. The second part of glycolysis extracts energy from the molecules and stores it in the form of ATP and NADH, the reduced form of NAD + . First Half of Glycolysis (Energy-Requiring Steps) 

Step 1. The first step in glycolysis ( [link] ) is catalyzed by hexokinase, an enzyme with broad specificity that catalyzes the phosphorylation of six-carbon sugars. Hexokinase phosphorylates glucose using ATP as the source of the phosphate, producing glucose-6-phosphate, a more reactive form of glucose. This reaction prevents the phosphorylated glucose molecule from continuing to interact with the GLUT proteins, and it can no longer leave the cell because the negatively charged phosphate will not allow it to cross the hydrophobic interior of the plasma membrane. 

Step 2. In the second step of glycolysis, an isomerase converts glucose-6-phosphate into one of its isomers, fructose-6-phosphate. An isomerase is an enzyme that catalyzes the conversion of a molecule into one of its isomers. (This change from phosphoglucose to phosphofructose allows the eventual split of the sugar into two three-carbon molecules.). 

Step 3. The third step is the phosphorylation of fructose-6-phosphate, catalyzed by the enzyme phosphofructokinase. A second ATP molecule donates a high-energy phosphate to fructose-6-phosphate, producing fructose-1,6- bi sphosphate. In this pathway, phosphofructokinase is a rate-limiting enzyme. It is active when the concentration of ADP is high; it is less active when ADP levels are low and the concentration of ATP is high. Thus, if there is sufficient ATP in the system, the pathway slows down. This is a type of end product inhibition, since ATP is the end product of glucose catabolism. 

Step 4. The newly added high-energy phosphates further destabilize fructose-1,6-bisphosphate. The fourth step in glycolysis employs an enzyme, aldolase, to cleave 1,6-bisphosphate into two three-carbon isomers: dihydroxyacetone-phosphate and glyceraldehyde-3-phosphate. 

Step 5. In the fifth step, an isomerase transforms the dihydroxyacetone-phosphate into its isomer, glyceraldehyde-3-phosphate. Thus, the pathway will continue with two molecules of a single isomer. At this point in the pathway, there is a net investment of energy from two ATP molecules in the breakdown of one glucose molecule. The first half of glycolysis uses two ATP molecules in the phosphorylation of glucose, which is then split into two three-carbon molecules. Second Half of Glycolysis (Energy-Releasing Steps) 

So far, glycolysis has cost the cell two ATP molecules and produced two small, three-carbon sugar molecules. Both of these molecules will proceed through the second half of the pathway, and sufficient energy will be extracted to pay back the two ATP molecules used as an initial investment and produce a profit for the cell of two additional ATP molecules and two even higher-energy NADH molecules. 

Step 6. The sixth step in glycolysis ( [link] ) oxidizes the sugar (glyceraldehyde-3-phosphate), extracting high-energy electrons, which are picked up by the electron carrier NAD + , producing NADH. The sugar is then phosphorylated by the addition of a second phosphate group, producing 1,3-bisphosphoglycerate. Note that the second phosphate group does not require another ATP molecule. The second half of glycolysis involves phosphorylation without ATP investment (step 6) and produces two NADH and four ATP molecules per glucose. 

Here again is a potential limiting factor for this pathway. The continuation of the reaction depends upon the availability of the oxidized form of the electron carrier, NAD + . Thus, NADH must be continuously oxidized back into NAD + in order to keep this step going. If NAD + is not available, the second half of glycolysis slows down or stops. If oxygen is available in the system, the NADH will be oxidized readily, though indirectly, and the high-energy electrons from the hydrogen released in this process will be used to produce ATP. In an environment without oxygen, an alternate pathway (fermentation) can provide the oxidation of NADH to NAD + . 

Step 7. In the seventh step, catalyzed by phosphoglycerate kinase (an enzyme named for the reverse reaction), 1,3-bisphosphoglycerate donates a high-energy phosphate to ADP, forming one molecule of ATP. (This is an example of substrate-level phosphorylation.) A carbonyl group on the 1,3-bisphosphoglycerate is oxidized to a carboxyl group, and 3-phosphoglycerate is formed. 

Step 8. In the eighth step, the remaining phosphate group in 3-phosphoglycerate moves from the third carbon to the second carbon, producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The enzyme catalyzing this step is a mutase (isomerase). 

Step 9. Enolase catalyzes the ninth step. This enzyme causes 2-phosphoglycerate to lose water from its structure; this is a dehydration reaction, resulting in the formation of a double bond that increases the potential energy in the remaining phosphate bond and produces phosphoenolpyruvate (PEP). 

Step 10. The last step in glycolysis is catalyzed by the enzyme pyruvate kinase (the enzyme in this case is named for the reverse reaction of pyruvate s conversion into PEP) and results in the production of a second ATP molecule by substrate-level phosphorylation and the compound pyruvic acid (or its salt form, pyruvate). Many enzymes in enzymatic pathways are named for the reverse reactions, since the enzyme can catalyze both forward and reverse reactions (these may have been described initially by the reverse reaction that takes place in vitro, under non-physiological conditions). 

Gain a better understanding of the breakdown of glucose by glycolysis by visiting this site to see the process in action. 

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Glycolysis occurs in the cytoplasm of nearly every cell. Organisms, from the small, circular colonies of bacteria pictured here to the human holding the petri dish, perform glycolysis using the same ten enzymes. Because of this, it is thought that glycolysis must have evolved in the very earliest forms of life. 

[link] Outcomes of Glycolysis 

Glycolysis starts with glucose and ends with two pyruvate molecules, a total of four ATP molecules and two molecules of NADH. Two ATP molecules were used in the first half of the pathway to prepare the six-carbon ring for cleavage, so the cell has a net gain of two ATP molecules and 2 NADH molecules for its use. If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. Mature mammalian red blood cells are not capable of aerobic respiration the process in which organisms convert energy in the presence of oxygen and glycolysis is their sole source of ATP. If glycolysis is interrupted, these cells lose their ability to maintain their sodium-potassium pumps, and eventually, they die. 

The last step in glycolysis will not occur if pyruvate kinase, the enzyme that catalyzes the formation of pyruvate, is not available in sufficient quantities. In this situation, the entire glycolysis pathway will proceed, but only two ATP molecules will be made in the second half. Thus, pyruvate kinase is a rate-limiting enzyme for glycolysis. Think About It Nearly all organisms on Earth carry out some form of glycolysis. How does that fact support or not support the assertion that glycolysis is one of the oldest metabolic pathways? Justify your answer. Human red blood cells do not perform aerobic respiration, but they do perform glycolysis. What might happen if glycolysis were blocked in a red blood cell? Could red blood cells tap into other sources of free energy needed for their functions? 

The first Think About It question is an application of Learning Objective 1.15 and Science Practice 7.2 because metabolic pathways are examples of conserved core processes shared by all organisms. 

The second Think About It question is an application of Learning Objective 2.4 and Science Practices 1.4 and 3.1 because students are addressing questions about how the features of cells can affect the cell s ability to harvest free energy from different sources. Possible answers: If glycolysis evolved relatively late, it likely would not be as universal in organisms as it is. It probably evolved in very primitive organisms and persisted, even when additional pathways of carbohydrate metabolism evolved later. All cells must consume energy in order to carry out basic functions, such as pumping ions across membranes. A red blood cell would lose its membrane potential if glycolysis was blocked, and it would eventually die. Mature mammalian red blood cells are not capable of aerobic respiration the process in which organisms convert energy in the presence of oxygen and glycolysis is their sole source of ATP. If glycolysis is interrupted, these cells lose their ability to maintain their sodium-potassium pumps, and eventually, they die. Section Summary 

Glycolysis is the first pathway used in the breakdown of glucose to extract energy. It was probably one of the earliest metabolic pathways to evolve and is used by nearly all of the organisms on earth. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for cleavage into two three-carbon sugars. ATP is invested in the process during this half to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD + . Two ATP molecules are invested in the first half and four ATP molecules are formed by substrate phosphorylation during the second half. This produces a net gain of two ATP and two NADH molecules for the cell. Review Questions 

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[link] Glossary aerobic respiration process in which organisms convert energy in the presence of oxygen anaerobic process that does not use oxygen glycolysis process of breaking glucose into two three-carbon molecules with the production of ATP and NADH isomerase enzyme that converts a molecule into its isomer pyruvate three-carbon sugar that can be decarboxylated and oxidized to make acetyl CoA, which enters the citric acid cycle under aerobic conditions; the end product of glycolysisOxidation of Pyruvate and the Citric Acid Cycle Oxidation of Pyruvate and the Citric Acid Cycle 

In this section, you will explore the following question: How is pyruvate, the product of glycolysis, prepared for entry into the citric acid cycle? What are the products of the citric acid cycle? Connection for AP Courses 

In the next stage of cellular respiration and in the presence of oxygen pyruvate produced in glycolysis is transformed into an acetyl group attached to a carrier molecule of coenzyme A. The resulting acetyl CoA is usually delivered from the cytoplasm to the mitochondria, a process that uses some ATP. In the mitochondria, acetyl CoA continues on to the citric acid cycle. The citric acid cycle (CAC or TCA- tricarboxylic acid cycle) is also known as the Krebs cycle. During the conversion of pyruvate into the acetyl group, a molecule of CO 2 and two high-energy electrons are removed. (Remember that glycolysis produces two molecules of pyruvate, and each can attach to a molecule of CoA and then enter the citric acid cycle. (A simple rule is to count the carbons. Because matter and energy cannot be created or destroyed, we must account for everything.) The electrons are picked up by NAD + , and NADH carries the electrons to a later pathway (the electron transport chain described below) for ATP production. The glucose molecule that originally entered cellular respiration in glycolysis has been completely oxidized. Chemical potential energy stored within the glucose molecules has been transferred to NADH or has been used to synthesize ATP molecules. 

The citric acid cycle occurs in the mitochondrial matrix and involves a series of redox and decarboxylation reactions that again remove high energy electrons and produce CO 2 . These electrons are carried by NADH and FADH 2 to the electron transport chain located in the cristae of the mitochondrion. (You do not need to memorize the steps in the citric acid cycle, but if provided with a diagram of the cycle, you should be able to interpret the steps.) During the cycle, ATP is synthesized from ADP and inorganic phosphate by substrate-level phosphorylation. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.2 Organisms capture and store free energy for use in biological processes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy. Essential Knowledge 2.A.2 Organisms capture and store free energy for use in biological processes Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.2 The structure and function of subcellular components, and their interactions, provide essential cellular processes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 4.6 The student is able to use representations and models to analyze situations qualitatively to describe how interactions of subcellular structures, which possess specialized functions, provide essential functions. 

Introduce the citric acid cycle using visuals such as this video . 

If oxygen is available, aerobic respiration will go forward. In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria. There, pyruvate will be transformed into an acetyl group that will be picked up and activated by a carrier compound called coenzyme A (CoA). The resulting compound is called acetyl CoA . CoA is made from vitamin B5, pantothenic acid. Acetyl CoA can be used in a variety of ways by the cell, but its major function is to deliver the acetyl group derived from pyruvate to the next stage of the pathway in glucose catabolism. Breakdown of Pyruvate 

In order for pyruvate, the product of glycolysis, to enter the next pathway, it must undergo several changes. The conversion is a three-step process ( [link] ). 

Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of carbon dioxide into the surrounding medium. The result of this step is a two-carbon hydroxyethyl group bound to the enzyme (pyruvate dehydrogenase). This is the first of the six carbons from the original glucose molecule to be removed. This step proceeds twice (remember: there are two pyruvate molecules produced at the end of glycolsis) for every molecule of glucose metabolized; thus, two of the six carbons will have been removed at the end of both steps. 

Step 2. The hydroxyethyl group is oxidized to an acetyl group, and the electrons are picked up by NAD + , forming NADH. The high-energy electrons from NADH will be used later to generate ATP. 

Step 3. The enzyme-bound acetyl group is transferred to CoA, producing a molecule of acetyl CoA. Upon entering the mitochondrial matrix, a multi-enzyme complex converts pyruvate into acetyl CoA. In the process, carbon dioxide is released and one molecule of NADH is formed. 

Note that during the second stage of glucose metabolism, whenever a carbon atom is removed, it is bound to two oxygen atoms, producing carbon dioxide, one of the major end products of cellular respiration. Acetyl CoA to CO 2 

In the presence of oxygen, acetyl CoA delivers its acetyl group to a four-carbon molecule, oxaloacetate, to form citrate, a six-carbon molecule with three carboxyl groups; this pathway will harvest the remainder of the extractable energy from what began as a glucose molecule. This single pathway is called by different names: the citric acid cycle (for the first intermediate formed citric acid, or citrate when acetate joins to the oxaloacetate), the TCA cycle (since citric acid or citrate and isocitrate are tricarboxylic acids), and the Krebs cycle , after Hans Krebs, who first identified the steps in the pathway in the 1930s in pigeon flight muscles. Citric Acid Cycle 

Like the conversion of pyruvate to acetyl CoA, the citric acid cycle takes place in the matrix of mitochondria. Almost all of the enzymes of the citric acid cycle are soluble, with the single exception of the enzyme succinate dehydrogenase, which is embedded in the inner membrane of the mitochondrion. Unlike glycolysis, the citric acid cycle is a closed loop: The last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one GTP/ATP, and reduced forms of NADH and FADH 2 ( [link] ). This is considered an aerobic pathway because the NADH and FADH 2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If this transfer does not occur, the oxidation steps of the citric acid cycle also do not occur. Note that the citric acid cycle produces very little ATP directly and does not directly consume oxygen. In the citric acid cycle, the acetyl group from acetyl CoA is attached to a four-carbon oxaloacetate molecule to form a six-carbon citrate molecule. Through a series of steps, citrate is oxidized, releasing two carbon dioxide molecules for each acetyl group fed into the cycle. In the process, three NAD + molecules are reduced to NADH, one FAD molecule is reduced to FADH 2 , and one ATP or GTP (depending on the cell type) is produced (by substrate-level phosphorylation). Because the final product of the citric acid cycle is also the first reactant, the cycle runs continuously in the presence of sufficient reactants. (credit: modification of work by Yikrazuul /Wikimedia Commons) Steps in the Citric Acid Cycle 

Step 1. Prior to the start of the first step, a transitional phase occurs during which pyruvic acid is converted to acetyl CoA. Then, the first step of the cycle begins: This is a condensation step, combining the two-carbon acetyl group with a four-carbon oxaloacetate molecule to form a six-carbon molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses away to eventually combine with another acetyl group. This step is irreversible because it is highly exergonic. The rate of this reaction is controlled by negative feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases. 

Step 2. In step two, citrate loses one water molecule and gains another as citrate is converted into its isomer, isocitrate. 

Step 3. In step three, isocitrate is oxidized, producing a five-carbon molecule, -ketoglutarate, together with a molecule of CO 2 and two electrons, which reduce NAD + to NADH. This step is also regulated by negative feedback from ATP and NADH, and a positive effect of ADP. 

Steps 3 and 4. Steps three and four are both oxidation and decarboxylation steps, which release electrons that reduce NAD + to NADH and release carboxyl groups that form CO 2 molecules. -Ketoglutarate is the product of step three, and a succinyl group is the product of step four. CoA binds the succinyl group to form succinyl CoA. The enzyme that catalyzes step four is regulated by feedback inhibition of ATP, succinyl CoA, and NADH. 

Step 5. In step five, a phosphate group is substituted for coenzyme A, and a high-energy bond is formed. This energy is used in substrate-level phosphorylation (during the conversion of the succinyl group to succinate) to form either guanine triphosphate (GTP) or ATP. There are two forms of the enzyme, called isoenzymes, for this step, depending upon the type of animal tissue in which they are found. One form is found in tissues that use large amounts of ATP, such as heart and skeletal muscle. This form produces ATP. The second form of the enzyme is found in tissues that have a high number of anabolic pathways, such as liver tissues. This form produces GTP. GTP is energetically equivalent to ATP; however, its use is more restricted. In particular, protein synthesis primarily uses GTP. 

Step 6. Step six is a dehydration process that converts succinate into fumarate. Two hydrogen atoms are transferred to FAD, producing FADH 2 . The energy contained in the electrons of these atoms is insufficient to reduce NAD + but adequate to reduce FAD. Unlike NADH, this carrier remains attached to the enzyme and transfers the electrons to the electron transport chain directly. This process is made possible by the localization of the enzyme catalyzing this step inside the inner membrane of the mitochondrion. 

Step 7. Water is added to fumarate during step seven, and malate is produced. The last step in the citric acid cycle regenerates oxaloacetate by oxidizing malate. Another molecule of NADH is produced in the process. 

Click through each step of the citric acid cycle here . 

[link] Products of the Citric Acid Cycle 

Two carbon atoms come into the citric acid cycle from each acetyl group, representing four out of the six carbons of one glucose molecule. Two carbon dioxide molecules are released on each turn of the cycle; however, these do not necessarily contain the most recently added carbon atoms. The two acetyl carbon atoms will eventually be released on later turns of the cycle; thus, all six carbon atoms from the original glucose molecule are eventually incorporated into carbon dioxide. Each turn of the cycle forms three NADH molecules and one FADH 2 molecule. These carriers will connect with the last portion of aerobic respiration to produce ATP molecules. One GTP or ATP is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential amino acids; therefore, the cycle is amphibolic (both catabolic and anabolic). Think About It 

Explain how citrate from the citric acid cycle might affect glycolysis. What other factors might affect the efficiency of the citric acid cycle and its products? 

This question is an application of Learning Objective 2.4 and Science Practice 6.2 because students are asked to explain the links between glycolysis and the citric acid cycle and factors that might affect the efficiency of these processes. Possible answer : High levels of citric acid inhibit glycolysis rate. Step one of the citric acid cycle is controlled by negative feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases. Section Summary 

In the presence of oxygen, pyruvate is transformed into an acetyl group attached to a carrier molecule of coenzyme A. The resulting acetyl CoA can enter several pathways, but most often, the acetyl group is delivered to the citric acid cycle for further catabolism. During the conversion of pyruvate into the acetyl group, a molecule of carbon dioxide and two high-energy electrons are removed. The carbon dioxide accounts for two (conversion of two pyruvate molecules) of the six carbons of the original glucose molecule. The electrons are picked up by NAD + , and the NADH carries the electrons to a later pathway for ATP production. At this point, the glucose molecule that originally entered cellular respiration has been completely oxidized. Chemical potential energy stored within the glucose molecule has been transferred to electron carriers or has been used to synthesize a few ATPs. 

The citric acid cycle is a series of redox and decarboxylation reactions that remove high-energy electrons and carbon dioxide. The electrons temporarily stored in molecules of NADH and FADH 2 are used to generate ATP in a subsequent pathway. One molecule of either GTP or ATP is produced by substrate-level phosphorylation on each turn of the cycle. There is no comparison of the cyclic pathway with a linear one. Review Questions 

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[link] Glossary acetyl CoA combination of an acetyl group derived from pyruvic acid and coenzyme A, which is made from pantothenic acid (a B-group vitamin) citric acid cycle (also, Krebs cycle) series of enzyme-catalyzed chemical reactions of central importance in all living cells Krebs cycle (also, citric acid cycle) alternate name for the citric acid cycle, named after Hans Krebs who first identified the steps in the pathway in the 1930s in pigeon flight muscles; see citric acid cycle TCA cycle (also, citric acid cycle) alternate name for the citric acid cycle, named after the group name for citric acid, tricarboxylic acid (TCA); see citric acid cycleOxidative Phosphorylation Oxidative Phosphorylation 

In this section, you will explore the following questions: How do electrons move through the electron transport chain and what happens to their energy levels? How is a proton (H + ) gradient established and maintained by the electron transport chain and how many ATP molecules are produced by chemiosmosis? Connection for AP Courses 

The electron transport chain (ETC) is the stage of aerobic respiration that uses free oxygen as the final electron acceptor of the electrons removed during glucose metabolism in glycolysis and the citric acid cycle. The ETC is located in membrane of the mitochondrial cristae, an area with many folds that increase the surface area available for chemical reactions. Electrons carried by NADH and FADH 2 are delivered to electron acceptor proteins embedded in the membrane as they move toward the final electron acceptor, O 2 , forming water. The electrons pass through a series of redox reactions, using free energy at three points to transport hydrogen ions across the membrane. This process contributes to the formation of the H + gradient used in chemiosmosis. As the protons are driven down their concentration gradient through ATP synthase, ATP is generated from ADP and inorganic phosphate. Under aerobic conditions, the stages of cellular respiration can generate 36-38 ATP. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 2 of the AP Biology Curriculum Framework, as shown in the table. As shown in the table, concepts covered in this section also align to the Learning Objectives listed in the Curriculum Framework that provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of living systems require free energy and matter. Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy. Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy. 

Introduce oxidative phosphorylation using visuals such as this video . 

Have students create a visual representation that shows an overview of glycolysis and the citric acid cycle and how the cycles relate to one another. 

An example is illustrated here . 

You have just read about two pathways Introduce glucose catabolism glycolysis and the citric acid cycle that generate ATP. Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Rather, it is derived from a process that begins with moving electrons through a series of electron transporters that undergo redox reactions. This causes hydrogen ions to accumulate within the matrix space. Therefore, a concentration gradient forms in which hydrogen ions diffuse out of the matrix space by passing through ATP synthase. The current of hydrogen ions powers the catalytic action of ATP synthase, which phosphorylates ADP, producing ATP. Electron Transport Chain 

The electron transport chain ( [link] ) is the last component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plants; in animals, it enters the body through the respiratory system. Electron transport is a series of redox reactions that resemble a relay race or bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where the electrons reduce molecular oxygen, producing water. There are four complexes composed of proteins, labeled I through IV in [link] , and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes. The electron transport chain is a series of electron transporters embedded in the inner mitochondrial membrane that shuttles electrons from NADH and FADH 2 to molecular oxygen. In the process, protons are pumped from the mitochondrial matrix to the intermembrane space, and oxygen is reduced to form water. Complex I 

To start, two electrons are carried to the first complex aboard NADH. This complex, labeled I, is composed of flavin mononucleotide (FMN) and an iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin B 2, also called riboflavin, is one of several prosthetic groups or co-factors in the electron transport chain. A prosthetic group is a non-protein molecule required for the activity of a protein. Prosthetic groups are organic or inorganic, non-peptide molecules bound to a protein that facilitate its function; prosthetic groups include co-enzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase and is a very large protein, containing 45 amino acid chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space, and it is in this way that the hydrogen ion gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane. Q and Complex II 

Complex II directly receives FADH 2 , which does not pass through complex I. The compound connecting the first and second complexes to the third is ubiquinone (Q). The Q molecule is lipid soluble and freely moves through the hydrophobic core of the membrane. Once it is reduced, (QH 2 ), ubiquinone delivers its electrons to the next complex in the electron transport chain. Q receives the electrons derived from NADH from complex I and the electrons derived from FADH 2 from complex II, including succinate dehydrogenase. This enzyme and FADH 2 form a small complex that delivers electrons directly to the electron transport chain, bypassing the first complex. Since these electrons bypass and thus do not energize the proton pump in the first complex, fewer ATP molecules are made from the FADH 2 electrons. The number of ATP molecules ultimately obtained is directly proportional to the number of protons pumped across the inner mitochondrial membrane. Complex III 

The third complex is composed of cytochrome b, another Fe-S protein, Rieske center (2Fe-2S center), and cytochrome c proteins; this complex is also called cytochrome oxidoreductase. Cytochrome proteins have a prosthetic group of heme. The heme molecule is similar to the heme in hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at its core is reduced and oxidized as it passes the electrons, fluctuating between different oxidation states: Fe ++ (reduced) and Fe +++ (oxidized). The heme molecules in the cytochromes have slightly different characteristics due to the effects of the different proteins binding them, giving slightly different characteristics to each complex. Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes (cytochrome c is the acceptor of electrons from Q; however, whereas Q carries pairs of electrons, cytochrome c can accept only one at a time). Complex IV 

The fourth complex is composed of cytochrome proteins c, a, and a 3 . This complex contains two heme groups (one in each of the two cytochromes, a, and a 3 ) and three copper ions (a pair of Cu A and one Cu B in cytochrome a 3 ). The cytochromes hold an oxygen molecule very tightly between the iron and copper ions until the oxygen is completely reduced. The reduced oxygen then picks up two hydrogen ions from the surrounding medium to make water (H 2 O). The removal of the hydrogen ions from the system contributes to the ion gradient used in the process of chemiosmosis. Chemiosmosis 

In chemiosmosis, the free energy from the series of redox reactions just described is used to pump hydrogen ions (protons) across the membrane. The uneven distribution of H + ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient), owing to the hydrogen ions positive charge and their aggregation on one side of the membrane. 

If the membrane were open to diffusion by the hydrogen ions, the ions would tend to diffuse back across into the matrix, driven by their electrochemical gradient. Recall that many ions cannot diffuse through the nonpolar regions of phospholipid membranes without the aid of ion channels. Similarly, hydrogen ions in the matrix space can only pass through the inner mitochondrial membrane through an integral membrane protein called ATP synthase ( [link] ). This complex protein acts as a tiny generator, turned by the force of the hydrogen ions diffusing through it, down their electrochemical gradient. The turning of parts of this molecular machine facilitates the addition of a phosphate to ADP, forming ATP, using the potential energy of the hydrogen ion gradient. 

ATP synthase is a complex, molecular machine that uses a proton (H + ) gradient to form ATP from ADP and inorganic phosphate (Pi). (Credit: modification of work by Klaus Hoffmeier) 

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Chemiosmosis ( [link] ) is used to generate 90 percent of the ATP made during aerobic glucose catabolism; it is also the method used in the light reactions of photosynthesis to harness the energy of sunlight in the process of photophosphorylation. Recall that the production of ATP using the process of chemiosmosis in mitochondria is called oxidative phosphorylation. The overall result of these reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally part of a glucose molecule. At the end of the pathway, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen attract hydrogen ions (protons) from the surrounding medium, and water is formed. 

In oxidative phosphorylation, the pH gradient formed by the electron transport chain is used by ATP synthase to form ATP. 

[link] ATP Yield 

The number of ATP molecules generated from the catabolism of glucose varies. For example, the number of hydrogen ions that the electron transport chain complexes can pump through the membrane varies between species. Another source of variance stems from the shuttle of electrons across the membranes of the mitochondria. (The NADH generated from glycolysis cannot easily enter mitochondria.) Thus, electrons are picked up on the inside of mitochondria by either NAD + or FAD + . As you have learned earlier, these FAD + molecules can transport fewer ions; consequently, fewer ATP molecules are generated when FAD + acts as a carrier. NAD + is used as the electron transporter in the liver and FAD + acts in the brain. 

Another factor that affects the yield of ATP molecules generated from glucose is the fact that intermediate compounds in these pathways are used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical compounds in cells, and the result is somewhat messier than the ideal situations described thus far. For example, sugars other than glucose are fed into the glycolytic pathway for energy extraction. Moreover, the five-carbon sugars that form nucleic acids are made from intermediates in glycolysis. Certain nonessential amino acids can be made from intermediates of both glycolysis and the citric acid cycle. Lipids, such as cholesterol and triglycerides, are also made from intermediates in these pathways, and both amino acids and triglycerides are broken down for energy through these pathways. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose. Activity 

Use construction paper and other art materials to create your own diagram of the electron transport chain (ETC). Be sure to include all parts of the electron transport chain, as well as the electrons themselves, NAD+ and NADH, and oxygen. On your diagram, label all parts of the ETC that transfers the free energy from electrons to another form. Then, use your model to make predictions about each of the following. Then, share your answers with the class. What would happen to free energy release if a cytochrome failed to undergo one of the redox reactions involved in the electron transport chain? What ultimately happens to the free energy in the electrons that travel down the ETC? Did you remember to have a pair of electrons travel down the ETC? What would happen if only one electron reached oxygen? Think About It Dinitrophenol (DNP) is an uncoupler that makes the inner mitochondrial membrane leaky to protons. It was used until 1938 as a weight loss drug. What effect would DNP have on the change in pH across the inner mitochondrial membrane and the overall process of cellular respiration? Why do you think DNP might be an effective weight-loss drug? Why is DNP no longer used? Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of the intermembrane space to increase or decrease? Explain the effect of cyanide on ATP synthesis. 

This activity is an application of Learning Objective 2.4 and Science Practices 1.4 and 3.1 and Learning Objective 2.5 and Science Practice 6.2 because students will have the opportunity to create a model of the electron transport chain, allowing students to study and discuss the components of the electron transport chain that allow organisms to capture, store, and use free energy. 

An extended lab investigation on cellular respiration is available from the College Board . This activity involves respirometry of plant seeds. It is available from the College Board s AP Biology Investigative Labs: An Inquiry-Based Approach , Investigation 6 . 

The Think About It questions are applications of Learning Objective 2.4 and Science Practices 1.4 and 3.1 and Learning Objective 2.5 and Science Practice 6.2 because students are provided with situations that raise questions about cellular respiration and are then asked to explain the effects of factors that affect the process. Students are also connecting the structure of the mitochondrion to its role in cellular respiration. Possible answers to Activity: If a cytochrome failed to perform a redox reaction, the electrons could not travel to the next cytochrome, and possibly not reach the proton pumps. Even if they did reach the pumps, the ETC could not offload the electrons into oxygen, preventing any additional electrons from travelling down the ETC and also preventing any further ATP production. The free energy in the electrons is transferred to the proton pumps, allowing them to pump protons. Some is also lost as heat and the rest is transferred to oxygen at the end of the ETC. If only one electron reached oxygen, water would not form at the end of the electron transport chain until another electron travelled through the chain. Possible answers to Think About It questions: In living cells, DNP acts as an agent that can directly shuttle protons across biological membranes. Therefore, it weakens the proton concentration gradient that drives protons to pass through ATP synthase. After DNP poisoning, the electron transport chain can no longer form a proton gradient, and ATP synthase can no longer make ATP. DNP is an effective diet drug because it uncouples ATP synthesis; in other words, after taking it, a person obtains less energy out of the food he or she eats. Interestingly, one of the worst side effects of this drug is hyperthermia, or overheating of the body. Since ATP cannot be formed, the energy from electron transport is lost as heat. After cyanide poisoning, the electron transport chain can no longer pump protons into the intermembrane space. The pH of the intermembrane space would increase, the pH gradient would decrease, and ATP synthesis would stop. Section Summary 

The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor of the electrons removed from the intermediate compounds in glucose catabolism. The electron transport chain is composed of four large, multiprotein complexes embedded in the inner mitochondrial membrane and two small diffusible electron carriers shuttling electrons between them. The electrons are passed through a series of redox reactions, with a small amount of free energy used at three points to transport hydrogen ions across a membrane. This process contributes to the gradient used in chemiosmosis. The electrons passing through the electron transport chain gradually lose energy, High-energy electrons donated to the chain by either NADH or FADH 2 complete the chain, as low-energy electrons reduce oxygen molecules and form water. The level of free energy of the electrons drops from about 60 kcal/mol in NADH or 45 kcal/mol in FADH 2 to about 0 kcal/mol in water. The end products of the electron transport chain are water and ATP. A number of intermediate compounds of the citric acid cycle can be diverted into the anabolism of other biochemical molecules, such as nonessential amino acids, sugars, and lipids. These same molecules can serve as energy sources for the glucose pathways. Review Questions 

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[link] Glossary ATP synthase (also, F1F0 ATP synthase) membrane-embedded protein complex that adds a phosphate to ADP with energy from protons diffusing through it prosthetic group (also, prosthetic cofactor) molecule bound to a protein that facilitates the function of the protein ubiquinone soluble electron transporter in the electron transport chain that connects the first or second complex to the thirdMetabolism without Oxygen Metabolism without Oxygen 

In this section, you will explore the following question: What is the fundamental difference between anaerobic cellular respiration and the different types of fermentation? Connection for AP Courses 

As was previously stated, under aerobic conditions cellular respiration can yield 36-38 ATP molecules. If oxygen is not present, ATP is only produced by substrate-level phosphorylation. Without oxygen, organisms must use another electron acceptor. Most organisms will use some form of fermentation to accomplish the regeneration of NAD + to ensure the continuation of glycolysis. In alcohol fermentation, pyruvate from glycolysis is converted to ethyl alcohol; during lactic acid fermentation, pyruvate is reduced to form lactate as an end-product. Without fermentation and anaerobic respiration, we wouldn t have yogurt or soy sauce. Nor would our muscle cells cramp from the buildup of lactate when we exercise vigorously and oxygen is scarce. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework, as shown in the table. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction, and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.2 Organisms capture and store free energy for use in biological processes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy. Essential Knowledge 2.A.2 Organisms capture and store free energy for use in biological processes. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy. 

Discuss with students the role of fermentation in processes such as the production of bread, yogurt, alcohol, and fuels. For example as discussed in this video . 

Students may not realize that fermentation functions to regenerate NAD + ; students may think that fermentation only functions to produce additional ATP. Fermentation can produce ATP as long as there is enough NAD + to accept electrons. Without NAD + regeneration from NADH, glycolysis will deplete NAD + and come to a stop. 

In aerobic respiration, the final electron acceptor is an oxygen molecule, O 2 . If aerobic respiration occurs, then ATP will be produced using the energy of high-energy electrons carried by NADH or FADH 2 to the electron transport chain. If aerobic respiration does not occur, NADH must be reoxidized to NAD + for reuse as an electron carrier for the glycolytic pathway to continue. How is this done? Some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to regenerate NAD + from NADH are collectively referred to as fermentation . In contrast, some living systems use an inorganic molecule as a final electron acceptor. Both methods are called anaerobic cellular respiration in which organisms convert energy for their use in the absence of oxygen. Anaerobic Cellular Respiration 

Certain prokaryotes, including some species of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, most of which are anaerobic ( [link] ), reduce sulfate to hydrogen sulfide to regenerate NAD + from NADH. The green color seen in these coastal waters is from an eruption of hydrogen sulfide-producing bacteria. These anaerobic, sulfate-reducing bacteria release hydrogen sulfide gas as they decompose algae in the water. (credit: modification of work by NASA/Jeff Schmaltz, MODIS Land Rapid Response Team at NASA GSFC, Visible Earth Catalog of NASA images) 

Visit this site to see anaerobic cellular respiration in action. 

[link] Lactic Acid Fermentation 

The fermentation method used by animals and certain bacteria, like those in yogurt, is lactic acid fermentation ( [link] ). This type of fermentation is used routinely in mammalian red blood cells and in skeletal muscle that has an insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid accumulation must be removed by the blood circulation and the lactate brought to the liver for further metabolism. The chemical reactions of lactic acid fermentation are the following: Pyruvic acid + NADH lactic acid + NAD + Pyruvic acid + NADH lactic acid + NAD + 

The enzyme used in this reaction is lactate dehydrogenase (LDH). The reaction can proceed in either direction, but the reaction from left to right is inhibited by acidic conditions. Such lactic acid accumulation was once believed to cause muscle stiffness, fatigue, and soreness, although more recent research disputes this hypothesis. Once the lactic acid has been removed from the muscle and circulated to the liver, it can be reconverted into pyruvic acid and further catabolized for energy. 

Lactic acid fermentation is common in muscle cells that have run out of oxygen. 

Tremetol, a metabolic poison found in the white snake root plant, prevents the metabolism of lactate. When cows eat this plant, it is concentrated in the milk they produce. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case? 

[link] Alcohol Fermentation 

Another familiar fermentation process is alcohol fermentation ( [link] ) that produces ethanol, an alcohol. The first chemical reaction of alcohol fermentation is the following (CO 2 does not participate in the second reaction): Pyruvic acid CO 2 + acetaldehyde + NADH ethanol + NAD + Pyruvic acid CO 2 + acetaldehyde + NADH ethanol + NAD + 

The first reaction is catalyzed by pyruvate decarboxylase, a cytoplasmic enzyme, with a coenzyme of thiamine pyrophosphate (TPP, derived from vitamin B 1 and also called thiamine). A carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the size of the molecule by one carbon, making acetaldehyde. The second reaction is catalyzed by alcohol dehydrogenase to oxidize NADH to NAD + and reduce acetaldehyde to ethanol. The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages. Ethanol tolerance of yeast is variable, ranging from about 5 percent to 21 percent, depending on the yeast strain and environmental conditions. Fermentation of grape juice into wine produces CO 2 as a byproduct. Fermentation tanks have valves so that the pressure inside the tanks created by the carbon dioxide produced can be released. Other Types of Fermentation 

Other fermentation methods occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like Clostridia , are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms and kills them on exposure. It should be noted that all forms of fermentation, except lactic acid fermentation, produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which plays a role in the laboratory identification of the bacteria. Various methods of fermentation are used by assorted organisms to ensure an adequate supply of NAD + for the sixth step in glycolysis. Without these pathways, that step would not occur and no ATP would be harvested from the breakdown of glucose. Lab Investigation 

Lab Investigation: Respiration of Sugars by Yeast. You are given the opportunity to design and conduct experiments to investigate whether yeasts are able to metabolize a variety of sugars, using gas pressure sensors or other means to measure CO 2 production. Think About It 

Tremetol, a metabolic poison found in the white snake plant root, prevents the metabolism of lactate. When female cows eat this plant, tremetol becomes concentrated in their milk. Humans who consume the milk become ill. Explain why the symptoms of this disease, which include vomiting, abdominal pain, and tremors, becomes worse after exercise. 

This investigation is an application of Learning Objective 2.5 and Science Practice 6.2 because in the course of their investigation, students will collect data and based on the results explain if different sugars can be metabolized in fermentation. 

Lab investigation: This lab can be done in one of several ways. A common one involves attaching a balloon to a chamber in which fermentation is occurring, allowing the carbon dioxide to gradually fill up the balloon. Please see this detailed lab description . 

The Think About It question is an application of Learning Objective 2.5 and Science Practice 6.2 because students are asked to explain how an environmental variable can interfere with the fermentation pathway. Possible answer: The illness is caused by lactate accumulation. Lactate levels rise after exercise, making the symptoms worse. Milk sickness is rare today, but was common in the Midwestern United States in the early 1800s. Section Summary 

If NADH cannot be oxidized through aerobic respiration, another electron acceptor is used. Most organisms will use some form of fermentation to accomplish the regeneration of NAD + , ensuring the continuation of glycolysis. The regeneration of NAD + in fermentation is not accompanied by ATP production; therefore, the potential of NADH to produce ATP using an electron transport chain is not utilized. Review Questions 

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[link] Glossary anaerobic cellular respiration process in which organisms convert energy for their use in the absence of oxygen fermentation process of regenerating NAD + with either an inorganic or organic compound serving as the final electron acceptor, occurs in the absence; occurs in the absence of oxygenConnections of Carbohydrate, Protein, and Lipid Metabolic Pathways Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways 

In this section, you will explore the following question: How do carbohydrate metabolic pathways, glycolysis, and the citric acid cycle interrelate with protein and lipid metabolism pathways? Connection for AP Courses 

The breakdown and synthesis of carbohydrates, proteins, lipids, and nucleic acids connect with the metabolic pathways of glycolysis and the citric acid cycle but enter the pathways at different points. Thus, these macromolecules can be used as sources of free energy. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework, as shown in the table. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.1 All living systems require constant input of free energy. Science Practice 6.1 The student can justify claims with evidence. Learning Objective 2.2 The student is able to justify a scientific claim that free energy is required for living systems to maintain organization, to grow or to reproduce, but that multiple strategies exist in different living systems. 

Discuss with students how metabolic reactions include both the breakdown of molecules and the synthesis of larger molecules. For example as discussed in Anatomy and Physiology here . 

Metabolic processes are constantly taking place in the body. Metabolism is the sum of all of the chemical reactions that are involved in catabolism and anabolism. The reactions governing the breakdown of food to obtain energy are called catabolic reactions. Conversely, anabolic reactions use the energy produced by catabolic reactions to synthesize larger molecules from smaller ones, such as when the body forms proteins by stringing together amino acids. Both sets of reactions are critical to maintaining life. 

Because catabolic reactions produce energy and anabolic reactions use energy, ideally, energy usage would balance the energy produced. If the net energy change is positive (catabolic reactions release more energy than the anabolic reactions use), then the body stores the excess energy by building fat molecules for long-term storage. On the other hand, if the net energy change is negative (catabolic reactions release less energy than anabolic reactions use), the body uses stored energy to compensate for the deficiency of energy released by catabolism. 

Have students create a visual representation of the interaction of various metabolic pathways. For example: 

You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than glucose for food. How does a turkey sandwich end up as ATP in your cells? This happens because all of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways (see [link] ). Metabolic pathways should be thought of as porous that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems. Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways. Connections of Other Sugars to Glucose Metabolism 

Glycogen, a polymer of glucose, is an energy storage molecule in animals. When there is adequate ATP present, excess glucose is shunted into glycogen for storage. Glycogen is made and stored in both liver and muscle. The glycogen will be hydrolyzed into glucose monomers (G-1-P) if blood sugar levels drop. The presence of glycogen as a source of glucose allows ATP to be produced for a longer period of time during exercise. Glycogen is broken down into G-1-P and converted into G-6-P in both muscle and liver cells, and this product enters the glycolytic pathway. 

Sucrose is a disaccharide with a molecule of glucose and a molecule of fructose bonded together with a glycosidic linkage. Fructose is one of the three dietary monosaccharides, along with glucose and galactose (which is part of the milk sugar, the disaccharide lactose), which are absorbed directly into the bloodstream during digestion. The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose. Connections of Proteins to Glucose Metabolism 

Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins. If there are excess amino acids, however, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism ( [link] ). Each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals produced from the nitrogen originating in amino acids, and it leaves the body in urine. The carbon skeletons of certain amino acids (indicated in boxes) derived from proteins can feed into the citric acid cycle. (credit: modification of work by Mikael H ggstr m) Connections of Lipid and Glucose Metabolisms 

The lipids that are connected to the glucose pathways are cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl groups and proceeds in only one direction. The process cannot be reversed. 

Triglycerides are a form of long-term energy storage in animals. Triglycerides are made of glycerol and three fatty acids. Animals can make most of the fatty acids they need. Triglycerides can be both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated to glycerol-3-phosphate, which continues through glycolysis. Fatty acids are catabolized in a process called beta-oxidation that takes place in the matrix of the mitochondria and converts their fatty acid chains into two carbon units of acetyl groups. The acetyl groups are picked up by CoA to form acetyl CoA that proceeds into the citric acid cycle. Glycogen from the liver and muscles, hydrolyzed into glucose-1-phosphate, together with fats and proteins, can feed into the catabolic pathways for carbohydrates. 

Pathways of Photosynthesis and Cellular Metabolism The processes of photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells arose in an aqueous environment a soup of nutrients probably on the surface of some porous clays. If these cells reproduced successfully and their numbers climbed steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived as they shifted the nutrients into the components of their own bodies. This hypothetical situation would have resulted in natural selection favoring those organisms that could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials upon which they could survive. Selection would favor those organisms that could extract maximal value from the nutrients to which they had access. 

An early form of photosynthesis developed that harnessed the sun s energy using water as a source of hydrogen atoms, but this pathway did not produce free oxygen (anoxygenic photosynthesis). (Early photosynthesis did not produce free oxygen because it did not use water as the source of hydrogen ions; instead, it used materials like hydrogen sulfide and consequently produced sulfur). It is thought that glycolysis developed at this time and could take advantage of the simple sugars being produced, but these reactions were unable to fully extract the energy stored in the carbohydrates. The development of glycolysis probably predated the evolution of photosynthesis, as it was well suited to extract energy from materials spontaneously accumulating in the primeval soup. A later form of photosynthesis used water as a source of electrons and hydrogen, and generated free oxygen. Over time, the atmosphere became oxygenated, but not before the oxygen released oxidized metals in the ocean and created a rust layer in the sediment, permitting the dating of the rise of the first oxygenic photosynthesizers. Living things adapted to exploit this new atmosphere that allowed aerobic respiration as we know it to evolve. When the full process of oxygenic photosynthesis developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract considerably more energy from the sugar molecules using the citric acid cycle and oxidative phosphorylation. 

[link] Think About It 

Explain how free energy can be obtained from the metabolism of carbohydrates, proteins, lipids, and even nucleic acids. Which of these molecules provides the largest amount of free energy? Justify your answer. 

This question is an application of Learning Objective 2.2 and Science Practice 6.1 because students are asked to justify the claim that organisms have multiple strategies to obtain free energy necessary to power cellular processes. Possible answer: Fatty acids and some amino acids contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle; carbohydrates, some amino acids and glycerol can enter glycolysis. Fats provide the most energy per molecule. Fats are broken down into fatty acids and glycerol. Glycerol is converted into glyceraldehyde phosphate, an intermediate of glycolysis. Also, the process of beta oxidation breaks fatty acids into two-carbon fragments, which enter the citric acid cycle as acetyl CoA. Section Summary 

The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The simple sugars are galactose, fructose, glycogen, and pentose. These are catabolized during glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl groups, and the components of triglycerides come from glycerol-3-phosphate from glycolysis and acetyl groups produced in the mitochondria from pyruvate. Review Questions 

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[link]Regulation of Cellular Respiration Regulation of Cellular Respiration 

In this section, you will explore the following question: What mechanisms control cellular respiration? Connection for AP Courses 

Cellular respiration is controlled by a variety of means. For example, the entry of glucose into a cell is controlled by the transport proteins that aid glucose passage through the cell membrane. However, most of the control of the respiration processes is accomplished through negative feedback inhibition of specific enzymes that respond to the intracellular concentrations of ATP, ADP, NAD + , and FAD, etc. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework, as shown in the table. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.C Organisms use feedback mechanisms to regulate growth and reproduction, and to maintain dynamic homeostasis. Essential Knowledge 2.C.1 Organisms use feedback mechanisms to maintain their internal environments and respond to external environmental changes. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 2.16 The student is able to connect how organisms use negative feedback to maintain their internal environments. Essential Knowledge 2.C.1 Organisms use feedback mechanisms to maintain their internal environments and respond to external environmental changes. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 2.17 The student is able to evaluate data that show the effect(s) of changes in concentration of key molecules on negative feedback mechanisms. 

Cellular respiration must be regulated in order to provide balanced amounts of energy in the form of ATP. The cell also must generate a number of intermediate compounds that are used in the anabolism and catabolism of macromolecules. Without controls, metabolic reactions would quickly come to a stand-still as the forward and backward reactions reached a state of equilibrium. Resources would be used inappropriately. A cell does not need the maximum amount of ATP that it can make all the time: At times, the cell needs to shunt some of the intermediates to pathways for amino acid, protein, glycogen, lipid, and nucleic acid production. In short, the cell needs to control its metabolism. Regulatory Mechanisms 

A variety of mechanisms is used to control cellular respiration. Some type of control exists at each stage of glucose metabolism. Access of glucose to the cell can be regulated using the GLUT proteins that transport glucose ( [link] ). Different forms of the GLUT protein control passage of glucose into the cells of specific tissues. GLUT4 is a glucose transporter that is stored in vesicles. A cascade of events that occurs upon insulin binding to a receptor in the plasma membrane causes GLUT4-containing vesicles to fuse with the plasma membrane so that glucose may be transported into the cell. 

Some reactions are controlled by having two different enzymes one each for the two directions of a reversible reaction. Reactions that are catalyzed by only one enzyme can go to equilibrium, stalling the reaction. In contrast, if two different enzymes (each specific for a given direction) are necessary for a reversible reaction, the opportunity to control the rate of the reaction increases, and equilibrium is not reached. 

A number of enzymes involved in each of the pathways in particular, the enzyme catalyzing the first committed reaction of the pathway are controlled by attachment of a molecule to an allosteric site on the protein. The molecules most commonly used in this capacity are the nucleotides ATP, ADP, AMP, NAD + , and NADH. These regulators, allosteric effectors, may increase or decrease enzyme activity, depending on the prevailing conditions. The allosteric effector alters the steric structure of the enzyme, usually affecting the configuration of the active site. This alteration of the protein s (the enzyme s) structure either increases or decreases its affinity for its substrate, with the effect of increasing or decreasing the rate of the reaction. The attachment signals to the enzyme. This binding can increase or decrease the enzyme s activity, providing feedback. This feedback type of control is effective as long as the chemical affecting it is attached to the enzyme. Once the overall concentration of the chemical decreases, it will diffuse away from the protein, and the control is relaxed. Control of Catabolic Pathways 

Enzymes, proteins, electron carriers, and pumps that play roles in glycolysis, the citric acid cycle, and the electron transport chain tend to catalyze non-reversible reactions. In other words, if the initial reaction takes place, the pathway is committed to proceeding with the remaining reactions. Whether a particular enzyme activity is released depends upon the energy needs of the cell (as reflected by the levels of ATP, ADP, and AMP). Glycolysis 

The control of glycolysis begins with the first enzyme in the pathway, hexokinase ( [link] ). This enzyme catalyzes the phosphorylation of glucose, which helps to prepare the compound for cleavage in a later step. The presence of the negatively charged phosphate in the molecule also prevents the sugar from leaving the cell. When hexokinase is inhibited, glucose diffuses out of the cell and does not become a substrate for the respiration pathways in that tissue. The product of the hexokinase reaction is glucose-6-phosphate, which accumulates when a later enzyme, phosphofructokinase, is inhibited. The glycolysis pathway is primarily regulated at the three key enzymatic steps (1, 2, and 7) as indicated. Note that the first two steps that are regulated occur early in the pathway and involve hydrolysis of ATP. 

Phosphofructokinase is the main enzyme controlled in glycolysis. High levels of ATP, citrate, or a lower, more acidic pH decrease the enzyme s activity. An increase in citrate concentration can occur because of a blockage in the citric acid cycle. Fermentation, with its production of organic acids like lactic acid, frequently accounts for the increased acidity in a cell; however, the products of fermentation do not typically accumulate in cells. 

The last step in glycolysis is catalyzed by pyruvate kinase. The pyruvate produced can proceed to be catabolized or converted into the amino acid alanine. If no more energy is needed and alanine is in adequate supply, the enzyme is inhibited. The enzyme s activity is increased when fructose-1,6-bisphosphate levels increase. (Recall that fructose-1,6-bisphosphate is an intermediate in the first half of glycolysis.) The regulation of pyruvate kinase involves phosphorylation by a kinase (pyruvate kinase kinase), resulting in a less-active enzyme. Dephosphorylation by a phosphatase reactivates it. Pyruvate kinase is also regulated by ATP (a negative allosteric effect). 

If more energy is needed, more pyruvate will be converted into acetyl CoA through the action of pyruvate dehydrogenase. If either acetyl groups or NADH accumulate, there is less need for the reaction and the rate decreases. Pyruvate dehydrogenase is also regulated by phosphorylation: A kinase phosphorylates it to form an inactive enzyme, and a phosphatase reactivates it. The kinase and the phosphatase are also regulated. Citric Acid Cycle 

The citric acid cycle is controlled through the enzymes that catalyze the reactions that make the first two molecules of NADH ( [link] ). These enzymes are isocitrate dehydrogenase and ketoglutarate dehydrogenase. When adequate ATP and NADH levels are available, the rates of these reactions decrease. When more ATP is needed, as reflected in rising ADP levels, the rate increases. -ketoglutarate dehydrogenase will also be affected by the levels of succinyl CoA a subsequent intermediate in the cycle causing a decrease in activity. A decrease in the rate of operation of the pathway at this point is not necessarily negative, as the increased levels of the -ketoglutarate not used by the citric acid cycle can be used by the cell for amino acid (glutamate) synthesis. Electron Transport Chain 

Specific enzymes of the electron transport chain are unaffected by feedback inhibition, but the rate of electron transport through the pathway is affected by the levels of ADP and ATP. Greater ATP consumption by a cell is indicated by a buildup of ADP. As ATP usage decreases, the concentration of ADP decreases, and now, ATP begins to build up in the cell. This change is the relative concentration of ADP to ATP triggers the cell to slow down the electron transport chain. 

Visit this site to see an animation of the electron transport chain and ATP synthesis. 

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For a summary of feedback controls in cellular respiration, see [link] . Summary of Feedback Controls in Cellular Respiration Pathway Enzyme affected Elevated levels of effector Effect on pathway activity glycolysis hexokinase glucose-6-phosphate decrease phosphofructokinase low-energy charge (ATP, AMP), fructose-6-phosphate via fructose-2,6-bisphosphate increase high-energy charge (ATP, AMP), citrate, acidic pH decrease pyruvate kinase fructose-1,6-bisphosphate increase high-energy charge (ATP, AMP), alanine decrease pyruvate to acetyl CoA conversion pyruvate dehydrogenase ADP, pyruvate increase acetyl CoA, ATP, NADH decrease citric acid cycle isocitrate dehydrogenase ADP increase ATP, NADH decrease -ketoglutarate dehydrogenase Calcium ions, ADP increase ATP, NADH, succinyl CoA decrease electron transport chain ADP increase ATP decrease Think About It 

Phosphofructokinase is a key enzyme in glycolysis. High levels of ATP or citrate or low pH can decrease the enzyme s activity. Explain why this is beneficial to the cell. 

This question is an application of Learning Objective 2.16 and Science Practice 7.1 and Learning Objective 2.17 and Science Practice 5.3 because students are connecting changes in concentrations of key molecules (ATP and citrate) and a change in an environmental variable (pH) to the regulation of glycolysis via negative feedback. Possible answer: Elevated levels of ATP, citrate, or a more acidic pH indicate a state of high cellular energy. Thus, phosphofructokinase activity is lowered to reduce the concentration of intracellular glucose in order to slow down cellular respiration and allow the cell to use the energy it has already captured. Section Summary 

Cellular respiration is controlled by a variety of means. The entry of glucose into a cell is controlled by the transport proteins that aid glucose passage through the cell membrane. Most of the control of the respiration processes is accomplished through the control of specific enzymes in the pathways. This is a type of negative feedback, turning the enzymes off. The enzymes respond most often to the levels of the available nucleosides ATP, ADP, AMP, NAD + , and FAD. Other intermediates of the pathway also affect certain enzymes in the systems. Review Questions 

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[link] Glossary GLUT protein integral membrane protein that transports glucoseIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" This world map shows Earth s distribution of photosynthesis as seen via chlorophyll a concentrations. On land, this is evident via terrestrial plants, and in oceanic zones, via phytoplankton. (credit: modification of work by SeaWiFS Project, NASA/Goddard Space Flight Center and ORBIMAGE) 

All biological processes require energy. To get this energy, many organisms access stored energy by eating, that is, by ingesting other organisms. But where does the stored energy in food originate? Almost all of this energy can be traced back to photosynthesis. 

Photosynthetic organisms are the basis for almost all of the food webs on the planet. For example, the Indian River Lagoon, a 156 mile mixture of fresh and salt water along the eastern coast of Florida, depends on its sea grass for the survival of its marine life. Unfortunately, when certain algal phytoplankton species grow in overabundance, it destroys the sea grass. Scientists conducted a 16 year study of algal blooms and found that extreme climate conditions, such as cold weather and low rainfall, change which particular species of phytoplankton is more likely to bloom, resulting in a die-off of sea grass, decrease in other marine life, and changes in salinity. The research study can be found here . 

Having studied the laws of thermodynamics in a previous chapter, it should be no surprise that the sun is a source of all the energy used by living organisms, that this energy can be converted, stored, and used, and that there is an interdependence between organisms with regard to that energy.Overview of Photosynthesis Overview of Photosynthesis 

In this section, you will explore the following questions: What is the relevance of photosynthesis to living organisms? What are the main cellular structures involved in photosynthesis? What are the substrates and products of photosynthesis? Connection for AP Courses 

As we learned in Chapter 7, all living organisms, from simple bacteria to complex plants and animals, require free energy to carry out cellular processes, such as growth and reproduction. Organisms use various strategies to capture, store, transform, and transfer free energy, including photosynthesis. Photosynthesis allows organisms to access enormous amounts of free energy from the sun and transform it to the chemical energy of sugars. Although all organisms carry out some form of cellular respiration, only certain organisms, called photoautotrophs, can perform photosynthesis. Examples of photoautotrophs include plants, algae, some unicellular eukaryotes, and cyanobacteria. They require the presence of chlorophyll, a specialized pigment that absorbs certain wavelengths of the visible light spectrum to harness free energy from the sun. Photosynthesis is a process where components of water and carbon dioxide are used to assemble carbohydrate molecules and where oxygen waste products are released into the atmosphere. In eukaryotes, the reactions of photosynthesis occur in chloroplasts; in prokaryotes, such as cyanobacteria, the reactions are less localized and occur within membranes and in the cytoplasm. (The structural features of the chloroplast that participate in photosynthesis will be explored in more detail later in The Light-Dependent Reactions of Photosynthesis and Using Light Energy to Make Organic Molecules.) Although photosynthesis and cellular respiration evolved as independent processes with photosynthesis creating an oxidizing atmosphere early in Earth s history today they are interdependent. As we studied in Cellular Respiration, aerobic cellular respiration taps into the oxidizing ability of oxygen to synthesize the organic compounds that are used to power cellular processes. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 1 and Big Idea 2 of the AP Biology Curriculum Framework, as shown in the table. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Structural and functional evidence supports the relatedness of all domains, with organisms shared many conserved core processes. Science Practice 6.1 The student can justify claims with evidence. Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains s or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.2 Organisms use various strategies to capture and store free energy for use in biological processes. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy. Essential Knowledge 2.A.2 Organisms use various strategies to capture and store free energy for use in biological processes. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy. 

Use this first part of the chapter to present an overview that will be filled out and completed in the later two portions. This will introduce the students to the biochemistry that they need to know and give them a chance to build up their understanding of the material. Importance of Photosynthesis 

Use this section to stress the importance of the interdependence between different species and the role played by photosynthesis in bringing energy to the living organisms. A number of terms, such as photoautotroph, heterotrophy, and chemoautotroph will be introduced here. 

Photosynthesis is essential to all life on earth; both plants and animals depend on it. It is the only biological process that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. In brief, the energy of sunlight is captured and used to energize electrons, which are then stored in the covalent bonds of sugar molecules. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis almost 200 million years ago. 

Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis ( [link] ). Because they use light to manufacture their own food, they are called photoautotrophs (literally, self-feeders using light ). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs ( other feeders ), because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight s energy, but by extracting energy from inorganic chemical compounds; hence, they are referred to as chemoautotrophs . Photoautotrophs including (a) plants, (b) algae, and (c) cyanobacteria synthesize their organic compounds via photosynthesis using sunlight as an energy source. Cyanobacteria and planktonic algae can grow over enormous areas in water, at times completely covering the surface. In a (d) deep sea vent, chemoautotrophs, such as these (e) thermophilic bacteria, capture energy from inorganic compounds to produce organic compounds. The ecosystem surrounding the vents has a diverse array of animals, such as tubeworms, crustaceans, and octopi that derive energy from the bacteria. (credit a: modification of work by Steve Hillebrand, U.S. Fish and Wildlife Service; credit b: modification of work by "eutrophication hypoxia"/Flickr; credit c: modification of work by NASA; credit d: University of Washington, NOAA; credit e: modification of work by Mark Amend, West Coast and Polar Regions Undersea Research Center, UAF, NOAA) 

The importance of photosynthesis is not just that it can capture sunlight s energy. A lizard sunning itself on a cold day can use the sun s energy to warm up. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the photo- part) as high-energy electrons in the carbon-carbon bonds of carbohydrate molecules (the -synthesis part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth s ecosystems. When a top predator, such as a wolf, preys on a deer ( [link] ), the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to vegetation, to deer, and finally to wolf. The energy stored in carbohydrate molecules from photosynthesis passes through the food chain. The predator that eats these deer receives a portion of the energy that originated in the photosynthetic vegetation that the deer consumed. (credit: modification of work by Steve VanRiper, U.S. Fish and Wildlife Service) Think About It Why do scientists think that photosynthesis evolved before aerobic cellular respiration? Why do carnivores, such as lions, depend on photosynthesis to survive? What evidence supports the claim that photosynthesis and cellular respiration are interdependent processes? The first Think About It question is an application of Learning Objective 1.15 and Science Practice 7.2 because students are describing the evolution of two energy-procuring processes that today are present in different organisms. The second Think About It question is an application of Learning Objective 2.5 and Science Practice 6.2 because you are explaining how the interdependent processes of photosynthesis and cellular respiration allow organisms to capture, store, and use free energy. Possible answers: Aerobic cellular respiration requires free oxygen, which was not available in the Earth s atmosphere until photosynthetic organisms produced enough oxygen as waste to support developing aerobic respiration. Carnivores at the top of the food chain eat herbivores that eat photoautotrophs. So no matter where you are in the food chain, every species depends on photosynthesis to convert light energy to chemical energy. In ecosystems that lack photosynthetic organisms (such as by forests burned by forest fire), organisms on all levels of the food chain die off. 

The structures, substrates and products of photosynthesis are introduced in this section. Remind them that [link] can also be read from right to left, if cellular respiration is the subject. This should help the students to connect the two pathways of photosynthesis and cellular respiration. 

Obtain diagrams of leaf structures to illustrate the content of this section. Try to bring in some leaves for students to look at. They have all seen lots of leaves, but probably never examined them for structural detail. A simple magnifying glass should allow them to see the inner structures discussed in this section. Main Structures and Summary of Photosynthesis 

Photosynthesis is a multi-step process that requires sunlight, carbon dioxide (which is low in energy), and water as substrates ( [link] ). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), simple carbohydrate molecules (which are high in energy) that can subsequently be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive. Photosynthesis uses solar energy, carbon dioxide, and water to produce energy-storing carbohydrates. Oxygen is generated as a waste product of photosynthesis. 

The following is the chemical equation for photosynthesis ( [link] ): The basic equation for photosynthesis is deceptively simple. In reality, the process takes place in many steps involving intermediate reactants and products. Glucose, the primary energy source in cells, is made from two three-carbon GA3Ps. 

Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the structures involved. 

In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll . The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes. 

In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast . For plants, chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane). Within the chloroplast are stacked, disc-shaped structures called thylakoids . Embedded in the thylakoid membrane is chlorophyll, a pigment (molecule that absorbs light) responsible for the initial interaction between light and plant material, and numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen . As shown in [link] , a stack of thylakoids is called a granum , and the liquid-filled space surrounding the granum is called stroma or bed (not to be confused with stoma or mouth, an opening on the leaf epidermis). 

Photosynthesis takes place in chloroplasts, which have an outer membrane and an inner membrane. Stacks of thylakoids called grana form a third membrane layer. 

[link] The Two Parts of Photosynthesis 

There are different terms that have been used for these reactions. Go over each pair of terms and discuss how they apply to the pathways. 

Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light independent-reactions. In the light-dependent reactions , energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions , the chemical energy harvested during the light-dependent reactions drive the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize certain molecules to temporarily store the energy: These are referred to as energy carriers. The energy carriers that move energy from light-dependent reactions to light-independent reactions can be thought of as full because they are rich in energy. After the energy is released, the empty energy carriers return to the light-dependent reaction to obtain more energy. [link] illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place. Photosynthesis takes place in two stages: light dependent reactions and the Calvin cycle. Light-dependent reactions, which take place in the thylakoid membrane, use light energy to make ATP and NADPH. The Calvin cycle, which takes place in the stroma, uses energy derived from these compounds to make GA3P from CO 2 . 

Click the link to learn more about photosynthesis. 

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Photosynthesis at the Grocery Store Foods that humans consume originate from photosynthesis. (credit: Associa o Brasileira de Supermercados) 

Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle ( [link] ) contains hundreds, if not thousands, of different products for customers to buy and consume. 

Although there is a large variety, each item links back to photosynthesis. Meats and dairy link, because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from starchy grains, which are the seeds of photosynthesis-dependent plants. What about desserts and drinks? All of these products contain sugar sucrose is a plant product, a disaccharide, a carbohydrate molecule, which is built directly from photosynthesis. Moreover, many items are less obviously derived from plants: For instance, paper goods are generally plant products, and many plastics (abundant as products and packaging) are derived from algae. Virtually every spice and flavoring in the spice aisle was produced by a plant as a leaf, root, bark, flower, fruit, or stem. Ultimately, photosynthesis connects to every meal and every food a person consumes. 

[link] Section Summary 

The process of photosynthesis transformed life on Earth. By harnessing energy from the sun, photosynthesis evolved to allow living things access to enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy that allowed them to build new structures and achieve the biodiversity evident today. 

Only certain organisms, called photoautotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that absorbs certain portions of the visible spectrum and can capture energy from sunlight. Photosynthesis uses carbon dioxide and water to assemble carbohydrate molecules and release oxygen as a waste product into the atmosphere. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place, and starch accumulates. In prokaryotes, such as cyanobacteria, the process is less localized and occurs within folded membranes, extensions of the plasma membrane, and in the cytoplasm. Review Questions 

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[link] Glossary chemoautotroph organism that can build organic molecules using energy derived from inorganic chemicals instead of sunlight chloroplast organelle in which photosynthesis takes place granum stack of thylakoids located inside a chloroplast heterotroph organism that consumes organic substances or other organisms for food light-dependent reaction first stage of photosynthesis where certain wavelengths of the visible light are absorbed to form two energy-carrying molecules (ATP and NADPH) light-independent reaction second stage of photosynthesis, though which carbon dioxide is used to build carbohydrate molecules using energy from ATP and NADPH mesophyll middle layer of chlorophyll-rich cells in a leaf photoautotroph organism capable of producing its own organic compounds from sunlight pigment molecule that is capable of absorbing certain wavelengths of light and reflecting others (which accounts for its color) stoma opening that regulates gas exchange and water evaporation between leaves and the environment, typically situated on the underside of leaves stroma fluid-filled space surrounding the grana inside a chloroplast where the light-independent reactions of photosynthesis take place thylakoid disc-shaped, membrane-bound structure inside a chloroplast where the light-dependent reactions of photosynthesis take place; stacks of thylakoids are called grana thylakoid lumen aqueous space bound by a thylakoid membrane where protons accumulate during light-driven electron transportThe Light-Dependent Reactions of Photosynthesis The Light-Dependent Reactions of Photosynthesis 

In this section, you will explore the following questions: How do plants absorb energy from sunlight? What are the differences between short and long wavelengths of light? What wavelengths are used in photosynthesis? How and where does photosynthesis occur within a plant? Connection for AP Courses 

Photosynthesis consists of two stages: the light-dependent reactions and the light-independent reactions or Calvin cycle. The light-dependent reactions occur when light is available. The overall equation for photosynthesis shows that is it a redox reaction; carbon dioxide is reduced and water is oxidized to produce oxygen: Energy + 6CO 2 + H 2 O C 6 H 12 O 6 + 6O 2 Energy + 6CO 2 + H 2 O C 6 H 12 O 6 + 6O 2 

The light-dependent reactions occur in the thylakoid membranes of chloroplasts, whereas the Calvin cycle occurs in the stroma of chloroplasts. Embedded in the thylakoid membranes are two photosystems (PS I and PS II), which are complexes of pigments that capture solar energy. Chlorophylls a and b absorb violet, blue, and red wavelengths from the visible light spectrum and reflect green. The carotenoid pigments absorb violet-blue-green light and reflect yellow-to-orange light. Environmental factors such as day length and temperature influence which pigments predominant at certain times of the year. Although the two photosystems run simultaneously, it is easier to explore them separately. Let s begin with photosystem II. 

A photon of light strikes the antenna pigments of PS II to initiate photosynthesis. In the noncyclic pathway, PS II captures photons at a slightly higher energy level than PS I. (Remember that shorter wavelengths of light carry more energy.) The absorbed energy travels to the reaction center of the antenna pigment that contains chlorophyll a and boosts chlorophyll a electrons to a higher energy level. The electrons are accepted by a primary electron acceptor protein and then pass to the electron transport chain also embedded in the thylakoid membrane. The energy absorbed in PS II is enough to oxidize (split) water, releasing oxygen into the atmosphere; the electrons released from the oxidation of water replace the electrons that were boosted from the reaction center chlorophyll. As the electrons from the reaction center chlorophyll pass through the series of electron carrier proteins, hydrogen ions (H + ) are pumped across the membrane via chemiosmosis into the interior of the thylakoid. (If this sounds familiar, it should. We studied chemiosmosis in our exploration of cellular respiration in Cellular Respiration.) This action builds up a high concentration of H+ ions, and as they flow through ATP synthase, molecules of ATP are formed. These molecules of ATP will be used to provide free energy for the synthesis of carbohydrate in the Calvin cycle, the second stage of photosynthesis. The electron transport chain connects PS II and PS I. Similar to the events occurring in PS II, this second photosystem absorbs a second photon of light, resulting in the formation of a molecule of NADPH from NADP + . The energy carried in NADPH also is used to power the chemical reactions of the Calvin cycle. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework, as shown in the table. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A All living systems require constant input of free energy. Essential Knowledge 2.A.2 The light-independent reactions of photosynthesis in eukaryotes involve a series of reactions that capture free energy present in light. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 3.1 The student can pose scientific questions. Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy. Essential Knowledge 2.A.2 The light-independent reactions of photosynthesis in eukaryotes involve a series of reactions that capture free energy present in light. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.2 Chloroplasts are specialized organelles that capture energy through photosynthesis. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 4.4 The student is able to make a prediction about the interactions of subcellular organelles. Essential Knowledge 4.A.2 Chloroplasts are specialized organelles that capture energy through photosynthesis. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 4.5 The student is able to construct explanations based on scientific evidence as to how interactions of subcellular structures provide essential functions. Essential Knowledge 4.A.2 Chloroplasts are specialized organelles that capture energy through photosynthesis. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 4.6 The student is able to use representations and models to analyze situations qualitatively to describe how interactions of subcellular structures, which possess specialized functions, provide essential functions. 

This section deals with the first half of photosynthesis. These reactions capture light energy and store it in chemicals for short periods of time to fuel the second half of photosynthesis. This is also where free oxygen can be released, but carbon dioxide is not captured or fixed. 

How can light be used to make food? When a person turns on a lamp, electrical energy becomes light energy. Like all other forms of kinetic energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is converted into chemical energy, which photoautotrophs use to build carbohydrate molecules ( [link] ). However, autotrophs only use a few specific components of sunlight. Photoautotrophs can capture light energy from the sun, converting it into the chemical energy used to build food molecules. (credit: Gerry Atwell) What Is Light Energy? 

Everybody knows what a rainbow is, but some students may not be able to connect it to actual light sources. Obtain some way of refracting light, such as a prism, and use it to separate the components of several light sources, such as an older, incandescent light bulb, a new fluorescent type of light bulb and actual sunlight. 

When discussing the electromagnetic spectrum, include the fact that when someone sets a radio station to its number, such as 92.1 or 1450 on the dial, they are really setting the radio to the specific wavelength of spectrum used by the station. 

The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy, which portion is therefore referred to as visible light. The manner in which solar energy travels is described as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength , the distance between consecutive points of a wave. A single wave is measured from two consecutive points, such as from crest to crest or from trough to trough ( [link] ). The wavelength of a single wave is the distance between two consecutive points of similar position (two crests or two troughs) along the wave. 

Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun and other stars. Scientists differentiate the various types of radiant energy from the sun within the electromagnetic spectrum. The electromagnetic spectrum is the range of all possible frequencies of radiation ( [link] ). The difference between wavelengths relates to the amount of energy carried by them. The sun emits energy in the form of electromagnetic radiation. This radiation exists at different wavelengths, each of which has its own characteristic energy. All electromagnetic radiation, including visible light, is characterized by its wavelength. 

Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength (or the more stretched out it appears in the diagram), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving a heavy rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy. 

The electromagnetic spectrum ( [link] ) shows several types of electromagnetic radiation originating from the sun, including X-rays and ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and damage cells and DNA, explaining why both X-rays and UV rays can be harmful to living organisms. Absorption of Light 

Stress the differences in the amount of energy at each wavelength, and the usefulness of the wavelengths for energy capture. Discuss what is in a grow light (artificial light source for plants grown indoors). 

Light energy initiates the process of photosynthesis when pigments absorb the light. Organic pigments, whether in the human retina or the chloroplast thylakoid, have a narrow range of energy levels that they can absorb. Energy levels lower than those represented by red light are insufficient to raise an orbital electron to a populatable, excited (quantum) state. Energy levels higher than those in blue light will physically tear the molecules apart, called bleaching. So retinal pigments can only see (absorb) 700 nm to 400 nm light, which is therefore called visible light. For the same reasons, plants pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically active radiation. 

The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal the colors to the human eye. The visible light portion of the electromagnetic spectrum shows the rainbow of colors, with violet and blue having shorter wavelengths, and therefore higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy ( [link] ). The colors of visible light do not carry the same amount of energy. Violet has the shortest wavelength and therefore carries the most energy, whereas red has the longest wavelength and carries the least amount of energy. (credit: modification of work by NASA) Understanding Pigments 

Concentrate on the types and functions of chlorophylls and carotenoids that are found in leaves. Discuss how all of them are always there even though they are not visible in the summer. They are visible in the fall. 

Ask the class what color coats people tend to wear in the summer and in the winter. Discuss why they do this. 

Different kinds of pigments exist, and each has evolved to absorb only certain wavelengths (colors) of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making them appear in the corresponding color. 

Chlorophylls and carotenoids are the two major classes of photosynthetic pigments found in plants and algae; each class has multiple types of pigment molecules. There are five major chlorophylls: a , b , c and d and a related molecule found in prokaryotes called bacteriochlorophyll. Chlorophyll a and chlorophyll b are found in higher plant chloroplasts and will be the focus of the following discussion. 

With dozens of different forms, carotenoids are a much larger group of pigments. The carotenoids found in fruit such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel ( -carotene) are used as advertisements to attract seed dispersers. In photosynthesis, carotenoids function as photosynthetic pigments that are very efficient molecules for the disposal of excess energy. When a leaf is exposed to full sun, the light-dependent reactions are required to process an enormous amount of energy; if that energy is not handled properly, it can do significant damage. Therefore, many carotenoids reside in the thylakoid membrane, absorb excess energy, and safely dissipate that energy as heat. 

Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is the absorption spectrum . The graph in [link] shows the absorption spectra for chlorophyll a , chlorophyll b , and a type of carotenoid pigment called -carotene (which absorbs blue and green light). Notice how each pigment has a distinct set of peaks and troughs, revealing a highly specific pattern of absorption. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not green. Because green is reflected or transmitted, chlorophyll appears green. Carotenoids absorb in the short-wavelength blue region, and reflect the longer yellow, red, and orange wavelengths. (a) Chlorophyll a , (b) chlorophyll b , and (c) -carotene are hydrophobic organic pigments found in the thylakoid membrane. Chlorophyll a and b , which are identical except for the part indicated in the red box, are responsible for the green color of leaves. -carotene is responsible for the orange color in carrots. Each pigment has (d) a unique absorbance spectrum. 

Many photosynthetic organisms have a mixture of pigments; using them, the organism can absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and quality decrease and change with depth. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees absorb most of the sunlight and scatter the remaining solar radiation ( [link] ). Plants that commonly grow in the shade have adapted to low levels of light by changing the relative concentrations of their chlorophyll pigments. (credit: Jason Hollinger) 

When studying a photosynthetic organism, scientists can determine the types of pigments present by generating absorption spectra. An instrument called a spectrophotometer can differentiate which wavelengths of light a substance can absorb. Spectrophotometers measure transmitted light and compute from it the absorption. By extracting pigments from leaves and placing these samples into a spectrophotometer, scientists can identify which wavelengths of light an organism can absorb. Additional methods for the identification of plant pigments include various types of chromatography that separate the pigments by their relative affinities to solid and mobile phases. How Light-Dependent Reactions Work 

Photosystems I and II can be confusing. Obtain diagrams of both systems and use them to go through the steps of the pathways. Discuss why some plants use the cyclic form of the systems and some the linear form. Discuss why oxygen is released during one pathway, but not the other. 

The overall function of light-dependent reactions is to convert solar energy into chemical energy in the form of NADPH and ATP. This chemical energy supports the light-independent reactions and fuels the assembly of sugar molecules. The light-dependent reactions are depicted in [link] . Protein complexes and pigment molecules work together to produce NADPH and ATP. A photosystem consists of a light-harvesting complex and a reaction center. Pigments in the light-harvesting complex pass light energy to two special chlorophyll a molecules in the reaction center. The light excites an electron from the chlorophyll a pair, which passes to the primary electron acceptor. The excited electron must then be replaced. In (a) photosystem II, the electron comes from the splitting of water, which releases oxygen as a waste product. In (b) photosystem I, the electron comes from the chloroplast electron transport chain discussed below. 

The actual step that converts light energy into chemical energy takes place in a multiprotein complex called a photosystem , two types of which are found embedded in the thylakoid membrane, photosystem II (PSII) and photosystem I (PSI) ( [link] ). The two complexes differ on the basis of what they oxidize (that is, the source of the low-energy electron supply) and what they reduce (the place to which they deliver their energized electrons). 

Both photosystems have the same basic structure; a number of antenna proteins to which the chlorophyll molecules are bound surround the reaction center where the photochemistry takes place. Each photosystem is serviced by the light-harvesting complex , which passes energy from sunlight to the reaction center; it consists of multiple antenna proteins that contain a mixture of 300 400 chlorophyll a and b molecules as well as other pigments like carotenoids. The absorption of a single photon or distinct quantity or packet of light by any of the chlorophylls pushes that molecule into an excited state. In short, the light energy has now been captured by biological molecules but is not stored in any useful form yet. The energy is transferred from chlorophyll to chlorophyll until eventually (after about a millionth of a second), it is delivered to the reaction center. Up to this point, only energy has been transferred between molecules, not electrons. 

In the photosystem II (PSII) reaction center, energy from sunlight is used to extract electrons from water. The electrons travel through the chloroplast electron transport chain to photosystem I (PSI), which reduces NADP + to NADPH. The electron transport chain moves protons across the thylakoid membrane into the lumen. At the same time, splitting of water adds protons to the lumen, and reduction of NADPH removes protons from the stroma. The net result is a low pH in the thylakoid lumen, and a high pH in the stroma. ATP synthase uses this electrochemical gradient to make ATP. 

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The reaction center contains a pair of chlorophyll a molecules with a special property. Those two chlorophylls can undergo oxidation upon excitation; they can actually give up an electron in a process called a photoact . It is at this step in the reaction center, this step in photosynthesis, that light energy is converted into an excited electron. All of the subsequent steps involve getting that electron onto the energy carrier NADPH for delivery to the Calvin cycle where the electron is deposited onto carbon for long-term storage in the form of a carbohydrate.PSII and PSI are two major components of the photosynthetic electron transport chain , which also includes the cytochrome complex . The cytochrome complex, an enzyme composed of two protein complexes, transfers the electrons from the carrier molecule plastoquinone (Pq) to the protein plastocyanin (Pc), thus enabling both the transfer of protons across the thylakoid membrane and the transfer of electrons from PSII to PSI. 

The reaction center of PSII (called P680 ) delivers its high-energy electrons, one at the time, to the primary electron acceptor , and through the electron transport chain (Pq to cytochrome complex to plastocyanine) to PSI. P680 s missing electron is replaced by extracting a low-energy electron from water; thus, water is split and PSII is re-reduced after every photoact. Splitting one H 2 O molecule releases two electrons, two hydrogen atoms, and one atom of oxygen. Splitting two molecules is required to form one molecule of diatomic O 2 gas. About 10 percent of the oxygen is used by mitochondria in the leaf to support oxidative phosphorylation. The remainder escapes to the atmosphere where it is used by aerobic organisms to support respiration. 

As electrons move through the proteins that reside between PSII and PSI, they lose energy. That energy is used to move hydrogen atoms from the stromal side of the membrane to the thylakoid lumen. Those hydrogen atoms, plus the ones produced by splitting water, accumulate in the thylakoid lumen and will be used synthesize ATP in a later step. Because the electrons have lost energy prior to their arrival at PSI, they must be re-energized by PSI, hence, another photon is absorbed by the PSI antenna. That energy is relayed to the PSI reaction center (called P700 ). P700 is oxidized and sends a high-energy electron to NADP + to form NADPH. Thus, PSII captures the energy to create proton gradients to make ATP, and PSI captures the energy to reduce NADP + into NADPH. The two photosystems work in concert, in part, to guarantee that the production of NADPH will roughly equal the production of ATP. Other mechanisms exist to fine tune that ratio to exactly match the chloroplast s constantly changing energy needs. Generating an Energy Carrier: ATP 

Discuss the similarities between ATP production in the light dependent reactions and in cellular respiration. 

As in the intermembrane space of the mitochondria during cellular respiration, the buildup of hydrogen ions inside the thylakoid lumen creates a concentration gradient. The passive diffusion of hydrogen ions from high concentration (in the thylakoid lumen) to low concentration (in the stroma) is harnessed to create ATP, just as in the electron transport chain of cellular respiration. The ions build up energy because of diffusion and because they all have the same electrical charge, repelling each other. 

To release this energy, hydrogen ions will rush through any opening, similar to water jetting through a hole in a dam. In the thylakoid, that opening is a passage through a specialized protein channel called the ATP synthase. The energy released by the hydrogen ion stream allows ATP synthase to attach a third phosphate group to ADP, which forms a molecule of ATP ( [link] ). The flow of hydrogen ions through ATP synthase is called chemiosmosis because the ions move from an area of high to an area of low concentration through a semi-permeable structure. 

Visit this site and click through the animation to view the process of photosynthesis within a leaf. 

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The anatomy of a leaf. The cuticle and epidermis are the outer layers of the leaf and protect it from drying out. Chloroplasts are found in the mesophyll cells and are where photosynthesis occurs. Gas is exchanged through pores called stomata, which are opened and closed by the guard cells. Legend: 1) cuticle 2) upper epidermis 3) palisade mesophyll 4) spongy mesophyll 5) lower epidermis 6) stoma 7) guard cells 8) xylem 9) phloem 10) vascular bundle. 

[link] Think About It 

On a hot, dry day, plants close their stomata to conserve water. Predict the impact of this on photosynthesis and justify your prediction. 

The Think About It question is an application of Learning Objective 4.4 and Science Practice 6.4 because students are making a prediction about how interactions of cellular organelles and structures affect the rate of photosynthesis. Possible answer: When the stomata are closed, carbon dioxide cannot enter the leaves to form glucose in the light independent reactions. When the light independent reactions are not occurring, energy stored in ATP and NADPH cannot be transferred to carbon-carbon bonds and so eventually the light-dependent reactions will run out of ADP and NADP to accept electrons. As a result, photosynthesis will slow. Section Summary 

The pigments of the first part of photosynthesis, the light-dependent reactions, absorb energy from sunlight. A photon strikes the antenna pigments of photosystem II to initiate photosynthesis. The energy travels to the reaction center that contains chlorophyll a to the electron transport chain, which pumps hydrogen ions into the thylakoid interior. This action builds up a high concentration of ions. The ions flow through ATP synthase via chemiosmosis to form molecules of ATP, which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule, another energy and reducing power carrier for the light-independent reactions. Review Questions 

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[link] Glossary absorption spectrum range of wavelengths of electromagnetic radiation absorbed by a given substance antenna protein pigment molecule that directly absorbs light and transfers the energy absorbed to other pigment molecules carotenoid photosynthetic pigment that functions to dispose of excess energy chlorophyll a form of chlorophyll that absorbs violet-blue and red light and consequently has a bluish-green color; the only pigment molecule that performs the photochemistry by getting excited and losing an electron to the electron transport chain chlorophyll b accessory pigment that absorbs blue and red-orange light and consequently has a yellowish-green tint cytochrome complex group of reversibly oxidizable and reducible proteins that forms part of the electron transport chain between photosystem II and photosystem I electromagnetic spectrum range of all possible frequencies of radiation electron transport chain group of proteins between PSII and PSI that pass energized electrons and use the energy released by the electrons to move hydrogen ions against their concentration gradient into the thylakoid lumen light harvesting complex complex that passes energy from sunlight to the reaction center in each photosystem; it consists of multiple antenna proteins that contain a mixture of 300 400 chlorophyll a and b molecules as well as other pigments like carotenoids P680 reaction center of photosystem II P700 reaction center of photosystem I photoact ejection of an electron from a reaction center using the energy of an absorbed photon photon distinct quantity or packet of light energy photosystem group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb light energy and convert it into chemical energy photosystem I integral pigment and protein complex in thylakoid membranes that uses light energy to transport electrons from plastocyanin to NADP + (which becomes reduced to NADPH in the process) photosystem II integral protein and pigment complex in thylakoid membranes that transports electrons from water to the electron transport chain; oxygen is a product of PSII primary electron acceptor pigment or other organic molecule in the reaction center that accepts an energized electron from the reaction center reaction center complex of chlorophyll molecules and other organic molecules that is assembled around a special pair of chlorophyll molecules and a primary electron acceptor; capable of undergoing oxidation and reduction spectrophotometer instrument that can measure transmitted light and compute the absorption wavelength distance between consecutive points of equal position (two crests or two troughs) of a wave in a graphic representation; inversely proportional to the energy of the radiationUsing Light Energy to Make Organic Molecules Using Light Energy to Make Organic Molecules 

In this section, you will explore the following questions: What are the reactions in the Calvin cycle described as the light-independent reactions? Why does the term carbon fixation describe the products of the Calvin cycle? What is the role of photosynthesis in the energy cycle of all living organisms? Connection for AP Courses 

The free energy stored in ATP and NADPH produced in the light-dependent reactions is used to power the chemical reactions of the light-independent reactions or Calvin cycle, which can occur during both the day and night. In the Calvin cycle, an enzyme called ribulose biphosphate carboxylase (RuBisCO), catalyzes a reaction with CO 2 and another molecule called ribulose biphosphate (RuBP) that is regenerated from a previous Calvin cycle. After a series of chemical reactions, the carbon from carbon dioxide in the atmosphere is fixed into carbohydrates, specifically a three-carbon molecule called glyceraldehydes-3-phosphate (G3P). (Again, count the carbons as we explore the Calvin cycle.) After three turns of the cycle, a three-carbon molecule of G3P leaves the cycle to become part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be regenerated into RuBP, which is then ready to react with more incoming CO 2 . In other words, the cell generates a stockpile of G3P to be assembled into organic molecules, including carbohydrates. Each step of the Calvin cycle is catalyzed by specific enzymes. (You do not have to memorize the reactions of the Calvin cycle; however, if provided with a diagram of the cycle, you should be able to interpret it.) Some plants evolved chemical modifications to more efficiently trap CO 2 if environmental conditions limit its availability. For example, when it s hot outside, plants tend to keep their stomata closed to prevent excessive water loss; when the outside temperature cools, stomata open and plants take in CO 2 and use a more efficient system to feed it into the Calvin cycle. 

As we explored in Overview of Photosynthesis, photosynthesis forms an energy link with cellular respiration. Plants need both photosynthesis and respiration in order to conduct metabolic processes during both light and dark times. Therefore, plant cells contain both chloroplasts and mitochondria. 

Information presented and the examples highlighted in the section, support concepts and learning objectives outlined in Big Idea 2 of the AP Biology Curriculum Framework, as shown in the table. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.A Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential Knowledge 2.A.2 Light energy captured in photosynthesis is stored in carbohydrates produced during the Calvin cycle. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy. Essential Knowledge 2.A.2 Light energy captured in photosynthesis is stored in carbohydrates produced during the Calvin cycle Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy. 

As with the light dependent reactions, obtain detailed diagrams of the Calvin cycle, such as Figure 8.18 and walk the students through it. Emphasize the roles of ATP and NADPH and where they enter and leave the pathway. Explain why the Calvin Cycle makes lots of G3P, but not all of it is used to make other carbohydrates. What happens to the rest? Why are all three stages of the cycle necessary? 

This is a good time to discuss the evolution of photosynthesis. Ask if it is possible to have the capture of energy without the release of oxygen? Could this have happened on Earth? Why would the release of oxygen be beneficial to organisms? Was it a good idea for all of the organisms living at that time? 

The light-independent reactions or Calvin cycle are not really independent of light. They depend on the earlier reactions to supply ATP and NADPH in order to proceed. This pathway makes the storage and transport form of energy used by nearly every living organism, sugars. It does not make glucose directly, but a chemical that is also an intermediate in cellular respiration, glyceraldehyde-3-phosphate (G3P). This can be used to make a variety of biologically important compounds, including glucose. The Calvin Cycle 

After the energy from the sun is converted into chemical energy and temporarily stored in ATP and NADPH molecules, the cell has the fuel needed to build carbohydrate molecules for long-term energy storage. The products of the light-dependent reactions, ATP and NADPH, have lifespans in the range of millionths of seconds, whereas the products of the light-independent reactions (carbohydrates and other forms of reduced carbon) can survive for hundreds of millions of years. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? It comes from carbon dioxide, the gas that is a waste product of respiration in microbes, fungi, plants, and animals. 

In plants, carbon dioxide (CO 2 ) enters the leaves through stomata, where it diffuses over short distances through intercellular spaces until it reaches the mesophyll cells. Once in the mesophyll cells, CO 2 diffuses into the stroma of the chloroplast the site of light-independent reactions of photosynthesis. These reactions actually have several names associated with them. Another term, the Calvin cycle , is named for the man who discovered it, and because these reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery. The most outdated name is dark reactions, because light is not directly required ( [link] ). However, the term dark reaction can be misleading because it implies incorrectly that the reaction only occurs at night or is independent of light, which is why most scientists and instructors no longer use it. Light reactions harness energy from the sun to produce chemical bonds, ATP, and NADPH. These energy-carrying molecules are made in the stroma where carbon fixation takes place. 

The light-independent reactions of the Calvin cycle can be organized into three basic stages: fixation, reduction, and regeneration. Stage 1: Fixation 

In the stroma, in addition to CO 2 , two other components are present to initiate the light-independent reactions: an enzyme called ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and three molecules of ribulose bisphosphate (RuBP), as shown in [link] . RuBP has five atoms of carbon, flanked by two phosphates. 

The Calvin cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic molecule, 3-PGA. In stage 2, the organic molecule is reduced using electrons supplied by NADPH. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the cycle can continue. Only one carbon dioxide molecule is incorporated at a time, so the cycle must be completed three times to produce a single three-carbon GA3P molecule, and six times to produce a six-carbon glucose molecule. 

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RuBisCO catalyzes a reaction between CO 2 and RuBP. For each CO 2 molecule that reacts with one RuBP, two molecules of another compound (3-PGA) form. PGA has three carbons and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 atoms from 3CO 2 + 15 atoms from 3RuBP = 18 atoms in 3 atoms of 3-PGA). This process is called carbon fixation , because CO 2 is fixed from an inorganic form into organic molecules. Stage 2: Reduction 

ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde 3-phosphate (G3P). That is a reduction reaction because it involves the gain of electrons by 3-PGA. Recall that a reduction is the gain of an electron by an atom or molecule. Six molecules of both ATP and NADPH are used. For ATP, energy is released with the loss of the terminal phosphate atom, converting it into ADP; for NADPH, both energy and a hydrogen atom are lost, converting it into NADP + . Both of these molecules return to the nearby light-dependent reactions to be reused and reenergized. Stage 3: Regeneration 

Interestingly, at this point, only one of the G3P molecules leaves the Calvin cycle and is sent to the cytoplasm to contribute to the formation of other compounds needed by the plant. Because the G3P exported from the chloroplast has three carbon atoms, it takes three turns of the Calvin cycle to fix enough net carbon to export one G3P. But each turn makes two G3Ps, thus three turns make six G3Ps. One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO 2 to be fixed. Three more molecules of ATP are used in these regeneration reactions. 

This link leads to an animation of the Calvin cycle. Click stage 1, stage 2, and then stage 3 to see G3P and ATP regenerate to form RuBP. 

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The harsh conditions of the desert have led plants like these cacti to evolve variations of the light-independent reactions of photosynthesis. These variations increase the efficiency of water usage, helping to conserve water and energy. (credit: Piotr Wojtkowski) 

[link] The Energy Cycle 

Whether the organism is a bacterium, plant, or animal, all living things access energy by breaking down carbohydrate molecules. But if plants make carbohydrate molecules, why would they need to break them down, especially when it has been shown that the gas organisms release as a waste product (CO 2 ) acts as a substrate for the formation of more food in photosynthesis? Remember, living things need energy to perform life functions. In addition, an organism can either make its own food or eat another organism either way, the food still needs to be broken down. Finally, in the process of breaking down food, called cellular respiration, heterotrophs release needed energy and produce waste in the form of CO 2 gas. 

In nature, there is no such thing as waste. Every single atom of matter and energy is conserved, recycling over and over infinitely. Substances change form or move from one type of molecule to another, but their constituent atoms never disappear. ( Figure 1.21 is an illustrative example of this process.) 

CO 2 is no more a form of waste than oxygen is wasteful to photosynthesis. Both are byproducts of reactions that move on to other reactions. Photosynthesis absorbs light energy to build carbohydrates in chloroplasts, and aerobic cellular respiration releases energy by using oxygen to metabolize carbohydrates in the cytoplasm and mitochondria. Both processes use electron transport chains to capture the energy necessary to drive other reactions. These two powerhouse processes, photosynthesis and cellular respiration, function in biological, cyclical harmony to allow organisms to access life-sustaining energy that originates millions of miles away in a burning star humans call the sun. Photosynthesis consumes carbon dioxide and produces oxygen. Aerobic respiration consumes oxygen and produces carbon dioxide. These two processes play an important role in the carbon cycle. (credit: modification of work by Stuart Bassil) 

Photosynthesis and aerobic respiration are interrelated in important ways. During photosynthesis, plants take in carbon dioxide and water. The water molecule is split, the oxygen is released into the atmosphere, and the carbon dioxide is used to build carbohydrates. During aerobic respiration, organisms take in water and oxygen for respiration and produce carbon dioxide. 

[link] Activity 

Create a model or diagram to show the links between photosynthesis and cellular respiration. Think About It 

What cellular features and processes are similar in both respiration and photosynthesis? 

This activity and question are applications of Learning Objective 2.4 and science practices 1.4 and 3.1 because students are creating and using a representation to explore the link between photosynthesis and cellular respiration, two processes that organisms use to capture, store, and use free energy. Additional information for students can be found here : Possible answer: Search for free images that show what the model or diagram should look like here , here , or here . Both cellular respiration and photosynthesis occur in/on double-membrane organelles in the cell. Both processes use electron carriers to shuttle electrons to and between membrane proteins that pump protons. The pumping of protons creates an electrochemical gradient that drives the synthesis of ATP. Section Summary 

Using the energy carriers formed in the first steps of photosynthesis, the light-independent reactions, or the Calvin cycle, take in CO 2 from the environment. An enzyme, RuBisCO, catalyzes a reaction with CO 2 and another molecule, RuBP. After three cycles, a three-carbon molecule of G3P leaves the cycle to become part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be regenerated into RuBP, which is then ready to react with more CO 2 . Photosynthesis forms an energy cycle with the process of cellular respiration. Plants need both photosynthesis and respiration for their ability to function in both the light and dark, and to be able to interconvert essential metabolites. Therefore, plants contain both chloroplasts and mitochondria. Review Questions 

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[link] Glossary Calvin cycle light-independent reactions of photosynthesis that convert carbon dioxide from the atmosphere into carbohydrates using the energy and reducing power of ATP and NADPH carbon fixation process of converting inorganic CO 2 gas into organic compounds reduction gain of electron(s) by an atom or moleculeIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Have you ever become separated from a friend while in a crowd? If so, you know the challenge of searching for someone when surrounded by thousands of other people. If you and your friend have cell phones, your chances of finding each other are good. A cell phone s ability to send and receive messages makes it an ideal communication device. (credit: modification of work by Vincent and Bella Productions) 

Imagine what life would be like if you and the people around you could not communicate. You would not be able to express your wishes, nor could you ask questions to find out more about your environment. Social organization is dependent on communication between the individuals; without communication, society would fall apart. 

As with people, it is vital for a cell to interact with its environment. This is true whether it is a unicellular organism or one of many cells forming a larger organism. In order to respond to external stimuli, cells have developed complex mechanisms of communication that can receive a message, transfer the information across the plasma membrane, and produce changes within the cell in response to the message. In multicellular organisms, cells send and receive chemical messages constantly to coordinate the actions of distant organs, tissues, and cells. 

While the necessity for cellular communication in larger organisms seems obvious, even single-celled organisms communicate with each other. Yeast cells signal each other to aid in mating. Some forms of bacteria coordinate their actions in order to form large complexes called biofilms (Figure 9.18) or to organize the production of toxins to remove competing organisms. The ability of cells to communicate through chemical signals originated in single cells and was essential for the evolution of multicellular organisms. 

Cell signaling is vital to the survival of organisms. For example, chemical signals tell cells when to make hormones such as insulin. Cell division also depends on chemical signals. When the chemical signals do not function properly, cells can divide uncontrollably, forming cancerous tumors. Scientists recently discovered a cell signaling pathway that protects cancer cells from being killed by the body s immune system. The hope is to use this knowledge to create treatments that target this cell signaling pathway so that the cancer cells self destruct. More about that can be found here : Scientists pinpoint a new line of defense used by cancer cells. 

Ask students to think about how a cell phone works. Draw on the board the sequence: signal, phone hardware, sound. What happens after the call? Immediate action if it is urgent, delayed action if not, or simply ignore and delete if the message is deemed irrelevant. Cells function similarly. The body is abuzz with messages. Not all cells can receive all messages, and the response to the same message can and should be different depending on the type of targeted cell.Signaling Molecules and Cellular Receptors Signaling Molecules and Cellular Receptors 

In this section, you will explore the following questions: What are the four types of signaling that are found in multicellular organisms? What are the differences between internal receptors and cell-surface receptors? What is the relationship between a ligand s structure and its mechanism of action? Connection for AP Courses 

Just like you communicate with your classmates face-to-face, using your phone, or via e-mail, cells communicate with each other by both inter and intracellular signaling. Cells detect and respond to changes in the environment using signaling pathways. Signaling pathways enable organisms to coordinate cellular activities and metabolic processes. Errors in these pathways can cause disease. Signaling cells secrete molecules called ligands that bind to target cells and initiate a chain of events within the target cell. For example, when epinephrine is released, binding to target cells, those cells respond by converting glycogen to glucose. Cell communication can happen over short distances. For example, neurotransmitters are released across a synapse to transfer messages between neurons Figure 1.3 . Gap junctions and plasmodesmata allow small molecules, including signaling molecules, to flow between neighboring cells. Cell communication can also happen over long distances using. For example, hormones released from endocrine cells travel to target cells in multiple body systems. How does a ligand such as a hormone traveling through the bloodstream know when it has reached its target organ to initiate a cellular response? Nearly all cell signaling pathways involve three stages: reception, signal transduction, and cellular response. 

Cell signaling pathways begin when the ligand binds to a receptor, a protein that is embedded in the plasma membrane of the target cell or found in the cell cytoplasm. The receptors are very specific, and each ligand is recognized by a different one. This stage of the pathway is called reception. Molecules that are nonpolar, such as steroids, diffuse across the cell membrane and bind to internal receptors. In turn, the receptor-ligand complex moves to the nucleus and interacts with cellular DNA. This changes how a gene is expressed. Polar ligands, on the other hand, interact with membrane receptor protein. Some membrane receptors work by changing conformation so that certain ions, such as Na + and K + , can pass through the plasma membrane. Other membrane receptors interact with a G-protein on the cytoplasmic side of the plasma membrane, which causes a series of reactions inside the cell. Disruptions to this process are linked to several diseases, including cholera. 

It is important to keep in mind that each cell has a variety of receptors, allowing it to respond to a variety of stimuli. Some receptors can bind several different ligands; for example, odorant molecules/receptors associated with the sense of smell in animals. Once the signaling molecule and receptor interact, a cascade of events called signal transduction usually amplifies the signal inside the cell. 

The content presented in this section supports the Learning Objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework listed. The AP Learning Objectives merge Essential knowledge content with one or more of the seven Science Practices. These objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP Exam questions. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.D Cells communicate by generating, transmitting and receiving chemical signals. Essential Knowledge 3.D.3 Signal transduction pathways link signal reception with cellular response. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 3.34 The student is able to construct explanations of cell communication through cell-to-cell direct contact or through chemical signaling. Essential Knowledge 3.D.3 Signal transduction pathways link signal reception with cellular response. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.35 The student is able to create representations that depict how cell-to-cell communication occurs by direct contact or from a distance through chemical signaling. 

Go back to the comparison to the phone. The signal is an incoming phone call and it must be directed to a specific phone number. That is the signaling molecule. It must reach the dialed phone number, not a wrong number. A signal targets a specific receptor. Ask students if they know the physical nature of a cell phone signal. It is an electromagnetic wave, a radio wave. Then discuss the nature of the signal sent and recognized by cells. Though most are chemical signals, mention the body receives other signals. Ask students to make a list: light, sound, pressure, temperature are all signals. 

When the signal is received by the phone, it is processed. Some calls are ignored, result in delayed action or are acted upon immediately depending on the originator and content. In the same way, cells prioritize signals or ignore them if not significant. For example, the strength of a signal must cross a threshold to cause a nerve response. 

The distance traveled by signals matches the intended response. Autocrine signals result in amplification because a cell responds to its own signal, proliferates, and increases the output of signal. For example, the activation of B-cells in the immune system is caused by signals from the helper T-cells. Paracrine signals, such as nerve impulses, are best for signaling between neighboring cells and often have fast responses. Some neurotransmitters which have delayed and long lasting effects use G-protein-linked receptors, not ligand-gated receptors. Long distance messages can integrate the body response by reaching several target tissues at once. The fight-or-flight response requires glucose for skeletal muscles, faster heartbeat, dilating bronchi, all geared towards the same goal. [link] summarizes this information. Signal Effect Examples Autocrine Amplification of signal by acting on self; increased output Bacterial autoinducers; T-helper cells response to cytokines Paracrine Affect only neighboring cells, localized effect Neurotransmitters; immune cells Endocrine Integration of response targeting several cells or organs at once; affect remote locations Hypothalamus-Pituitary-organ axis; Inflammatory mediators secreted by macrophages 

Ask students if all nervous system signaling should be mediated by ligand-gated receptors, which render a rapid and short duration response. Skeletal muscles use ligand-gated receptors, which give rapid and time-limited responses. Some situations require a lasting effect. Smooth muscles carry G-protein-linked receptors because smooth muscle responses, bladder, intestine, etc., have prolonged action. This is an example of the same ligand, acetylcholine, binding to two different types of receptors. 

Distribute large sheets of paper and markers. Divide the class in groups and assign each group a specific type of receptor: ion channel-linked receptors (gated ion channels), G-protein-linked receptors, receptor tyrosine kinases, and internal (intracellular) receptors. More than one group of students may work on the same receptor. Ask students to set up a concept map starting with signal types: water soluble molecules or lipophilic molecules for each receptor molecule. For each receptor type, diagram the second messenger and amplification scheme. Allow enough time to create the posters and ask each group to present the receptor to the class. Here the goal is to divide and conquer the receptors because cellular signaling is confusing. Show this animation from Davidson College in class or provide a link for later view by students. 

There are two kinds of communication in the world of living cells. Communication between cells is called intercellular signaling , and communication within a cell is called intracellular signaling . An easy way to remember the distinction is by understanding the Latin origin of the prefixes: inter- means "between" (for example, intersecting lines are those that cross each other) and intra- means "inside" (like intravenous). 

Chemical signals are released by signaling cells in the form of small, usually volatile or soluble molecules called ligands. A ligand is a molecule that binds another specific molecule, in some cases, delivering a signal in the process. Ligands can thus be thought of as signaling molecules. Ligands interact with proteins in target cells , which are cells that are affected by chemical signals; these proteins are also called receptors . Ligands and receptors exist in several varieties; however, a specific ligand will have a specific receptor that typically binds only that ligand. Forms of Signaling 

There are four categories of chemical signaling found in multicellular organisms: paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions ( [link] ). The main difference between the different categories of signaling is the distance that the signal travels through the organism to reach the target cell. Not all cells are affected by the same signals. In chemical signaling, a cell may target itself (autocrine signaling), a cell connected by gap junctions, a nearby cell (paracrine signaling), or a distant cell (endocrine signaling). Paracrine signaling acts on nearby cells, endocrine signaling uses the circulatory system to transport ligands, and autocrine signaling acts on the signaling cell. Signaling via gap junctions involves signaling molecules moving directly between adjacent cells. Paracrine Signaling 

Signals that act locally between cells that are close together are called paracrine signals . Paracrine signals move by diffusion through the extracellular matrix. These types of signals usually elicit quick responses that last only a short amount of time. In order to keep the response localized, paracrine ligand molecules are normally quickly degraded by enzymes or removed by neighboring cells. Removing the signals will reestablish the concentration gradient for the signal, allowing them to quickly diffuse through the intracellular space if released again. 

One example of paracrine signaling is the transfer of signals across synapses between nerve cells. A nerve cell consists of a cell body, several short, branched extensions called dendrites that receive stimuli, and a long extension called an axon, which transmits signals to other nerve cells or muscle cells. The junction between nerve cells where signal transmission occurs is called a synapse. A synaptic signal is a chemical signal that travels between nerve cells. Signals within the nerve cells are propagated by fast-moving electrical impulses. When these impulses reach the end of the axon, the signal continues on to a dendrite of the next cell by the release of chemical ligands called neurotransmitters by the presynaptic cell (the cell emitting the signal). The neurotransmitters are transported across the very small distances between nerve cells, which are called chemical synapses ( [link] ). The small distance between nerve cells allows the signal to travel quickly; this enables an immediate response, such as, Take your hand off the stove! 

When the neurotransmitter binds the receptor on the surface of the postsynaptic cell, the electrochemical potential of the target cell changes, and the next electrical impulse is launched. The neurotransmitters that are released into the chemical synapse are degraded quickly or get reabsorbed by the presynaptic cell so that the recipient nerve cell can recover quickly and be prepared to respond rapidly to the next synaptic signal. The distance between the presynaptic cell and the postsynaptic cell called the synaptic gap is very small and allows for rapid diffusion of the neurotransmitter. Enzymes in the synapatic cleft degrade some types of neurotransmitters to terminate the signal. Endocrine Signaling 

Signals from distant cells are called endocrine signals , and they originate from endocrine cells . (In the body, many endocrine cells are located in endocrine glands, such as the thyroid gland, the hypothalamus, and the pituitary gland.) These types of signals usually produce a slower response but have a longer-lasting effect. The ligands released in endocrine signaling are called hormones, signaling molecules that are produced in one part of the body but affect other body regions some distance away. 

Hormones travel the large distances between endocrine cells and their target cells via the bloodstream, which is a relatively slow way to move throughout the body. Because of their form of transport, hormones get diluted and are present in low concentrations when they act on their target cells. This is different from paracrine signaling, in which local concentrations of ligands can be very high. Autocrine Signaling 

Autocrine signals are produced by signaling cells that can also bind to the ligand that is released. This means the signaling cell and the target cell can be the same or a similar cell (the prefix auto- means self, a reminder that the signaling cell sends a signal to itself). This type of signaling often occurs during the early development of an organism to ensure that cells develop into the correct tissues and take on the proper function. Autocrine signaling also regulates pain sensation and inflammatory responses. Further, if a cell is infected with a virus, the cell can signal itself to undergo programmed cell death, killing the virus in the process. In some cases, neighboring cells of the same type are also influenced by the released ligand. In embryological development, this process of stimulating a group of neighboring cells may help to direct the differentiation of identical cells into the same cell type, thus ensuring the proper developmental outcome. Direct Signaling Across Gap Junctions 

Gap junctions in animals and plasmodesmata in plants are connections between the plasma membranes of neighboring cells. These water-filled channels allow small signaling molecules, called intracellular mediators , to diffuse between the two cells. Small molecules, such as calcium ions (Ca 2+ ), are able to move between cells, but large molecules like proteins and DNA cannot fit through the channels. The specificity of the channels ensures that the cells remain independent but can quickly and easily transmit signals. The transfer of signaling molecules communicates the current state of the cell that is directly next to the target cell; this allows a group of cells to coordinate their response to a signal that only one of them may have received. In plants, plasmodesmata are ubiquitous, making the entire plant into a giant, communication network. Types of Receptors 

Receptors are protein molecules in the target cell or on its surface that bind ligand. There are two types of receptors, internal receptors and cell-surface receptors. Internal receptors 

Internal receptors , also known as intracellular or cytoplasmic receptors, are found in the cytoplasm of the cell and respond to hydrophobic ligand molecules that are able to travel across the plasma membrane. Once inside the cell, many of these molecules bind to proteins that act as regulators of mRNA synthesis (transcription) to mediate gene expression. Gene expression is the cellular process of transforming the information in a cell's DNA into a sequence of amino acids, which ultimately forms a protein. When the ligand binds to the internal receptor, a conformational change is triggered that exposes a DNA-binding site on the protein. The ligand-receptor complex moves into the nucleus, then binds to specific regulatory regions of the chromosomal DNA and promotes the initiation of transcription ( [link] ). Transcription is the process of copying the information in a cells DNA into a special form of RNA called messenger RNA (mRNA); the cell uses information in the mRNA (which moves out into the cytoplasm and associates with ribosomes) to link specific amino acids in the correct order, producing a protein. Internal receptors can directly influence gene expression without having to pass the signal on to other receptors or messengers. Hydrophobic signaling molecules typically diffuse across the plasma membrane and interact with intracellular receptors in the cytoplasm. Many intracellular receptors are transcription factors that interact with DNA in the nucleus and regulate gene expression. Cell-Surface Receptors 

Cell-surface receptors , also known as transmembrane receptors, are cell surface, membrane-anchored (integral) proteins that bind to external ligand molecules. This type of receptor spans the plasma membrane and performs signal transduction, in which an extracellular signal is converted into an intercellular signal. Ligands that interact with cell-surface receptors do not have to enter the cell that they affect. Cell-surface receptors are also called cell-specific proteins or markers because they are specific to individual cell types. 

Because cell-surface receptor proteins are fundamental to normal cell functioning, it should come as no surprise that a malfunction in any one of these proteins could have severe consequences. Errors in the protein structures of certain receptor molecules have been shown to play a role in hypertension (high blood pressure), asthma, heart disease, and cancer. 

Each cell-surface receptor has three main components: an external ligand-binding domain, a hydrophobic membrane-spanning region, and an intracellular domain inside the cell. The ligand-binding domain is also called the extracellular domain . The size and extent of each of these domains vary widely, depending on the type of receptor. 

How Viruses Recognize a Host Unlike living cells, many viruses do not have a plasma membrane or any of the structures necessary to sustain life. Some viruses are simply composed of an inert protein shell containing DNA or RNA. To reproduce, viruses must invade a living cell, which serves as a host, and then take over the hosts cellular apparatus. But how does a virus recognize its host? 

Viruses often bind to cell-surface receptors on the host cell. For example, the virus that causes human influenza (flu) binds specifically to receptors on membranes of cells of the respiratory system. Chemical differences in the cell-surface receptors among hosts mean that a virus that infects a specific species (for example, humans) cannot infect another species (for example, chickens). 

However, viruses have very small amounts of DNA or RNA compared to humans, and, as a result, viral reproduction can occur rapidly. Viral reproduction invariably produces errors that can lead to changes in newly produced viruses; these changes mean that the viral proteins that interact with cell-surface receptors may evolve in such a way that they can bind to receptors in a new host. Such changes happen randomly and quite often in the reproductive cycle of a virus, but the changes only matter if a virus with new binding properties comes into contact with a suitable host. In the case of influenza, this situation can occur in settings where animals and people are in close contact, such as poultry and swine farms. 1 Once a virus jumps to a new host, it can spread quickly. Scientists watch newly appearing viruses (called emerging viruses) closely in the hope that such monitoring can reduce the likelihood of global viral epidemics. 

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Cell-surface receptors are involved in most of the signaling in multicellular organisms. There are three general categories of cell-surface receptors: ion channel-linked receptors, G-protein-linked receptors, and enzyme-linked receptors. 

Ion channel-linked receptors bind a ligand and open a channel through the membrane that allows specific ions to pass through. To form a channel, this type of cell-surface receptor has an extensive membrane-spanning region. In order to interact with the phospholipid fatty acid tails that form the center of the plasma membrane, many of the amino acids in the membrane-spanning region are hydrophobic in nature. Conversely, the amino acids that line the inside of the channel are hydrophilic to allow for the passage of water or ions. When a ligand binds to the extracellular region of the channel, there is a conformational change in the proteins structure that allows ions such as sodium, calcium, magnesium, and hydrogen to pass through ( [link] ). Gated ion channels form a pore through the plasma membrane that opens when the signaling molecule binds. The open pore then allows ions to flow into or out of the cell. 

G-protein-linked receptors bind a ligand and activate a membrane protein called a G-protein. The activated G-protein then interacts with either an ion channel or an enzyme in the membrane ( [link] ). All G-protein-linked receptors have seven transmembrane domains, but each receptor has its own specific extracellular domain and G-protein-binding site. 

Cell signaling using G-protein-linked receptors occurs as a cyclic series of events. Before the ligand binds, the inactive G-protein can bind to a newly revealed site on the receptor specific for its binding. Once the G-protein binds to the receptor, the resultant shape change activates the G-protein, which releases GDP and picks up GTP. The subunits of the G-protein then split into the subunit and the subunit. One or both of these G-protein fragments may be able to activate other proteins as a result. After awhile, the GTP on the active subunit of the G-protein is hydrolyzed to GDP and the subunit is deactivated. The subunits reassociate to form the inactive G-protein and the cycle begins anew. Heterotrimeric G proteins have three subunits: , , and . When a signaling molecule binds to a G-protein-coupled receptor in the plasma membrane, a GDP molecule associated with the subunit is exchanged for GTP. The and subunits dissociate from the subunit, and a cellular response is triggered either by the subunit or the dissociated pair. Hydrolysis of GTP to GDP terminates the signal. 

G-protein-linked receptors have been extensively studied and much has been learned about their roles in maintaining health. Bacteria that are pathogenic to humans can release poisons that interrupt specific G-protein-linked receptor function, leading to illnesses such as pertussis, botulism, and cholera. In cholera ( [link] ), for example, the water-borne bacterium Vibrio cholerae produces a toxin, choleragen, that binds to cells lining the small intestine. The toxin then enters these intestinal cells, where it modifies a G-protein that controls the opening of a chloride channel and causes it to remain continuously active, resulting in large losses of fluids from the body and potentially fatal dehydration as a result. Transmitted primarily through contaminated drinking water, cholera is a major cause of death in the developing world and in areas where natural disasters interrupt the availability of clean water. The cholera bacterium, Vibrio cholerae , creates a toxin that modifies G-protein-mediated cell signaling pathways in the intestines. Modern sanitation eliminates the threat of cholera outbreaks, such as the one that swept through New York City in 1866. This poster from that era shows how, at that time, the way that the disease was transmitted was not understood. (credit: New York City Sanitary Commission) 

Enzyme-linked receptors are cell-surface receptors with intracellular domains that are associated with an enzyme. In some cases, the intracellular domain of the receptor itself is an enzyme. Other enzyme-linked receptors have a small intracellular domain that interacts directly with an enzyme. The enzyme-linked receptors normally have large extracellular and intracellular domains, but the membrane-spanning region consists of a single alpha-helical region of the peptide strand. When a ligand binds to the extracellular domain, a signal is transferred through the membrane, activating the enzyme. Activation of the enzyme sets off a chain of events within the cell that eventually leads to a response. One example of this type of enzyme-linked receptor is the tyrosine kinase receptor ( [link] ). A kinase is an enzyme that transfers phosphate groups from ATP to another protein. The tyrosine kinase receptor transfers phosphate groups to tyrosine molecules (tyrosine residues). First, signaling molecules bind to the extracellular domain of two nearby tyrosine kinase receptors. The two neighboring receptors then bond together, or dimerize. Phosphates are then added to tyrosine residues on the intracellular domain of the receptors (phosphorylation). The phosphorylated residues can then transmit the signal to the next messenger within the cytoplasm. 

A receptor tyrosine kinase is an enzyme-linked receptor with a single transmembrane region, and extracellular and intracellular domains. Binding of a signaling molecule to the extracellular domain causes the receptor to dimerize. Tyrosine residues on the intracellular domain are then autophosphorylated, triggering a downstream cellular response. The signal is terminated by a phosphatase that removes the phosphates from the phosphotyrosine residues. 

[link] Signaling Molecules 

Produced by signaling cells and the subsequent binding to receptors in target cells, ligands act as chemical signals that travel to the target cells to coordinate responses. The types of molecules that serve as ligands are incredibly varied and range from small proteins to small ions like calcium (Ca 2+ ). Small Hydrophobic Ligands 

Small hydrophobic ligands can directly diffuse through the plasma membrane and interact with internal receptors. Important members of this class of ligands are the steroid hormones. Steroids are lipids that have a hydrocarbon skeleton with four fused rings; different steroids have different functional groups attached to the carbon skeleton. Steroid hormones include the female sex hormone, estradiol, which is a type of estrogen; the male sex hormone, testosterone; and cholesterol, which is an important structural component of biological membranes and a precursor of steriod hormones ( [link] ). Other hydrophobic hormones include thyroid hormones and vitamin D. In order to be soluble in blood, hydrophobic ligands must bind to carrier proteins while they are being transported through the bloodstream. Steroid hormones have similar chemical structures to their precursor, cholesterol. Because these molecules are small and hydrophobic, they can diffuse directly across the plasma membrane into the cell, where they interact with internal receptors. Water-Soluble Ligands 

Water-soluble ligands are polar and therefore cannot pass through the plasma membrane unaided; sometimes, they are too large to pass through the membrane at all. Instead, most water-soluble ligands bind to the extracellular domain of cell-surface receptors. This group of ligands is quite diverse and includes small molecules, peptides, and proteins. Other Ligands 

Nitric oxide (NO) is a gas that also acts as a ligand. It is able to diffuse directly across the plasma membrane, and one of its roles is to interact with receptors in smooth muscle and induce relaxation of the tissue. NO has a very short half-life and therefore only functions over short distances. Nitroglycerin, a treatment for heart disease, acts by triggering the release of NO, which causes blood vessels to dilate (expand), thus restoring blood flow to the heart. NO has become better known recently because the pathway that it affects is targeted by prescription medications for erectile dysfunction, such as Viagra (erection involves dilated blood vessels). Think About It Cells grown in the laboratory are placed in a solution containing a dye that is unable to pass through the plasma membrane. If a ligand is then added to the solution, observations show that the dye enters the cell. Describe the type of receptor the ligand most likely binds to and explain your reasoning. HER2 is a receptor tyrosine kinase. In 30 percent of human breast cancers, HER2 is permanently activated, resulting in unregulated cell division. Lapatinib, a drug used to treat breast cancer, inhibits HER2 receptor tyrosine kinase autophosphorylation (the process by which the receptor adds phosphate onto itself), thus reducing tumor growth. Besides autophosphorylation, explain another feature of the cell signaling pathway that can be affected by Lapatinib. In certain cancers, the GTPase activity of RAS G-protein in inhibited. This means that the RAS G-protein can no longer hydrolyze GTP into GDP. Explain what effect this would have on downstream cellular events. 

The first question is an application of Learning Objective 3.34 and Science Practice 6.3 because students are explaining how cells communicate through signaling pathways, beginning with the interaction between a signal molecule and receptor protein. 

The second and third questions are applications of Learning Objective 3.34 and Science Practice 6.3 because students are explaining how disruptions in cell signaling pathways can affect a cell s normal function. Answers: Presumably the dye is a large molecule, most likely hydrophilic. The ligand may change the permeability of the cell membrane; for example, it binds to gated channels that allow passage of the dye. Give acetylcholine binding to its receptor and allowing the passage of Na + as an example. In both cases the answer is the same; all the reactions downstream of phosphorylation do not take place because they depend on the first reaction. The last step, transcription and translation of proteins needed for cell division, does not take place and cell proliferation is inhibited. Section Summary 

Cells communicate by both inter- and intracellular signaling. Signaling cells secrete ligands that bind to target cells and initiate a chain of events within the target cell. The four categories of signaling in multicellular organisms are paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions. Paracrine signaling takes place over short distances. Endocrine signals are carried long distances through the bloodstream by hormones, and autocrine signals are received by the same cell that sent the signal or other nearby cells of the same kind. Gap junctions allow small molecules, including signaling molecules, to flow between neighboring cells. 

Internal receptors are found in the cell cytoplasm. Here, they bind ligand molecules that cross the plasma membrane; these receptor-ligand complexes move to the nucleus and interact directly with cellular DNA. Cell-surface receptors transmit a signal from outside the cell to the cytoplasm. Ion channel-linked receptors, when bound to their ligands, form a pore through the plasma membrane through which certain ions can pass. G-protein-linked receptors interact with a G-protein on the cytoplasmic side of the plasma membrane, promoting the exchange of bound GDP for GTP and interacting with other enzymes or ion channels to transmit a signal. Enzyme-linked receptors transmit a signal from outside the cell to an intracellular domain of a membrane-bound enzyme. Ligand binding causes activation of the enzyme. Small hydrophobic ligands (like steroids) are able to penetrate the plasma membrane and bind to internal receptors. Water-soluble hydrophilic ligands are unable to pass through the membrane; instead, they bind to cell-surface receptors, which transmit the signal to the inside of the cell. Review Questions 

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A. B. Sigalov, The School of Nature. IV. Learning from Viruses, Self/Nonself 1, no. 4 (2010): 282-298. Y. Cao, X. Koh, L. Dong, X. Du, A. Wu, X. Ding, H. Deng, Y. Shu, J. Chen, T. Jiang, Rapid Estimation of Binding Activity of Influenza Virus Hemagglutinin to Human and Avian Receptors, PLoS One 6, no. 4 (2011): e18664. Glossary autocrine signal signal that is sent and received by the same or similar nearby cells cell-surface receptor cell-surface protein that transmits a signal from the exterior of the cell to the interior, even though the ligand does not enter the cell chemical synapse small space between axon terminals and dendrites of nerve cells where neurotransmitters function endocrine cell cell that releases ligands involved in endocrine signaling (hormones) endocrine signal long-distance signal that is delivered by ligands (hormones) traveling through an organisms circulatory system from the signaling cell to the target cell enzyme-linked receptor cell-surface receptor with intracellular domains that are associated with membrane-bound enzymes extracellular domain region of a cell-surface receptor that is located on the cell surface G-protein-linked receptor cell-surface receptor that activates membrane-bound G-proteins to transmit a signal from the receptor to nearby membrane components intercellular signaling communication between cells internal receptor (also, intracellular receptor) receptor protein that is located in the cytosol of a cell and binds to ligands that pass through the plasma membrane intracellular mediator (also, second messenger) small molecule that transmits signals within a cell intracellular signaling communication within cells ion channel-linked receptor cell-surface receptor that forms a plasma membrane channel, which opens when a ligand binds to the extracellular domain (ligand-gated channels) ligand molecule produced by a signaling cell that binds with a specific receptor, delivering a signal in the process neurotransmitter chemical ligand that carries a signal from one nerve cell to the next paracrine signal signal between nearby cells that is delivered by ligands traveling in the liquid medium in the space between the cells receptor protein in or on a target cell that bind to ligands signaling cell cell that releases signal molecules that allow communication with another cell synaptic signal chemical signal (neurotransmitter) that travels between nerve cells target cell cell that has a receptor for a signal or ligand from a signaling cellPropagation of the Signal Propagation of the Signal 

In this section, you will explore the following questions: How does the binding of a ligand initiate signal transduction throughout a cell? What is the role of second messengers in signal transduction? Connection for AP Courses 

During signal transduction, a series of relay proteins inside the cytoplasm of the target cell activate target proteins, resulting in a cellular response. These cascades are complex because of the interplay between proteins. A significant contributor to cell signaling cascades is the phosphorylation of molecules by enzymes known as kinases. (Substrate level phosphorylation was studied when you learned about glycolysis.) By adding a phosphate group, phosphorylation changes the shapes of proteins. This change in shape activates or inactivates them. Second messengers, e.g., cAMP and Ca 2+ , are often used to transmit signals within a cell. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.D Cells communicate by generating, transmitting and receiving chemical signals. Essential Knowledge 3.D.3 Signal transduction pathways link signal reception with cellular response. Science Practice 1.5 The student can re-express key elements of natural phenomena across multiple representations in the domain. Learning Objective 3.36 The student is able to describe a model that expresses the key elements of signal transduction pathways by which a signal is converted to a cellular response. 

Ask students what would happen if suddenly the fire alarm went off. It should trigger the fight-or-flight response. Some organs must be activated for the response: skeletal muscle, heart, and the release of glucose from liver. Other organs have their activities dampened: the stomach halts digestion and salivary glands stop production. 

Ask students what happens if they get a loud alarm sound while eating. The likely response is that nauseous feeling and digestion cut short, courtesy of our sympathetic system. The same signal that activates all the systems needed for survival also shuts down the systems which are not essential for the rapid reaction needed to escape danger. An animation of fight-or-flight response can be seen here . 

Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. Continuation of a signal in this manner is called signal transduction . Signal transduction only occurs with cell-surface receptors because internal receptors are able to interact directly with DNA in the nucleus to initiate protein synthesis. 

When a ligand binds to its receptor, conformational changes occur that affect the receptor s intracellular domain. Conformational changes of the extracellular domain upon ligand binding can propagate through the membrane region of the receptor and lead to activation of the intracellular domain or its associated proteins. In some cases, binding of the ligand causes dimerization of the receptor, which means that two receptors bind to each other to form a stable complex called a dimer. A dimer is a chemical compound formed when two molecules (often identical) join together. The binding of the receptors in this manner enables their intracellular domains to come into close contact and activate each other. Binding Initiates a Signaling Pathway 

After the ligand binds to the cell-surface receptor, the activation of the receptor s intracellular components sets off a chain of events that is called a signaling pathway or a signaling cascade. In a signaling pathway, second messengers, enzymes, and activated proteins interact with specific proteins, which are in turn activated in a chain reaction that eventually leads to a change in the cell s environment ( [link] ). The events in the cascade occur in a series, much like a current flows in a river. Interactions that occur before a certain point are defined as upstream events, and events after that point are called downstream events. 

The epidermal growth factor (EGF) receptor (EGFR) is a receptor tyrosine kinase involved in the regulation of cell growth, wound healing, and tissue repair. When EGF binds to the EGFR, a cascade of downstream events causes the cell to grow and divide. If EGFR is activated at inappropriate times, uncontrolled cell growth (cancer) may occur. 

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Signaling pathways can get very complicated very quickly because most cellular proteins can affect different downstream events, depending on the conditions within the cell. A single pathway can branch off toward different endpoints based on the interplay between two or more signaling pathways, and the same ligands are often used to initiate different signals in different cell types. This variation in response is due to differences in protein expression in different cell types. Another complicating element is signal integration of the pathways, in which signals from two or more different cell-surface receptors merge to activate the same response in the cell. This process can ensure that multiple external requirements are met before a cell commits to a specific response. 

The effects of extracellular signals can also be amplified by enzymatic cascades. At the initiation of the signal, a single ligand binds to a single receptor. However, activation of a receptor-linked enzyme can activate many copies of a component of the signaling cascade, which amplifies the signal. Methods of Intracellular Signaling 

The induction of a signaling pathway depends on the modification of a cellular component by an enzyme. There are numerous enzymatic modifications that can occur, and they are recognized in turn by the next component downstream. The following are some of the more common events in intracellular signaling. 

Observe an animation of cell signaling at this site . 

[link] Phosphorylation 

One of the most common chemical modifications that occurs in signaling pathways is the addition of a phosphate group (PO 4 3 ) to a molecule such as a protein in a process called phosphorylation. The phosphate can be added to a nucleotide such as GMP to form GDP or GTP. Phosphates are also often added to serine, threonine, and tyrosine residues of proteins, where they replace the hydroxyl group of the amino acid ( [link] ). The transfer of the phosphate is catalyzed by an enzyme called a kinase . Various kinases are named for the substrate they phosphorylate. Phosphorylation of serine and threonine residues often activates enzymes. Phosphorylation of tyrosine residues can either affect the activity of an enzyme or create a binding site that interacts with downstream components in the signaling cascade. Phosphorylation may activate or inactivate enzymes, and the reversal of phosphorylation, dephosphorylation by a phosphatase, will reverse the effect. In protein phosphorylation, a phosphate group (PO 4 -3 ) is added to residues of the amino acids serine, threonine, and tyrosine. Second Messengers 

Second messengers are small molecules that propagate a signal after it has been initiated by the binding of the signaling molecule to the receptor. These molecules help to spread a signal through the cytoplasm by altering the behavior of certain cellular proteins. 

Calcium ion is a widely used second messenger. The free concentration of calcium ions (Ca 2+ ) within a cell is very low because ion pumps in the plasma membrane continuously use adenosine-5'-triphosphate (ATP) to remove it. For signaling purposes, Ca 2+ is stored in cytoplasmic vesicles, such as the endoplasmic reticulum, or accessed from outside the cell. When signaling occurs, ligand-gated calcium ion channels allow the higher levels of Ca 2+ that are present outside the cell (or in intracellular storage compartments) to flow into the cytoplasm, which raises the concentration of cytoplasmic Ca 2+ . The response to the increase in Ca 2+ varies, depending on the cell type involved. For example, in the -cells of the pancreas, Ca 2+ signaling leads to the release of insulin, and in muscle cells, an increase in Ca 2+ leads to muscle contractions. 

Another second messenger utilized in many different cell types is cyclic AMP (cAMP) . Cyclic AMP is synthesized by the enzyme adenylyl cyclase from ATP ( [link] ). The main role of cAMP in cells is to bind to and activate an enzyme called cAMP-dependent kinase (A-kinase) . A-kinase regulates many vital metabolic pathways: It phosphorylates serine and threonine residues of its target proteins, activating them in the process. A-kinase is found in many different types of cells, and the target proteins in each kind of cell are different. Differences give rise to the variation of the responses to cAMP in different cells. This diagram shows the mechanism for the formation of cyclic AMP (cAMP). cAMP serves as a second messenger to activate or inactivate proteins within the cell. Termination of the signal occurs when an enzyme called phosphodiesterase converts cAMP into AMP. 

Present in small concentrations in the plasma membrane, inositol phospholipids are lipids that can also be converted into second messengers. Because these molecules are membrane components, they are located near membrane-bound receptors and can easily interact with them. Phosphatidylinositol (PI) is the main phospholipid that plays a role in cellular signaling. Enzymes known as kinases phosphorylate PI to form PI-phosphate (PIP) and PI-bisphosphate (PIP 2 ). 

The enzyme phospholipase C cleaves PIP 2 to form diacylglycerol (DAG) and inositol triphosphate (IP 3 ) ( [link] ). These products of the cleavage of PIP 2 serve as second messengers. Diacylglycerol (DAG) remains in the plasma membrane and activates protein kinase C (PKC), which then phosphorylates serine and threonine residues in its target proteins. IP 3 diffuses into the cytoplasm and binds to ligand-gated calcium channels in the endoplasmic reticulum to release Ca 2+ that continues the signal cascade. The enzyme phospholipase C breaks down PIP 2 into IP 3 and DAG, both of which serve as second messengers. Think About It 

The same second messengers are used in many different cells, but the response to second messengers is different in each cell. How is this possible? 

This question is an application of Learning Objective 3.36 and Science Practice 1.5 because students are using a model of a cell signaling pathway to describe how signal transduction is converted to a cellular response. Answer: The second messenger interacts with protein targets and these proteins vary according to the cell. Review Questions 

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Ligand binding to the receptor allows for signal transduction through the cell. The chain of events that conveys the signal through the cell is called a signaling pathway or cascade. Signaling pathways are often very complex because of the interplay between different proteins. A major component of cell signaling cascades is the phosphorylation of molecules by enzymes known as kinases. Phosphorylation adds a phosphate group to serine, threonine, and tyrosine residues in a protein, changing their shapes, and activating or inactivating the protein. Small molecules like nucleotides can also be phosphorylated. Second messengers are small, non-protein molecules that are used to transmit a signal within a cell. Some examples of second messengers are calcium ions (Ca 2+ ), cyclic AMP (cAMP), diacylglycerol (DAG), and inositol triphosphate (IP 3 ). Glossary cyclic AMP (cAMP) second messenger that is derived from ATP cyclic AMP-dependent kinase (also, protein kinase A, or PKA) kinase that is activated by binding to cAMP diacylglycerol (DAG) cleavage product of PIP 2 that is used for signaling within the plasma membrane dimer chemical compound formed when two molecules join together dimerization (of receptor proteins) interaction of two receptor proteins to form a functional complex called a dimer inositol phospholipid lipid present at small concentrations in the plasma membrane that is converted into a second messenger; it has inositol (a carbohydrate) as its hydrophilic head group inositol triphosphate (IP 3 ) cleavage product of PIP 2 that is used for signaling within the cell kinase enzyme that catalyzes the transfer of a phosphate group from ATP to another molecule second messenger small, non-protein molecule that propagates a signal within the cell after activation of a receptor causes its release signal integration interaction of signals from two or more different cell-surface receptors that merge to activate the same response in the cell signal transduction propagation of the signal through the cytoplasm (and sometimes also the nucleus) of the cell signaling pathway (also signaling cascade) chain of events that occurs in the cytoplasm of the cell to propagate the signal from the plasma membrane to produce a responseResponse to the Signal Response to the Signal 

In this section you will explore the following questions: How do signaling pathways direct protein expression, cellular metabolism, and cell growth? What is the role of apoptosis in the development and maintenance of a healthy organism? Connection for AP Courses 

The initiation of a signaling pathway results in a cellular response to changes in the external environment. This response can take many different forms, including protein synthesis, a change in cell metabolism, cell division and growth, or even cell death. As we will explore in more detail in later chapters, some pathways activate enzymes that interact within DNA transcription factors to promote gene expression, others can cause cells to store energy as glycogen as fat, or result in free energy availability in the form of glucose. Cell division and growth are almost always stimulated by external signals called growth factors; left unregulated, cell growth leads to cancer. Programmed cell death, or apoptosis, removes damaged or unnecessary cells and plays a vital role in development, including morphogenesis of fingers and toes. Termination of the cell signaling cascade is important to ensure that the response to a signal is appropriate in timing and intensity. Degradation of signaling molecules and dephosphorylation of intermediates of the pathway are two ways signals are terminated within cells. Conditions where signaling pathways are blocked or defective can be deleterious, preventative, or prophylactic; examples include diabetes, heart disease, autoimmune disease, toxins, anesthetics, and birth control pills. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 3 and Big Idea 2 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.D Cells communicate by generating, transmitting and receiving chemical signals. Essential Knowledge 3.D.4 Changes in signal transduction pathways can alter cellular response. Science Practice 1.5 The student can re-express key elements of natural phenomena across multiple representations in the domain. Learning Objective 3.36 The student is able to describe a model that expresses the key elements of signal transduction pathways by which a signal is converted to a cellular response. Essential Knowledge 3.D.4 Changes in signal transduction pathways can alter cellular response. Science Practice 6.1 The student can justify claims with evidence. Learning Objective 3.37 The student is able to justify claims based on scientific evidence that changes in signal transduction pathways can alter cellular response. Essential Knowledge 3.D.4 Changes in signal transduction pathways can alter cellular response. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 3.39 The student is able to construct an explanation of how certain drugs affect signal reception and, consequently, signal transduction pathways. 

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. 

Enduring Understanding 2.E Many biological processes involved in growth, reproduction and dynamic homeostasis include temporal regulation and coordination. Essential Knowledge 2.E.1 Timing and coordination of specific events are necessary for the normal development of an organism, and these events are regulated by a variety of mechanisms. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 2.34 The student is able to describe the role of programmed cell death in development and differentiation, the reuse of molecules, and the maintenance of dynamic homeostasis. 

Remind students that response to the environment is one of the characteristics of life. Organisms must be able to perceive changes in the environment in order to survive. Ask students to make a list of which changes an organism should perceive to survive. The list may include availability of nutrients, changes in physical conditions, perception of noxious chemicals and the presence of predators. Multicellular organisms must be able to coordinate the responses of their cells. The integration of responses first requires signal transmission, then reception and transduction. The signaling pathways can easily confuse students. Many enzymes and other proteins are involved in cascading reactions. This website offers clear explanations of signal transduction and a number of activities to engage students using the flight-or-flight response as an example. The activity, Dealing Signals, can help students understand signaling pathways asks them to act as the components of a signaling pathway by taking cues from cell communication cards. Students mimic signaling pathways by running in place, interacting with specific classmates by either bumping into them or holding them, and leaning or lifting arms to simulate conformational changes. Further information about his activity can be found here . 

Inside the cell, ligands bind to their internal receptors, allowing them to directly affect the cell s DNA and protein-producing machinery. Using signal transduction pathways, receptors in the plasma membrane produce a variety of effects on the cell. The results of signaling pathways are extremely varied and depend on the type of cell involved as well as the external and internal conditions. A small sampling of responses is described below. Gene Expression 

Some signal transduction pathways regulate the transcription of RNA. Others regulate the translation of proteins from mRNA. An example of a protein that regulates translation in the nucleus is the MAP kinase ERK. ERK is activated in a phosphorylation cascade when epidermal growth factor (EGF) binds the EGF receptor (see [link] ). Upon phosphorylation, ERK enters the nucleus and activates a protein kinase that, in turn, regulates protein translation ( [link] ). ERK is a MAP kinase that activates translation when it is phosphorylated. ERK phosphorylates MNK1, which in turn phosphorylates eIF-4E, an elongation initiation factor that, with other initiation factors, is associated with mRNA. When eIF-4E becomes phosphorylated, the mRNA unfolds, allowing protein synthesis in the nucleus to begin. (See [link] for the phosphorylation pathway that activates ERK.) 

The second kind of protein with which PKC can interact is a protein that acts as an inhibitor. An inhibitor is a molecule that binds to a protein and prevents it from functioning or reduces its function. In this case, the inhibitor is a protein called I -B, which binds to the regulatory protein NF- B. (The symbol represents the Greek letter kappa.) When I -B is bound to NF- B, the complex cannot enter the nucleus of the cell, but when I -B is phosphorylated by PKC, it can no longer bind NF- B, and NF- B (a transcription factor) can enter the nucleus and initiate RNA transcription. In this case, the effect of phosphorylation is to inactivate an inhibitor and thereby activate the process of transcription. Increase in Cellular Metabolism 

The result of another signaling pathway affects muscle cells. The activation of -adrenergic receptors in muscle cells by adrenaline leads to an increase in cyclic AMP (cAMP) inside the cell. Also known as epinephrine, adrenaline is a hormone (produced by the adrenal gland attached to the kidney) that readies the body for short-term emergencies. Cyclic AMP activates PKA (protein kinase A), which in turn phosphorylates two enzymes. The first enzyme promotes the degradation of glycogen by activating intermediate glycogen phosphorylase kinase (GPK) that in turn activates glycogen phosphorylase (GP) that catabolizes glycogen into glucose. (Recall that your body converts excess glucose to glycogen for short-term storage. When energy is needed, glycogen is quickly reconverted to glucose.) Phosphorylation of the second enzyme, glycogen synthase (GS), inhibits its ability to form glycogen from glucose. In this manner, a muscle cell obtains a ready pool of glucose by activating its formation via glycogen degradation and by inhibiting the use of glucose to form glycogen, thus preventing a futile cycle of glycogen degradation and synthesis. The glucose is then available for use by the muscle cell in response to a sudden surge of adrenaline the fight or flight reflex. Cell Growth 

Cell signaling pathways also play a major role in cell division. Cells do not normally divide unless they are stimulated by signals from other cells. The ligands that promote cell growth are called growth factors . Most growth factors bind to cell-surface receptors that are linked to tyrosine kinases. These cell-surface receptors are called receptor tyrosine kinases (RTKs). Activation of RTKs initiates a signaling pathway that includes a G-protein called RAS, which activates the MAP kinase pathway described earlier. The enzyme MAP kinase then stimulates the expression of proteins that interact with other cellular components to initiate cell division. Cancer Biologist 

Cancer biologists study the molecular origins of cancer with the goal of developing new prevention methods and treatment strategies that will inhibit the growth of tumors without harming the normal cells of the body. As mentioned earlier, signaling pathways control cell growth. These signaling pathways are controlled by signaling proteins, which are, in turn, expressed by genes. Mutations in these genes can result in malfunctioning signaling proteins. This prevents the cell from regulating its cell cycle, triggering unrestricted cell division and cancer. The genes that regulate the signaling proteins are one type of oncogene which is a gene that has the potential to cause cancer. The gene encoding RAS is an oncogene that was originally discovered when mutations in the RAS protein were linked to cancer. Further studies have indicated that 30 percent of cancer cells have a mutation in the RAS gene that leads to uncontrolled growth. If left unchecked, uncontrolled cell division can lead tumor formation and metastasis, the growth of cancer cells in new locations in the body. 

Cancer biologists have been able to identify many other oncogenes that contribute to the development of cancer. For example, HER2 is a cell-surface receptor that is present in excessive amounts in 20 percent of human breast cancers. Cancer biologists realized that gene duplication led to HER2 overexpression in 25 percent of breast cancer patients and developed a drug called Herceptin (trastuzumab). Herceptin is a monoclonal antibody that targets HER2 for removal by the immune system. Herceptin therapy helps to control signaling through HER2. The use of Herceptin in combination with chemotherapy has helped to increase the overall survival rate of patients with metastatic breast cancer. 

More information on cancer biology research can be found at the National Cancer Institute website . Cell Death 

When a cell is damaged, superfluous, or potentially dangerous to an organism, a cell can initiate a mechanism to trigger programmed cell death, or apoptosis . Apoptosis allows a cell to die in a controlled manner that prevents the release of potentially damaging molecules from inside the cell. There are many internal checkpoints that monitor a cell s health; if abnormalities are observed, a cell can spontaneously initiate the process of apoptosis. However, in some cases, such as a viral infection or uncontrolled cell division due to cancer, the cell s normal checks and balances fail. External signaling can also initiate apoptosis. For example, most normal animal cells have receptors that interact with the extracellular matrix, a network of glycoproteins that provides structural support for cells in an organism. The binding of cellular receptors to the extracellular matrix initiates a signaling cascade within the cell. However, if the cell moves away from the extracellular matrix, the signaling ceases, and the cell undergoes apoptosis. This system keeps cells from traveling through the body and proliferating out of control, as happens with tumor cells that metastasize. 

Another example of external signaling that leads to apoptosis occurs in T-cell development. T-cells are immune cells that bind to foreign macromolecules and particles, and target them for destruction by the immune system. Normally, T-cells do not target self proteins (those of their own organism), a process that can lead to autoimmune diseases. In order to develop the ability to discriminate between self and non-self, immature T-cells undergo screening to determine whether they bind to so-called self proteins. If the T-cell receptor binds to self proteins, the cell initiates apoptosis to remove the potentially dangerous cell. 

Apoptosis is also essential for normal embryological development. In vertebrates, for example, early stages of development include the formation of web-like tissue between individual fingers and toes ( [link] ). During the course of normal development, these unneeded cells must be eliminated, enabling fully separated fingers and toes to form. A cell signaling mechanism triggers apoptosis, which destroys the cells between the developing digits. The histological section of a foot of a 15-day-old mouse embryo, visualized using light microscopy, reveals areas of tissue between the toes, which apoptosis will eliminate before the mouse reaches its full gestational age at 27 days. (credit: modification of work by Michal Ma as) Termination of the Signal Cascade 

The aberrant signaling often seen in tumor cells is proof that the termination of a signal at the appropriate time can be just as important as the initiation of a signal. One method of stopping a specific signal is to degrade the ligand or remove it so that it can no longer access its receptor. One reason that hydrophobic hormones like estrogen and testosterone trigger long-lasting events is because they bind carrier proteins. These proteins allow the insoluble molecules to be soluble in blood, but they also protect the hormones from degradation by circulating enzymes. 

Inside the cell, many different enzymes reverse the cellular modifications that result from signaling cascades. For example, phosphatases are enzymes that remove the phosphate group attached to proteins by kinases in a process called dephosphorylation. Cyclic AMP (cAMP) is degraded into AMP by phosphodiesterase , and the release of calcium stores is reversed by the Ca 2+ pumps that are located in the external and internal membranes of the cell. Activity 

Explain the mechanism by which a specific disease is caused by a defective signaling pathway. Then, investigate online how a specific drug works by blocking a signaling pathway. 

This activity is an application of Learning Objective 3.37, Science Practice 6.1, Learning Objective 3.39, and Science Practice 6.2 because the students are asked to justify the claim based on evidence that changes in signaling pathways can alter cellular response and cause disease, and explain how a specific drug can affect a signaling pathway. 

Another example is Parkinson s disease, in which the brain cells that make dopamine slowly die. Without dopamine, the cells that control movement cannot send messages to the muscles. The primary treatment helps increase dopamine levels in the brain by supplementing with L-dopa, a drug that converts to dopamine in the brain, or drugs that mimic dopamine and bind to the receptor. Like dopamine, serotonin is a neurotransmitter. It is linked to positive mood, emotion, and sleep. Most antidepressants block the reuptake or breakdown of serotonin and are called selective serotonin reuptake inhibitors (SSRIs). 

Stopping uncontrolled cell division is a major cancer research goal. The MAP kinase pathway stimulates the expression of proteins that interact with other cellular components to initiate cell division. By attacking proteins acting downstream in the MAP kinase, or MAPK pathway, cell division can be stopped or slowed down. One such protein is MEK. The Food and Drug Administration (FDA) recently approved one MEK inhibitor, trametinib (Mekinist ), for the treatment of certain patients with advanced melanoma. Section Summary 

The initiation of a signaling pathway is a response to external stimuli. This response can take many different forms, including protein synthesis, a change in the cell s metabolism, cell growth, or even cell death. Many pathways influence the cell by initiating gene expression, and the methods utilized are quite numerous. Some pathways activate enzymes that interact with DNA transcription factors. Others modify proteins and induce them to change their location in the cell. Depending on the status of the organism, cells can respond by storing energy as glycogen or fat, or making it available in the form of glucose. A signal transduction pathway allows muscle cells to respond to immediate requirements for energy in the form of glucose. Cell growth is almost always stimulated by external signals called growth factors. Uncontrolled cell growth leads to cancer, and mutations in the genes encoding protein components of signaling pathways are often found in tumor cells. Programmed cell death, or apoptosis, is important for removing damaged or unnecessary cells. The use of cellular signaling to organize the dismantling of a cell ensures that harmful molecules from the cytoplasm are not released into the spaces between cells, as they are in uncontrolled death, necrosis. Apoptosis also ensures the efficient recycling of the components of the dead cell. Termination of the cellular signaling cascade is very important so that the response to a signal is appropriate in both timing and intensity. Degradation of signaling molecules and dephosphorylation of phosphorylated intermediates of the pathway by phosphatases are two ways to terminate signals within the cell. Review Questions 

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[link] Glossary apoptosis programmed cell death growth factor ligand that binds to cell-surface receptors and stimulates cell growth inhibitor molecule that binds to a protein (usually an enzyme) and keeps it from functioning phosphatase enzyme that removes the phosphate group from a molecule that has been previously phosphorylated phosphodiesterase enzyme that degrades cAMP, producing AMP, to terminate signalingSignaling in Single-Celled Organisms Signaling in Single-Celled Organisms 

In this section, you will explore the following questions: How do single-celled yeasts use cell signaling to communicate with each other? How does quorum sensing allow some bacteria to form biofilms? Connection for AP Courses 

Cell signaling allows bacteria to respond to environmental cues, such as nutrient levels and quorum sensing (cell density). Yeasts are eukaryotes (fungi), and the components and processes found in yeast signals are similar to those of cell-surface receptor signals in multicellular organisms. For example, budding yeasts often release mating factors that enable them to participate in a process that is similar to sexual reproduction. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.D Cells communicate by generating, transmitting and receiving chemical signals. Essential Knowledge 3.D.1 Cell communication processes share common features that reflect a shared evolutionary history. Science Practice 1.5 The student can re-express key elements of natural phenomena across multiple representations in the domain. Learning Objective 3.36 The student is able to describe a model that expresses the key elements of signal transduction pathways by which a signal is converted to a cellular response. Essential Knowledge 3.D.1 Cell communication processes share common features that reflect a shared evolutionary history. Science Practice 6.1 The student can justify claims with evidence. Learning Objective 3.37 The student is able to justify claims based on scientific evidence that changes in signal transduction pathways can alter cellular response. 

Unicellular organisms were assumed to communicate at a very primitive level, but current research reveals the existence more complex signaling systems. Examples of these forms of communication are the formation of biofilms and quorum sensing. Biofilms have received the attention of researchers only recently for several historical and technical reasons. Since the germ theory of disease was established, the interest had been to isolate and characterize pathogens, not to study microorganisms as a community. 

It is much easier to grow bacteria as pure cultures than replicate mixed populations biofilms, making the latter difficult to study in the laboratory setting. Such slime layers, previously considered haphazard assemblies of microorganisms, have been found to be highly organized ecosystems. The slime layer is made of extracellular polymers crisscrossed with channels for gases, nutrients, waste exchanges. Microbes attach to the solid substrate in a succession of populations. 

Quorum sensing exists both within a same species and across species. It allows microbes to behave as multicellular populations and coordinate responses. One such example is the expression of genes encoding toxins in Staphylococcus aureus . Dr. Bonnie Bassler presents quorum sensing communication in Vibrio harveyi in this Ted Talk . Her enthusiasm and clear explanations make this video a thoroughly engaging experience. This is an opportunity to show a strong female role model in science. 

Also available is this video clip : Quorum sensing molecules presented by Dr. Bonnie Bassler: 

And an animation on quorum sensing in Vibrio harveyi can be found here . 

Further reading: Painter, Kimberley L. et al. (2014). What role does the quorum-sensing accessory gene regulator system play during Staphylococcus aureus bacteremia? Trends in Microbiology 22:676 685 

Within-cell signaling allows bacteria to respond to environmental cues, such as nutrient levels, some single-celled organisms also release molecules to signal to each other. Signaling in Yeast 

Yeasts are eukaryotes (fungi), and the components and processes found in yeast signals are similar to those of cell-surface receptor signals in multicellular organisms. Budding yeasts ( [link] ) are able to participate in a process that is similar to sexual reproduction that entails two haploid cells (cells with one-half the normal number of chromosomes) combining to form a diploid cell (a cell with two sets of each chromosome, which is what normal body cells contain). In order to find another haploid yeast cell that is prepared to mate, budding yeasts secrete a signaling molecule called mating factor . When mating factor binds to cell-surface receptors in other yeast cells that are nearby, they stop their normal growth cycles and initiate a cell signaling cascade that includes protein kinases and GTP-binding proteins that are similar to G-proteins. Budding Saccharomyces cerevisiae yeast cells can communicate by releasing a signaling molecule called mating factor. In this micrograph, they are visualized using differential interference contrast microscopy, a light microscopy technique that enhances the contrast of the sample. Signaling in Bacteria 

Signaling in bacteria enables bacteria to monitor extracellular conditions, ensure that there are sufficient amounts of nutrients, and ensure that hazardous situations are avoided. There are circumstances, however, when bacteria communicate with each other. 

The first evidence of bacterial communication was observed in a bacterium that has a symbiotic relationship with Hawaiian bobtail squid. When the population density of the bacteria reaches a certain level, specific gene expression is initiated, and the bacteria produce bioluminescent proteins that emit light. Because the number of cells present in the environment (cell density) is the determining factor for signaling, bacterial signaling was named quorum sensing . In politics and business, a quorum is the minimum number of members required to be present to vote on an issue. 

Quorum sensing uses autoinducers as signaling molecules. Autoinducers are signaling molecules secreted by bacteria to communicate with other bacteria of the same kind. The secreted autoinducers can be small, hydrophobic molecules such as acyl-homoserine lactone, (AHL) or larger peptide-based molecules; each type of molecule has a different mode of action. When AHL enters target bacteria, it binds to transcription factors, which then switch gene expression on or off ( [link] ). The peptide autoinducers stimulate more complicated signaling pathways that include bacterial kinases. The changes in bacteria following exposure to autoinducers can be quite extensive. The pathogenic bacterium Pseudomonas aeruginosa has 616 different genes that respond to autoinducers. 

Autoinducers are small molecules or proteins produced by bacteria that regulate gene expression. 

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Some species of bacteria that use quorum sensing form biofilms, complex colonies of bacteria (often containing several species) that exchange chemical signals to coordinate the release of toxins that will attack the host. Bacterial biofilms ( [link] ) can sometimes be found on medical equipment; when biofilms invade implants such as hip or knee replacements or heart pacemakers, they can cause life-threatening infections. Think About It 

Why is signaling in multicellular organisms more complicated than signaling in single-celled organisms such as microbes? 

This question is an application of LO 3.36 and Science Practice 1.5 because students are describing and comparing models of signaling pathways in different types of organisms. Presumably, unicellular organisms do not need to coordinate the response of many tissue types and organs. Point out to students that the study of cell-to-cell communication in microorganisms is only beginning. Assuming that multicellular organisms have more complicated signaling may well be a premature conclusion. 

Cell-cell communication enables these (a) Staphylococcus aureus bacteria to work together to form a biofilm inside a hospital patient s catheter, seen here via scanning electron microscopy. S. aureus is the main cause of hospital-acquired infections. (b) Hawaiian bobtail squid have a symbiotic relationship with the bioluminescent bacteria Vibrio fischeri . The luminescence makes it difficult to see the squid from below because it effectively eliminates its shadow. In return for camouflage, the squid provides food for the bacteria. Free-living V. fischeri do not produce luciferase, the enzyme responsible for luminescence, but V. fischeri living in a symbiotic relationship with the squid do. Quorum sensing determines whether the bacteria should produce the luciferase enzyme. (credit a: modifications of work by CDC/Janice Carr; credit b: modifications of work by Cliff1066/Flickr) 

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Research on the details of quorum sensing has led to advances in growing bacteria for industrial purposes. Recent discoveries suggest that it may be possible to exploit bacterial signaling pathways to control bacterial growth; this process could replace or supplement antibiotics that are no longer effective in certain situations. 

Watch geneticist Bonnie Bassler discuss her discovery of quorum sensing in biofilm bacteria in squid. 

[link] Cellular Communication in Yeasts 

The first life on our planet consisted of single-celled prokaryotic organisms that had limited interaction with each other. While some external signaling occurs between different species of single-celled organisms, the majority of signaling within bacteria and yeasts concerns only other members of the same species. The evolution of cellular communication is an absolute necessity for the development of multicellular organisms, and this innovation is thought to have required approximately 2.5 billion years to appear in early life forms. 

Yeasts are single-celled eukaryotes, and therefore have a nucleus and organelles characteristic of more complex life forms. Comparisons of the genomes of yeasts, nematode worms, fruit flies, and humans illustrate the evolution of increasingly complex signaling systems that allow for the efficient inner workings that keep humans and other complex life forms functioning correctly. 

Kinases are a major component of cellular communication, and studies of these enzymes illustrate the evolutionary connectivity of different species. Yeasts have 130 types of kinases. More complex organisms such as nematode worms and fruit flies have 454 and 239 kinases, respectively. Of the 130 kinase types in yeast, 97 belong to the 55 subfamilies of kinases that are found in other eukaryotic organisms. The only obvious deficiency seen in yeasts is the complete absence of tyrosine kinases. It is hypothesized that phosphorylation of tyrosine residues is needed to control the more sophisticated functions of development, differentiation, and cellular communication used in multicellular organisms. 

Because yeasts contain many of the same classes of signaling proteins as humans, these organisms are ideal for studying signaling cascades. Yeasts multiply quickly and are much simpler organisms than humans or other multicellular animals. Therefore, the signaling cascades are also simpler and easier to study, although they contain similar counterparts to human signaling. 1 

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Watch this collection of interview clips with biofilm researchers in What Are Bacterial Biofilms? 

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Yeasts and multicellular organisms have similar signaling mechanisms. Yeasts use cell-surface receptors and signaling cascades to communicate information on mating with other yeast cells. The signaling molecule secreted by yeasts is called mating factor. 

Bacterial signaling is called quorum sensing. Bacteria secrete signaling molecules called autoinducers that are either small, hydrophobic molecules or peptide-based signals. The hydrophobic autoinducers, such as AHL, bind transcription factors and directly affect gene expression. The peptide-based molecules bind kinases and initiate signaling cascades in the cells. Review Questions 

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G. Manning, G.D. Plowman, T. Hunter, S. Sudarsanam, Evolution of Protein Kinase Signaling from Yeast to Man, Trends in Biochemical Sciences 27, no. 10 (2002): 514 520. Glossary autoinducer signaling molecule secreted by bacteria to communicate with other bacteria of its kind and others mating factor signaling molecule secreted by yeast cells to communicate to nearby yeast cells that they are available to mate and communicating their mating orientation quorum sensing method of cellular communication used by bacteria that informs them of the abundance of similar (or different) bacteria in the environmentIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for sup AP #174; /sup Courses" A sea urchin begins life as a single cell that (a) divides to form two cells, visible by scanning electron microscopy. After four rounds of cell division, (b) there are 16 cells, as seen in this SEM image. After many rounds of cell division, the individual develops into a complex, multicellular organism, as seen in this (c) mature sea urchin. (credit a: modification of work by Evelyn Spiegel, Louisa Howard; credit b: modification of work by Evelyn Spiegel, Louisa Howard; credit c: modification of work by Marco Busdraghi; scale-bar data from Matt Russell) 

A human, as well as every sexually reproducing organism, begins life as a fertilized egg (embryo) or zygote. Trillions of cell divisions subsequently occur in a controlled manner to produce a complex, multicellular human. In other words, that original single cell is the ancestor of every other cell in the body. Once a being is fully grown, cell reproduction is still necessary to repair or regenerate tissues. For example, new blood and skin cells are constantly being produced. All multicellular organisms use cell division for growth, maintenance, and repair of tissues. Cell division is tightly regulated, and the occasional failure of regulation can have life-threatening consequences. Single-celled organisms use cell division as their method of reproduction. 

Not all cells in the body reproduce to repair tissues. Most nerve tissues, for example, are not capable of regeneration. This means people who have damaged their nerves or nervous system are often left paralyzed. 

However, this may change in the future; scientists have discovered a new drug called intracellular signal peptide (ISP), which helps nerve cells regenerate in rats. It works by blocking an enzyme that causes scar tissue in damaged nerve cells allowing the nervous system a chance to repair itself. The full research study is located here . 

Before students begin this chapter, it is useful to review these concepts: the differences between prokaryotes and eukaryotes; cell structure; cell signaling; cell growth and cell death.Cell Division Cell Division 

In this section, you will explore the following question: What is the relationship between chromosomes, genes, and traits in prokaryotes and eukaryotes? Connection for AP Courses 

All organisms, from bacteria to complex animals, must be able to store, retrieve, and transmit genetic information to continue life. In later chapters, we will explore how a cell s genetic information encoded in DNA, its genome, is replicated and passed to the next generation to direct the production of proteins, determining an organism s traits. Prokaryotes have single circular chromosome of DNA, whereas eukaryotes have multiple, linear chromosomes composed of chromatin (DNA wrapped around a histone protein) surrounded by a nuclear membrane. Cell division involves both mitosis, the division of the chromosomes, and cytokinesis, the division of the cytoplasm. Human somatic cells consist of 46 chromosomes 22 pairs of autosomal chromosomes and a pair of sex chromosomes. Prior to mitosis, each chromosome is duplicated to ensure that daughter cells receive the full amount of hereditary material contributed by both parents. The total number of autosomal chromosomes is referred to as the diploid (2 n ) number. (In the next chapter, we will study meiosis, the second type of cell division in sexually reproducing organisms.) 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework, as shown in the table. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA, and in some cases, RNA are the primary sources of heritable information. 

Ask students to bring in a picture of themselves as a baby, and a current picture. Ask them how do we change from a baby to an adult? What process is required to generate new cells? 

The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle is an orderly sequence of events that describes the stages of a cell s life from the division of a single parent cell to the production of two new daughter cells. The mechanisms involved in the cell cycle are highly regulated. Genomic DNA 

Before discussing the steps a cell must undertake to replicate, a deeper understanding of the structure and function of a cell s genetic information is necessary. A cell s DNA, packaged as a double-stranded DNA molecule, is called its genome . In prokaryotes, the genome is composed of a single, double-stranded DNA molecule in the form of a loop or circle ( [link] ). The region in the cell containing this genetic material is called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth. Bacteria can exchange these plasmids with other bacteria, sometimes receiving beneficial new genes that the recipient can add to their chromosomal DNA. Antibiotic resistance is one trait that often spreads through a bacterial colony through plasmid exchange. Prokaryotes, including bacteria and archaea, have a single, circular chromosome located in a central region called the nucleoid. 

In eukaryotes, the genome consists of several double-stranded linear DNA molecules ( [link] ). Each species of eukaryotes has a characteristic number of chromosomes in the nuclei of its cells. Human body cells have 46 chromosomes, while human gametes (sperm or eggs) have 23 chromosomes each. A typical body cell, or somatic cell, contains two matched sets of chromosomes, a configuration known as diploid . The letter n is used to represent a single set of chromosomes; therefore, a diploid organism is designated 2 n . Human cells that contain one set of chromosomes are called gametes, or sex cells; these are eggs and sperm, and are designated 1n , or haploid . There are 23 pairs of homologous chromosomes in a female human somatic cell. The condensed chromosomes are viewed within the nucleus (top), removed from a cell in mitosis and spread out on a slide (right), and artificially arranged according to length (left); an arrangement like this is called a karyotype. In this image, the chromosomes were exposed to fluorescent stains for differentiation of the different chromosomes. A method of staining called chromosome painting employs fluorescent dyes that highlight chromosomes in different colors. (credit: National Human Genome Project/NIH) 

Matched pairs of chromosomes in a diploid organism are called homologous ( same knowledge ) chromosomes . Homologous chromosomes are the same length and have specific nucleotide segments called genes in exactly the same location, or locus . Genes, the functional units of chromosomes, determine specific characteristics by coding for specific proteins. Traits are the variations of those characteristics. For example, hair color is a characteristic with traits that are blonde, brown, or black. 

Each copy of a homologous pair of chromosomes originates from a different parent; therefore, the genes themselves are not identical. The variation of individuals within a species is due to the specific combination of the genes inherited from both parents. Even a slightly altered sequence of nucleotides within a gene can result in an alternative trait. For example, there are three possible gene sequences on the human chromosome that code for blood type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that determines blood type, the blood type (the trait) is determined by which two versions of the marker gene are inherited. It is possible to have two copies of the same gene sequence on both homologous chromosomes, with one on each (for example, AA, BB, or OO), or two different sequences, such as AB. 

Minor variations of traits, such as blood type, eye color, and handedness, contribute to the natural variation found within a species. However, if the entire DNA sequence from any pair of human homologous chromosomes is compared, the difference is less than one percent. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosome uniformity: Other than a small amount of homology that is necessary to accurately produce gametes, the genes found on the X and Y chromosomes are different. Eukaryotic Chromosomal Structure and Compaction 

If the DNA from all 46 chromosomes in a human cell nucleus was laid out end to end, it would measure approximately two meters; however, its diameter would be only 2 nm. Considering that the size of a typical human cell is about 10 m (100,000 cells lined up to equal one meter), DNA must be tightly packaged to fit in the cell s nucleus. At the same time, it must also be readily accessible for the genes to be expressed. During some stages of the cell cycle, the long strands of DNA are condensed into compact chromosomes. There are a number of ways that chromosomes are compacted. 

In the first level of compaction, short stretches of the DNA double helix wrap around a core of eight histone proteins at regular intervals along the entire length of the chromosome ( [link] ). The DNA-histone complex is called chromatin. The beadlike, histone DNA complex is called a nucleosome , and DNA connecting the nucleosomes is called linker DNA. A DNA molecule in this form is about seven times shorter than the double helix without the histones, and the beads are about 10 nm in diameter, in contrast with the 2-nm diameter of a DNA double helix. The next level of compaction occurs as the nucleosomes and the linker DNA between them are coiled into a 30-nm chromatin fiber. This coiling further shortens the chromosome so that it is now about 50 times shorter than the extended form. In the third level of packing, a variety of fibrous proteins is used to pack the chromatin. These fibrous proteins also ensure that each chromosome in a non-dividing cell occupies a particular area of the nucleus that does not overlap with that of any other chromosome (see the top image in [link] ). Double-stranded DNA wraps around histone proteins to form nucleosomes that have the appearance of beads on a string. The nucleosomes are coiled into a 30-nm chromatin fiber. When a cell undergoes mitosis, the chromosomes condense even further. 

DNA replicates in the S phase of interphase. After replication, the chromosomes are composed of two linked sister chromatids . When fully compact, the pairs of identically packed chromosomes are bound to each other by cohesin proteins. The connection between the sister chromatids is closest in a region called the centromere . The conjoined sister chromatids, with a diameter of about 1 m, are visible under a light microscope. The centromeric region is highly condensed and thus will appear as a constricted area. 

This animation illustrates the different levels of chromosome packing. 

[link] Think About It 

What is the relationship between a genome and chromosomes? 

This question is an application of Learning Objective 3.1 and Science Practice 6.5 because the student is explaining the link between chromosomes and DNA as the source of hereditary information. 

Answer 

The genome consists of the sum total of an organism s chromosomes. Each chromosome contains hundreds and sometimes thousands of genes, segments of DNA that code for a polypeptide or RNA, and a large amount of DNA with no known function. This noncoding DNA, in the past called junk DNA, accounts for approximately 98% of the human genome. Noncoding DNA includes introns. Some noncoding DNA controls the expression of nearby genes, but most of it has unknown functions yet to be discovered. Section Summary 

Prokaryotes have a single circular chromosome composed of double-stranded DNA, whereas eukaryotes have multiple, linear chromosomes composed of chromatin surrounded by a nuclear membrane. The 46 chromosomes of human somatic cells are composed of 22 pairs of autosomes (matched pairs) and a pair of sex chromosomes, which may or may not be matched. This is the 2 n or diploid state. Human gametes have 23 chromosomes or one complete set of chromosomes; a set of chromosomes is complete with either one of the sex chromosomes. This is the n or haploid state. Genes are segments of DNA that code for a specific protein. An organism s traits are determined by the genes inherited from each parent. Duplicated chromosomes are composed of two sister chromatids. Chromosomes are compacted using a variety of mechanisms during certain stages of the cell cycle. Several classes of protein are involved in the organization and packing of the chromosomal DNA into a highly condensed structure. The condensing complex compacts chromosomes, and the resulting condensed structure is necessary for chromosomal segregation during mitosis. Review Questions 

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[link] Glossary cell cycle ordered sequence of events that a cell passes through between one cell division and the next centromere region at which sister chromatids are bound together; a constricted area in condensed chromosomes chromatid single DNA molecule of two strands of duplicated DNA and associated proteins held together at the centromere diploid cell, nucleus, or organism containing two sets of chromosomes (2 n ) gamete haploid reproductive cell or sex cell (sperm, pollen grain, or egg) gene physical and functional unit of heredity, a sequence of DNA that codes for a protein. genome total genetic information of a cell or organism haploid cell, nucleus, or organism containing one set of chromosomes ( n ) histone one of several similar, highly conserved, low molecular weight, basic proteins found in the chromatin of all eukaryotic cells; associates with DNA to form nucleosomes homologous chromosomes chromosomes of the same morphology with genes in the same location; diploid organisms have pairs of homologous chromosomes (homologs), with each homolog derived from a different parent locus position of a gene on a chromosome nucleosome subunit of chromatin composed of a short length of DNA wrapped around a core of histone proteinsThe Cell Cycle The Cell Cycle 

In this section, you will explore the following questions: What processes occur during the three stages of interphase? How do the chromosomes behave during the mitotic phase? Connection for AP Courses 

The cell cycle describes an orderly sequence of events that are highly regulated. In eukaryotes, the cell cycle consists of a long preparatory period (interphase) followed by mitosis and cytokinesis. Interphase is divided into three phases: Gap 1 (G 1 ), DNA synthesis (S), and Gap 2 (G 2 ). Interphase represents the portion of the cell cycle between nuclear divisions. During this phase, preparations are made for division that include growth, duplication of most cellular contents, and replication of DNA. The cell s DNA is replicated during the S stage. (We will study the details of DNA replication in the chapter on DNA structure and function.) Following the G 2 stage of interphase, the cell begins mitosis, the process of active division by which duplicated chromosomes (chromatids) attach to spindle fibers, align themselves along the equator of the cell, and then separate from each other. 

Following mitosis, the cell undergoes cytokinesis, the splitting of the parent cell into two daughter cells, complete with a full complement of genetic material. In animal cells, daughter cells are separated by an actin ring, whereas plant cells are separated by the cell plate, which will grow into a new cell wall. Sometimes cells enter a Gap zero (G 0 ) phase, during which they do not actively prepare to divide; the G 0 phase can be temporary until triggered by an external signal to enter G 1 , or permanent, such as mature cardiac muscle cells and nerve cells. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework, as shown in the tables. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.7 The student can make predictions about natural phenomena occurring during the cell cycle. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.8 The student can describe the events that occur in the cell cycle. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 6.3 The student can articulate the reasons that scientific explanations and theories are refined or replaced. Learning Objective 3.9 The student is able to construct an explanation, using visual representations or narratives, as to how DNA in chromosomes is transmitted to the next generation via mitosis. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 3.11 The student is able to evaluate evidence provided by data sets to support the claim that heritable information is passed from one generation to another generation through mitosis. 

Discuss with students the difference between diploid and haploid cells. Show students a graphic of the difference. 

Discuss with students how in mitosis, the ploidy of the cell remains constant. In a cell culture of human somatic cells, all of the cells will be diploid. In contrast the DNA content, the amount of DNA in a cell culture will change as the cells replicate (undergo S-phase and replicate their DNA). In relative amounts, the initial amount of DNA is considered to be 1x, after S-phase it will be 2x, and so on. More information on the methods used by scientists to track ploidy can be found here . 

Introduce mitosis using visuals such as this video . 

Show Crash Course or Bozeman Videos such as Cell Cycle, Mitosis Meiosis , Development: Timing Coordination , Mechanisms of Timing Control , DNA, Hot Pockets, The Longest Word Ever: Crash Course Biology #11 , and HHMI: Mix 1 

Students may think that interphase is a resting phase, where no events occur. Remind students that cells are metabolically active in this phase. Cells in G 0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage that occurs when cells exit the cell cycle. Some cells enter G 0 temporarily until an external signal triggers the onset of G 1 . Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G 0 permanently. 

In addition, students may not realize that the events of mitosis are continuous, and the organization into discrete stages is for convenience. Show students a time lapse video to illustrate this, such as found here . 

The stages of the cell cycle can be taught using the images available here . 

The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and division that produces two identical (clone) cells. The cell cycle has two major phases: interphase and the mitotic phase ( [link] ). During interphase , the cell grows and DNA is replicated. During the mitotic phase , the replicated DNA and cytoplasmic contents are separated, and the cell divides. The cell cycle consists of interphase and the mitotic phase. During interphase, the cell grows and the nuclear DNA is duplicated. Interphase is followed by the mitotic phase. During the mitotic phase, the duplicated chromosomes are segregated and distributed into daughter nuclei. The cytoplasm is usually divided as well, resulting in two daughter cells. Interphase 

During interphase, the cell undergoes normal growth processes while also preparing for cell division. In order for a cell to move from interphase into the mitotic phase, many internal and external conditions must be met. The three stages of interphase are called G 1 , S, and G 2 . G 1 Phase (First Gap) 

The first stage of interphase is called the G 1 phase (first gap) because, from a microscopic aspect, little change is visible. However, during the G 1 stage, the cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated proteins as well as accumulating sufficient energy reserves to complete the task of replicating each chromosome in the nucleus. S Phase (Synthesis of DNA) 

Throughout interphase, nuclear DNA remains in a semi-condensed chromatin configuration. In the S phase , DNA replication can proceed through the mechanisms that result in the formation of identical pairs of DNA molecules sister chromatids that are firmly attached to the centromeric region. The centrosome is duplicated during the S phase. The two centrosomes will give rise to the mitotic spindle , the apparatus that orchestrates the movement of chromosomes during mitosis. At the center of each animal cell, the centrosomes of animal cells are associated with a pair of rod-like objects, the centrioles , which are at right angles to each other. Centrioles help organize cell division. Centrioles are not present in the centrosomes of other eukaryotic species, such as plants and most fungi. G 2 Phase (Second Gap) 

In the G 2 phase , the cell replenishes its energy stores and synthesizes proteins necessary for chromosome manipulation. Some cell organelles are duplicated, and the cytoskeleton is dismantled to provide resources for the mitotic phase. There may be additional cell growth during G 2 . The final preparations for the mitotic phase must be completed before the cell is able to enter the first stage of mitosis. The Mitotic Phase 

The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and move into two new, identical daughter cells. The first portion of the mitotic phase is called karyokinesis , or nuclear division. The second portion of the mitotic phase, called cytokinesis, is the physical separation of the cytoplasmic components into the two daughter cells. 

Revisit the stages of mitosis at this site . 

[link] Karyokinesis (Mitosis) 

Karyokinesis, also known as mitosis , is divided into a series of phases prophase, prometaphase, metaphase, anaphase, and telophase that result in the division of the cell nucleus ( [link] ). Karyokinesis is also called mitosis. 

These budding plants demonstrate asexual reproduction, one of the main purposes of mitosis. The other two purposes are growth and repair. 

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Karyokinesis (or mitosis) is divided into five stages prophase, prometaphase, metaphase, anaphase, and telophase. The pictures at the bottom were taken by fluorescence microscopy (hence, the black background) of cells artificially stained by fluorescent dyes: blue fluorescence indicates DNA (chromosomes) and green fluorescence indicates microtubules (spindle apparatus). (credit mitosis drawings : modification of work by Mariana Ruiz Villareal; credit micrographs : modification of work by Roy van Heesbeen; credit cytokinesis micrograph : Wadsworth Center/New York State Department of Health; scale-bar data from Matt Russell) 

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During prophase , the first phase, the nuclear envelope starts to dissociate into small vesicles, and the membranous organelles (such as the Golgi complex or Golgi apparatus, and endoplasmic reticulum), fragment and disperse toward the periphery of the cell. The nucleolus disappears (disperses). The centrosomes begin to move to opposite poles of the cell. Microtubules that will form the mitotic spindle extend between the centrosomes, pushing them farther apart as the microtubule fibers lengthen. The sister chromatids begin to coil more tightly with the aid of condensin proteins and become visible under a light microscope. 

During prometaphase , the first change phase, many processes that were begun in prophase continue to advance. The remnants of the nuclear envelope fragment. The mitotic spindle continues to develop as more microtubules assemble and stretch across the length of the former nuclear area. Chromosomes become more condensed and discrete. Each sister chromatid develops a protein structure called a kinetochore in the centromeric region ( [link] ). The proteins of the kinetochore attract and bind mitotic spindle microtubules. As the spindle microtubules extend from the centrosomes, some of these microtubules come into contact with and firmly bind to the kinetochores. Once a mitotic fiber attaches to a chromosome, the chromosome will be oriented until the kinetochores of sister chromatids face the opposite poles. Eventually, all the sister chromatids will be attached via their kinetochores to microtubules from opposing poles. Spindle microtubules that do not engage the chromosomes are called polar microtubules. These microtubules overlap each other midway between the two poles and contribute to cell elongation. Astral microtubules are located near the poles, aid in spindle orientation, and are required for the regulation of mitosis. During prometaphase, mitotic spindle microtubules from opposite poles attach to each sister chromatid at the kinetochore. In anaphase, the connection between the sister chromatids breaks down, and the microtubules pull the chromosomes toward opposite poles. 

During metaphase , the change phase, all the chromosomes are aligned in a plane called the metaphase plate , or the equatorial plane, midway between the two poles of the cell. The sister chromatids are still tightly attached to each other by cohesin proteins. At this time, the chromosomes are maximally condensed. 

During anaphase , the upward phase, the cohesin proteins degrade, and the sister chromatids separate at the centromere. Each chromatid, now called a chromosome, is pulled rapidly toward the centrosome to which its microtubule is attached. The cell becomes visibly elongated (oval shaped) as the polar microtubules slide against each other at the metaphase plate where they overlap. 

During telophase , the distance phase, the chromosomes reach the opposite poles and begin to decondense (unravel), relaxing into a chromatin configuration. The mitotic spindles are depolymerized into tubulin monomers that will be used to assemble cytoskeletal components for each daughter cell. Nuclear envelopes form around the chromosomes, and nucleosomes appear within the nuclear area. Cytokinesis 

Cytokinesis , or cell motion, is the second main stage of the mitotic phase during which cell division is completed via the physical separation of the cytoplasmic components into two daughter cells. Division is not complete until the cell components have been apportioned and completely separated into the two daughter cells. Although the stages of mitosis are similar for most eukaryotes, the process of cytokinesis is quite different for eukaryotes that have cell walls, such as plant cells. 

In cells such as animal cells that lack cell walls, cytokinesis follows the onset of anaphase. A contractile ring composed of actin filaments forms just inside the plasma membrane at the former metaphase plate. The actin filaments pull the equator of the cell inward, forming a fissure. This fissure, or crack, is called the cleavage furrow . The furrow deepens as the actin ring contracts, and eventually the membrane is cleaved in two ( [link] ). 

In plant cells, a new cell wall must form between the daughter cells. During interphase, the Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules prior to breaking into vesicles and dispersing throughout the dividing cell. During telophase, these Golgi vesicles are transported on microtubules to form a phragmoplast (a vesicular structure) at the metaphase plate. There, the vesicles fuse and coalesce from the center toward the cell walls; this structure is called a cell plate . As more vesicles fuse, the cell plate enlarges until it merges with the cell walls at the periphery of the cell. Enzymes use the glucose that has accumulated between the membrane layers to build a new cell wall. The Golgi membranes become parts of the plasma membrane on either side of the new cell wall ( [link] ). During cytokinesis in animal cells, a ring of actin filaments forms at the metaphase plate. The ring contracts, forming a cleavage furrow, which divides the cell in two. In plant cells, Golgi vesicles coalesce at the former metaphase plate, forming a phragmoplast. A cell plate formed by the fusion of the vesicles of the phragmoplast grows from the center toward the cell walls, and the membranes of the vesicles fuse to form a plasma membrane that divides the cell in two. Activity Use a set of pipe cleaners (or other materials as directed by your teacher) that you can use to model chromosomes during mitosis and meiosis: Each of the pipe cleaners represents a single, unreplicated chromosome. Each chromosome should differ in size, as they do in most organisms. Assume that your dividing cell contains 3 chromosomes: numbered chromosome 1, 2, and 3. Using both members of each homologous pair for chromosomes 1 3, model how the chromosomes would appear in a cell that had just finished the S phase of the cell cycle. Once your teacher has approved your model, have one member of your group document the model by photographing or drawing it. Now, repeat step 2 but show the cell at metaphase during mitosis. Finally, model the two daughter cells that will result from mitosis. Again, have one member of your group document the model. Repeat steps 2 5 for both meiosis I and meiosis II. Remember that you should have four daughter cells at the end of meiosis II. Also remember to ask your teacher for approval and document your model before moving on to the next phase of meiosis. Exchange/ copy all of the drawings or photographs that your group took of your models. As a group or individually (as directed by your teacher) create a report to turn in that labels and explain each picture of your model. An organism s ploidy count is the total number of chromosome sets contained in each body cell. Most organisms have a ploidy level of 2, meaning that they have two sets of chromosomes due to presence of homologous pairs. However, some plants are multiploid, meaning they can have ploidy levels greater than 2. The table shows possible multiploid levels of some common crop plants. Common name Multiploid chromosome count Normal chromosome count Bananas 33 11 Potatoes 48 12 Wheat 42 7 Sugar cane 80 10 

Analyze the data with a partner of in a group as directed by your teacher. On a separate sheet of paper, answer the following questions. How does the multiploid count of the crop plants relate to their normal chromosome count? Explain the basis for the relationship you described in part a, in terms of what occurs to chromosomes during replication and meiosis. Give one additional example of a possible multiploid chromosome count for each species in the table above. Think About It 

Chemotherapy drugs such as vincristine and colchicines disrupt mitosis by binding to tubulin (the subunit of microtubules) and interfering with microtubule assembly and disassembly. What mitotic structure is targeted by these drugs, and what effect would this have on cell division? 

The first activity is an application of Learning Objective 3.8 and Science Practice 1.2 because students are modelling steps of the cell cycle, including mitosis and meiosis. A variety of materials can be used to represent chromosomes in the model as long as the students can easily distinguish between the three chromosomes (such as by having different-sized pipe cleaners) as well as distinguish between homologs (such as by using two colors of pipe cleaner). Be sure to provide enough chromosomes to represent sister chromatids in both the mitosis and meiosis models. The critical point to stress is that, in modelling mitosis, students should place homologous chromosomes (each with a sister chromatid) above and below each other during metaphase, ensuring a sister chromosome from each homolog enters each daughter cell. Conversely, in metaphase I of meiosis, the homologous chromosomes (each with a sister chromatid) will pair together side-by-side so that each cell only receives one of the two homologs. 

The second activity is an application of Learning Objective 3.11 and Science Practice 5.3 because students are using their knowledge of meiosis to explain and predict possible ploidy levels in crop plants. Students should work in pairs or as a group. 

An expanded lab investigation for mitosis and meiosis, involving studying onion cells undergoing mitosis (part 2), and karyotype analysis (part 3) is available from the College Board s AP Biology Investigative Labs: An Inquiry-Based Approach in Investigation 7 . Possible Answer The multiploid count is always a whole-number multiple of the normal chromosome count. Before meiosis (and mitosis) all of an organism s chromosomes are replicated before any segregation takes place. Therefore, ploidy levels will always involve whole-number multiples of the original chromosome levels. Answers will vary but all answers should be whole-number multiples of the normal chromosome numbers. 

The Think About It question is an application of Learning Objective 3.7 and Science Practice 6.4 because the student must be able to describe the events that occur in the cell cycle before you can make a prediction about the effects of a disruption in mitosis. Possible Answer 

The mitotic spindle is formed of microtubules. Microtubules are polymers of the protein tubulin; therefore, it is the mitotic spindle that is disrupted by these drugs. Without a functional mitotic spindle, the chromosomes will not be sorted or separated during mitosis. The cell will arrest in mitosis and die. G 0 Phase 

Not all cells adhere to the classic cell cycle pattern in which a newly formed daughter cell immediately enters the preparatory phases of interphase, closely followed by the mitotic phase. Cells in G 0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage that occurs when cells exit the cell cycle. Some cells enter G 0 temporarily until an external signal triggers the onset of G 1 . Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G 0 permanently. 

Determine the Time Spent in Cell Cycle Stages 

Problem : How long does a cell spend in interphase compared to each stage of mitosis? 

Background : A prepared microscope slide of blastula cross-sections will show cells arrested in various stages of the cell cycle. It is not visually possible to separate the stages of interphase from each other, but the mitotic stages are readily identifiable. If 100 cells are examined, the number of cells in each identifiable cell cycle stage will give an estimate of the time it takes for the cell to complete that stage. 

Problem Statement : Given the events included in all of interphase and those that take place in each stage of mitosis, estimate the length of each stage based on a 24-hour cell cycle. Before proceeding, state your hypothesis. 

Test your hypothesis : Test your hypothesis by doing the following: Place a fixed and stained microscope slide of whitefish blastula cross-sections under the scanning objective of a light microscope. Locate and focus on one of the sections using the scanning objective of your microscope. Notice that the section is a circle composed of dozens of closely packed individual cells. Switch to the low-power objective and refocus. With this objective, individual cells are visible. 

Switch to the high-power objective and slowly move the slide left to right, and up and down to view all the cells in the section ( [link] ). As you scan, you will notice that most of the cells are not undergoing mitosis but are in the interphase period of the cell cycle. 

Slowly scan whitefish blastula cells with the high-power objective as illustrated in image (a) to identify their mitotic stage. (b) A microscopic image of the scanned cells is shown. (credit micrograph : modification of work by Linda Flora; scale-bar data from Matt Russell) Practice identifying the various stages of the cell cycle, using the drawings of the stages as a guide ( [link] ). Once you are confident about your identification, begin to record the stage of each cell you encounter as you scan left to right, and top to bottom across the blastula section. Keep a tally of your observations and stop when you reach 100 cells identified. The larger the sample size (total number of cells counted), the more accurate the results. If possible, gather and record group data prior to calculating percentages and making estimates. 

Record your observations : Make a table similar to [link] in which you record your observations. Results of Cell Stage Identification Phase or Stage Individual Totals Group Totals Percent Interphase Prophase Metaphase Anaphase Telophase Cytokinesis Totals 100 100 100 percent 

Analyze your data/report your results : To find the length of time whitefish blastula cells spend in each stage, multiply the percent (recorded as a decimal) by 24 hours. Make a table similar to [link] to illustrate your data. Estimate of Cell Stage Length Phase or Stage Percent (as Decimal) Time in Hours Interphase Prophase Metaphase Anaphase Telophase Cytokinesis Section Summary 

The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase. Interphase is divided into G 1 , S, and G 2 phases. The mitotic phase begins with karyokinesis (mitosis), which consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase. The final stage of the mitotic phase is cytokinesis, during which the cytoplasmic components of the daughter cells are separated either by an actin ring (animal cells) or by cell plate formation (plant cells). Review Questions 

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[link] Glossary anaphase stage of mitosis during which sister chromatids are separated from each other cell cycle ordered series of events involving cell growth and cell division that produces two new daughter cells cell plate structure formed during plant cell cytokinesis by Golgi vesicles, forming a temporary structure (phragmoplast) and fusing at the metaphase plate; ultimately leads to the formation of cell walls that separate the two daughter cells centriole rod-like structure constructed of microtubules at the center of each animal cell centrosome cleavage furrow constriction formed by an actin ring during cytokinesis in animal cells that leads to cytoplasmic division condensin proteins that help sister chromatids coil during prophase cytokinesis division of the cytoplasm following mitosis that forms two daughter cells. G 0 phase distinct from the G 1 phase of interphase; a cell in G 0 is not preparing to divide G 1 phase (also, first gap) first phase of interphase centered on cell growth during mitosis G 2 phase (also, second gap) third phase of interphase during which the cell undergoes final preparations for mitosis interphase period of the cell cycle leading up to mitosis; includes G 1 , S, and G 2 phases (the interim period between two consecutive cell divisions karyokinesis mitotic nuclear division kinetochore protein structure associated with the centromere of each sister chromatid that attracts and binds spindle microtubules during prometaphase metaphase plate equatorial plane midway between the two poles of a cell where the chromosomes align during metaphase metaphase stage of mitosis during which chromosomes are aligned at the metaphase plate mitosis (also, karyokinesis) period of the cell cycle during which the duplicated chromosomes are separated into identical nuclei; includes prophase, prometaphase, metaphase, anaphase, and telophase mitotic phase period of the cell cycle during which duplicated chromosomes are distributed into two nuclei and cytoplasmic contents are divided; includes karyokinesis (mitosis) and cytokinesis mitotic spindle apparatus composed of microtubules that orchestrates the movement of chromosomes during mitosis prometaphase stage of mitosis during which the nuclear membrane breaks down and mitotic spindle fibers attach to kinetochores prophase stage of mitosis during which chromosomes condense and the mitotic spindle begins to form quiescent refers to a cell that is performing normal cell functions and has not initiated preparations for cell division S phase second, or synthesis, stage of interphase during which DNA replication occurs telophase stage of mitosis during which chromosomes arrive at opposite poles, decondense, and are surrounded by a new nuclear envelopeControl of the Cell Cycle Control of the Cell Cycle 

In this section, you will explore the following questions: What are examples of internal and external mechanisms that control the cell cycle? What molecules are involved in controlling the cell cycle through positive and negative regulation? Connection for AP Courses 

Each step of the cell cycle is closely monitored by external signals and internal controls called checkpoints. There are three major checkpoints in the cell cycle: one near the end of G 1 , a second at the G 2 /M transition, and the third during metaphase. Growth factor proteins arriving at the dividing cell s plasma membrane can trigger the cell to begin dividing. Cyclins and cyclin-dependent kinases (Cdks) are internal molecular signals that regulate cell transitions through the various checkpoints. Passage through the G 1 checkpoint makes sure that the cell is ready for DNA replication in the S stage of interphase; passage through the G 2 checkpoint triggers the separation of chromatids during mitosis. Positive regulator molecules like the cyclins and Cdks allow the cell cycle to advance to the next stage; negative regulator molecules, such as tumor suppressor proteins, monitor cellular conditions and can halt the cycle until specific requirements are met. Errors in the regulation of the cell cycle can cause cancer, which is characterized by uncontrolled cell division. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework, as shown in the tables. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.7 The student can make predictions about natural phenomena occurring during the cell cycle. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.8 The student can describe the events that occur in the cell cycle. 

Introduce the topic of control of the cell cycle using visuals such as this video . 

The length of the cell cycle is highly variable, even within the cells of a single organism. In humans, the frequency of cell turnover ranges from a few hours in early embryonic development, to an average of two to five days for epithelial cells, and to an entire human lifetime spent in G 0 by specialized cells, such as cortical neurons or cardiac muscle cells. There is also variation in the time that a cell spends in each phase of the cell cycle. When fast-dividing mammalian cells are grown in culture (outside the body under optimal growing conditions), the length of the cycle is about 24 hours. In rapidly dividing human cells with a 24-hour cell cycle, the G 1 phase lasts approximately nine hours, the S phase lasts 10 hours, the G 2 phase lasts about four and one-half hours, and the M phase lasts approximately one-half hour. In early embryos of fruit flies, the cell cycle is completed in about eight minutes. The timing of events in the cell cycle is controlled by mechanisms that are both internal and external to the cell. Regulation of the Cell Cycle by External Events 

Both the initiation and inhibition of cell division are triggered by events external to the cell when it is about to begin the replication process. An event may be as simple as the death of a nearby cell or as sweeping as the release of growth-promoting hormones, such as human growth hormone (HGH). A lack of HGH can inhibit cell division, resulting in dwarfism, whereas too much HGH can result in gigantism. Crowding of cells can also inhibit cell division. Another factor that can initiate cell division is the size of the cell; as a cell grows, it becomes inefficient due to its decreasing surface-to-volume ratio. The solution to this problem is to divide. 

Whatever the source of the message, the cell receives the signal, and a series of events within the cell allows it to proceed into interphase. Moving forward from this initiation point, every parameter required during each cell cycle phase must be met or the cycle cannot progress. Regulation at Internal Checkpoints 

It is essential that the daughter cells produced be exact duplicates of the parent cell. Mistakes in the duplication or distribution of the chromosomes lead to mutations that may be passed forward to every new cell produced from an abnormal cell. To prevent a compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell cycle checkpoints . A checkpoint is one of several points in the eukaryotic cell cycle at which the progression of a cell to the next stage in the cycle can be halted until conditions are favorable. These checkpoints occur near the end of G 1 , at the G 2 /M transition, and during metaphase ( [link] ). The cell cycle is controlled at three checkpoints. The integrity of the DNA is assessed at the G 1 checkpoint. Proper chromosome duplication is assessed at the G 2 checkpoint. Attachment of each kinetochore to a spindle fiber is assessed at the M checkpoint. The G 1 Checkpoint 

The G 1 checkpoint determines whether all conditions are favorable for cell division to proceed. The G 1 checkpoint, also called the restriction point (in yeast), is a point at which the cell irreversibly commits to the cell division process. External influences, such as growth factors, play a large role in carrying the cell past the G 1 checkpoint. In addition to adequate reserves and cell size, there is a check for genomic DNA damage at the G 1 checkpoint. A cell that does not meet all the requirements will not be allowed to progress into the S phase. The cell can halt the cycle and attempt to remedy the problematic condition, or the cell can advance into G 0 and await further signals when conditions improve. The G 2 Checkpoint 

The G 2 checkpoint bars entry into the mitotic phase if certain conditions are not met. As at the G 1 checkpoint, cell size and protein reserves are assessed. However, the most important role of the G 2 checkpoint is to ensure that all of the chromosomes have been replicated and that the replicated DNA is not damaged. If the checkpoint mechanisms detect problems with the DNA, the cell cycle is halted, and the cell attempts to either complete DNA replication or repair the damaged DNA. The M Checkpoint 

The M checkpoint occurs near the end of the metaphase stage of karyokinesis. The M checkpoint is also known as the spindle checkpoint, because it determines whether all the sister chromatids are correctly attached to the spindle microtubules. Because the separation of the sister chromatids during anaphase is an irreversible step, the cycle will not proceed until the kinetochores of each pair of sister chromatids are firmly anchored to at least two spindle fibers arising from opposite poles of the cell. 

Watch what occurs at the G 1 , G 2 , and M checkpoints by visiting this website to see an animation of the cell cycle. 

[link] Regulator Molecules of the Cell Cycle 

In addition to the internally controlled checkpoints, there are two groups of intracellular molecules that regulate the cell cycle. These regulatory molecules either promote progress of the cell to the next phase (positive regulation) or halt the cycle (negative regulation). Regulator molecules may act individually, or they can influence the activity or production of other regulatory proteins. Therefore, the failure of a single regulator may have almost no effect on the cell cycle, especially if more than one mechanism controls the same event. Conversely, the effect of a deficient or non-functioning regulator can be wide-ranging and possibly fatal to the cell if multiple processes are affected. Positive Regulation of the Cell Cycle 

Two groups of proteins, called cyclins and cyclin-dependent kinases (Cdks), are responsible for the progress of the cell through the various checkpoints. The levels of the four cyclin proteins fluctuate throughout the cell cycle in a predictable pattern ( [link] ). Increases in the concentration of cyclin proteins are triggered by both external and internal signals. After the cell moves to the next stage of the cell cycle, the cyclins that were active in the previous stage are degraded. The concentrations of cyclin proteins change throughout the cell cycle. There is a direct correlation between cyclin accumulation and the three major cell cycle checkpoints. Also note the sharp decline of cyclin levels following each checkpoint (the transition between phases of the cell cycle), as cyclin is degraded by cytoplasmic enzymes. (credit: modification of work by "WikiMiMa"/Wikimedia Commons) 

Cyclins regulate the cell cycle only when they are tightly bound to Cdks. To be fully active, the Cdk/cyclin complex must also be phosphorylated in specific locations. Like all kinases, Cdks are enzymes (kinases) that phosphorylate other proteins. Phosphorylation activates the protein by changing its shape. The proteins phosphorylated by Cdks are involved in advancing the cell to the next phase. ( [link] ). The levels of Cdk proteins are relatively stable throughout the cell cycle; however, the concentrations of cyclin fluctuate and determine when Cdk/cyclin complexes form. The different cyclins and Cdks bind at specific points in the cell cycle and thus regulate different checkpoints. Cyclin-dependent kinases (Cdks) are protein kinases that, when fully activated, can phosphorylate and thus activate other proteins that advance the cell cycle past a checkpoint. To become fully activated, a Cdk must bind to a cyclin protein and then be phosphorylated by another kinase. 

Since the cyclic fluctuations of cyclin levels are based on the timing of the cell cycle and not on specific events, regulation of the cell cycle usually occurs by either the Cdk molecules alone or the Cdk/cyclin complexes. Without a specific concentration of fully activated cyclin/Cdk complexes, the cell cycle cannot proceed through the checkpoints. 

Although the cyclins are the main regulatory molecules that determine the forward momentum of the cell cycle, there are several other mechanisms that fine-tune the progress of the cycle with negative, rather than positive, effects. These mechanisms essentially block the progression of the cell cycle until problematic conditions are resolved. Molecules that prevent the full activation of Cdks are called Cdk inhibitors. Many of these inhibitor molecules directly or indirectly monitor a particular cell cycle event. The block placed on Cdks by inhibitor molecules will not be removed until the specific event that the inhibitor monitors is completed. Negative Regulation of the Cell Cycle 

The second group of cell cycle regulatory molecules are negative regulators. Negative regulators halt the cell cycle. Remember that in positive regulation, active molecules cause the cycle to progress. 

The best understood negative regulatory molecules are retinoblastoma protein (Rb) , p53 , and p21 . Retinoblastoma proteins are a group of tumor-suppressor proteins common in many cells. The 53 and 21 designations refer to the functional molecular masses of the proteins (p) in kilodaltons. Much of what is known about cell cycle regulation comes from research conducted with cells that have lost regulatory control. All three of these regulatory proteins were discovered to be damaged or non-functional in cells that had begun to replicate uncontrollably (became cancerous). In each case, the main cause of the unchecked progress through the cell cycle was a faulty copy of the regulatory protein. 

Rb, p53, and p21 act primarily at the G 1 checkpoint. p53 is a multi-functional protein that has a major impact on the commitment of a cell to division because it acts when there is damaged DNA in cells that are undergoing the preparatory processes during G 1 . If damaged DNA is detected, p53 halts the cell cycle and recruits enzymes to repair the DNA. If the DNA cannot be repaired, p53 can trigger apoptosis, or cell suicide, to prevent the duplication of damaged chromosomes. As p53 levels rise, the production of p21 is triggered. p21 enforces the halt in the cycle dictated by p53 by binding to and inhibiting the activity of the Cdk/cyclin complexes. As a cell is exposed to more stress, higher levels of p53 and p21 accumulate, making it less likely that the cell will move into the S phase. 

Rb exerts its regulatory influence on other positive regulator proteins. Chiefly, Rb monitors cell size. In the active, dephosphorylated state, Rb binds to proteins called transcription factors, most commonly, E2F ( [link] ). Transcription factors turn on specific genes, allowing the production of proteins encoded by that gene. When Rb is bound to E2F, production of proteins necessary for the G 1 /S transition is blocked. As the cell increases in size, Rb is slowly phosphorylated until it becomes inactivated. Rb releases E2F, which can now turn on the gene that produces the transition protein, and this particular block is removed. For the cell to move past each of the checkpoints, all positive regulators must be turned on, and all negative regulators must be turned off. 

Rb halts the cell cycle and releases its hold in response to cell growth. 

[link] Rb is a negative regulator that blocks the cell cycle at the G 1 checkpoint until the cell achieves a requisite size. What is the most likely mechanism that Rb employs to halt the cell cycle? A cell has a mutation that results in the production of an abnormal cyclin-dependent kinase at the G 2 /M checkpoint. What is a likely consequence of the mutation on the cell cycle? 

The Think About It questions are applications of Learning Objective 3.7 and Science Practice 6.4 and Learning Objective 3.8 and Science Practice 1.2 because the students are making predictions based on their understanding of the events occurring during the cell cycle. 

Answers Rb is active when it is dephosphorylated. In this state, Rb binds to E2F, which is a transcription factor required for the transcription and eventual translation of molecules required for the G 1 /S transition. E2F cannot transcribe certain genes when it is bound to Rb. As the cell increases in size, Rb becomes phosphorylated, inactivated, and releases E2F. E2F can then promote the transcription of the genes it controls, and the transition proteins will be produced. Cyclins and cyclin-dependent kinases (Cdks), are responsible for the progress of the cell through the various checkpoints including the G 2 /M checkpoint. Without a specific concentration of fully activated cyclin/Cdk complexes, or if an abnormal cdk is produced, the cell cycle cannot proceed through the checkpoint and will arrest at the G 2 /M checkpoint. Section Summary 

Each step of the cell cycle is monitored by internal controls called checkpoints. There are three major checkpoints in the cell cycle: one near the end of G 1 , a second at the G 2 /M transition, and the third during metaphase. Positive regulator molecules allow the cell cycle to advance to the next stage. Negative regulator molecules monitor cellular conditions and can halt the cycle until specific requirements are met. Review Questions 

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[link] Glossary cell cycle checkpoint mechanism that monitors the preparedness of a eukaryotic cell to advance through the various cell cycle stages cyclin one of a group of proteins that act in conjunction with cyclin-dependent kinases to help regulate the cell cycle by phosphorylating key proteins; the concentrations of cyclins fluctuate throughout the cell cycle cyclin-dependent kinase one of a group of protein kinases that helps to regulate the cell cycle when bound to cyclin; it functions to phosphorylate other proteins that are either activated or inactivated by phosphorylation p21 cell cycle regulatory protein that inhibits the cell cycle; its levels are controlled by p53 p53 cell cycle regulatory protein that regulates cell growth and monitors DNA damage; it halts the progression of the cell cycle in cases of DNA damage and may induce apoptosis retinoblastoma protein (Rb) regulatory molecule that exhibits negative effects on the cell cycle by interacting with a transcription factor (E2F)Cancer and the Cell Cycle Cancer and the Cell Cycle 

In this section, you will explore the following question: What causes uncontrolled cell growth, and why does it often cause cancer? Connection for AP Courses 

Cancer results from unchecked cell division caused by a breakdown of the mechanisms that regulate the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. One culprit that has been identified is the p53 protein (coded for by the p53 gene), a major regulator at the G 1 checkpoint. Normally, p53 proteins monitor DNA. If they find cells with damaged DNA, p53 will trigger repair mechanisms or destroy the cells, thus suppressing the formation of a tumor. However, mutations in p53 can result in abnormal p53 proteins that fail to stop cell division if the cell s DNA is damaged. This results in an increased number of mutations, leading to abnormal daughter cells. Eventually, all checkpoints in the cell become nonfunctional, and the abnormal cells can crowd out normal cells. 

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework, as shown in the table. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.7 The student can make predictions about natural phenomena occurring during the cell cycle. 

This chapter reviews the fidelity with which undamaged and damaged DNA is copied. Students who want more background on how gene mutations can occur maybe interested in reading the review The fidelity of DNA synthesis by eukaryotic replicative and translation synthesis polymerases here . 

Introduce the topic of loss of control of the cell cycle using visuals such as these videos: The Eukaryotic Cell Cycle and Cancer , Tumor Suppressor Genes , Click and Learn: p53 Gene and Cancer , and Using p53 to Fight Cancer . 

Students may believe that the presence of a mutation in p53 or any of the tumor suppressor genes or proto-oncogenes leads to the formation of cancer in every case. However, the development of cancer is a complex process. The presence of a gene mutation does not in and of itself mean cancer will develop. Three main factors can cause cancer: environmental factors, carcinogens, viruses, and genetics. Additional overview of the development of cancer can be given to students in this video . 

Cancer comprises many different diseases caused by a common mechanism: uncontrolled cell growth. Despite the redundancy and overlapping levels of cell cycle control, errors do occur. One of the critical processes monitored by the cell cycle checkpoint surveillance mechanism is the proper replication of DNA during the S phase. Even when all of the cell cycle controls are fully functional, a small percentage of replication errors (mutations) will be passed on to the daughter cells. If changes to the DNA nucleotide sequence occur within a coding portion of a gene and are not corrected, a gene mutation results. All cancers start when a gene mutation gives rise to a faulty protein that plays a key role in cell reproduction. The change in the cell that results from the malformed protein may be minor: perhaps a slight delay in the binding of Cdk to cyclin or an Rb protein that detaches from its target DNA while still phosphorylated. Even minor mistakes, however, may allow subsequent mistakes to occur more readily. Over and over, small uncorrected errors are passed from the parent cell to the daughter cells and amplified as each generation produces more non-functional proteins from uncorrected DNA damage. Eventually, the pace of the cell cycle speeds up as the effectiveness of the control and repair mechanisms decreases. Uncontrolled growth of the mutated cells outpaces the growth of normal cells in the area, and a tumor ( -oma ) can result. Proto-oncogenes 

The genes that code for the positive cell cycle regulators are called proto-oncogenes . Proto-oncogenes are normal genes that, when mutated in certain ways, become oncogenes , genes that cause a cell to become cancerous. Consider what might happen to the cell cycle in a cell with a recently acquired oncogene. In most instances, the alteration of the DNA sequence will result in a less functional (or non-functional) protein. The result is detrimental to the cell and will likely prevent the cell from completing the cell cycle; however, the organism is not harmed because the mutation will not be carried forward. If a cell cannot reproduce, the mutation is not propagated and the damage is minimal. Occasionally, however, a gene mutation causes a change that increases the activity of a positive regulator. For example, a mutation that allows Cdk to be activated without being partnered with cyclin could push the cell cycle past a checkpoint before all of the required conditions are met. If the resulting daughter cells are too damaged to undergo further cell divisions, the mutation would not be propagated and no harm would come to the organism. However, if the atypical daughter cells are able to undergo further cell divisions, subsequent generations of cells will probably accumulate even more mutations, some possibly in additional genes that regulate the cell cycle. 

The Cdk gene in the above example is only one of many genes that are considered proto-oncogenes. In addition to the cell cycle regulatory proteins, any protein that influences the cycle can be altered in such a way as to override cell cycle checkpoints. An oncogene is any gene that, when altered, leads to an increase in the rate of cell cycle progression. Tumor Suppressor Genes 

Like proto-oncogenes, many of the negative cell cycle regulatory proteins were discovered in cells that had become cancerous. Tumor suppressor genes are segments of DNA that code for negative regulator proteins, the type of regulators that, when activated, can prevent the cell from undergoing uncontrolled division. The collective function of the best-understood tumor suppressor gene proteins, Rb, p53, and p21, is to put up a roadblock to cell cycle progression until certain events are completed. A cell that carries a mutated form of a negative regulator might not be able to halt the cell cycle if there is a problem. Tumor suppressors are similar to brakes in a vehicle: Malfunctioning brakes can contribute to a car crash. 

Mutated p53 genes have been identified in more than one-half of all human tumor cells. This discovery is not surprising in light of the multiple roles that the p53 protein plays at the G 1 checkpoint. A cell with a faulty p53 may fail to detect errors present in the genomic DNA ( [link] ). Even if a partially functional p53 does identify the mutations, it may no longer be able to signal the necessary DNA repair enzymes. Either way, damaged DNA will remain uncorrected. At this point, a functional p53 will deem the cell unsalvageable and trigger programmed cell death (apoptosis). The damaged version of p53 found in cancer cells, however, cannot trigger apoptosis. 

The role of normal p53 is to monitor DNA and the supply of oxygen (hypoxia is a condition of reduced oxygen supply). If damage is detected, p53 triggers repair mechanisms. If repairs are unsuccessful, p53 signals apoptosis. A cell with an abnormal p53 protein cannot repair damaged DNA and thus cannot signal apoptosis. Cells with abnormal p53 can become cancerous. (credit: modification of work by Thierry Soussi) 

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The loss of p53 function has other repercussions for the cell cycle. Mutated p53 might lose its ability to trigger p21 production. Without adequate levels of p21, there is no effective block on Cdk activation. Essentially, without a fully functional p53, the G 1 checkpoint is severely compromised and the cell proceeds directly from G 1 to S regardless of internal and external conditions. At the completion of this shortened cell cycle, two daughter cells are produced that have inherited the mutated p53 gene. Given the non-optimal conditions under which the parent cell reproduced, it is likely that the daughter cells will have acquired other mutations in addition to the faulty tumor suppressor gene. Cells such as these daughter cells quickly accumulate both oncogenes and non-functional tumor suppressor genes. Again, the result is tumor growth. 

Go to this website to watch an animation of how cancer results from errors in the cell cycle. 

[link] Think About It 

Human papillomavirus (HPV) can cause cervical cancer. The virus encodes E6, a protein that binds p53. Predict the most likely effect of E6 binding on p53 activity, and explain the basis for your prediction. 

This question is an application of Learning Objectives 3.7 and Science Practice 7.4 because the students are predicting how a change in regulation of the cell cycle can result in cancer. Answer 

The role of normal p53 is to monitor DNA for damage. If damage is detected, p53 triggers repair mechanisms. If repairs are unsuccessful, p53 signals apoptosis. A cell with an abnormal p53 protein cannot repair damaged DNA or signal apoptosis. Cells with abnormal p53 can become cancerous. Because E6 leads to the development of cancer, it must bind p53 is such a way that p53 cannot monitor DNA for damage, cannot trigger a repair mechanism, or signal apoptosis. Section Summary 

Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms that regulate the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to the daughter cells. Each successive cell division will give rise to daughter cells with even more accumulated damage. Eventually, all checkpoints become nonfunctional, and rapidly reproducing cells crowd out normal cells, resulting in a tumor or leukemia (blood cancer). Review Questions 

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[link] Glossary oncogene mutated version of a normal gene involved in the positive regulation of the cell cycle proto-oncogene normal gene that when mutated becomes an oncogene tumor suppressor gene segment of DNA that codes for regulator proteins that prevent the cell from undergoing uncontrolled divisionProkaryotic Cell Division Prokaryotic Cell Division 

In this section, you will explore the following question: How does the process of binary fission in prokaryotes differ from cell division in eukaryotes? 

Prokaryotes, such as bacteria, propagate by binary fission. For unicellular organisms, cell division is the only method to produce new individuals. In both prokaryotic and eukaryotic cells, the outcome of cell reproduction is a pair of daughter cells that are genetically identical to the parent cell. In unicellular organisms, daughter cells are individuals. 

To achieve the outcome of cloned offspring, certain steps are essential. The genomic DNA must be replicated and then allocated into the daughter cells; the cytoplasmic contents must also be divided to give both new cells the machinery to sustain life. In bacterial cells, the genome consists of a single, circular DNA chromosome; therefore, the process of cell division is simplified. Karyokinesis is unnecessary because there is no nucleus and thus no need to direct one copy of the multiple chromosomes into each daughter cell. This type of cell division is called binary (prokaryotic) fission . Binary Fission 

Due to the relative simplicity of the prokaryotes, the cell division process, called binary fission, is a less complicated and much more rapid process than cell division in eukaryotes. The single, circular DNA chromosome of bacteria is not enclosed in a nucleus, but instead occupies a specific location, the nucleoid, within the cell ( [link] ). Although the DNA of the nucleoid is associated with proteins that aid in packaging the molecule into a compact size, there are no histone proteins and thus no nucleosomes in prokaryotes. The packing proteins of bacteria are, however, related to the cohesin and condensin proteins involved in the chromosome compaction of eukaryotes. 

The bacterial chromosome is attached to the plasma membrane at about the midpoint of the cell. The starting point of replication, the origin , is close to the binding site of the chromosome to the plasma membrane ( [link] ). Replication of the DNA is bidirectional, moving away from the origin on both strands of the loop simultaneously. As the new double strands are formed, each origin point moves away from the cell wall attachment toward the opposite ends of the cell. As the cell elongates, the growing membrane aids in the transport of the chromosomes. After the chromosomes have cleared the midpoint of the elongated cell, cytoplasmic separation begins. The formation of a ring composed of repeating units of a protein called FtsZ directs the partition between the nucleoids. Formation of the FtsZ ring triggers the accumulation of other proteins that work together to recruit new membrane and cell wall materials to the site. A septum is formed between the nucleoids, extending gradually from the periphery toward the center of the cell. When the new cell walls are in place, the daughter cells separate. These images show the steps of binary fission in prokaryotes. (credit: modification of work by Mcstrother /Wikimedia Commons) Mitotic Spindle Apparatus 

The precise timing and formation of the mitotic spindle is critical to the success of eukaryotic cell division. Prokaryotic cells, on the other hand, do not undergo karyokinesis and therefore have no need for a mitotic spindle. However, the FtsZ protein that plays such a vital role in prokaryotic cytokinesis is structurally and functionally very similar to tubulin, the building block of the microtubules that make up the mitotic spindle fibers that are necessary for eukaryotes. FtsZ proteins can form filaments, rings, and other three-dimensional structures that resemble the way tubulin forms microtubules, centrioles, and various cytoskeletal components. In addition, both FtsZ and tubulin employ the same energy source, GTP (guanosine triphosphate), to rapidly assemble and disassemble complex structures. 

FtsZ and tubulin are homologous structures derived from common evolutionary origins. In this example, FtsZ is the ancestor protein to tubulin (a modern protein). While both proteins are found in extant organisms, tubulin function has evolved and diversified tremendously since evolving from its FtsZ prokaryotic origin. A survey of mitotic assembly components found in present-day unicellular eukaryotes reveals crucial intermediary steps to the complex membrane-enclosed genomes of multicellular eukaryotes ( [link] ). Cell Division Apparatus among Various Organisms Structure of genetic material Division of nuclear material Separation of daughter cells Prokaryotes There is no nucleus. The single, circular chromosome exists in a region of cytoplasm called the nucleoid. Occurs through binary fission. As the chromosome is replicated, the two copies move to opposite ends of the cell by an unknown mechanism. FtsZ proteins assemble into a ring that pinches the cell in two. Some protists Linear chromosomes exist in the nucleus. Chromosomes attach to the nuclear envelope, which remains intact. The mitotic spindle passes through the envelope and elongates the cell. No centrioles exist. Microfilaments form a cleavage furrow that pinches the cell in two. Other protists Linear chromosomes exist in the nucleus. A mitotic spindle forms from the centrioles and passes through the nuclear membrane, which remains intact. Chromosomes attach to the mitotic spindle, which separates the chromosomes and elongates the cell. Microfilaments form a cleavage furrow that pinches the cell in two. Animal cells Linear chromosomes exist in the nucleus. A mitotic spindle forms from the centrosomes. The nuclear envelope dissolves. Chromosomes attach to the mitotic spindle, which separates the chromosomes and elongates the cell. Microfilaments form a cleavage furrow that pinches the cell in two. 

[link] Section Summary 

In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and then each copy is allocated into a daughter cell. In addition, the cytoplasmic contents are divided evenly and distributed to the new cells. However, there are many differences between prokaryotic and eukaryotic cell division. Bacteria have a single, circular DNA chromosome but no nucleus. Therefore, mitosis is not necessary in bacterial cell division. Bacterial cytokinesis is directed by a ring composed of a protein called FtsZ. Ingrowth of membrane and cell wall material from the periphery of the cells results in the formation of a septum that eventually constructs the separate cell walls of the daughter cells. Review Questions 

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[link] Glossary binary fission prokaryotic cell division process FtsZ tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin: F ilamenting t emperature- s ensitive mutant Z ) origin (also, ORI) region of the prokaryotic chromosome where replication begins (origin of replication) septum structure formed in a bacterial cell as a precursor to the separation of the cell into two daughter cellsIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP #174; Courses" Each of us, like these other large multicellular organisms, begins life as a fertilized egg. After trillions of cell divisions, each of us develops into a complex, multicellular organism. (credit a: modification of work by Frank Wouters; credit b: modification of work by Ken Cole, USGS; credit c: modification of work by Martin Pettitt) 

The ability to reproduce in kind is a basic characteristic of all living things. In kind means that the offspring of an organism closely resembles its parent or parents. Hippopotamuses give birth to hippopotamus calves, Joshua trees produce Joshua tree seedlings, and flamingos lay eggs that hatch into flamingo chicks. In kind can mean exactly the same. Many unicellular organisms, such as yeast, and a few multicellular organisms, such as sponges, can produce genetically identical clones of themselves through cell division. However, many single-celled organisms and most multicellular organisms reproduce regularly using a method requiring two parents. Sexual reproduction occurs through the production by each parent of a haploid cell (containing one half of an offspring s required genetic material) and the fusion of these two haploid cells to form a single, unique diploid cell with a complete set of genetic information. In most plants and animals, through multiple rounds of mitotic cell division, this diploid cell will develop into an adult organism. Haploid cells that are necessary for sexual reproduction are produced by a type of cell division called meiosis. Sexual reproduction, specifically meiosis and fertilization, introduces variation into offspring. Variation is an important component of a species evolutionary success. The vast majority of eukaryotic organisms employs some form of meiosis and fertilization to reproduce. 

Not all sexually reproducing eukaryotes reproduce solely by sexual reproduction. For example, an Asian termite species, Reticulitermes speratus , can reproduce sexually or asexually. In a young colony, a single termite pair the king and queen produce worker offspring sexually by the union of haploid cells. However, after several years, as the queen begins to age, she produces some offspring asexually in a process called parthenogenesis. These offspring, which are destined to become new queens, are not fertilized by the king. They are genetic clones of the queen. More information about parthenogenesis in these termites can be found at this article . 

It is important to stress how critical sexual reproduction is for the adaptation and survival of many species. Natural selection works only because there are variations in genes, and genetic variations are a natural result of sexual reproduction.The Process of Meiosis The Process of Meiosis 

In this section, you will explore the following questions: How do chromosomes behave during meiosis? What cellular events occur during meiosis? What are the similarities and differences between meiosis and mitosis? How can the process of meiosis generate genetic variation? Connection for AP Courses 

As we explored the cell cycle and mitosis in a previous chapter, we learned that cells divide to grow, replace other cells, and reproduce asexually. Without mutation, or changes in the DNA, the daughter cells produced by mitosis receive a set of genetic instructions that is identical to that of the parent cell. Because changes in genes drive both the unity and diversity of life, organisms without genetic variation cannot evolve through natural selection. Evolution occurs only because organisms have developed ways to vary their genetic material. This occurs through mutations in DNA, recombination of genes during meiosis, and meiosis followed by fertilization in sexually reproducing organisms. 

Sexual reproduction requires that diploid (2 n ) organisms produce haploid (1 n ) cells through meiosis and that these haploid cells fuse to form new, diploid offspring. The union of these two haploid cells, one from each parent, is fertilization. Although the processes of meiosis and mitosis share similarities, their end products are different. Recall that eukaryotic DNA is contained in chromosomes, and that chromosomes occur in homologous pairs (homologues). At fertilization, the male parent contributes one member of each homologous pair to the offspring, and the female parent contributes the other. With the exception of the sex chromosomes, homologous chromosomes contain the same genes, but these genes can have different variations, called alleles. (For example, you might have inherited an allele for brown eyes from your father and an allele for blue eyes from your mother.) As in mitosis, homologous chromosomes are duplicated during the S-stage (synthesis) of interphase. However, unlike mitosis, in which there is just one nuclear division, meiosis has two complete rounds of nuclear division meiosis I and meiosis II. These result in four nuclei and (usually) four daughter cells, each with half the number of chromosomes as the parent cell (1 n ). The first division, meiosis I, separates homologous chromosomes, and the second division, meiosis II, separates chromatids. (Remember: during meiosis, DNA replicates ONCE but divides TWICE, whereas in mitosis, DNA replicates ONCE but divides only ONCE.). 

Although mitosis and meiosis are similar in many ways, they have different outcomes. The main difference is in the type of cell produced: mitosis produces identical cells, allowing growth or repair of tissues; meiosis generates reproductive cells, or gametes. Gametes, often called sex cells, unite with other sex cells to produce new, unique organisms. 

Genetic variation occurs during meiosis I, in which homologous chromosomes pair and exchange non-sister chromatid segments (crossover). Here the homologous chromosomes separate into different nuclei, causing a reduction in ploidy. During meiosis II which is more similar to a mitotic division the chromatids separate and segregate into four haploid sex cells. However, because of crossover, the resultant daughter cells do not contain identical genomes. As in mitosis, external factors and internal signals regulate the meiotic cell cycle. As we will explore in more detail in a later chapter, errors in meiosis can cause genetic disorders, such as Down syndrome. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 3.9 The student is able to construct an explanation, using visual representations or narratives, as to how DNA in chromosomes is transmitted to the next generation via mitosis, or meiosis followed by fertilization. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 3.10 The student is able to represent the connection between meiosis and increased genetic diversity necessary for evolution. 

The process of meiosis can be confusing, especially if it is taught as just a series of steps. Initially, discuss the goal of the process. Explain that meiosis serves to produce reproductive cells with exactly half the number of chromosomes, and that once these haploid cells are fused during fertilization, a complete set of genetic instructions for a new individual is formed. Meiosis starts in a cell with chromosomes in pairs. Each chromosome has already been duplicated and the two sister strands are held together. Therefore, each pair consists of four chromatids. Because students have already learned about mitosis (the process whereby chromosomes are sorted and allocated to daughter cells), it might be helpful to teach meiosis as a special case of mitosis. The first division separates the pairs of chromosomes, reducing the number of duplicated chromosomes in the daughter cells by half. The second division separates the chromatids, creating daughter cells that each has one half of the total number of chromosomes of the original cell. An added benefit to an organism using meiosis is the increase in genetic variation that occurs during the process. Each individual born as a result of sexual reproduction truly has a unique assortment of genes. 

You read that fertilization is the union of two sex cells from two individual organisms. If these two cells each contain one set of chromosomes, the resulting fertilized cell contains two sets of chromosomes. Haploid cells contain one set of chromosomes. Cells containing two sets of chromosomes are called diploid. The number of sets of chromosomes in a cell is called its ploidy level. If the reproductive cycle is to continue, a diploid cell must reduce the number of its chromosome sets before fertilization can occur again. Otherwise, the number of chromosome sets would double, and continue to double in every generation. So, in addition to fertilization, sexual reproduction includes a nuclear division that reduces the number of chromosome sets. 

Most animals and plants are diploid, containing two sets of chromosomes. In an organism s somatic cells , sometimes referred to as body cells (all cells of a multicellular organism except the reproductive cells), the nucleus contains two copies of each chromosome, called homologous chromosomes. Homologous chromosomes are matched pairs containing the same genes in identical locations along their length. Diploid organisms inherit one copy of each homologous chromosome from each parent; all together, they are considered a full set of chromosomes. Haploid cells, containing a single copy of each homologous chromosome, are found only within an organism s reproductive structures, such as the ovaries and testes. Haploid cells can be either gametes or spores. Male gametes are sperm and female gametes are eggs. All animals and most plants produce gametes. Spores are haploid cells that can produce a haploid organism or can fuse with another spore to form a diploid cell. Some plants and all fungi produce spores. 

As you have learned, the nuclear division that forms haploid cells meiosis is closely related to mitosis. Mitosis is the part of a cell reproduction cycle that results in identical daughter nuclei that are also genetically identical to the original parent nucleus. In mitosis, both the parent and the daughter nuclei are at the same ploidy level diploid for most plants and animals. Meiosis employs many of the same mechanisms as mitosis. However, the starting nucleus is always diploid and the nuclei that result at the end of a meiotic cell division are haploid. To achieve this reduction in chromosome number, meiosis consists of one round of chromosome duplication and two rounds of nuclear division. Because the events that occur during each of the division stages are analogous to the events of mitosis, the same stage names are assigned. However, because there are two rounds of division, the major process and the stages are designated with a I or a II. Thus, meiosis I is the first round of meiotic division and consists of prophase I, prometaphase I, and so on. Meiosis II , in which the second round of meiotic division takes place, includes prophase II, prometaphase II, and so on. 

Meiosis I has the same steps as mitosis, with the exception that the chromosome pairs, not the chromatids, are separated at anaphase I. Two other events occur during the first cell division to produce the genetic variation that results. In prophase I, when the pairs of chromosomes condense and tentatively join, parts of the arms and legs of the chromosomes can crossover, or exchange places, with corresponding parts on the other homologous chromosome. The resulting pair now has a configuration that was not present initially. The pairs line up in a double line during metaphase I, but the distribution of the pairs at the equator is random. Half of the original chromosomes came from one parent, half from the other. As the chromosomes line up and are pulled apart during anaphase I, each daughter cell will receive a chromosome mixture that was not present in the original germ cells. [link] illustrates crossing over and [link] illustrates the random distribution of pairs of chromosomes. Also use the Link to Learning: Meiosis: An Interactive Animation. Meiosis II finishes the process and closely resembles mitosis, except for the number of chromosomes present, as compared to somatic cells. 

Comparing meiosis and mitosis should be a review of the two processes, with a reinforcement of the similarities and differences. Meiosis I 

Meiosis is preceded by an interphase consisting of the G 1 , S, and G 2 phases, which are nearly identical to the phases preceding mitosis. The G 1 phase, which is also called the first gap phase, is the first phase of the interphase and is focused on cell growth. The S phase is the second phase of interphase, during which the DNA of the chromosomes is replicated. Finally, the G 2 phase, also called the second gap phase, is the third and final phase of interphase; in this phase, the cell undergoes the final preparations for meiosis. 

During DNA duplication in the S phase, each chromosome is replicated to produce two identical copies, called sister chromatids, that are held together at the centromere by cohesin proteins. Cohesin holds the chromatids together until anaphase II. The centrosomes, which are the structures that organize the microtubules of the meiotic spindle, also replicate. This prepares the cell to enter prophase I, the first meiotic phase. Prophase I 

Early in prophase I, before the chromosomes can be seen clearly microscopically, the homologous chromosomes are attached at their tips to the nuclear envelope by proteins. As the nuclear envelope begins to break down, the proteins associated with homologous chromosomes bring the pair close to each other. Recall that, in mitosis, homologous chromosomes do not pair together. In mitosis, homologous chromosomes line up end-to-end so that when they divide, each daughter cell receives a sister chromatid from both members of the homologous pair. The synaptonemal complex , a lattice of proteins between the homologous chromosomes, first forms at specific locations and then spreads to cover the entire length of the chromosomes. The tight pairing of the homologous chromosomes is called synapsis . In synapsis, the genes on the chromatids of the homologous chromosomes are aligned precisely with each other. The synaptonemal complex supports the exchange of chromosomal segments between non-sister homologous chromatids, a process called crossing over. Crossing over can be observed visually after the exchange as chiasmata (singular = chiasma) ( [link] ). 

In species such as humans, even though the X and Y sex chromosomes are not homologous (most of their genes differ), they have a small region of homology that allows the X and Y chromosomes to pair up during prophase I. A partial synaptonemal complex develops only between the regions of homology. Early in prophase I, homologous chromosomes come together to form a synapse. The chromosomes are bound tightly together and in perfect alignment by a protein lattice called a synaptonemal complex and by cohesin proteins at the centromere. 

Located at intervals along the synaptonemal complex are large protein assemblies called recombination nodules . These assemblies mark the points of later chiasmata and mediate the multistep process of crossover or genetic recombination between the non-sister chromatids. Near the recombination nodule on each chromatid, the double-stranded DNA is cleaved, the cut ends are modified, and a new connection is made between the non-sister chromatids. As prophase I progresses, the synaptonemal complex begins to break down and the chromosomes begin to condense. When the synaptonemal complex is gone, the homologous chromosomes remain attached to each other at the centromere and at chiasmata. The chiasmata remain until anaphase I. The number of chiasmata varies according to the species and the length of the chromosome. There must be at least one chiasma per chromosome for proper separation of homologous chromosomes during meiosis I, but there may be as many as 25. Following crossover, the synaptonemal complex breaks down and the cohesin connection between homologous pairs is also removed. At the end of prophase I, the pairs are held together only at the chiasmata ( [link] ) and are called tetrads because the four sister chromatids of each pair of homologous chromosomes are now visible. 

The crossover events are the first source of genetic variation in the nuclei produced by meiosis. A single crossover event between homologous non-sister chromatids leads to a reciprocal exchange of equivalent DNA between a maternal chromosome and a paternal chromosome. Now, when that sister chromatid is moved into a gamete cell it will carry some DNA from one parent of the individual and some DNA from the other parent. The sister recombinant chromatid has a combination of maternal and paternal genes that did not exist before the crossover. Multiple crossovers in an arm of the chromosome have the same effect, exchanging segments of DNA to create recombinant chromosomes. Crossover occurs between non-sister chromatids of homologous chromosomes. The result is an exchange of genetic material between homologous chromosomes. Prometaphase I 

The key event in prometaphase I is the attachment of the spindle fiber microtubules to the kinetochore proteins at the centromeres. Kinetochore proteins are multiprotein complexes that bind the centromeres of a chromosome to the microtubules of the mitotic spindle. Microtubules grow from centrosomes placed at opposite poles of the cell. The microtubules move toward the middle of the cell and attach to one of the two fused homologous chromosomes. The microtubules attach at each chromosomes' kinetochores. With each member of the homologous pair attached to opposite poles of the cell, in the next phase, the microtubules can pull the homologous pair apart. A spindle fiber that has attached to a kinetochore is called a kinetochore microtubule. At the end of prometaphase I, each tetrad is attached to microtubules from both poles, with one homologous chromosome facing each pole. The homologous chromosomes are still held together at chiasmata. In addition, the nuclear membrane has broken down entirely. Metaphase I 

During metaphase I, the homologous chromosomes are arranged in the center of the cell with the kinetochores facing opposite poles. The homologous pairs orient themselves randomly at the equator. For example, if the two homologous members of chromosome 1 are labeled a and b, then the chromosomes could line up a-b, or b-a. This is important in determining the genes carried by a gamete, as each will only receive one of the two homologous chromosomes. Recall that homologous chromosomes are not identical. They contain slight differences in their genetic information, causing each gamete to have a unique genetic makeup. 

This randomness is the physical basis for the creation of the second form of genetic variation in offspring. Consider that the homologous chromosomes of a sexually reproducing organism are originally inherited as two separate sets, one from each parent. Using humans as an example, one set of 23 chromosomes is present in the egg donated by the mother. The father provides the other set of 23 chromosomes in the sperm that fertilizes the egg. Every cell of the multicellular offspring has copies of the original two sets of homologous chromosomes. In prophase I of meiosis, the homologous chromosomes form the tetrads. In metaphase I, these pairs line up at the midway point between the two poles of the cell to form the metaphase plate. Because there is an equal chance that a microtubule fiber will encounter a maternally or paternally inherited chromosome, the arrangement of the tetrads at the metaphase plate is random. Any maternally inherited chromosome may face either pole. Any paternally inherited chromosome may also face either pole. The orientation of each tetrad is independent of the orientation of the other 22 tetrads. 

This event the random (or independent) assortment of homologous chromosomes at the metaphase plate is the second mechanism that introduces variation into the gametes or spores. In each cell that undergoes meiosis, the arrangement of the tetrads is different. The number of variations is dependent on the number of chromosomes making up a set. There are two possibilities for orientation at the metaphase plate; the possible number of alignments therefore equals 2 n , where n is the number of chromosomes per set. Humans have 23 chromosome pairs, which results in over eight million (2 23 ) possible genetically-distinct gametes. This number does not include the variability that was previously created in the sister chromatids by crossover. Given these two mechanisms, it is highly unlikely that any two haploid cells resulting from meiosis will have the same genetic composition ( [link] ). 

To summarize the genetic consequences of meiosis I, the maternal and paternal genes are recombined by crossover events that occur between each homologous pair during prophase I. In addition, the random assortment of tetrads on the metaphase plate produces a unique combination of maternal and paternal chromosomes that will make their way into the gametes. Random, independent assortment during metaphase I can be demonstrated by considering a cell with a set of two chromosomes ( n = 2). In this case, there are two possible arrangements at the equatorial plane in metaphase I. The total possible number of different gametes is 2 n , where n equals the number of chromosomes in a set. In this example, there are four possible genetic combinations for the gametes. With n = 23 in human cells, there are over 8 million possible combinations of paternal and maternal chromosomes. Anaphase I 

In anaphase I, the microtubules pull the linked chromosomes apart. The sister chromatids remain tightly bound together at the centromere. The chiasmata are broken in anaphase I as the microtubules attached to the fused kinetochores pull the homologous chromosomes apart ( [link] ). Telophase I and Cytokinesis 

In telophase, the separated chromosomes arrive at opposite poles. The remainder of the typical telophase events may or may not occur, depending on the species. In some organisms, the chromosomes decondense and nuclear envelopes form around the chromatids in telophase I. In other organisms, cytokinesis the physical separation of the cytoplasmic components into two daughter cells occurs without reformation of the nuclei. In nearly all species of animals and some fungi, cytokinesis separates the cell contents via a cleavage furrow (constriction of the actin ring that leads to cytoplasmic division). In plants, a cell plate is formed during cell cytokinesis by Golgi vesicles fusing at the metaphase plate. This cell plate will ultimately lead to the formation of cell walls that separate the two daughter cells. 

Two haploid cells are the end result of the first meiotic division. The cells are haploid because at each pole, there is just one of each pair of the homologous chromosomes. Therefore, only one full set of the chromosomes is present. This is why the cells are considered haploid there is only one chromosome set, even though each homolog still consists of two sister chromatids. Recall that sister chromatids are merely duplicates of one of the two homologous chromosomes (except for changes that occurred during crossing over). In meiosis II, these two sister chromatids will separate, creating four haploid daughter cells. 

Review the process of meiosis, observing how chromosomes align and migrate, at Meiosis: An Interactive Animation . 

[link] Meiosis II 

In some species, cells enter a brief interphase, or interkinesis , before entering meiosis II. Interkinesis lacks an S phase, so chromosomes are not duplicated. The two cells produced in meiosis I go through the events of meiosis II in synchrony. During meiosis II, the sister chromatids within the two daughter cells separate, forming four new haploid gametes. The mechanics of meiosis II is similar to mitosis, except that each dividing cell has only one set of homologous chromosomes. Therefore, each cell has half the number of sister chromatids to separate out as a diploid cell undergoing mitosis. Prophase II 

If the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes were formed, they fragment into vesicles. The centrosomes that were duplicated during interkinesis move away from each other toward opposite poles, and new spindles are formed. Prometaphase II 

The nuclear envelopes are completely broken down, and the spindle is fully formed. Each sister chromatid forms an individual kinetochore that attaches to microtubules from opposite poles. Metaphase II 

The sister chromatids are maximally condensed and aligned at the equator of the cell. Anaphase II 

The sister chromatids are pulled apart by the kinetochore microtubules and move toward opposite poles. Non-kinetochore microtubules elongate the cell. The process of chromosome alignment differs between meiosis I and meiosis II. In prometaphase I, microtubules attach to the fused kinetochores of homologous chromosomes, and the homologous chromosomes are arranged at the midpoint of the cell in metaphase I. In anaphase I, the homologous chromosomes are separated. In prometaphase II, microtubules attach to the kinetochores of sister chromatids, and the sister chromatids are arranged at the midpoint of the cells in metaphase II. In anaphase II, the sister chromatids are separated. Telophase II and Cytokinesis 

The chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form around the chromosomes. Cytokinesis separates the two cells into four unique haploid cells. At this point, the newly formed nuclei are both haploid. The cells produced are genetically unique because of the random assortment of paternal and maternal homologs and because of the recombining of maternal and paternal segments of chromosomes (with their sets of genes) that occurs during crossover. The entire process of meiosis is outlined in [link] . An animal cell with a diploid number of four (2 n = 4) proceeds through the stages of meiosis to form four haploid daughter cells. Comparing Meiosis and Mitosis 

Mitosis and meiosis are both forms of division of the nucleus in eukaryotic cells. They share some similarities, but also exhibit distinct differences that lead to very different outcomes ( [link] ). Mitosis is a single nuclear division that results in two nuclei that are usually partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical to the original nucleus. They have the same number of sets of chromosomes, one set in the case of haploid cells and two sets in the case of diploid cells. In most plants and all animal species, it is typically diploid cells that undergo mitosis to form new diploid cells. In contrast, meiosis consists of two nuclear divisions resulting in four nuclei that are usually partitioned into four new cells. The nuclei resulting from meiosis are not genetically identical and they contain one chromosome set only. This is half the number of chromosome sets in the original cell, which is diploid. 

The main differences between mitosis and meiosis occur in meiosis I, which is a very different nuclear division than mitosis. In meiosis I, the homologous chromosome pairs become associated with each other, are bound together with the synaptonemal complex, develop chiasmata and undergo crossover between sister chromatids, and line up along the metaphase plate in tetrads with kinetochore fibers from opposite spindle poles attached to each kinetochore of a homolog in a tetrad. All of these events occur only in meiosis I. 

When the chiasmata resolve and the tetrad is broken up with the homologs moving to one pole or another, the ploidy level the number of sets of chromosomes in each future nucleus has been reduced from two to one. For this reason, meiosis I is referred to as a reduction division . There is no such reduction in ploidy level during mitosis. 

Meiosis II is much more analogous to a mitotic division. In this case, the duplicated chromosomes (only one set of them) line up on the metaphase plate with divided kinetochores attached to kinetochore fibers from opposite poles. During anaphase II, as in mitotic anaphase, the kinetochores divide and one sister chromatid now referred to as a chromosome is pulled to one pole while the other sister chromatid is pulled to the other pole. If it were not for the fact that there had been crossover, the two products of each individual meiosis II division would be identical (like in mitosis). Instead, they are different because there has always been at least one crossover per chromosome. Meiosis II is not a reduction division because although there are fewer copies of the genome in the resulting cells, there is still one set of chromosomes, as there was at the end of meiosis I. Meiosis and mitosis are both preceded by one round of DNA replication; however, meiosis includes two nuclear divisions. The four daughter cells resulting from meiosis are haploid and genetically distinct. The daughter cells resulting from mitosis are diploid and identical to the parent cell. 

The Mystery of the Evolution of Meiosis Some characteristics of organisms are so widespread and fundamental that it is sometimes difficult to remember that they evolved like other simpler traits. Meiosis is such an extraordinarily complex series of cellular events that biologists have had trouble hypothesizing and testing how it may have evolved. Although meiosis is inextricably entwined with sexual reproduction and its advantages and disadvantages, it is important to separate the questions of the evolution of meiosis and the evolution of sex, because early meiosis may have been advantageous for different reasons than it is now. Thinking outside the box and imagining what the early benefits from meiosis might have been is one approach to uncovering how it may have evolved. 

Meiosis and mitosis share obvious cellular processes and it makes sense that meiosis evolved from mitosis. The difficulty lies in the clear differences between meiosis I and mitosis. Adam Wilkins and Robin Holliday 1 summarized the unique events that needed to occur for the evolution of meiosis from mitosis. These steps are homologous chromosome pairing, crossover exchanges, sister chromatids remaining attached during anaphase, and suppression of DNA replication in interphase. They argue that the first step is the hardest and most important, and that understanding how it evolved would make the evolutionary process clearer. They suggest genetic experiments that might shed light on the evolution of synapsis. 

There are other approaches to understanding the evolution of meiosis in progress. Different forms of meiosis exist in single-celled protists. Some appear to be simpler or more primitive forms of meiosis. Comparing the meiotic divisions of different protists may shed light on the evolution of meiosis. Marilee Ramesh and colleagues 2 compared the genes involved in meiosis in protists to understand when and where meiosis might have evolved. Although research is still ongoing, recent scholarship into meiosis in protists suggests that some aspects of meiosis may have evolved later than others. This kind of genetic comparison can tell us what aspects of meiosis are the oldest and what cellular processes they may have borrowed from in earlier cells. 

[link] 

Click through the steps of this interactive animation to compare the meiotic process of cell division to that of mitosis: How Cells Divide . 

[link] Activity 

Create a series of diagrams with annotations to compare and contrast the processes of mitosis and meiosis in an organism with a haploid number of six. Then, using specific examples, explain how meiosis followed by fertilization increases genetic variation in a family of organisms. 

This activity is an application of Learning Objectives 3.9 and science practice 6.2, Learning Objectives 3.10 and science practice 7.1, and Learning Objectives 3.28 and science practice 6.2 because students are creating a visual representation to show how DNA is transmitted to the next generation by mitosis and meiosis followed by fertilization and then are using the representation to explain how meiosis increases genetic variation. Section Summary 

Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid offspring. As with mitosis, DNA replication occurs prior to meiosis during the S-phase of the cell cycle. Meiosis is a series of events that arrange and separate chromosomes and chromatids into daughter cells. During the interphases of meiosis, each chromosome is duplicated. In meiosis, there are two rounds of nuclear division resulting in four nuclei and usually four daughter cells, each with half the number of chromosomes as the parent cell. The first separates homologs, and the second like mitosis separates chromatids into individual chromosomes. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I and random alignment of tetrads at metaphase I. The cells that are produced by meiosis are genetically unique. 

Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions include two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set instead of the two sets of chromosomes in the parent cell. The main differences between the processes occur in the first division of meiosis, in which homologous chromosomes are paired and exchange non-sister chromatid segments. The homologous chromosomes separate into different nuclei during meiosis I, causing a reduction of ploidy level in the first division. The second division of meiosis is more similar to a mitotic division, except that the daughter cells do not contain identical genomes because of crossover. Review Questions 

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[link] Footnotes 1 

Adam S. Wilkins and Robin Holliday, The Evolution of Meiosis from Mitosis, Genetics 181 (2009): 3 12. 2 

Marilee A. Ramesh, Shehre-Banoo Malik and John M. Logsdon, Jr, A Phylogenetic Inventory of Meiotic Genes: Evidence for Sex in Giardia and an Early Eukaryotic Origin of Meiosis, Current Biology 15 (2005):185 91. Glossary chiasmata (singular, chiasma ) the structure that forms at the crossover points after genetic material is exchanged cohesin proteins that form a complex that seals sister chromatids together at their centromeres until anaphase II of meiosis crossover exchange of genetic material between non-sister chromatids resulting in chromosomes that incorporate genes from both parents of the organism fertilization union of two haploid cells from two individual organisms interkinesis (also, interphase II ) brief period of rest between meiosis I and meiosis II meiosis a nuclear division process that results in four haploid cells meiosis I first round of meiotic cell division; referred to as reduction division because the ploidy level is reduced from diploid to haploid meiosis II second round of meiotic cell division following meiosis I; sister chromatids are separated into individual chromosomes, and the result is four unique haploid cells recombination nodules protein assemblies formed on the synaptonemal complex that mark the points of crossover events and mediate the multistep process of genetic recombination between non-sister chromatids reduction division nuclear division that produces daughter nuclei each having one-half as many chromosome sets as the parental nucleus; meiosis I is a reduction division somatic cell all the cells of a multicellular organism except the gametes or reproductive cells spore haploid cell that can produce a haploid multicellular organism or can fuse with another spore to form a diploid cell synapsis formation of a close association between homologous chromosomes during prophase I synaptonemal complex protein lattice that forms between homologous chromosomes during prophase I, supporting crossover tetrad two duplicated homologous chromosomes (four chromatids) bound together by chiasmata during prophase ISexual Reproduction Sexual Reproduction 

In this section, you will explore the following questions: Why are meiosis and sexual reproduction considered evolved traits? Why is variation among offspring a potential evolutionary advantage to sexual reproduction? What are the three different life-cycles among sexual multicellular organisms and their commonalities? Connection for AP Courses 

Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells (gametes or spores) by meiosis is advantageous for evolution via natural selection. Meiosis and fertilization alternate as the organisms pass through the haploid and diploid stages of their life cycles. In most animals, the diploid stage dominates, whereas in fungi, the haploid stage dominates. Identifying the haploid and diploid stages within the life cycles of different organisms is vital in understanding how organisms reproduce and in determining when mitosis and meiosis occur. 

Information presented and the examples highlighted in the section support concepts and learning objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven science practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.C.2 Biological systems have multiple processes that increase genetic variation. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 3.27 The student is able to compare and contrast processes by which genetic variation is produced and maintained in organisms from multiple domains. 

Sexual reproduction in this chapter deals with sexual life cycles of animals, plants, fungi, and algae. Divide the class into small groups of 4 5 students and assign each group one of these categories. The students are to identify at least three examples of life cycles among organisms in their group s category. Have each group report back to the class with its findings, explaining the reproductive cycles it has identified (with real life examples, if possible). 

Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells. It appears to have been very successful because most eukaryotes are able to reproduce sexually, and in many animals, it is the only mode of reproduction. And yet, scientists recognize some real disadvantages to sexual reproduction. On the surface, creating offspring that are genetic clones of the parent appears to be a better system. If the parent organism is successfully occupying a habitat, offspring with the same traits would be similarly successful. There is also the obvious benefit to an organism that can produce offspring whenever circumstances are favorable by asexual budding, fragmentation, or asexual eggs. These methods of reproduction do not require another organism of the opposite sex. Indeed, some organisms that lead a solitary lifestyle have retained the ability to reproduce asexually. In addition, in asexual populations, every individual is capable of reproduction. In sexual populations, the males are not producing the offspring themselves, so in theory an asexual population could grow twice as fast. 

However, multicellular organisms that exclusively depend on asexual reproduction are exceedingly rare. Why is sexuality (and meiosis) so common? This is one of the important unanswered questions in biology and has been the focus of much research beginning in the latter half of the twentieth century. There are several possible explanations, one of which is that the variation that sexual reproduction creates among offspring is very important to the survival and reproduction of the population. Thus, on average, a sexually reproducing population will leave more descendants than an otherwise similar asexually reproducing population. The only source of variation in asexual organisms is mutation. This is the ultimate source of variation in sexual organisms, but in addition, those different mutations are continually reshuffled from one generation to the next when different parents combine their unique genomes and the genes are mixed into different combinations by crossovers during prophase I and random assortment at metaphase I. 

The Red Queen Hypothesis It is not in dispute that sexual reproduction provides evolutionary advantages to organisms that employ this mechanism to produce offspring. But why, even in the face of fairly stable conditions, does sexual reproduction persist when it is more difficult and costly for individual organisms? Variation is the outcome of sexual reproduction, but why are ongoing variations necessary? Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in 1973. 1 The concept was named in reference to the Red Queen's race in Lewis Carroll's book, Through the Looking-Glass . 

All species co-evolve with other organisms; for example predators evolve with their prey, and parasites evolve with their hosts. Each tiny advantage gained by favorable variation gives a species an edge over close competitors, predators, parasites, or even prey. The only method that will allow a co-evolving species to maintain its own share of the resources is to also continually improve its fitness. As one species gains an advantage, this increases selection on the other species; they must also develop an advantage or they will be outcompeted. No single species progresses too far ahead because genetic variation among the progeny of sexual reproduction provides all species with a mechanism to improve rapidly. Species that cannot keep up become extinct. The Red Queen s catchphrase was, It takes all the running you can do to stay in the same place. This is an apt description of co-evolution between competing species. 

[link] Life Cycles of Sexually Reproducing Organisms 

Fertilization and meiosis alternate in sexual life cycles . What happens between these two events depends on the organism. The process of meiosis reduces the chromosome number by half. Fertilization, the joining of two haploid gametes, restores the diploid condition. There are three main categories of life cycles in multicellular organisms: diploid-dominant , in which the multicellular diploid stage is the most obvious life stage, such as with most animals including humans; haploid-dominant , in which the multicellular haploid stage is the most obvious life stage, such as with all fungi and some algae; and alternation of generations , in which the two stages are apparent to different degrees depending on the group, as with plants and some algae. Diploid-Dominant Life Cycle 

Nearly all animals employ a diploid-dominant life-cycle strategy in which the only haploid cells produced by the organism are the gametes. Early in the development of the embryo, specialized diploid cells, called germ cells , are produced within the gonads, such as the testes and ovaries. Germ cells are capable of mitosis to perpetuate the cell line and meiosis to produce gametes. Once the haploid gametes are formed, they lose the ability to divide again. There is no multicellular haploid life stage. Fertilization occurs with the fusion of two gametes, usually from different individuals, restoring the diploid state ( [link] ). In animals, sexually reproducing adults form haploid gametes from diploid germ cells. Fusion of the gametes gives rise to a fertilized egg cell, or zygote. The zygote will undergo multiple rounds of mitosis to produce a multicellular offspring. The germ cells are generated early in the development of the zygote. Haploid-Dominant Life Cycle 

Most fungi and algae employ a life-cycle type in which the body of the organism the ecologically important part of the life cycle is haploid. The haploid cells that make up the tissues of the dominant multicellular stage are formed by mitosis. During sexual reproduction, specialized haploid cells from two individuals, designated the (+) and ( ) mating types, join to form a diploid zygote. The zygote immediately undergoes meiosis to form four haploid cells called spores. Although haploid like the parents, these spores contain a new genetic combination from two parents. The spores can remain dormant for various time periods. Eventually, when conditions are conducive, the spores form multicellular haploid structures by many rounds of mitosis ( [link] ). 

Fungi, such as black bread mold ( Rhizopus nigricans ), have haploid-dominant life cycles. The haploid multicellular stage produces specialized haploid cells by mitosis that fuse to form a diploid zygote. The zygote undergoes meiosis to produce haploid spores. Each spore gives rise to a multicellular haploid organism by mitosis. (credit zygomycota micrograph: modification of work by Fanaberka /Wikimedia Commons) 

[link] Alternation of Generations 

The third life-cycle type, employed by some algae and all plants, is a blend of the haploid-dominant and diploid-dominant extremes. Species with alternation of generations have both haploid and diploid multicellular organisms as part of their life cycle. The haploid multicellular plants are called gametophytes , because they produce gametes from specialized cells. Meiosis is not directly involved in the production of gametes in this case, because the organism that produces the gametes is already a haploid. Fertilization between the gametes forms a diploid zygote. The zygote will undergo many rounds of mitosis and give rise to a diploid multicellular plant called a sporophyte . Specialized cells of the sporophyte will undergo meiosis and produce haploid spores. The spores will subsequently develop into the gametophytes ( [link] ). Plants have a life cycle that alternates between a multicellular haploid organism and a multicellular diploid organism. In some plants, such as ferns, both the haploid and diploid plant stages are free-living. The diploid plant is called a sporophyte because it produces haploid spores by meiosis. The spores develop into multicellular, haploid plants called gametophytes because they produce gametes. The gametes of two individuals will fuse to form a diploid zygote that becomes the sporophyte. (credit fern : modification of work by Cory Zanker; credit sporangia : modification of work by "Obsidian Soul"/Wikimedia Commons; credit gametophyte and sporophyte : modification of work by Vlmastra /Wikimedia Commons) 

Although all plants utilize some version of the alternation of generations, the relative size of the sporophyte and the gametophyte and the relationship between them vary greatly. In plants such as moss, the gametophyte organism is the free-living plant, and the sporophyte is physically dependent on the gametophyte. In other plants, such as ferns, both the gametophyte and sporophyte plants are free-living; however, the sporophyte is much larger. In seed plants, such as magnolia trees and daisies, the gametophyte is composed of only a few cells and, in the case of the female gametophyte, is completely retained within the sporophyte. 

Sexual reproduction takes many forms in multicellular organisms. However, at some point in each type of life cycle, meiosis produces haploid cells that will fuse with the haploid cell of another organism. The mechanisms of variation crossover, random assortment of homologous chromosomes, and random fertilization are present in all versions of sexual reproduction. The fact that nearly every multicellular organism on Earth employs sexual reproduction is strong evidence for the benefits of producing offspring with unique gene combinations, though there are other possible benefits as well. Think About It 

Compare and contrast the three main types of life cycles in multicellular organisms and give an example of an organism that employs each. 

This question is an application of learning objective 3.27 and science practice 7.2 because students are comparing processes by which genetic variation is produced and maintained in different types of organisms. 

Describe in simple terms the three main types of life cycles in multicellular organisms and give an example of an organism that employs each. Possible Answer 

1. diploid-dominant, in which the multicellular diploid stage is dominant; examples are most animals, including humans 

2. haploid-dominant, in which the multicellular haploid stage is dominant; examples are all fungi and some algae 

3. alternation of generations, in which two stages are apparent to different degrees depending on the group; examples are plants and some algae Section Summary 

Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be one of the advantages of sexual reproduction that has made it so successful. Meiosis and fertilization alternate in sexual life cycles. The process of meiosis produces unique reproductive cells called gametes, which have half the number of chromosomes as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced and the timing between meiosis and fertilization vary greatly. There are three main categories of life cycles: diploid-dominant, demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and the alternation of generations, demonstrated by plants and some algae. Review Questions 

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Leigh Van Valen, A New Evolutionary Law, Evolutionary Theory 1 (1973): 1 30 Glossary alternation of generations life-cycle type in which the diploid and haploid stages alternate diploid-dominant life-cycle type in which the multicellular diploid stage is prevalent haploid-dominant life-cycle type in which the multicellular haploid stage is prevalent gametophyte a multicellular haploid life-cycle stage that produces gametes germ cells specialized cell line that produces gametes, such as eggs or sperm life cycle the sequence of events in the development of an organism and the production of cells that produce offspring sporophyte a multicellular diploid life-cycle stage that produces haploid spores by meiosisIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Experimenting with thousands of garden peas, Mendel uncovered the fundamentals of genetics. (credit: modification of work by Jerry Kirkhart) 

During the 19 th century, long before chromosomes or genes had been identified, Johann Gregor Mendel set the framework for genetics by studying a simple biological system, the garden pea. He conducted methodical, quantitative analyses using large sample sizes. Mendel s work laid the foundation for the fundamental principles of heredity. We now know that genes, carried on chromosomes, are the basic functional units of heredity with the capacity to be replicated, expressed, repressed, modified and mutated. Today, the postulates put forth by Mendel form the basis of classical, or Mendelian, genetics. Genes do not all obey the tenets of Mendelian genetics, but Mendel s experiments serve as an excellent starting point for thinking about inheritance. 

An understanding of genetic inheritance enables scientists to study and explain complex phenomena. For example, scientists studied the remains of 84 ancient dogs from North and South America. They found that some of the dogs had greater genetic diversity, indicating that these dogs might have interbred with American wolves. Other dogs in their sample had low diversity, indicating that ancient humans were purposely breeding dogs. The study also found that dogs migrated to the Americas with humans only about 10,000 years ago. You can read more about this fascinating story here . 

Introduce the topic of genetics to the students. Ask them what they think genetics is about. Can it explain why children resemble their parents? This warm up is a good opportunity to assess how familiar students are with the topic, which is very often front page news and usually poorly explained or misunderstood. Present the warm up topic of dogs interbreeding with wolves and the concepts of humans breeding animals and plants. It will be an opportunity to remind students that genetically modified organisms are not a new concept. What is new is the modification of traits at the molecular level. 

Ask students if they like Brussels sprouts or broccoli. Usually there is a diversity of responses. Some truly hate them while other students will insist that they are very good. Tell them that their genes can contribute to their like or dislike of these vegetables. Ask students to look at their hairlines and compare. The widow s peak is considered dominant and, for simplification purposes, a monogenic trait.Mendel s Experiments and the Laws of Probability Mendel s Experiments and the Laws of Probability 

In this section, you will explore the following questions: Why was Mendel s experimental work so successful? How do the sum and product rules of probability predict the outcomes of monohybrid crosses involving dominant and recessive alleles? Connection for AP Courses 

Genetics is the science of heredity. Austrian monk Gregor Mendel set the framework for genetics long before chromosomes or genes had been identified, at a time when meiosis was not well understood. Working with garden peas, Mendel found that crosses between true-breading parents (P) that differed in one trait (e.g., color: green peas versus yellow peas) produced first generation (F1) offspring that all expressed the trait of one parent (e.g., all green or all yellow). Mendel used the term dominant to refer to the trait that was observed, and recessive to denote that non-expressed trait, or the trait that had disappeared in this first generation. When the F1 offspring were crossed with each other, the F2 offspring exhibited both traits in a 3:1 ratio. Other crosses (e.g., height: tall plants versus short plants) generated the same 3:1 ratio (in this example, tall to short) in the F2 offspring. By mathematically examining sample sizes, Mendel showed that genetic crosses behaved according to the laws of probability, and that the traits were inherited as independent events. In other words, Mendel used statistical methods to build his model of inheritance. 

As you have likely noticed, the AP Biology course emphasizes the application of mathematics. Two rules of probability can be used to find the expected proportions of different traits in offspring from different crosses. To find the probability of two or more independent events (events where the outcome of one event has no influence on the outcome of the other event) occurring together, apply the product rule and multiply the probabilities of the individual events. To find the probability that one of two or more events occur, apply the sum rule and add their probabilities together. 

The content presented in this section supports the learning objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework. The AP learning objectives merge essential knowledge content with one or more of the seven science practices. These objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP exam questions. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.3 The chromosomal basis of inheritance proposed by Mendel provides an understanding of the pattern of passage of genes from parent to offspring. Science Practice 3.1 The student can pose scientific questions. Learning Objective 3.13 The student is able to pose questions about ethical, social, or medical issues surrounding human genetic disorders. Essential Knowledge 3.A.3 The chromosomal basis of inheritance proposed by Mendel provides an understanding of the pattern of passage of genes from parent to offspring. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Learning Objective 3.14 The student is able to apply mathematical routines to determine Mendelian patterns of inheritance provided by data sets. 

Two rules of probability are used in solving genetics problems: the rule of multiplication and the rule of addition. The probability that independent events will occur simultaneously is the product of their individual probabilities. If two dices are tossed, what is the probability of landing two ones? A die has 6 faces, and assuming the die is not loaded, each face has the same probability of outcome. The probability of obtaining the number 1 is equal to the number on the die divided by the total number of sides: 1 6 1 6 . The probability of rolling two ones is equal to 1 6 1 6 = 1 36 1 6 1 6 = 1 36 . 

The probability that any one of a set of mutually exclusive events will occur is the sum of their individual probabilities. The probability of rolling a 1 or a 2 is equal to 1 6 + 1 6 = 1 3 1 6 + 1 6 = 1 3 because the two outcomes are mutually exclusive. If we roll a 1, it cannot be a 2. 

Tell students that Gregor Mendel was a monk who had received a solid scientific education and had excelled at mathematics. He brought this knowledge of science into his experiments with peas. 

Engage students in describing what makes a good organism to study genetics. One approach is to ask the class if they would use elephants to study genetics. The disadvantages of using elephants actually highlight the advantages of using peas, corn, fruit flies, or mice for genetics studies: short life cycle, easy to maintain and handle, large number of offspring for statistical analysis, etc. 

The concepts of statistics are not intuitive. Practice with dice and coins. Explain that the probability ratios are achieved with large numbers of trials. 

Dominant traits are the ones expressed in a dominant/recessive situation. They do not usually repress the recessive trait. A dominant trait is not necessarily the most common trait in a population. For example, type O blood is a recessive trait, but it is the most frequent blood group in many ethnic groups. A dominant trait can be lethal. A dominant allele is not better than the recessive allele. Whether a trait is beneficial depends on the environment. Give the example of wing color in moths. Dark pigmentation is beneficial in a polluted environment where predators would not pick up the moths on dark tree barks. For example, the population peppered moths in 19th century London shifted so that their wing colors were darker to blend in with the soot of the Industrial Revolution. After pollution levels dropped, light pigmentation became more prevalent because it helped the moths to escape notice. Johann Gregor Mendel is considered the father of genetics. 

Johann Gregor Mendel (1822 1884) ( [link] ) was a lifelong learner, teacher, scientist, and man of faith. As a young adult, he joined the Augustinian Abbey of St. Thomas in Brno in what is now the Czech Republic. Supported by the monastery, he taught physics, botany, and natural science courses at the secondary and university levels. In 1856, he began a decade-long research pursuit involving inheritance patterns in honeybees and plants, ultimately settling on pea plants as his primary model system (a system with convenient characteristics used to study a specific biological phenomenon to be applied to other systems). In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the local Natural History Society. He demonstrated that traits are transmitted faithfully from parents to offspring independently of other traits and in dominant and recessive patterns. In 1866, he published his work, Experiments in Plant Hybridization, 1 in the proceedings of the Natural History Society of Br nn. 

Mendel s work went virtually unnoticed by the scientific community that believed, incorrectly, that the process of inheritance involved a blending of parental traits that produced an intermediate physical appearance in offspring; this hypothetical process appeared to be correct because of what we know now as continuous variation. Continuous variation results from the action of many genes to determine a characteristic like human height. Offspring appear to be a blend of their parents traits when we look at characteristics that exhibit continuous variation. The blending theory of inheritance asserted that the original parental traits were lost or absorbed by the blending in the offspring, but we now know that this is not the case. Mendel was the first researcher to see it. Instead of continuous characteristics, Mendel worked with traits that were inherited in distinct classes (specifically, violet versus white flowers); this is referred to as discontinuous variation . Mendel s choice of these kinds of traits allowed him to see experimentally that the traits were not blended in the offspring, nor were they absorbed, but rather that they kept their distinctness and could be passed on. In 1868, Mendel became abbot of the monastery and exchanged his scientific pursuits for his pastoral duties. He was not recognized for his extraordinary scientific contributions during his lifetime. In fact, it was not until 1900 that his work was rediscovered, reproduced, and revitalized by scientists on the brink of discovering the chromosomal basis of heredity. Mendel s Model System 

Mendel s seminal work was accomplished using the garden pea, Pisum sativum , to study inheritance. This species naturally self-fertilizes, such that pollen encounters ova within individual flowers. The flower petals remain sealed tightly until after pollination, preventing pollination from other plants. The result is highly inbred, or true-breeding, pea plants. These are plants that always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance. Mendelian Crosses 

Mendel performed hybridizations , which involve mating two true-breeding individuals that have different traits. In the pea, which is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant of one variety to the stigma of a separate mature pea plant of the second variety. In plants, pollen carries the male gametes (sperm) to the stigma, a sticky organ that traps pollen and allows the sperm to move down the pistil to the female gametes (ova) below. To prevent the pea plant that was receiving pollen from self-fertilizing and confounding his results, Mendel painstakingly removed all of the anthers from the plant s flowers before they had a chance to mature. 

Plants used in first-generation crosses were called P 0 , or parental generation one, plants ( [link] ). Mendel collected the seeds belonging to the P 0 plants that resulted from each cross and grew them the following season. These offspring were called the F 1 , or the first filial ( filial = offspring, daughter or son), generation. Once Mendel examined the characteristics in the F 1 generation of plants, he allowed them to self-fertilize naturally. He then collected and grew the seeds from the F 1 plants to produce the F 2 , or second filial, generation. Mendel s experiments extended beyond the F 2 generation to the F 3 and F 4 generations, and so on, but it was the ratio of characteristics in the P 0 F 1 F 2 generations that were the most intriguing and became the basis for Mendel s postulates. In one of his experiments on inheritance patterns, Mendel crossed plants that were true-breeding for violet flower color with plants true-breeding for white flower color (the P generation). The resulting hybrids in the F 1 generation all had violet flowers. In the F 2 generation, approximately three quarters of the plants had violet flowers, and one quarter had white flowers. Garden Pea Characteristics Revealed the Basics of Heredity 

In his 1865 publication, Mendel reported the results of his crosses involving seven different characteristics, each with two contrasting traits. A trait is defined as a variation in the physical appearance of a heritable characteristic. The characteristics included plant height, seed texture, seed color, flower color, pea pod size, pea pod color, and flower position. For the characteristic of flower color, for example, the two contrasting traits were white versus violet. To fully examine each characteristic, Mendel generated large numbers of F 1 and F 2 plants, reporting results from 19,959 F 2 plants alone. His findings were consistent. 

What results did Mendel find in his crosses for flower color? First, Mendel confirmed that he had plants that bred true for white or violet flower color. Regardless of how many generations Mendel examined, all self-crossed offspring of parents with white flowers had white flowers, and all self-crossed offspring of parents with violet flowers had violet flowers. In addition, Mendel confirmed that, other than flower color, the pea plants were physically identical. 

Once these validations were complete, Mendel applied the pollen from a plant with violet flowers to the stigma of a plant with white flowers. After gathering and sowing the seeds that resulted from this cross, Mendel found that 100 percent of the F 1 hybrid generation had violet flowers. Conventional wisdom at that time would have predicted the hybrid flowers to be pale violet or for hybrid plants to have equal numbers of white and violet flowers. In other words, the contrasting parental traits were expected to blend in the offspring. Instead, Mendel s results demonstrated that the white flower trait in the F 1 generation had completely disappeared. 

Importantly, Mendel did not stop his experimentation there. He allowed the F 1 plants to self-fertilize and found that, of F 2 -generation plants, 705 had violet flowers and 224 had white flowers. This was a ratio of 3.15 violet flowers per one white flower, or approximately 3:1. When Mendel transferred pollen from a plant with violet flowers to the stigma of a plant with white flowers and vice versa, he obtained about the same ratio regardless of which parent, male or female, contributed which trait. This is called a reciprocal cross a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross. For the other six characteristics Mendel examined, the F 1 and F 2 generations behaved in the same way as they had for flower color. One of the two traits would disappear completely from the F 1 generation only to reappear in the F 2 generation at a ratio of approximately 3:1 ( [link] ). The Results of Mendel s Garden Pea Hybridizations Characteristic Contrasting P 0 Traits F 1 Offspring Traits F 2 Offspring Traits F 2 Trait Ratios Flower color Violet vs. white 100 percent violet 705 violet 224 white 3.15:1 Flower position Axial vs. terminal 100 percent axial 651 axial 207 terminal 3.14:1 Plant height Tall vs. dwarf 100 percent tall 787 tall 277 dwarf 2.84:1 Seed texture Round vs. wrinkled 100 percent round 5,474 round 1,850 wrinkled 2.96:1 Seed color Yellow vs. green 100 percent yellow 6,022 yellow 2,001 green 3.01:1 Pea pod texture Inflated vs. constricted 100 percent inflated 882 inflated 299 constricted 2.95:1 Pea pod color Green vs. yellow 100 percent green 428 green 152 yellow 2.82:1 

Upon compiling his results for many thousands of plants, Mendel concluded that the characteristics could be divided into expressed and latent traits. He called these, respectively, dominant and recessive traits. Dominant traits are those that are inherited unchanged in a hybridization. Recessive traits become latent, or disappear, in the offspring of a hybridization. The recessive trait does, however, reappear in the progeny of the hybrid offspring. An example of a dominant trait is the violet-flower trait. For this same characteristic (flower color), white-colored flowers are a recessive trait. The fact that the recessive trait reappeared in the F 2 generation meant that the traits remained separate (not blended) in the plants of the F 1 generation. Mendel also proposed that plants possessed two copies of the trait for the flower-color characteristic, and that each parent transmitted one of its two copies to its offspring, where they came together. Moreover, the physical observation of a dominant trait could mean that the genetic composition of the organism included two dominant versions of the characteristic or that it included one dominant and one recessive version. Conversely, the observation of a recessive trait meant that the organism lacked any dominant versions of this characteristic. 

So why did Mendel repeatedly obtain 3:1 ratios in his crosses? To understand how Mendel deduced the basic mechanisms of inheritance that lead to such ratios, we must first review the laws of probability. Think About It 

Students are performing a cross involving seed color in garden pea plants. Yellow seed color is dominant to green seed color. What F1 offspring would be expected when cross true-breeding plants with green seeds with true-breading plants with yellow seeds? Express the answer(s) as percentage. 

This question is an application of Learning Objectives 3.14 and Science Practice 2.2 because students are applying a mathematical routine (probability) to determine a Mendelian pattern of inheritance. Possible answer: 100% would be yellow seeds. The dominant trait is the only one displayed in F1. Probability Basics 

Probabilities are mathematical measures of likelihood. The empirical probability of an event is calculated by dividing the number of times the event occurs by the total number of opportunities for the event to occur. It is also possible to calculate theoretical probabilities by dividing the number of times that an event is expected to occur by the number of times that it could occur. Empirical probabilities come from observations, like those of Mendel. Theoretical probabilities come from knowing how the events are produced and assuming that the probabilities of individual outcomes are equal. A probability of one for some event indicates that it is guaranteed to occur, whereas a probability of zero indicates that it is guaranteed not to occur. An example of a genetic event is a round seed produced by a pea plant. In his experiment, Mendel demonstrated that the probability of the event round seed occurring was one in the F 1 offspring of true-breeding parents, one of which has round seeds and one of which has wrinkled seeds. When the F 1 plants were subsequently self-crossed, the probability of any given F 2 offspring having round seeds was now three out of four. In other words, in a large population of F 2 offspring chosen at random, 75 percent were expected to have round seeds, whereas 25 percent were expected to have wrinkled seeds. Using large numbers of crosses, Mendel was able to calculate probabilities and use these to predict the outcomes of other crosses. The Product Rule and Sum Rule 

Mendel demonstrated that the pea-plant characteristics he studied were transmitted as discrete units from parent to offspring. As will be discussed, Mendel also determined that different characteristics, like seed color and seed texture, were transmitted independently of one another and could be considered in separate probability analyses. For instance, performing a cross between a plant with green, wrinkled seeds and a plant with yellow, round seeds still produced offspring that had a 3:1 ratio of green:yellow seeds (ignoring seed texture) and a 3:1 ratio of round:wrinkled seeds (ignoring seed color). The characteristics of color and texture did not influence each other. 

The product rule of probability can be applied to this phenomenon of the independent transmission of characteristics. The product rule states that the probability of two independent events occurring together can be calculated by multiplying the individual probabilities of each event occurring alone. To demonstrate the product rule, imagine that you are rolling a six-sided die (D) and flipping a penny (P) at the same time. The die may roll any number from 1 6 (D # ), whereas the penny may turn up heads (P H ) or tails (P T ). The outcome of rolling the die has no effect on the outcome of flipping the penny and vice versa. There are 12 possible outcomes of this action ( [link] ), and each event is expected to occur with equal probability. Twelve Equally Likely Outcomes of Rolling a Die and Flipping a Penny Rolling Die Flipping Penny D 1 P H D 1 P T D 2 P H D 2 P T D 3 P H D 3 P T D 4 P H D 4 P T D 5 P H D 5 P T D 6 P H D 6 P T 

Of the 12 possible outcomes, the die has a 2/12 (or 1/6) probability of rolling a two, and the penny has a 6/12 (or 1/2) probability of coming up heads. By the product rule, the probability that you will obtain the combined outcome 2 and heads is: (D 2 ) x (P H ) = (1/6) x (1/2) or 1/12 ( [link] ). Notice the word and in the description of the probability. The and is a signal to apply the product rule. For example, consider how the product rule is applied to the dihybrid cross: the probability of having both dominant traits in the F 2 progeny is the product of the probabilities of having the dominant trait for each characteristic, as shown here: 3 4 3 4 = 9 16 3 4 3 4 = 9 16 

On the other hand, the sum rule of probability is applied when considering two mutually exclusive outcomes that can come about by more than one pathway. The sum rule states that the probability of the occurrence of one event or the other event, of two mutually exclusive events, is the sum of their individual probabilities. Notice the word or in the description of the probability. The or indicates that you should apply the sum rule. In this case, let s imagine you are flipping a penny (P) and a quarter (Q). What is the probability of one coin coming up heads and one coin coming up tails? This outcome can be achieved by two cases: the penny may be heads (P H ) and the quarter may be tails (Q T ), or the quarter may be heads (Q H ) and the penny may be tails (P T ). Either case fulfills the outcome. By the sum rule, we calculate the probability of obtaining one head and one tail as [(P H ) (Q T )] + [(Q H ) (P T )] = [(1/2) (1/2)] + [(1/2) (1/2)] = 1/2 ( [link] ). You should also notice that we used the product rule to calculate the probability of P H and Q T , and also the probability of P T and Q H , before we summed them. Again, the sum rule can be applied to show the probability of having just one dominant trait in the F 2 generation of a dihybrid cross: 3 16 + 3 4 = 15 16 3 16 + 3 4 = 15 16 The Product Rule and Sum Rule Product Rule Sum Rule For independent events A and B, the probability (P) of them both occurring (A and B) is (P A P B ) For mutually exclusive events A and B, the probability (P) that at least one occurs (A or B) is (P A + P B ) 

To use probability laws in practice, it is necessary to work with large sample sizes because small sample sizes are prone to deviations caused by chance. The large quantities of pea plants that Mendel examined allowed him calculate the probabilities of the traits appearing in his F 2 generation. As you will learn, this discovery meant that when parental traits were known, the offspring s traits could be predicted accurately even before fertilization. Section Summary 

Working with garden pea plants, Mendel found that crosses between parents that differed by one trait produced F 1 offspring that all expressed the traits of one parent. Observable traits are referred to as dominant, and non-expressed traits are described as recessive. When the offspring in Mendel s experiment were self-crossed, the F 2 offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully from the original P 0 parent. Reciprocal crosses generated identical F 1 and F 2 offspring ratios. By examining sample sizes, Mendel showed that his crosses behaved reproducibly according to the laws of probability, and that the traits were inherited as independent events. 

Two rules in probability can be used to find the expected proportions of offspring of different traits from different crosses. To find the probability of two or more independent events occurring together, apply the product rule and multiply the probabilities of the individual events. The use of the word and suggests the appropriate application of the product rule. To find the probability of two or more events occurring in combination, apply the sum rule and add their individual probabilities together. The use of the word or suggests the appropriate application of the sum rule. Review Questions 

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Johann Gregor Mendel, Versuche ber Pflanzenhybriden Verhandlungen des naturforschenden Vereines in Br nn, Bd. IV f r das Jahr , 1865 Abhandlungen, 3 47. [go here for the English translation here ] Glossary blending theory of inheritance hypothetical inheritance pattern in which parental traits are blended together in the offspring to produce an intermediate physical appearance continuous variation inheritance pattern in which a character shows a range of trait values with small gradations rather than large gaps between them discontinuous variation inheritance pattern in which traits are distinct and are transmitted independently of one another dominant trait which confers the same physical appearance whether an individual has two copies of the trait or one copy of the dominant trait and one copy of the recessive trait F 1 first filial generation in a cross; the offspring of the parental generation F 2 second filial generation produced when F 1 individuals are self-crossed or fertilized with each other hybridization process of mating two individuals that differ with the goal of achieving a certain characteristic in their offspring model system species or biological system used to study a specific biological phenomenon to be applied to other different species P 0 parental generation in a cross product rule probability of two independent events occurring simultaneously can be calculated by multiplying the individual probabilities of each event occurring alone recessive trait that appears latent or non-expressed when the individual also carries a dominant trait for that same characteristic; when present as two identical copies, the recessive trait is expressed reciprocal cross paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross sum rule probability of the occurrence of at least one of two mutually exclusive events is the sum of their individual probabilities trait variation in the physical appearance of a heritable characteristicCharacteristics and Traits Characteristics and Traits 

In this section, you will explore the following questions: What is the relationship between genotypes and phenotypes in dominant and recessive gene systems? How can a Punnett square be used to calculate expected proportions of genotypes and phenotypes in a monohybrid cross? How do phenomena such as incomplete dominance, codominance, recessive lethals, multiple alleles, and sex linkage explain deviations from Mendel s model of inheritance? Connection for AP Courses 

The characteristics that Mendel evaluated in his pea plants were each expressed as one of two versions, or traits (e.g., green peas versus yellow peas). As we will explore in more detail in later chapters, the physical expression of characteristics is accomplished through the expression of genes (sequences of DNA), carried on chromosomes. The genetic makeup of peas consists of two similar, or homologous (remember this term from Chapter 11), copies of each chromosome, one from each parent. Through meiosis, diploid organisms utilize meiosis to produce haploid (1 n ) gametes that participate in fertilization. For cases in which a single gene controls a single characteristic, such as pea color, a diploid organism has genetic copies that may or may not encode the same version of the characteristic. These gene variations (e.g., green peas versus yellow peas) are called alleles. 

Different alleles for a given gene in a diploid organism interact to express physical characteristics such as pea color in plants or hairline appearance in humans. The observable traits of an organism are referred to as its phenotype. The organism s underlying genetic makeup, i.e., the combination of alleles, is called its genotype. When diploid organisms carry the same alleles for a given trait, they are said to be homozygous for the genotype; when they carry different alleles, they are said to be heterozygous. For a gene whose expression is Mendelian (Section 12.1), homozygous dominant and heterozygous organisms will look identical; that is, they will have different genotypes but the same phenotype. The recessive allele will only be observed in homozygous recessive individuals. 

However, alleles do not always behave in dominant and recessive patterns. In other words, there are exceptions to Mendel s model of inheritance. For example, incomplete dominance describes situation in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes (e.g., a pink-flowered offspring is produced from a cross between a red-flowered parent and a white-flowered parent). Codominance describes the simultaneous expression of both of the alleles in the heterozygote (e.g., human blood types). It is also common for more than two alleles of a gene to exist in a population (e.g., variations in sizes of pumpkins). In humans, as in many animals and some plants, females have two X chromosomes, and males have one X chromosome and one Y chromosome. Genes on the X chromosome are X-linked, and males inherit and express only one allele for the gene (e.g., hemophilia, color-blindness). Some alleles can also be lethal, so their phenotype will never be observed. 

Many human genetic disorders, including albinism, cystic fibrosis, and Huntington s disease can be explained on the basis of simple Mendelian inheritance patterns created by pedigree analysis. (In later Chapters we will learn how DNA analysis can be used to diagnose genetic disorders). Punnett squares are useful tools that apply the rules of probability and meiosis to predict the possible outcomes of genetic crosses. Test crosses are done to determine whether or not an individual is homozygous or heterozygous by crossing the individual with a homozygous recessive. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The learning objectives (LO) listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices (SP). 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.3 The chromosomal basis of inheritance proposed by Mendel provides an understanding of the pattern of passage of genes from parent to offspring. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 3.12 The student is able to construct a representation (e.g., Punnett square) that connects the process of meiosis to the passage of traits from parent to offspring. Essential Knowledge 3.A.3 The chromosomal basis of inheritance proposed by Mendel provides an understanding of the pattern of passage of genes from parent to offspring. Science Practice 3.1 The student can pose scientific questions. Learning Objective 3.13 The student is able to pose questions about ethical, social or medical issues surrounding human genetic disorders. Essential Knowledge 3.A.3 The chromosomal basis of inheritance proposed by Mendel provides an understanding of the pattern of passage of genes from parent to offspring. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Learning Objective 3.14 The student is able to apply mathematical routines to determine Mendelian patterns of inheritance provided by data sets. Essential Knowledge 3.A.4 The inheritance patterns of many traits cannot be explained by simple Mendelian genetics. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.15 The student is able to explain deviations from Mendel s model of the inheritance of traits. Essential Knowledge 3.A.4 The inheritance patterns of many traits cannot be explained by simple Mendelian genetics. Science Practice 6.3 The student can articulate the reasons that scientific explanations and theories are refined or replaced. Learning Objective 3.16 The student is able to explain how the inheritance pattern of many traits cannot be accounted for by Mendelian genetics. Essential Knowledge 3.A.4 The inheritance patterns of many traits cannot be explained by simple Mendelian genetics. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.17 The student is able to describe representations of an appropriate example of inheritance patterns that cannot be explained by Mendel s model of the inheritance of traits. 

Emphasize to the class the importance of using a Punnett s square rather than guessing the right answer. Students should show their reasoning to solve Mendelian genetics problems. This site contains a wealth of problems. Ask students to answer questions after designing a Punnett s square. 

It is recommended to work through all problems and assessments before assigning them to students. Verify that there is only one correct answer or alert students that there might be several correct answers. 

Choose easily observable traits such as widow s peak or attached ear lobe. Divide the class into groups of 5 6 students. Each group will draw possible Punnett squares for the traits of students in their group. Because the students can only observe their phenotype, each student may have several possible Punnett squares, depending on his/her parent s genotypes. 

Another exercise to be performed by the students is measuring the distribution of tasters and non-tasters of the bitter chemical phenylthiocarbamide (PTC). Paper strips impregnated with PTC are available from scientific suppliers and can be used to survey the class. Ask students to put a strip of paper on their tongue and record the taste. Some individuals can react strongly to an intensely bitter taste, other can detect a bitter taste, and, for some, it is just insipid paper. The ability to taste PTC is controlled by the gene TAS2R38 whose taster allele is dominant over the non-taster allele. 

Detailed worksheets available at: A Tree of Genetic Traits . 

For more information, go here this site . You may also find worksheets here . For resources on human genetics visit the Online Mendelian Inheritance in Man Online Mendelian Inheritance in Man and the Genetics Home References . 

The seven characteristics that Mendel evaluated in his pea plants were each expressed as one of two versions, or traits. The physical expression of characteristics is accomplished through the expression of genes carried on chromosomes. The genetic makeup of peas consists of two similar or homologous copies of each chromosome, one from each parent. Each pair of homologous chromosomes has the same linear order of genes. In other words, peas are diploid organisms in that they have two copies of each chromosome. The same is true for many other plants and for virtually all animals. Diploid organisms utilize meiosis to produce haploid gametes, which contain one copy of each homologous chromosome that unite at fertilization to create a diploid zygote. 

For cases in which a single gene controls a single characteristic, a diploid organism has two genetic copies that may or may not encode the same version of that characteristic. Gene variants that arise by mutation and exist at the same relative locations on homologous chromosomes are called alleles . Mendel examined the inheritance of genes with just two allele forms, but it is common to encounter more than two alleles for any given gene in a natural population. Phenotypes and Genotypes 

Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype . An organism s underlying genetic makeup, consisting of both physically visible and non-expressed alleles, is called its genotype . Mendel s hybridization experiments demonstrate the difference between phenotype and genotype. When true-breeding plants in which one parent had yellow pods and one had green pods were cross-fertilized, all of the F 1 hybrid offspring had yellow pods. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow pods. However, we know that the allele donated by the parent with green pods was not simply lost because it reappeared in some of the F 2 offspring. Therefore, the F 1 plants must have been genotypically different from the parent with yellow pods. 

The P 1 plants that Mendel used in his experiments were each homozygous for the trait he was studying. Diploid organisms that are homozygous at a given gene, or locus, have two identical alleles for that gene on their homologous chromosomes. Mendel s parental pea plants always bred true because both of the gametes produced carried the same trait. When P 1 plants with contrasting traits were cross-fertilized, all of the offspring were heterozygous for the contrasting trait, meaning that their genotype reflected that they had different alleles for the gene being examined. Dominant and Recessive Alleles 

Our discussion of homozygous and heterozygous organisms brings us to why the F 1 heterozygous offspring were identical to one of the parents, rather than expressing both alleles. In all seven pea-plant characteristics, one of the two contrasting alleles was dominant, and the other was recessive. Mendel called the dominant allele the expressed unit factor; the recessive allele was referred to as the latent unit factor. We now know that these so-called unit factors are actually genes on homologous chromosome pairs. For a gene that is expressed in a dominant and recessive pattern, homozygous dominant and heterozygous organisms will look identical (that is, they will have different genotypes but the same phenotype). The recessive allele will only be observed in homozygous recessive individuals ( [link] ). Human Inheritance in Dominant and Recessive Patterns Dominant Traits Recessive Traits Achondroplasia Albinism Brachydactyly Cystic fibrosis Huntington s disease Duchenne muscular dystrophy Marfan syndrome Galactosemia Neurofibromatosis Phenylketonuria Widow s peak Sickle-cell anemia Wooly hair Tay-Sachs disease 

Several conventions exist for referring to genes and alleles. For the purposes of this chapter, we will abbreviate genes using the first letter of the gene s corresponding dominant trait. For example, violet is the dominant trait for a pea plant s flower color, so the flower-color gene would be abbreviated as V (note that it is customary to italicize gene designations). Furthermore, we will use uppercase and lowercase letters to represent dominant and recessive alleles, respectively. Therefore, we would refer to the genotype of a homozygous dominant pea plant with violet flowers as VV , a homozygous recessive pea plant with white flowers as vv , and a heterozygous pea plant with violet flowers as Vv . The Punnett Square Approach for a Monohybrid Cross 

When fertilization occurs between two true-breeding parents that differ in only one characteristic, the process is called a monohybrid cross, and the resulting offspring are monohybrids. Mendel performed seven monohybrid crosses involving contrasting traits for each characteristic. On the basis of his results in F 1 and F 2 generations, Mendel postulated that each parent in the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors was equally likely. 

To demonstrate a monohybrid cross, consider the case of true-breeding pea plants with yellow versus green pea seeds. The dominant seed color is yellow; therefore, the parental genotypes were YY for the plants with yellow seeds and yy for the plants with green seeds, respectively. A Punnett square , devised by the British geneticist Reginald Punnett, can be drawn that applies the rules of probability to predict the possible outcomes of a genetic cross or mating and their expected frequencies. To prepare a Punnett square, all possible combinations of the parental alleles are listed along the top (for one parent) and side (for the other parent) of a grid, representing their meiotic segregation into haploid gametes. Then the combinations of egg and sperm are made in the boxes in the table to show which alleles are combining. Each box then represents the diploid genotype of a zygote, or fertilized egg, that could result from this mating. Because each possibility is equally likely, genotypic ratios can be determined from a Punnett square. If the pattern of inheritance (dominant or recessive) is known, the phenotypic ratios can be inferred as well. For a monohybrid cross of two true-breeding parents, each parent contributes one type of allele. In this case, only one genotype is possible. All offspring are Yy and have yellow seeds ( [link] ). In the P generation, pea plants that are true-breeding for the dominant yellow phenotype are crossed with plants with the recessive green phenotype. This cross produces F 1 heterozygotes with a yellow phenotype. Punnett square analysis can be used to predict the genotypes of the F 2 generation. 

A self-cross of one of the Yy heterozygous offspring can be represented in a 2 2 Punnett square because each parent can donate one of two different alleles. Therefore, the offspring can potentially have one of four allele combinations: YY , Yy , yY , or yy ( [link] ). Notice that there are two ways to obtain the Yy genotype: a Y from the egg and a y from the sperm, or a y from the egg and a Y from the sperm. Both of these possibilities must be counted. Recall that Mendel s pea-plant characteristics behaved in the same way in reciprocal crosses. Therefore, the two possible heterozygous combinations produce offspring that are genotypically and phenotypically identical despite their dominant and recessive alleles deriving from different parents. They are grouped together. Because fertilization is a random event, we expect each combination to be equally likely and for the offspring to exhibit a ratio of YY : Yy : yy genotypes of 1:2:1 ( [link] ). Furthermore, because the YY and Yy offspring have yellow seeds and are phenotypically identical, applying the sum rule of probability, we expect the offspring to exhibit a phenotypic ratio of 3 yellow:1 green. Indeed, working with large sample sizes, Mendel observed approximately this ratio in every F 2 generation resulting from crosses for individual traits. 

Mendel validated these results by performing an F 3 cross in which he self-crossed the dominant- and recessive-expressing F 2 plants. When he self-crossed the plants expressing green seeds, all of the offspring had green seeds, confirming that all green seeds had homozygous genotypes of yy . When he self-crossed the F 2 plants expressing yellow seeds, he found that one-third of the plants bred true, and two-thirds of the plants segregated at a 3:1 ratio of yellow:green seeds. In this case, the true-breeding plants had homozygous ( YY ) genotypes, whereas the segregating plants corresponded to the heterozygous ( Yy ) genotype. When these plants self-fertilized, the outcome was just like the F 1 self-fertilizing cross. The Test Cross Distinguishes the Dominant Phenotype 

Beyond predicting the offspring of a cross between known homozygous or heterozygous parents, Mendel also developed a way to determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote. Called the test cross , this technique is still used by plant and animal breeders. In a test cross, the dominant-expressing organism is crossed with an organism that is homozygous recessive for the same characteristic. If the dominant-expressing organism is a homozygote, then all F 1 offspring will be heterozygotes expressing the dominant trait ( [link] ). Alternatively, if the dominant expressing organism is a heterozygote, the F 1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes ( [link] ). The test cross further validates Mendel s postulate that pairs of unit factors segregate equally. 

A test cross can be performed to determine whether an organism expressing a dominant trait is a homozygote or a heterozygote. 

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Many human diseases are genetically inherited. A healthy person in a family in which some members suffer from a recessive genetic disorder may want to know if he or she has the disease-causing gene and what risk exists of passing the disorder on to his or her offspring. Of course, doing a test cross in humans is unethical and impractical. Instead, geneticists use pedigree analysis to study the inheritance pattern of human genetic diseases ( [link] ). 

Alkaptonuria is a recessive genetic disorder in which two amino acids, phenylalanine and tyrosine, are not properly metabolized. Affected individuals may have darkened skin and brown urine, and may suffer joint damage and other complications. In this pedigree, individuals with the disorder are indicated in blue and have the genotype aa . Unaffected individuals are indicated in yellow and have the genotype AA or Aa . Note that it is often possible to determine a person s genotype from the genotype of their offspring. For example, if neither parent has the disorder but their child does, they must be heterozygous. Two individuals on the pedigree have an unaffected phenotype but unknown genotype. Because they do not have the disorder, they must have at least one normal allele, so their genotype gets the A? designation. 

[link] Alternatives to Dominance and Recessiveness 

Mendel s experiments with pea plants suggested that: (1) two units or alleles exist for every gene; (2) alleles maintain their integrity in each generation (no blending); and (3) in the presence of the dominant allele, the recessive allele is hidden and makes no contribution to the phenotype. Therefore, recessive alleles can be carried and not expressed by individuals. Such heterozygous individuals are sometimes referred to as carriers. Further genetic studies in other plants and animals have shown that much more complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider some of the extensions of Mendelism. If Mendel had chosen an experimental system that exhibited these genetic complexities, it s possible that he would not have understood what his results meant. Incomplete Dominance 

Mendel s results, that traits are inherited as dominant and recessive pairs, contradicted the view at that time that offspring exhibited a blend of their parents traits. However, the heterozygote phenotype occasionally does appear to be intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus ( [link] ), a cross between a homozygous parent with white flowers ( C W C W ) and a homozygous parent with red flowers ( C R C R ) will produce offspring with pink flowers ( C R C W ). (Note that different genotypic abbreviations are used for Mendelian extensions to distinguish these patterns from simple dominance and recessiveness.) This pattern of inheritance is described as incomplete dominance , denoting the expression of two contrasting alleles such that the individual displays an intermediate phenotype. The allele for red flowers is incompletely dominant over the allele for white flowers. However, the results of a heterozygote self-cross can still be predicted, just as with Mendelian dominant and recessive crosses. In this case, the genotypic ratio would be 1 C R C R :2 C R C W :1 C W C W , and the phenotypic ratio would be 1:2:1 for red:pink:white. These pink flowers of a heterozygote snapdragon result from incomplete dominance. (credit: storebukkebruse /Flickr) Codominance 

A variation on incomplete dominance is codominance , in which both alleles for the same characteristic are simultaneously expressed in the heterozygote. An example of codominance is the MN blood groups of humans. The M and N alleles are expressed in the form of an M or N antigen present on the surface of red blood cells. Homozygotes ( L M L M and L N L N ) express either the M or the N allele, and heterozygotes ( L M L N ) express both alleles equally. In a self-cross between heterozygotes expressing a codominant trait, the three possible offspring genotypes are phenotypically distinct. However, the 1:2:1 genotypic ratio characteristic of a Mendelian monohybrid cross still applies. Multiple Alleles 

Mendel implied that only two alleles, one dominant and one recessive, could exist for a given gene. We now know that this is an oversimplification. Although individual humans (and all diploid organisms) can only have two alleles for a given gene, multiple alleles may exist at the population level such that many combinations of two alleles are observed. Note that when many alleles exist for the same gene, the convention is to denote the most common phenotype or genotype among wild animals as the wild type (often abbreviated + ); this is considered the standard or norm. All other phenotypes or genotypes are considered variants of this standard, meaning that they deviate from the wild type. The variant may be recessive or dominant to the wild-type allele. 

An example of multiple alleles is coat color in rabbits ( [link] ). Here, four alleles exist for the c gene. The wild-type version, C + C + , is expressed as brown fur. The chinchilla phenotype, c ch c ch , is expressed as black-tipped white fur. The Himalayan phenotype, c h c h , has black fur on the extremities and white fur elsewhere. Finally, the albino, or colorless phenotype, cc , is expressed as white fur. In cases of multiple alleles, dominance hierarchies can exist. In this case, the wild-type allele is dominant over all the others, chinchilla is incompletely dominant over Himalayan and albino, and Himalayan is dominant over albino. This hierarchy, or allelic series, was revealed by observing the phenotypes of each possible heterozygote offspring. Four different alleles exist for the rabbit coat color ( C ) gene. 

The complete dominance of a wild-type phenotype over all other mutants often occurs as an effect of dosage of a specific gene product, such that the wild-type allele supplies the correct amount of gene product whereas the mutant alleles cannot. For the allelic series in rabbits, the wild-type allele may supply a given dosage of fur pigment, whereas the mutants supply a lesser dosage or none at all. Interestingly, the Himalayan phenotype is the result of an allele that produces a temperature-sensitive gene product that only produces pigment in the cooler extremities of the rabbit s body. 

Alternatively, one mutant allele can be dominant over all other phenotypes, including the wild type. This may occur when the mutant allele somehow interferes with the genetic message so that even a heterozygote with one wild-type allele copy expresses the mutant phenotype. One way in which the mutant allele can interfere is by enhancing the function of the wild-type gene product or changing its distribution in the body. One example of this is the Antennapedia mutation in Drosophila ( [link] ). In this case, the mutant allele expands the distribution of the gene product, and as a result, the Antennapedia heterozygote develops legs on its head where its antennae should be. As seen in comparing the wild-type Drosophila (left) and the Antennapedia mutant (right), the Antennapedia mutant has legs on its head in place of antennae. 

Multiple Alleles Confer Drug Resistance in the Malaria Parasite Malaria is a parasitic disease in humans that is transmitted by infected female mosquitoes, including Anopheles gambiae ( [link] a ), and is characterized by cyclic high fevers, chills, flu-like symptoms, and severe anemia. Plasmodium falciparum and P. vivax are the most common causative agents of malaria, and P. falciparum is the most deadly ( [link] b ) . When promptly and correctly treated, P. falciparum malaria has a mortality rate of 0.1 percent. However, in some parts of the world, the parasite has evolved resistance to commonly used malaria treatments, so the most effective malarial treatments can vary by geographic region. The (a) Anopheles gambiae , or African malaria mosquito, acts as a vector in the transmission to humans of the malaria-causing parasite (b) Plasmodium falciparum , here visualized using false-color transmission electron microscopy. (credit a: James D. Gathany; credit b: Ute Frevert; false color by Margaret Shear; scale-bar data from Matt Russell) 

In Southeast Asia, Africa, and South America, P. falciparum has developed resistance to the anti-malarial drugs chloroquine, mefloquine, and sulfadoxine-pyrimethamine. P. falciparum , which is haploid during the life stage in which it is infectious to humans, has evolved multiple drug-resistant mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance are associated with each of these alleles. Being haploid, P. falciparum needs only one drug-resistant allele to express this trait. 

In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene are localized to different geographic regions. This is a common evolutionary phenomenon that occurs because drug-resistant mutants arise in a population and interbreed with other P. falciparum isolates in close proximity. Sulfadoxine-resistant parasites cause considerable human hardship in regions where this drug is widely used as an over-the-counter malaria remedy. As is common with pathogens that multiply to large numbers within an infection cycle, P. falciparum evolves relatively rapidly (over a decade or so) in response to the selective pressure of commonly used anti-malarial drugs. For this reason, scientists must constantly work to develop new drugs or drug combinations to combat the worldwide malaria burden. 1 

[link] X-Linked Traits 

In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes. The sex chromosomes are one pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or autosomes . In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas human males have an XY chromosome pair. Although the Y chromosome contains a small region of similarity to the X chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains many fewer genes. When a gene being examined is present on the X chromosome, but not on the Y chromosome, it is said to be X-linked . 

Eye color in Drosophila was one of the first X-linked traits to be identified. Thomas Hunt Morgan mapped this trait to the X chromosome in 1910. Like humans, Drosophila males have an XY chromosome pair, and females are XX. In flies, the wild-type eye color is red (X W ) and it is dominant to white eye color (X w ) ( [link] ). Because of the location of the eye-color gene, reciprocal crosses do not produce the same offspring ratios. Males are said to be hemizygous , because they have only one allele for any X-linked characteristic. Hemizygosity makes the descriptions of dominance and recessiveness irrelevant for XY males. Drosophila males lack a second allele copy on the Y chromosome; that is, their genotype can only be X W Y or X w Y. In contrast, females have two allele copies of this gene and can be X W X W , X W X w , or X w X w . In Drosophila , the gene for eye color is located on the X chromosome. Clockwise from top left are brown, cinnabar, sepia, vermilion, white, and red. Red eye color is wild-type and is dominant to white eye color. 

In an X-linked cross, the genotypes of F 1 and F 2 offspring depend on whether the recessive trait was expressed by the male or the female in the P 1 generation. With regard to Drosophila eye color, when the P 1 male expresses the white-eye phenotype and the female is homozygous red-eyed, all members of the F 1 generation exhibit red eyes ( [link] ). The F 1 females are heterozygous (X W X w ), and the males are all X W Y, having received their X chromosome from the homozygous dominant P 1 female and their Y chromosome from the P 1 male. A subsequent cross between the X W X w female and the X W Y male would produce only red-eyed females (with X W X W or X W X w genotypes) and both red- and white-eyed males (with X W Y or X w Y genotypes). Now, consider a cross between a homozygous white-eyed female and a male with red eyes. The F 1 generation would exhibit only heterozygous red-eyed females (X W X w ) and only white-eyed males (X w Y). Half of the F 2 females would be red-eyed (X W X w ) and half would be white-eyed (X w X w ). Similarly, half of the F 2 males would be red-eyed (X W Y) and half would be white-eyed (X w Y). 

Punnett square analysis is used to determine the ratio of offspring from a cross between a red-eyed male fruit fly and a white-eyed female fruit fly. 

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Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X-linked trait, she will pass the trait on to 100 percent of her offspring. Her male offspring are, therefore, destined to express the trait, as they will inherit their father's Y chromosome. In humans, the alleles for certain conditions (some forms of color blindness, hemophilia, and muscular dystrophy) are X-linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These females will pass the disease to half of their sons and will pass carrier status to half of their daughters; therefore, recessive X-linked traits appear more frequently in males than females. 

In some groups of organisms with sex chromosomes, the gender with the non-homologous sex chromosomes is the female rather than the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in which they are hemizygous. Human Sex-linked Disorders 

Sex-linkage studies in Morgan s laboratory provided the fundamentals for understanding X-linked recessive disorders in humans, which include red-green color blindness, and Types A and B hemophilia. Because human males need to inherit only one recessive mutant X allele to be affected, X-linked disorders are disproportionately observed in males. Females must inherit recessive X-linked alleles from both of their parents in order to express the trait. When they inherit one recessive X-linked mutant allele and one dominant X-linked wild-type allele, they are carriers of the trait and are typically unaffected. Carrier females can manifest mild forms of the trait due to the inactivation of the dominant allele located on one of the X chromosomes. However, female carriers can contribute the trait to their sons, resulting in the son exhibiting the trait, or they can contribute the recessive allele to their daughters, resulting in the daughters being carriers of the trait ( [link] ). Although some Y-linked recessive disorders exist, typically they are associated with infertility in males and are therefore not transmitted to subsequent generations. The son of a woman who is a carrier of a recessive X-linked disorder will have a 50 percent chance of being affected. A daughter will not be affected, but she will have a 50 percent chance of being a carrier like her mother. 

Watch this video to learn more about sex-linked traits. 

[link] Lethality 

A large proportion of genes in an individual s genome are essential for survival. Occasionally, a nonfunctional allele for an essential gene can arise by mutation and be transmitted in a population as long as individuals with this allele also have a wild-type, functional copy. The wild-type allele functions at a capacity sufficient to sustain life and is therefore considered to be dominant over the nonfunctional allele. However, consider two heterozygous parents that have a genotype of wild-type/nonfunctional mutant for a hypothetical essential gene. In one quarter of their offspring, we would expect to observe individuals that are homozygous recessive for the nonfunctional allele. Because the gene is essential, these individuals might fail to develop past fertilization, die in utero , or die later in life, depending on what life stage requires this gene. An inheritance pattern in which an allele is only lethal in the homozygous form and in which the heterozygote may be normal or have some altered non-lethal phenotype is referred to as recessive lethal . 

For crosses between heterozygous individuals with a recessive lethal allele that causes death before birth when homozygous, only wild-type homozygotes and heterozygotes would be observed. The genotypic ratio would therefore be 2:1. In other instances, the recessive lethal allele might also exhibit a dominant (but not lethal) phenotype in the heterozygote. For instance, the recessive lethal Curly allele in Drosophila affects wing shape in the heterozygote form but is lethal in the homozygote. 

A single copy of the wild-type allele is not always sufficient for normal functioning or even survival. The dominant lethal inheritance pattern is one in which an allele is lethal both in the homozygote and the heterozygote; this allele can only be transmitted if the lethality phenotype occurs after reproductive age. Individuals with mutations that result in dominant lethal alleles fail to survive even in the heterozygote form. Dominant lethal alleles are very rare because, as you might expect, the allele only lasts one generation and is not transmitted. However, just as the recessive lethal allele might not immediately manifest the phenotype of death, dominant lethal alleles also might not be expressed until adulthood. Once the individual reaches reproductive age, the allele may be unknowingly passed on, resulting in a delayed death in both generations. An example of this in humans is Huntington s disease, in which the nervous system gradually wastes away ( [link] ). People who are heterozygous for the dominant Huntington allele ( Hh ) will inevitably develop the fatal disease. However, the onset of Huntington s disease may not occur until age 40, at which point the afflicted persons may have already passed the allele to 50 percent of their offspring. The neuron in the center of this micrograph (yellow) has nuclear inclusions characteristic of Huntington s disease (orange area in the center of the neuron). Huntington s disease occurs when an abnormal dominant allele for the Huntington gene is present. (credit: Dr. Steven Finkbeiner, Gladstone Institute of Neurological Disease, The Taube-Koret Center for Huntington's Disease Research, and the University of California San Francisco/Wikimedia) Activity 

This section includes descriptions of genetically-inherited human diseases, such as sickle cell anemia, alkaptonuria, hemophilia, color blindness and Huntington s disease. One issue surrounding genetic disorders is the right to privacy. Can you think of other examples of ethical, social, or medical issue surrounding human genetic disorders? Lab Investigation 

Investigate inheritance patterns in an organism of choice, such as Wisconsin Fast Plants or Drosophila melanogaster , by performing several genetic crosses and comparing expected and observed phenotypic ratios. Virtual labs exploring Mendelian inheritance patterns are also available online. Think About It In pea plants, round peas ( R ) are dominant to wrinkles peas ( r ) ( [link] ). You do a test cross between a pea plant with wrinkled peas (genotype rr ) and a plant of unknown genotype that has round peas (genotype either RR or Rr ). You end up with three offspring plants, all which have round peas. Based on the phenotype of the offspring plants, can you deduce the genotype of the round pea parent plant? If the round pea parent plant is heterozygous, calculate the probability that a random sample of 3 progeny peas will all be round. Can a human male be a carrier of red-green color blindness? Justify your answer. In pea plants, violet flowers ( V ) are dominant to white flowers ( v ). What are the possible genotypes and phenotypes for a cross between Vv and vv pea plants? Use a Punnett square to show all work. The activity is an application of Learning Objective 3.13 and SP 3.1 because students are exploring issues that surround human genetic disorders. This lab investigation is an application of Learning Objective 3.12 and Science Practices 1.1 and 7.2 because students will connect the process of meiosis to the passage of traits from parent to offspring to make predictions about expected phenotypic ratios resulting from genetic crosses. Students will also apply Learning Objective 3.14 and Science Practice 2.2 because they will use mathematical routine to determine inheritance patterns provided by experimental data. The first Think About It question is an application of Learning Objective 3.12 and Science Practices 1.1 and 7.2 because students will use Punnett squares to connect the process of meiosis to the passage of traits from parent to offspring. In addition, students will use probability, a mathematical routine, to explain the inheritance pattern provided by data. The second Think About It question is an application of Learning Objective 3.15 and Science Practice 6.5 and Learning Objective 3.27 and Science Practice 1.2 because students are asked to explain an appropriate example of an inheritance pattern that deviates from Mendel s model. The third Think About It question is an application of Learning Objective 3.12 and Science Practices 1.1 and 7.2 because students will use Punnett squares to connect the process of meiosis to the passage of traits from parent to offspring. In addition, students will use probability, a mathematical routine, to explain the inheritance pattern provided by data. Possible answer to activity: Other issues might be insurance concerns, employment, and personal relationships. On the other hand, by knowing one s genetic predispositions to certain diseases, life style adjustments and treatments can be started early. There are no simple, one-size fits all answers. Be prepared for heated discussions. Possible answers to Think About It: You cannot be sure if the plant is homozygous or heterozygous as the data set is too small; by random chance, all three plants might have inherited only the dominant gene even if the recessive one is present. If the round pea parent is heterozygous, there is a one-eighth probability that a random sample of three progeny peas will all be round. No, color blindness is X-linked. A male has only one X chromosome, so red-green blindness is not masked by the normal allele. 

Violet flowers 1/2 

White flowers: 1/2 Section Summary 

When true-breeding or homozygous individuals that differ for a certain trait are crossed, all of the offspring will be heterozygotes for that trait. If the traits are inherited as dominant and recessive, the F 1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F 2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F 2 offspring will exhibit a ratio of three dominant to one recessive. 

Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles of a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two. Finally, some alleles can be lethal. Recessive lethal alleles are only lethal in homozygotes, but dominant lethal alleles are fatal in heterozygotes as well. Review Questions 

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Sumiti Vinayak, et al., Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum , Public Library of Science Pathogens 6, no. 3 (2010): e1000830, doi:10.1371/journal.ppat.1000830. Glossary allele gene variations that arise by mutation and exist at the same relative locations on homologous chromosomes autosomes any of the non-sex chromosomes codominance in a heterozygote, complete and simultaneous expression of both alleles for the same characteristic dominant lethal inheritance pattern in which an allele is lethal both in the homozygote and the heterozygote; this allele can only be transmitted if the lethality phenotype occurs after reproductive age genotype underlying genetic makeup, consisting of both physically visible and non-expressed alleles, of an organism hemizygous presence of only one allele for a characteristic, as in X-linkage; hemizygosity makes descriptions of dominance and recessiveness irrelevant heterozygous having two different alleles for a given gene on the homologous chromosome homozygous having two identical alleles for a given gene on the homologous chromosome incomplete dominance in a heterozygote, expression of two contrasting alleles such that the individual displays an intermediate phenotype monohybrid result of a cross between two true-breeding parents that express different traits for only one characteristic phenotype observable traits expressed by an organism Punnett square visual representation of a cross between two individuals in which the gametes of each individual are denoted along the top and side of a grid, respectively, and the possible zygotic genotypes are recombined at each box in the grid recessive lethal inheritance pattern in which an allele is only lethal in the homozygous form; the heterozygote may be normal or have some altered, non-lethal phenotype sex-linked any gene on a sex chromosome test cross cross between a dominant expressing individual with an unknown genotype and a homozygous recessive individual; the offspring phenotypes indicate whether the unknown parent is heterozygous or homozygous for the dominant trait X-linked gene present on the X, but not the Y chromosomeLaws of Inheritance Laws of Inheritance 

In this section, you will explore the following questions: What is the relationship between Mendel s law of segregation and independent assortment in terms of genetics and the events of meiosis? How can the forked-lined method and probability rules be used to calculate the probability of genotypes and phenotypes from multiple gene crosses? How do linkage, cross-over, epistasis, and recombination violate Mendel s laws of inheritance? Connection for AP Courses 

As was described previously, Mendel proposed that genes are inherited as pairs of alleles that behave in a dominant and recessive pattern. During meiosis, alleles segregate, or separate, such that each gamete is equally likely to receive either one of the two alleles present in the diploid individual. Mendel called this phenomenon the law of segregation, which can be demonstrated in a monohybrid cross. In addition, genes carried on different chromosomes sort into gametes independently of one another. This is Mendel s law of independent assortment. This law can be demonstrated in a dihybrid cross involving two different traits located on different chromosomes. Punnett squares can be used to predict genotypes and phenotypes of offspring involving one or two genes. 

Although chromosomes sort independently into gametes during meiosis, Mendel s law of independent assortment refers to genes, not chromosomes. In humans, single chromosomes may carry more than 1,000 genes. Genes located close together on the same chromosome are said to be linked genes. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together unless recombination occurs. This results in offspring ratios that violate Mendel s law of independent assortment. Genes that are located far apart on the same chromosome are likely to assort independently. The rules of probability can help to sort this out (pun intended). The law states that alleles of different genes assort independently of one another during gamete formation. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.3 The chromosomal basis of inheritance provides an understanding of the pattern of passage (transmission) of genes from parent to offspring. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Learning Objective 3.14 The student is able to apply mathematical routines to determine Mendelian patterns of inheritance provided by data. Essential Knowledge 3.A.4 The inheritance pattern of many traits cannot be explained by simple Mendelian genetics. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.15 The student is able to explain deviations from Mendel s model of the inheritance of traits. Essential Knowledge 3.A.4 The inheritance pattern of many traits cannot be explained by simple Mendelian genetics. Science Practice 6.3 The student can articulate the reasons that scientific explanations and theories are refined or replaced. Learning Objective 3.16 The student is able to explain how the inheritance patterns of many traits cannot be accounted for by Mendelian genetics. Essential Knowledge 3.A.4 The inheritance pattern of many traits cannot be explained by simple Mendelian genetics. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.17 The student is able to describe representations of an appropriate example of inheritance patterns that cannot be explained by Mendel s model of the inheritance of traits. 

Emphasize that very few traits depend on a single genes. Multiallelic traits are much more common but are much more difficult to study because of the complexity of multi-gene interactions. Cite height, skin and eye pigmentation. Also introduce the concept of environmental effects on the expression of traits (i.e. nature versus nurture). 

A good example of environmental effect is the color of petals in hydrangeas. The enzyme that converts the pigment from pink to blue requires aluminum ions as cofactors. The uptake of aluminum ions is inhibited in neutral or alkaline soils, and the blooms appear pink. Gardeners can amend acidic soil with lime to neutralize the pH. The blooms will turn to pink once the soil reaches a neutral to alkaline pH. 

Many students think that lethal or rare traits in human are always recessive. This is not the case. Huntington disease, which is fully expressed when people reach middle age, is a dominant trait. Dwarfism and polydactyly are examples of dominant traits that are not frequent in the population. 

Many students also think that genetics is as simple as the examples we use to teach Mendelian genetics. In fact, most traits diverge from Mendelian genetics. 

Mendel generalized the results of his pea-plant experiments into four postulates, some of which are sometimes called laws, that describe the basis of dominant and recessive inheritance in diploid organisms. As you have learned, more complex extensions of Mendelism exist that do not exhibit the same F 2 phenotypic ratios (3:1). Nevertheless, these laws summarize the basics of classical genetics. Pairs of Unit Factors, or Genes 

Mendel proposed first that paired unit factors of heredity were transmitted faithfully from generation to generation by the dissociation and reassociation of paired factors during gametogenesis and fertilization, respectively. After he crossed peas with contrasting traits and found that the recessive trait resurfaced in the F 2 generation, Mendel deduced that hereditary factors must be inherited as discrete units. This finding contradicted the belief at that time that parental traits were blended in the offspring. Alleles Can Be Dominant or Recessive 

Mendel s law of dominance states that in a heterozygote, one trait will conceal the presence of another trait for the same characteristic. Rather than both alleles contributing to a phenotype, the dominant allele will be expressed exclusively. The recessive allele will remain latent but will be transmitted to offspring by the same manner in which the dominant allele is transmitted. The recessive trait will only be expressed by offspring that have two copies of this allele ( [link] ), and these offspring will breed true when self-crossed. 

Since Mendel s experiments with pea plants, other researchers have found that the law of dominance does not always hold true. Instead, several different patterns of inheritance have been found to exist. The child in the photo expresses albinism, a recessive trait. Equal Segregation of Alleles 

Observing that true-breeding pea plants with contrasting traits gave rise to F 1 generations that all expressed the dominant trait and F 2 generations that expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed the law of segregation . This law states that paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor. For the F 2 generation of a monohybrid cross, the following three possible combinations of genotypes could result: homozygous dominant, heterozygous, or homozygous recessive. Because heterozygotes could arise from two different pathways (receiving one dominant and one recessive allele from either parent), and because heterozygotes and homozygous dominant individuals are phenotypically identical, the law supports Mendel s observed 3:1 phenotypic ratio. The equal segregation of alleles is the reason we can apply the Punnett square to accurately predict the offspring of parents with known genotypes. The physical basis of Mendel s law of segregation is the first division of meiosis, in which the homologous chromosomes with their different versions of each gene are segregated into daughter nuclei. The role of the meiotic segregation of chromosomes in sexual reproduction was not understood by the scientific community during Mendel s lifetime. Independent Assortment 

Mendel s law of independent assortment states that genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur. The independent assortment of genes can be illustrated by the dihybrid cross, a cross between two true-breeding parents that express different traits for two characteristics. Consider the characteristics of seed color and seed texture for two pea plants, one that has green, wrinkled seeds ( yyrr ) and another that has yellow, round seeds ( YYRR ). Because each parent is homozygous, the law of segregation indicates that the gametes for the green/wrinkled plant all are yr , and the gametes for the yellow/round plant are all YR . Therefore, the F 1 generation of offspring all are YyRr ( [link] ). 

This dihybrid cross of pea plants involves the genes for seed color and texture. 

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For the F2 generation, the law of segregation requires that each gamete receive either an R allele or an r allele along with either a Y allele or a y allele. The law of independent assortment states that a gamete into which an r allele sorted would be equally likely to contain either a Y allele or a y allele. Thus, there are four equally likely gametes that can be formed when the YyRr heterozygote is self-crossed, as follows: YR , Yr , yR , and yr . Arranging these gametes along the top and left of a 4 4 Punnett square ( [link] ) gives us 16 equally likely genotypic combinations. From these genotypes, we infer a phenotypic ratio of 9 round/yellow:3 round/green:3 wrinkled/yellow:1 wrinkled/green ( [link] ). These are the offspring ratios we would expect, assuming we performed the crosses with a large enough sample size. 

Because of independent assortment and dominance, the 9:3:3:1 dihybrid phenotypic ratio can be collapsed into two 3:1 ratios, characteristic of any monohybrid cross that follows a dominant and recessive pattern. Ignoring seed color and considering only seed texture in the above dihybrid cross, we would expect that three quarters of the F 2 generation offspring would be round, and one quarter would be wrinkled. Similarly, isolating only seed color, we would assume that three quarters of the F 2 offspring would be yellow and one quarter would be green. The sorting of alleles for texture and color are independent events, so we can apply the product rule. Therefore, the proportion of round and yellow F 2 offspring is expected to be (3/4) (3/4) = 9/16, and the proportion of wrinkled and green offspring is expected to be (1/4) (1/4) = 1/16. These proportions are identical to those obtained using a Punnett square. Round, green and wrinkled, yellow offspring can also be calculated using the product rule, as each of these genotypes includes one dominant and one recessive phenotype. Therefore, the proportion of each is calculated as (3/4) (1/4) = 3/16. 

The law of independent assortment also indicates that a cross between yellow, wrinkled ( YYrr ) and green, round ( yyRR ) parents would yield the same F 1 and F 2 offspring as in the YYRR x yyrr cross. 

The physical basis for the law of independent assortment also lies in meiosis I, in which the different homologous pairs line up in random orientations. Each gamete can contain any combination of paternal and maternal chromosomes (and therefore the genes on them) because the orientation of tetrads on the metaphase plane is random. Forked-Line Method 

When more than two genes are being considered, the Punnett-square method becomes unwieldy. For instance, examining a cross involving four genes would require a 16 16 grid containing 256 boxes. It would be extremely cumbersome to manually enter each genotype. For more complex crosses, the forked-line and probability methods are preferred. 

To prepare a forked-line diagram for a cross between F 1 heterozygotes resulting from a cross between AABBCC and aabbcc parents, we first create rows equal to the number of genes being considered, and then segregate the alleles in each row on forked lines according to the probabilities for individual monohybrid crosses ( [link] ). We then multiply the values along each forked path to obtain the F 2 offspring probabilities. Note that this process is a diagrammatic version of the product rule. The values along each forked pathway can be multiplied because each gene assorts independently. For a trihybrid cross, the F 2 phenotypic ratio is 27:9:9:9:3:3:3:1. The forked-line method can be used to analyze a trihybrid cross. Here, the probability for color in the F 2 generation occupies the top row (3 yellow:1 green). The probability for shape occupies the second row (3 round:1 wrinked), and the probability for height occupies the third row (3 tall:1 dwarf). The probability for each possible combination of traits is calculated by multiplying the probability for each individual trait. Thus, the probability of F 2 offspring having yellow, round, and tall traits is 3 3 3, or 27. Probability Method 

While the forked-line method is a diagrammatic approach to keeping track of probabilities in a cross, the probability method gives the proportions of offspring expected to exhibit each phenotype (or genotype) without the added visual assistance. Both methods make use of the product rule and consider the alleles for each gene separately. Earlier, we examined the phenotypic proportions for a trihybrid cross using the forked-line method; now we will use the probability method to examine the genotypic proportions for a cross with even more genes. 

For a trihybrid cross, writing out the forked-line method is tedious, albeit not as tedious as using the Punnett-square method. To fully demonstrate the power of the probability method, however, we can consider specific genetic calculations. For instance, for a tetrahybrid cross between individuals that are heterozygotes for all four genes, and in which all four genes are sorting independently and in a dominant and recessive pattern, what proportion of the offspring will be expected to be homozygous recessive for all four alleles? Rather than writing out every possible genotype, we can use the probability method. We know that for each gene, the fraction of homozygous recessive offspring will be 1/4. Therefore, multiplying this fraction for each of the four genes, (1/4) (1/4) (1/4) (1/4), we determine that 1/256 of the offspring will be quadruply homozygous recessive. 

For the same tetrahybrid cross, what is the expected proportion of offspring that have the dominant phenotype at all four loci? We can answer this question using phenotypic proportions, but let s do it the hard way using genotypic proportions. The question asks for the proportion of offspring that are 1) homozygous dominant at A or heterozygous at A, and 2) homozygous at B or heterozygous at B , and so on. Noting the or and and in each circumstance makes clear where to apply the sum and product rules. The probability of a homozygous dominant at A is 1/4 and the probability of a heterozygote at A is 1/2. The probability of the homozygote or the heterozygote is 1/4 + 1/2 = 3/4 using the sum rule. The same probability can be obtained in the same way for each of the other genes, so that the probability of a dominant phenotype at A and B and C and D is, using the product rule, equal to 3/4 3/4 3/4 3/4, or 27/64. If you are ever unsure about how to combine probabilities, returning to the forked-line method should make it clear. Rules for Multihybrid Fertilization 

Predicting the genotypes and phenotypes of offspring from given crosses is the best way to test your knowledge of Mendelian genetics. Given a multihybrid cross that obeys independent assortment and follows a dominant and recessive pattern, several generalized rules exist; you can use these rules to check your results as you work through genetics calculations ( [link] ). To apply these rules, first you must determine n , the number of heterozygous gene pairs (the number of genes segregating two alleles each). For example, a cross between AaBb and AaBb heterozygotes has an n of 2. In contrast, a cross between AABb and AABb has an n of 1 because A is not heterozygous. General Rules for Multihybrid Crosses General Rule Number of Heterozygous Gene Pairs Number of different F 1 gametes 2 n Number of different F 2 genotypes 3 n Given dominant and recessive inheritance, the number of different F 2 phenotypes 2 n Linked Genes Violate the Law of Independent Assortment 

Although all of Mendel s pea characteristics behaved according to the law of independent assortment, we now know that some allele combinations are not inherited independently of each other. Genes that are located on separate non-homologous chromosomes will always sort independently. However, each chromosome contains hundreds or thousands of genes, organized linearly on chromosomes like beads on a string. The segregation of alleles into gametes can be influenced by linkage , in which genes that are located physically close to each other on the same chromosome are more likely to be inherited as a pair. However, because of the process of recombination, or crossover, it is possible for two genes on the same chromosome to behave independently, or as if they are not linked. To understand this, let s consider the biological basis of gene linkage and recombination. 

Homologous chromosomes possess the same genes in the same linear order. The alleles may differ on homologous chromosome pairs, but the genes to which they correspond do not. In preparation for the first division of meiosis, homologous chromosomes replicate and synapse. Like genes on the homologs align with each other. At this stage, segments of homologous chromosomes exchange linear segments of genetic material ( [link] ). This process is called recombination, or crossover, and it is a common genetic process. Because the genes are aligned during recombination, the gene order is not altered. Instead, the result of recombination is that maternal and paternal alleles are combined onto the same chromosome. Across a given chromosome, several recombination events may occur, causing extensive shuffling of alleles. The process of crossover, or recombination, occurs when two homologous chromosomes align during meiosis and exchange a segment of genetic material. Here, the alleles for gene C were exchanged. The result is two recombinant and two non-recombinant chromosomes. 

When two genes are located in close proximity on the same chromosome, they are considered linked, and their alleles tend to be transmitted through meiosis together. To exemplify this, imagine a dihybrid cross involving flower color and plant height in which the genes are next to each other on the chromosome. If one homologous chromosome has alleles for tall plants and red flowers, and the other chromosome has genes for short plants and yellow flowers, then when the gametes are formed, the tall and red alleles will go together into a gamete and the short and yellow alleles will go into other gametes. These are called the parental genotypes because they have been inherited intact from the parents of the individual producing gametes. But unlike if the genes were on different chromosomes, there will be no gametes with tall and yellow alleles and no gametes with short and red alleles. If you create the Punnett square with these gametes, you will see that the classical Mendelian prediction of a 9:3:3:1 outcome of a dihybrid cross would not apply. As the distance between two genes increases, the probability of one or more crossovers between them increases, and the genes behave more like they are on separate chromosomes. Geneticists have used the proportion of recombinant gametes (the ones not like the parents) as a measure of how far apart genes are on a chromosome. Using this information, they have constructed elaborate maps of genes on chromosomes for well-studied organisms, including humans. 

Mendel s seminal publication makes no mention of linkage, and many researchers have questioned whether he encountered linkage but chose not to publish those crosses out of concern that they would invalidate his independent assortment postulate. The garden pea has seven chromosomes, and some have suggested that his choice of seven characteristics was not a coincidence. However, even if the genes he examined were not located on separate chromosomes, it is possible that he simply did not observe linkage because of the extensive shuffling effects of recombination. 

Testing the Hypothesis of Independent Assortment To better appreciate the amount of labor and ingenuity that went into Mendel s experiments, proceed through one of Mendel s dihybrid crosses. 

Question : What will be the offspring of a dihybrid cross? 

Background : Consider that pea plants mature in one growing season, and you have access to a large garden in which you can cultivate thousands of pea plants. There are several true-breeding plants with the following pairs of traits: tall plants with inflated pods, and dwarf plants with constricted pods. Before the plants have matured, you remove the pollen-producing organs from the tall/inflated plants in your crosses to prevent self-fertilization. Upon plant maturation, the plants are manually crossed by transferring pollen from the dwarf/constricted plants to the stigmata of the tall/inflated plants. 

Hypothesis : Both trait pairs will sort independently according to Mendelian laws. When the true-breeding parents are crossed, all of the F 1 offspring are tall and have inflated pods, which indicates that the tall and inflated traits are dominant over the dwarf and constricted traits, respectively. A self-cross of the F 1 heterozygotes results in 2,000 F 2 progeny. 

Test the hypothesis : Because each trait pair sorts independently, the ratios of tall:dwarf and inflated:constricted are each expected to be 3:1. The tall/dwarf trait pair is called T/t , and the inflated/constricted trait pair is designated I/i . Each member of the F 1 generation therefore has a genotype of TtIi . Construct a grid analogous to [link] , in which you cross two TtIi individuals. Each individual can donate four combinations of two traits: TI , Ti , tI , or ti , meaning that there are 16 possibilities of offspring genotypes. Because the T and I alleles are dominant, any individual having one or two of those alleles will express the tall or inflated phenotypes, respectively, regardless if they also have a t or i allele. Only individuals that are tt or ii will express the dwarf and constricted alleles, respectively. As shown in [link] , you predict that you will observe the following offspring proportions: tall/inflated:tall/constricted:dwarf/inflated:dwarf/constricted in a 9:3:3:1 ratio. Notice from the grid that when considering the tall/dwarf and inflated/constricted trait pairs in isolation, they are each inherited in 3:1 ratios. This figure shows all possible combinations of offspring resulting from a dihybrid cross of pea plants that are heterozygous for the tall/dwarf and inflated/constricted alleles. 

Test the hypothesis : You cross the dwarf and tall plants and then self-cross the offspring. For best results, this is repeated with hundreds or even thousands of pea plants. What special precautions should be taken in the crosses and in growing the plants? 

Analyze your data : You observe the following plant phenotypes in the F 2 generation: 2706 tall/inflated, 930 tall/constricted, 888 dwarf/inflated, and 300 dwarf/constricted. Reduce these findings to a ratio and determine if they are consistent with Mendelian laws. 

Form a conclusion : Were the results close to the expected 9:3:3:1 phenotypic ratio? Do the results support the prediction? What might be observed if far fewer plants were used, given that alleles segregate randomly into gametes? Try to imagine growing that many pea plants, and consider the potential for experimental error. For instance, what would happen if it was extremely windy one day? Think About It 

In the shepherd s-purse plant ( Capsella bursa-pastoris ), seed shape is controlled by two genes, A and B . When both the A and B loci are homozygous recessive ( aabb ), the seeds are ovoid. However, if the dominant allele for either or both of these genes is present, the seeds are triangular. Based on this information, what are the expected phenotypic ratios for a cross between plants that are heterozygous for both traits? 

What is the expected ratio of phenotypes from a dihybrid cross? How do you explain the difference between the expected dihybrid cross ratio and ratio observed in the shepherd s-purse plant? 

This question is an application of Learning Objectives 3.14, 3.15, 3.16, and 3.17 and Science Practices 2.2, 6.5, 6.3, 1.2, and 6.2 because students are applying mathematical routines to analyze data to explain deviations from Mendel s model of inheritance. (Note: The data in this question can be analyzed for statistical difference using Chi-square.) 

Possible answers: The ratios from the shepherd s-purse plant is 15 triangular seeds to 1 ovoid seed. The reason this diverges from the expected 9:3:3:1 ratio is because the genes A and B express the same phenotype. One copy is sufficient for the dominant trait to be expressed. It is an example of dominant epistasis. Epistasis 

Mendel s studies in pea plants implied that the sum of an individual s phenotype was controlled by genes (or as he called them, unit factors), such that every characteristic was distinctly and completely controlled by a single gene. In fact, single observable characteristics are almost always under the influence of multiple genes (each with two or more alleles) acting in unison. For example, at least eight genes contribute to eye color in humans. 

Eye color in humans is determined by multiple genes. Use the Eye Color Calculator to predict the eye color of children from parental eye color. 

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In some cases, several genes can contribute to aspects of a common phenotype without their gene products ever directly interacting. In the case of organ development, for instance, genes may be expressed sequentially, with each gene adding to the complexity and specificity of the organ. Genes may function in complementary or synergistic fashions, such that two or more genes need to be expressed simultaneously to affect a phenotype. Genes may also oppose each other, with one gene modifying the expression of another. 

In epistasis , the interaction between genes is antagonistic, such that one gene masks or interferes with the expression of another. Epistasis is a word composed of Greek roots that mean standing upon. The alleles that are being masked or silenced are said to be hypostatic to the epistatic alleles that are doing the masking. Often the biochemical basis of epistasis is a gene pathway in which the expression of one gene is dependent on the function of a gene that precedes or follows it in the pathway. 

An example of epistasis is pigmentation in mice. The wild-type coat color, agouti ( AA ), is dominant to solid-colored fur ( aa ). However, a separate gene ( C ) is necessary for pigment production. A mouse with a recessive c allele at this locus is unable to produce pigment and is albino regardless of the allele present at locus A ( [link] ). Therefore, the genotypes AAcc , Aacc , and aacc all produce the same albino phenotype. A cross between heterozygotes for both genes ( AaCc x AaCc ) would generate offspring with a phenotypic ratio of 9 agouti:3 solid color:4 albino ( [link] ). In this case, the C gene is epistatic to the A gene. In mice, the mottled agouti coat color ( A ) is dominant to a solid coloration, such as black or gray. A gene at a separate locus ( C ) is responsible for pigment production. The recessive c allele does not produce pigment, and a mouse with the homozygous recessive cc genotype is albino regardless of the allele present at the A locus. Thus, the C gene is epistatic to the A gene. 

Epistasis can also occur when a dominant allele masks expression at a separate gene. Fruit color in summer squash is expressed in this way. Homozygous recessive expression of the W gene ( ww ) coupled with homozygous dominant or heterozygous expression of the Y gene ( YY or Yy ) generates yellow fruit, and the wwyy genotype produces green fruit. However, if a dominant copy of the W gene is present in the homozygous or heterozygous form, the summer squash will produce white fruit regardless of the Y alleles. A cross between white heterozygotes for both genes ( WwYy WwYy ) would produce offspring with a phenotypic ratio of 12 white:3 yellow:1 green. 

Finally, epistasis can be reciprocal such that either gene, when present in the dominant (or recessive) form, expresses the same phenotype. In the shepherd s purse plant ( Capsella bursa-pastoris ), the characteristic of seed shape is controlled by two genes in a dominant epistatic relationship. When the genes A and B are both homozygous recessive ( aabb ), the seeds are ovoid. If the dominant allele for either of these genes is present, the result is triangular seeds. That is, every possible genotype other than aabb results in triangular seeds, and a cross between heterozygotes for both genes ( AaBb x AaBb ) would yield offspring with a phenotypic ratio of 15 triangular:1 ovoid. 

As you work through genetics problems, keep in mind that any single characteristic that results in a phenotypic ratio that totals 16 is typical of a two-gene interaction. Recall the phenotypic inheritance pattern for Mendel s dihybrid cross, which considered two non-interacting genes 9:3:3:1. Similarly, we would expect interacting gene pairs to also exhibit ratios expressed as 16 parts. Note that we are assuming the interacting genes are not linked; they are still assorting independently into gametes. 

For an excellent review of Mendel s experiments and to perform your own crosses and identify patterns of inheritance, visit the Mendel s Peas web lab. 

[link] Section Summary 

Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a diploid individual. In addition, genes are assorted into gametes independently of one another. That is, alleles are generally not more likely to segregate into a gamete with a particular allele of another gene. A dihybrid cross demonstrates independent assortment when the genes in question are on different chromosomes or distant from each other on the same chromosome. For crosses involving more than two genes, use the forked line or probability methods to predict offspring genotypes and phenotypes rather than a Punnett square. 

Although chromosomes sort independently into gametes during meiosis, Mendel s law of independent assortment refers to genes, not chromosomes, and a single chromosome may carry more than 1,000 genes. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together. This results in offspring ratios that violate Mendel's law of independent assortment. However, recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together. Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal space. 

Whether or not they are sorting independently, genes may interact at the level of gene products such that the expression of an allele for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis. Review Questions 

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[link] Glossary dihybrid result of a cross between two true-breeding parents that express different traits for two characteristics epistasis antagonistic interaction between genes such that one gene masks or interferes with the expression of another law of dominance in a heterozygote, one trait will conceal the presence of another trait for the same characteristic law of independent assortment genes do not influence each other with regard to sorting of alleles into gametes; every possible combination of alleles is equally likely to occur law of segregation paired unit factors (i.e., genes) segregate equally into gametes such that offspring have an equal likelihood of inheriting any combination of factors linkage phenomenon in which alleles that are located in close proximity to each other on the same chromosome are more likely to be inherited togetherIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Chromosomes are threadlike nuclear structures consisting of DNA and proteins that serve as the repositories for genetic information. The chromosomes depicted here were isolated from a fruit fly s salivary gland, stained with dye, and visualized under a microscope. Akin to miniature bar codes, chromosomes absorb different dyes to produce characteristic banding patterns, which allows for their routine identification. (credit: modification of work by LPLT /Wikimedia Commons; scale-bar data from Matt Russell) 

According to the United Nations Office on Drugs and Crime, approximately 95% of those who commit homicide are men. While behavior is shaped by the environment one grows up and lives in, genetics also play a role. For example, scientists have discovered genes that appear to increase one s tendency to exhibit aggressive behavior. One of the genes, called MAOA, is located on the X chromosome. In one recent study involving a group of male prisoners in Finland, scientists found that the prisoners who inherited a variant of this gene were between 5% and 10% more likely to have committed a violent crime. Men only have one copy of the gene, since men only have one X chromosome. Women, however, have two copies of the X chromosome and therefore two copies of the gene. Therefore, women who inherit the variant allele will most likely also have a normal allele to counteract its effects. It is important to note that many men inherit the variant copy of MAOA and only some commit violent crimes. The environment seems to play a much more critical role. You can read more about nature/nurture roles in crime in this article . 

Before students begin this chapter, it is useful to review these concepts: DNA and chromosome structure; relationships among DNA, genes, and chromosomes; overview of the steps of mitosis and meiosis; overview of independent assortment; ploidy (haploid versus diploid).Chromosomal Theory and Genetic Linkage Chromosomal Theory and Genetic Linkage 

In this section, you will explore the following question: What is the relationship among genetic linkage, crossing over, and genetic variation? Connection for AP Courses 

Proposed independently by Sutton and Boveri in the early 1900s, the Chromosomal Theory of Inheritance states that chromosomes are vehicles of genetic heredity. As we have discovered, patterns of inheritance are more complex than Mendel could have imagined. Mendel was investigating the behavior of genes. He was fortunate in choosing traits coded by genes that happened to be on different chromosomes or far apart on the same chromosome. When genes are linked or near each other on the same chromosome, patterns of segregation and independent assortment change. In 1913, Sturtevant devised a method to assess recombination frequency and infer the relative positions and distances of linked genes on a chromosome based on the average number of crossovers between them during meiosis. 

The content presented in this section supports the Learning Objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework. The AP Learning Objectives merge essential knowledge content with one or more of the seven Science Practices. These objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP exam questions. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 3.10 The student is able to represent the connection between meiosis and increased genetic diversity necessary for evolution. Essential Knowledge 3.A.3 The chromosomal basis of inheritance provides an understanding of the pattern of passage (transmission) of genes from parent to offspring. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 3.12 The student is able to construct a representation that connects the process of meiosis to the passage of traits from parent to offspring. 

Introduce genetic linkage using visuals such as this video . 

Students can read about corn genetics in this review article . 

Students can read about linked genes and Mendel s work in this article . 

Have students work through inheritance scenarios where genes are linked and where they are on different chromosomes using the following activity sheet . 

Teacher preparation notes for this activity are available here . 

Long before chromosomes were visualized under a microscope, the father of modern genetics, Gregor Mendel, began studying heredity in 1843. With the improvement of microscopic techniques during the late 1800s, cell biologists could stain and visualize subcellular structures with dyes and observe their actions during cell division and meiosis. With each mitotic division, chromosomes replicated, condensed from an amorphous (no constant shape) nuclear mass into distinct X-shaped bodies (pairs of identical sister chromatids), and migrated to separate cellular poles. Chromosomal Theory of Inheritance 

The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel s publications and re-evaluate his model in terms of the behavior of chromosomes during mitosis and meiosis. In 1902, Theodor Boveri observed that proper embryonic development of sea urchins does not occur unless chromosomes are present. That same year, Walter Sutton observed the separation of chromosomes into daughter cells during meiosis ( [link] ). Together, these observations led to the development of the Chromosomal Theory of Inheritance , which identified chromosomes as the genetic material responsible for Mendelian inheritance. (a) Walter Sutton and (b) Theodor Boveri are credited with developing the Chromosomal Theory of Inheritance, which states that chromosomes carry the unit of heredity (genes). 

The Chromosomal Theory of Inheritance was consistent with Mendel s laws and was supported by the following observations: During meiosis, homologous chromosome pairs migrate as discrete structures that are independent of other chromosome pairs. The sorting of chromosomes from each homologous pair into pre-gametes appears to be random. Each parent synthesizes gametes that contain only half of their chromosomal complement. Even though male and female gametes (sperm and egg) differ in size and morphology, they have the same number of chromosomes, suggesting equal genetic contributions from each parent. The gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents. 

Despite compelling correlations between the behavior of chromosomes during meiosis and Mendel s abstract laws, the Chromosomal Theory of Inheritance was proposed long before there was any direct evidence that traits were carried on chromosomes. Critics pointed out that individuals had far more independently segregating traits than they had chromosomes. It was only after several years of carrying out crosses with the fruit fly, Drosophila melanogaster , that Thomas Hunt Morgan provided experimental evidence to support the Chromosomal Theory of Inheritance. Genetic Linkage and Distances 

Mendel s work suggested that traits are inherited independently of each other. Morgan identified a 1:1 correspondence between a segregating trait and the X chromosome, suggesting that the random segregation of chromosomes was the physical basis of Mendel s model. This also demonstrated that linked genes disrupt Mendel s predicted outcomes. The fact that each chromosome can carry many linked genes explains how individuals can have many more traits than they have chromosomes. However, observations by researchers in Morgan s laboratory suggested that alleles positioned on the same chromosome were not always inherited together. During meiosis, linked genes somehow became unlinked. Homologous Recombination 

In 1909, Frans Janssen observed chiasmata the point at which chromatids are in contact with each other and may exchange segments prior to the first division of meiosis. He suggested that alleles become unlinked and chromosomes physically exchange segments. As chromosomes condensed and paired with their homologs, they appeared to interact at distinct points. Janssen suggested that these points corresponded to regions in which chromosome segments were exchanged. It is now known that the pairing and interaction between homologous chromosomes, known as synapsis, does more than simply organize the homologs for migration to separate daughter cells. When synapsed, homologous chromosomes undergo reciprocal physical exchanges at their arms in a process called homologous recombination , or more simply, crossing over. 

To better understand the type of experimental results that researchers were obtaining at this time, consider a heterozygous individual that inherited dominant maternal alleles for two genes on the same chromosome (such as AB ) and two recessive paternal alleles for those same genes (such as ab ). If the genes are linked, one would expect this individual to produce gametes that are either AB or ab with a 1:1 ratio. If the genes are unlinked, the individual should produce AB , Ab , aB , and ab gametes with equal frequencies, according to the Mendelian concept of independent assortment. Because they correspond to new allele combinations, the genotypes Ab and aB are nonparental types that result from homologous recombination during meiosis. Parental types are progeny that exhibit the same allelic combination as their parents. Morgan and his colleagues, however, found that when such heterozygous individuals were test crossed to a homozygous recessive parent ( AaBb aabb ), both parental and nonparental cases occurred. For example, 950 offspring might be recovered that were either AaBb or aabb , but 50 offspring would also be obtained that were either Aabb or aaBb . These results suggested that linkage occurred most often, but a significant minority of offspring were the products of recombination. 

Inheritance patterns of unlinked and linked genes are shown. In (a), two genes are located on different chromosomes so independent assortment occurs during meiosis. The offspring have an equal chance of being the parental type (inheriting the same combination of traits as the parents) or a nonparental type (inheriting a different combination of traits than the parents). In (b), two genes are very close together on the same chromosome so that no crossing over occurs between them. The genes are therefore always inherited together and all of the offspring are the parental type. In (c), two genes are far apart on the chromosome such that crossing over occurs during every meiotic event. The recombination frequency will be the same as if the genes were on separate chromosomes. (d) The actual recombination frequency of fruit fly wing length and body color that Thomas Morgan observed in 1912 was 17 percent. A crossover frequency between 0 percent and 50 percent indicates that the genes are on the same chromosome and crossover occurs some of the time. 

[link] Think About It 

A test cross involving F 1 dihybrid flies produces more parental-type offspring than recombinant-type offspring. How can you explain these observed results? 

The question is an application of Learning Objective 3.12 and Science Practices 1.1 and 7.2, and Learning Objective 3.10 and Science Practice 7.1 because students are explaining how meiosis can result in gametes with genetic variation; in turn, these gametes can introduce variation in offspring. Answer 

More parental type offspring are produced because the genes that are being examined in the dihybrid cross are linked. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during meiosis as a result of chromosomal crossover. Therefore, there will be more offspring with the parental phenotype than the recombinant phenotype. 

More information about linked genes can be found at the following resources: 

Linked genes: Youtube video 

Chromosomal inheritance: Youtube video 

Genetic Markers for Cancers 

Scientists have used genetic linkage to discover the location in the human genome of many genes that cause disease. They locate disease genes by tracking inheritance of traits through generations of families and creating linkage maps that measure recombination among groups of genetic markers. The two BRCA genes, mutations which can lead to breast and ovarian cancers, were some of the first genes discovered by genetic mapping. Women who have family histories of these cancers can now be screened to determine if one or both of these genes carry a mutation. If so, they can opt to have their breasts and ovaries surgically removed. This decreases their chances of getting cancer later in life. The actress Angelia Jolie brought this to the public s attention when she opted for surgery in 2014 and again in 2015 after doctors found she carried a mutated BRCA1 gene. 

[link] Genetic Maps 

Janssen did not have the technology to demonstrate crossing over so it remained an abstract idea that was not widely accepted. Scientists thought chiasmata were a variation on synapsis and could not understand how chromosomes could break and rejoin. Yet, the data were clear that linkage did not always occur. Ultimately, it took a young undergraduate student and an all-nighter to mathematically elucidate the problem of linkage and recombination. 

In 1913, Alfred Sturtevant, a student in Morgan s laboratory, gathered results from researchers in the laboratory, and took them home one night to mull them over. By the next morning, he had created the first chromosome map, a linear representation of gene order and relative distance on a chromosome ( [link] ). 

This genetic map orders Drosophila genes on the basis of recombination frequency. 

[link] 

As shown in [link] , by using recombination frequency to predict genetic distance, the relative order of genes on chromosome 2 could be inferred. The values shown represent map distances in centimorgans (cM), which correspond to recombination frequencies (in percent). Therefore, the genes for body color and wing size were 65.5 48.5 = 17 cM apart, indicating that the maternal and paternal alleles for these genes recombine in 17 percent of offspring, on average. 

To construct a chromosome map, Sturtevant assumed that genes were ordered serially on threadlike chromosomes. He also assumed that the incidence of recombination between two homologous chromosomes could occur with equal likelihood anywhere along the length of the chromosome. Operating under these assumptions, Sturtevant postulated that alleles that were far apart on a chromosome were more likely to dissociate during meiosis simply because there was a larger region over which recombination could occur. Conversely, alleles that were close to each other on the chromosome were likely to be inherited together. The average number of crossovers between two alleles that is, their recombination frequency correlated with their genetic distance from each other, relative to the locations of other genes on that chromosome. Considering the example cross between AaBb and aabb above, the frequency of recombination could be calculated as 50/1000 = 0.05. That is, the likelihood of a crossover between genes A/a and B/b was 0.05, or 5 percent. Such a result would indicate that the genes were definitively linked, but that they were far enough apart for crossovers to occasionally occur. Sturtevant divided his genetic map into map units, or centimorgans (cM) , in which a recombination frequency of 0.01 corresponds to 1 cM. 

By representing alleles in a linear map, Sturtevant suggested that genes can range from being perfectly linked (recombination frequency = 0) to being perfectly unlinked (recombination frequency = 0.5) when genes are on different chromosomes or genes are separated very far apart on the same chromosome. Perfectly unlinked genes correspond to the frequencies predicted by Mendel to assort independently in a dihybrid cross. A recombination frequency of 0.5 indicates that 50 percent of offspring are recombinants and the other 50 percent are parental types. That is, every type of allele combination is represented with equal frequency. This representation allowed Sturtevant to additively calculate distances between several genes on the same chromosome. However, as the genetic distances approached 0.50, his predictions became less accurate because it was not clear whether the genes were very far apart on the same chromosome or on different chromosomes. 

In 1931, Barbara McClintock and Harriet Creighton demonstrated the crossover of homologous chromosomes in corn plants. Weeks later, homologous recombination in Drosophila was demonstrated microscopically by Curt Stern. Stern observed several X-linked phenotypes that were associated with a structurally unusual and dissimilar X chromosome pair in which one X was missing a small terminal segment, and the other X was fused to a piece of the Y chromosome. By crossing flies, observing their offspring, and then visualizing the offspring s chromosomes, Stern demonstrated that every time the offspring allele combination deviated from either of the parental combinations, there was a corresponding exchange of an X chromosome segment. Using mutant flies with structurally distinct X chromosomes was the key to observing the products of recombination because DNA sequencing and other molecular tools were not yet available. It is now known that homologous chromosomes regularly exchange segments in meiosis by reciprocally breaking and rejoining their DNA at precise locations. 

Review Sturtevant s process to create a genetic map on the basis of recombination frequencies here . 

[link] Mendel s Mapped Traits 

Homologous recombination is a common genetic process, yet Mendel never observed it. Had he investigated both linked and unlinked genes, it would have been much more difficult for him to create a unified model of his data on the basis of probabilistic calculations. Researchers who have since mapped the seven traits investigated by Mendel onto the seven chromosomes of the pea plant genome have confirmed that all of the genes he examined are either on separate chromosomes or are sufficiently far apart as to be statistically unlinked. Some have suggested that Mendel was enormously lucky to select only unlinked genes, whereas others question whether Mendel discarded any data suggesting linkage. In any case, Mendel consistently observed independent assortment because he examined genes that were effectively unlinked. Section Summary 

The Chromosomal Theory of inheritance, proposed by Sutton and Boveri, states that chromosomes are the vehicles of genetic heredity. Neither Mendelian genetics nor gene linkage is perfectly accurate; instead, chromosome behavior involves segregation, independent assortment, and occasionally, linkage. Sturtevant devised a method to assess recombination frequency and infer the relative positions and distances of linked genes on a chromosome on the basis of the average number of crossovers in the intervening region between the genes. Sturtevant correctly presumed that genes are arranged in serial order on chromosomes and that recombination between homologs can occur anywhere on a chromosome with equal likelihood. Whereas linkage causes alleles on the same chromosome to be inherited together, homologous recombination biases alleles toward an inheritance pattern of independent assortment. Review Questions 

[link] 

[link] Critical Thinking Questions 

[link] Test Prep for AP Courses 

[link] 

[link] Glossary centimorgan (cM) (also, map unit) relative distance that corresponds to a recombination frequency of 0.01 Chromosomal Theory of Inheritance theory proposing that chromosomes are the vehicles of genes and that their behavior during meiosis is the physical basis of the inheritance patterns that Mendel observed homologous recombination process by which homologous chromosomes undergo reciprocal physical exchanges at their arms, also known as crossing over nonparental (recombinant) type progeny resulting from homologous recombination that exhibits a different allele combination compared with its parents parental types progeny that exhibits the same allelic combination as its parents recombination frequency average number of crossovers between two alleles; observed as the number of nonparental types in a population of progenyChromosomal Basis of Inherited Disorders Chromosomal Basis of Inherited Disorders 

In this section, you will explore the following question: What are the genetic consequences that result from nondisjunction and errors in chromosome structure through inversions and translocations? Connection for AP Courses 

The number, size, shape, and banding patterns of chromosomes make them easily identifiable in a karyogram and allows for the assessment of many chromosomal abnormalities. Although the cell cycle, mitosis, and meiosis are highly regulated to prevent errors, the processes are not perfect. One example is the failure of homologous chromosomes or sister chromatids to separate properly during meiosis I or meiosis II (a phenomenon referred to as nondisjunction). This results in gametes with too many or too few chromosomes. Disorders in chromosome number (aneuploidy) are typically lethal to the embryo, although a few trisomic genotypes are viable (e.g., Down syndrome). Because of X inactivation, aberrations in sex chromosomes typically have milder phenotypic effects (e.g., Turner syndrome) than aneuploidy. Sometimes segments of chromosome are duplicated, deleted, or rearranged by inversion or translocation. These aberrations can result in problematic phenotypic effects. Diagnostic testing can detect many of these chromosomal disorders in individuals well before birth, resulting in medical, ethical, and civic issues, such as the right to privacy. 

A condition in which an organism has more than the normal number of chromosome sets (two for diploid species) is called polyploidy. Polyploidy resulting in odd numbers of chromosomes is rare because it results in sterile organisms. One set of chromosomes has no pair so meiosis cannot proceed normally. In contrast, polyploidy resulting in even chromosome numbers is very common in the plant kingdom. Polyploid plants tend to be larger and more robust than individuals with the normal number of chromosomes. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 3.9 The student is able to construct an explanation, using visual representations or narratives, as to how DNA in chromosomes is transmitted to the next generation via mitosis, or meiosis followed by fertilization. Essential Knowledge 3.A.3 The chromosomal basis of inheritance provides an understanding of the pattern of passage (transmission) of genes from parent to offspring. Science Practice 3.1 The student can pose scientific questions. Learning Objective 3.13 The student is able to pose questions about ethical, social or medical issues surrounding human genetic disorders. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.A.3 Changes in genotype can result in changes in phenotype. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 3.24 The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection. 

Introduce karyotyping using this activity, which has students create a karyotype by matching chromosomes, this activity or this activity . 

Background information on karyotyping is available at this site . 

Some students have difficulties connecting the idea of chromosome structure with inheritance, as discussed in this paper . 

Students may therefore have trouble understanding the role of chromosomal abnormalities in inherited disorders. It may help students to review meiosis, using videos such as this . 

Inherited disorders can arise when chromosomes behave abnormally during meiosis. Chromosome disorders can be divided into two categories: abnormalities in chromosome number and chromosomal structural rearrangements. Because even small segments of chromosomes can span many genes, chromosomal disorders are characteristically dramatic and often fatal. Identification of Chromosomes 

The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, and includes their length, banding pattern, and centromere position. To obtain a view of an individual s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram , also known as an ideogram ( [link] ). This karyotype is of a female human. Notice that homologous chromosomes are the same size, and have the same centromere positions and banding patterns. A human male would have an XY chromosome pair instead of the XX pair shown. (credit: Andreas Blozer et al) 

In a given species, chromosomes can be identified by their number, size, centromere position, and banding pattern. In a human karyotype, autosomes or body chromosomes (all of the non sex chromosomes) are generally organized in order of size from largest (chromosome 1) to smallest (chromosome 22). (The X and Y chromosomes, the 23 rd pair, are not autosomes.) However, chromosome 21 is actually shorter than chromosome 22. This was discovered after the naming of Down syndrome as trisomy 21, reflecting how this disease results from possessing one extra chromosome 21 (three total). Not wanting to change the name of this disease, scientists retained the original numbering system. The chromosome arms projecting from either end of the centromere may be designated as short or long, depending on their relative lengths. The short arm is abbreviated p (for petite ), whereas the long arm is abbreviated q (because it follows p alphabetically). Each arm is further subdivided and denoted by a number. For example, locus 3 on the short arm of chromosome 21 is denoted 21p3. Using this naming system, locations on chromosomes can be described consistently in the scientific literature. 

Geneticists Use Karyograms to Identify Chromosomal Aberrations Although Mendel is referred to as the father of modern genetics, he performed his experiments with none of the tools that the geneticists of today routinely employ. One such powerful cytological technique is karyotyping, a method in which traits characterized by chromosomal abnormalities can be identified from a single cell. To observe an individual s karyotype, a person s cells (like white blood cells) are first collected from a blood sample or other tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical called colchicine is then applied to cells to arrest condensed chromosomes in metaphase. Cells are then made to swell using a hypotonic solution so the chromosomes spread apart. Finally, the sample is preserved in a fixative and applied to a slide. 

The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding patterns of each chromosome pair. Following staining, the chromosomes are viewed using bright-field microscopy. A common stain choice is the Giemsa stain. Giemsa staining results in approximately 400 800 bands (of tightly coiled DNA and condensed proteins) arranged along all of the 23 chromosome pairs; an experienced geneticist can identify each band. In addition to the banding patterns, chromosomes are further identified on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern ( [link] ). 

At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down Syndrome, which is identified by a third copy of chromosome 21, and Turner Syndrome, which is characterized by the presence of only one X chromosome in women instead of the normal two. Geneticists can also identify large deletions or insertions of DNA. For instance, Jacobsen Syndrome which involves distinctive facial features as well as heart and bleeding defects is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations , which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia. 

During Mendel s lifetime, inheritance was an abstract concept that could only be inferred by performing crosses and observing the traits expressed by offspring. By observing a karyogram, today s geneticists can actually visualize the chromosomal composition of an individual to confirm or predict genetic abnormalities in offspring, even before birth. Disorders in Chromosome Number 

Of all of the chromosomal disorders, abnormalities in chromosome number are the most obviously identifiable from a karyogram. Disorders of chromosome number include the duplication or loss of entire chromosomes, as well as changes in the number of complete sets of chromosomes. They are caused by nondisjunction , which occurs when pairs of homologous chromosomes or sister chromatids fail to separate during meiosis. Misaligned or incomplete synapsis, or a dysfunction of the spindle apparatus that facilitates chromosome migration, can cause nondisjunction. The risk of nondisjunction occurring increases with the age of the parents. 

Nondisjunction can occur during either meiosis I or II, with differing results ( [link] ). If homologous chromosomes fail to separate during meiosis I, the result is two gametes that lack that particular chromosome and two gametes with two copies of the chromosome. If sister chromatids fail to separate during meiosis II, the result is one gamete that lacks that chromosome, two normal gametes with one copy of the chromosome, and one gamete with two copies of the chromosome. 

Nondisjunction occurs when homologous chromosomes or sister chromatids fail to separate during meiosis, resulting in an abnormal chromosome number. Nondisjunction may occur during meiosis I or meiosis II. 

[link] Aneuploidy 

An individual with the appropriate number of chromosomes for their species is called euploid ; in humans, euploidy corresponds to 22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as aneuploid , a term that includes monosomy (loss of one chromosome) or trisomy (gain of an extraneous chromosome). Monosomic human zygotes missing any one copy of an autosome invariably fail to develop to birth because they lack essential genes. This underscores the importance of gene dosage in humans. Most autosomal trisomies also fail to develop to birth; however, duplications of some of the smaller chromosomes (13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a different type of genetic imbalance: an excess in gene dose. Individuals with an extra chromosome may synthesize an abundance of the gene products encoded by that chromosome. This extra dose (150 percent) of specific genes can lead to a number of functional challenges and often precludes development. The most common trisomy among viable births is that of chromosome 21, which corresponds to Down Syndrome. Individuals with this inherited disorder are characterized by short stature and stunted digits, facial distinctions that include a broad skull and large tongue, and significant developmental delays. The incidence of Down syndrome is correlated with maternal age; older women are more likely to become pregnant with fetuses carrying the trisomy 21 genotype ( [link] ). The incidence of having a fetus with trisomy 21 increases dramatically with maternal age. 

Visualize the addition of a chromosome that leads to Down syndrome in this video simulation . 

[link] Polyploidy 

An individual with more than the correct number of chromosome sets (two for diploid species) is called polyploid . For instance, fertilization of an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards. Polyploid animals are sterile because meiosis cannot proceed normally and instead produces mostly aneuploid daughter cells that cannot yield viable zygotes. Rarely, polyploid animals can reproduce asexually by haplodiploidy, in which an unfertilized egg divides mitotically to produce offspring. In contrast, polyploidy is very common in the plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species ( [link] ). As with many polyploid plants, this triploid orange daylily ( Hemerocallis fulva ) is particularly large and robust, and grows flowers with triple the number of petals of its diploid counterparts. (credit: Steve Karg) Sex Chromosome Nondisjunction in Humans 

Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. Rather than a gain or loss of autosomes, variations in the number of sex chromosomes are associated with relatively mild effects. In part, this occurs because of a molecular process called X inactivation . Early in development, when female mammalian embryos consist of just a few thousand cells (relative to trillions in the newborn), one X chromosome in each cell inactivates by tightly condensing into a quiescent (dormant) structure called a Barr body. The chance that an X chromosome (maternally or paternally derived) is inactivated in each cell is random, but once the inactivation occurs, all cells derived from that one will have the same inactive X chromosome or Barr body. By this process, females compensate for their double genetic dose of X chromosome. In so-called tortoiseshell cats, embryonic X inactivation is observed as color variegation ( [link] ). Females that are heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome is inactivated in the embryonic cell progenitor of that region. In cats, the gene for coat color is located on the X chromosome. In the embryonic development of female cats, one of the two X chromosomes is randomly inactivated in each cell, resulting in a tortoiseshell pattern if the cat has two different alleles for coat color. Male cats, having only one X chromosome, never exhibit a tortoiseshell coat color. (credit: Michael Bodega) 

An individual carrying an abnormal number of X chromosomes will inactivate all but one X chromosome in each of her cells. However, even inactivated X chromosomes continue to express a few genes, and X chromosomes must reactivate for the proper maturation of female ovaries. As a result, X-chromosomal abnormalities are typically associated with mild mental and physical defects, as well as sterility. If the X chromosome is absent altogether, the individual will not develop in utero. 

Several errors in sex chromosome number have been characterized. Individuals with three X chromosomes, called triplo-X, are phenotypically female but express developmental delays and reduced fertility. The XXY genotype, corresponding to one type of Klinefelter syndrome, corresponds to phenotypically male individuals with small testes, enlarged breasts, and reduced body hair. More complex types of Klinefelter syndrome exist in which the individual has as many as five X chromosomes. In all types, every X chromosome except one undergoes inactivation to compensate for the excess genetic dosage. This can be seen as several Barr bodies in each cell nucleus. Turner syndrome, characterized as an X0 genotype (i.e., only a single sex chromosome), corresponds to a phenotypically female individual with short stature, webbed skin in the neck region, hearing and cardiac impairments, and sterility. Duplications and Deletions 

In addition to the loss or gain of an entire chromosome, a chromosomal segment may be duplicated or lost. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Duplicated chromosomal segments may fuse to existing chromosomes or may be free in the nucleus. Cri-du-chat (from the French for cry of the cat ) is a syndrome associated with nervous system abnormalities and identifiable physical features that result from a deletion of most of 5p (the small arm of chromosome 5) ( [link] ). Infants with this genotype emit a characteristic high-pitched cry on which the disorder s name is based. This individual with cri-du-chat syndrome is shown at two, four, nine, and 12 years of age. (credit: Paola Cerruti Mainardi) Chromosomal Structural Rearrangements 

Cytologists have characterized numerous structural rearrangements in chromosomes, but chromosome inversions and translocations are the most common. Both are identified during meiosis by the adaptive pairing of rearranged chromosomes with their former homologs to maintain appropriate gene alignment. If the genes carried on two homologs are not oriented correctly, a recombination event could result in the loss of genes from one chromosome and the gain of genes on the other. This would produce aneuploid gametes. Chromosome Inversions 

A chromosome inversion is the detachment, 180 rotation, and reinsertion of part of a chromosome. Inversions may occur in nature as a result of mechanical shear, or from the action of transposable elements (special DNA sequences capable of facilitating the rearrangement of chromosome segments with the help of enzymes that cut and paste DNA sequences). Unless they disrupt a gene sequence, inversions only change the orientation of genes and are likely to have more mild effects than aneuploid errors. However, altered gene orientation can result in functional changes because regulators of gene expression could be moved out of position with respect to their targets, causing aberrant levels of gene products. 

An inversion can be pericentric and include the centromere, or paracentric and occur outside of the centromere ( [link] ). A pericentric inversion that is asymmetric about the centromere can change the relative lengths of the chromosome arms, making these inversions easily identifiable. Pericentric inversions include the centromere, and paracentric inversions do not. A pericentric inversion can change the relative lengths of the chromosome arms; a paracentric inversion cannot. 

When one homologous chromosome undergoes an inversion but the other does not, the individual is described as an inversion heterozygote. To maintain point-for-point synapsis during meiosis, one homolog must form a loop, and the other homolog must mold around it. Although this topology can ensure that the genes are correctly aligned, it also forces the homologs to stretch and can be associated with regions of imprecise synapsis ( [link] ). When one chromosome undergoes an inversion but the other does not, one chromosome must form an inverted loop to retain point-for-point interaction during synapsis. This inversion pairing is essential to maintaining gene alignment during meiosis and to allow for recombination. 

The Chromosome 18 Inversion Not all structural rearrangements of chromosomes produce nonviable, impaired, or infertile individuals. In rare instances, such a change can result in the evolution of a new species. In fact, a pericentric inversion in chromosome 18 appears to have contributed to the evolution of humans. This inversion is not present in our closest genetic relatives, the chimpanzees. Humans and chimpanzees differ cytogenetically by pericentric inversions on several chromosomes and by the fusion of two separate chromosomes in chimpanzees that correspond to chromosome two in humans. 

The pericentric chromosome 18 inversion is believed to have occurred in early humans following their divergence from a common ancestor with chimpanzees approximately five million years ago. Researchers characterizing this inversion have suggested that approximately 19,000 nucleotide bases were duplicated on 18p, and the duplicated region inverted and reinserted on chromosome 18 of an ancestral human. 

A comparison of human and chimpanzee genes in the region of this inversion indicates that two genes ROCK1 and USP14 that are adjacent on chimpanzee chromosome 17 (which corresponds to human chromosome 18) are more distantly positioned on human chromosome 18. This suggests that one of the inversion breakpoints occurred between these two genes. Interestingly, humans and chimpanzees express USP14 at distinct levels in specific cell types, including cortical cells and fibroblasts. Perhaps the chromosome 18 inversion in an ancestral human repositioned specific genes and reset their expression levels in a useful way. Because both ROCK1 and USP14 encode cellular enzymes, a change in their expression could alter cellular function. It is not known how this inversion contributed to hominid evolution, but it appears to be a significant factor in the divergence of humans from other primates. 1 

[link] Translocations 

A translocation occurs when a segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome. Translocations can be benign or have devastating effects depending on how the positions of genes are altered with respect to regulatory sequences. Notably, specific translocations have been associated with several cancers and with schizophrenia. Reciprocal translocations result from the exchange of chromosome segments between two nonhomologous chromosomes such that there is no gain or loss of genetic information ( [link] ). A reciprocal translocation occurs when a segment of DNA is transferred from one chromosome to another, nonhomologous chromosome. (credit: modification of work by National Human Genome Research/USA) Activity 

A Day in the Life . Compose a short story, PowerPoint presentation, video, poem, or significant piece of art to describe a day in the life of a teenager afflicted with a single gene disorder or chromosomal abnormality. You need to include the causes and effects of the disorder and pose a question about a social, medical, or ethical issue(s) associated with human genetic disorders. Think About It 

Create a series of representations to show how nondisjunction can result in a trisomic zygote from a cell with 2n = 4. 

The activity is an application of Learning Objective 3.24 and Science Practices 6.4 and 7.2, and Learning Objective 3.13 and Science Practice 3.1 because students are asked to show how a change in a human genotype, either by a single gene mutation or a chromosomal abnormality, can produce a change in phenotype; then students pose a question about an ethical, social, or medical issue surrounding human genetic disorders in general. 

The Think About It question is an application of Learning Objective 3.9 and Science Practice 6.2 because students are creating a diagram to explain how errors in meiosis can result in an abnormal zygote following fertilization. Answer Nondisjunction occurs when homologous chromosomes or sister chromatids fail to separate during meiosis, resulting in an abnormal chromosome number. Nondisjunction may occur during meiosis I or meiosis II. Section Summary 

The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allows for the assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have milder phenotypic effects. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted. Chromosome structures may also be rearranged, for example by inversion or translocation. Both of these aberrations can result in problematic phenotypic effects. Because they force chromosomes to assume unnatural topologies during meiosis, inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction. Review Questions 

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Violaine Goidts et al., Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates, Human Genetics . 115 (2004):116-122 Glossary aneuploid individual with an error in chromosome number; includes deletions and duplications of chromosome segments autosome any of the non-sex chromosomes chromosome inversion detachment, 180 rotation, and reinsertion of a chromosome arm euploid individual with the appropriate number of chromosomes for their species karyogram photographic image of a karyotype karyotype number and appearance of an individuals chromosomes; includes the size, banding patterns, and centromere position monosomy otherwise diploid genotype in which one chromosome is missing nondisjunction failure of synapsed homologs to completely separate and migrate to separate poles during the first cell division of meiosis paracentric inversion that occurs outside of the centromere pericentric inversion that involves the centromere polyploid individual with an incorrect number of chromosome sets translocation process by which one segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome trisomy otherwise diploid genotype in which one entire chromosome is duplicated X inactivation condensation of X chromosomes into Barr bodies during embryonic development in females to compensate for the double genetic doseIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Michael Morton went to jail in 1986 for the murder of this wife. Twenty-five years later, in 2011, he was exonerated of her murder by DNA evidence. (credit: Lauren Gerson) 

Each person s DNA is unique, and it is possible to detect differences among individuals within a species on the basis of these unique features. DNA analysis has many practical applications, including identifying criminals (forensics), determining paternity, tracing genealogy, identifying pathogens, researching archeological finds, tracing disease outbreaks, and studying human migration patterns. In the medical field, DNA is used in diagnostics, new vaccine development, and cancer therapy. It is often possible to determine predisposition to diseases by sequencing genes. 

Sometimes an innocent person is erroneously convicted of a crime and sent to jail. Between 2000 and 2015, evidence from DNA was used to exonerate over 250 innocent people. Twenty of those people were on death row after being convicted of a murder they didn t commit. To learn more about the intense scientific and legal processes used to exonerate those wrongfully convicted, go to The Innocence Project website here . 

Determination of DNA patterns has many uses. In criminal proceedings, DNA analysis has become almost routine and many juries depend on it. However, DNA samples for analysis may not be available in all cases, or DNA might be contaminated. Occasionally, DNA preserved from a crime committed before DNA analysis was available is used as evidence at a retrial.Historical Basis of Modern Understanding Historical Basis of Modern Understanding 

In this section, you will explore the following questions: What is transformation of DNA? How do Griffith s experiments in 1928 relate to our modern understanding of DNA and how it works? What are key historic experiments that helped identify DNA as the genetic material? What are Chargaff s rules of nitrogenous base pairing? Connection for AP Courses 

Today the three letters DNA have become synonymous with crime solving, paternity testing, human identification, and genetic testing. All of these procedures are possible because of the discovery, in the middle of the twentieth century, that DNA is the genetic material. The results of several classic experiments set the stage for an explosion of our knowledge about DNA and how it stores and transmits genetic information. DNA was first isolated from white blood cells by Miescher in the 1860s. Over fifty years later, Griffith s work transforming strains of the bacterium Streptococcus pneumoniae provided the first clue that DNA and not protein (as others argued) is the universal molecule of heredity. Griffith s conclusions were later supported by Avery, MacLeod, and McCarty. 

Subsequent experiments by Hershey and Chase using the bacteriophage T2 proved decisively that DNA is the genetic material. Shortly thereafter, Chargaff determined the ratios of adenine, thymine, cytosine, and guanine in DNA, suggesting paired relationships (A = T and C = G). He also found that the percentages of A, T, C, and G are different for different species. All of these historically important experiments shaped our current understanding of DNA. 

The content presented in this section supports the learning objectives outlined in Big Ideas 3 and 4 of the AP Biology Curriculum Framework. The AP learning objectives merge essential knowledge content with one or more of the seven science practices. These objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP exam questions. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA to support the claim that DNA is the primary source of heritable information. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question. Learning Objective 3.2 The student is able to justify the selection of data from historical investigations that support the claim that DNA is the source of heritable information. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.1 The subcomponents of biological molecules and their sequence determine the properties of that molecule. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. 

Stress to students that while DNA was discovered in the 1860s, the understanding that DNA is the genetic material came only in the middle of the 20 th century. Prior to that time, most scientists thought that genetic information was transmitted by proteins. There were good reasons for this belief. Scientists had observed that there were many more proteins in cells than there were DNA molecules. They also observed that the chromosomes in eukaryotic cells were packed with large protein complexes. Today scientists call those chromosomal protein complexes histones. Histones play no role in transmitting genetic information. Instead, they help package and order the chromosomes in a cell s nucleus. 

Explain the experiments demonstrating DNA s structure and function and focus on the logic behind the findings. Ask students if they can think of alternative methods to illustrate the same findings based on what they know today. 

Modern understandings of DNA have evolved from the discovery of nucleic acid to the development of the double-helix model. In the 1860s, Friedrich Miescher ( [link] ), a physician by profession, was the first person to isolate phosphate-rich chemicals from white blood cells or leukocytes. He named these chemicals (which would eventually be known as RNA and DNA) nuclein because they were isolated from the nuclei of the cells. Friedrich Miescher (1844 1895) discovered nucleic acids. 

To see Miescher conduct an experiment step-by-step, click through this review of how he discovered the key role of DNA and proteins in the nucleus. 

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A half century later, British bacteriologist Frederick Griffith was perhaps the first person to show that hereditary information could be transferred from one cell to another horizontally, rather than by descent. In 1928, he reported the first demonstration of bacterial transformation , a process in which external DNA is taken up by a cell, thereby changing morphology and physiology. He was working with Streptococcus pneumoniae, the bacterium that causes pneumonia. Griffith worked with two strains, rough (R) and smooth (S). The R strain is non-pathogenic (does not cause disease) and is called rough because its outer surface is a cell wall and lacks a capsule; as a result, the cell surface appears uneven under the microscope. The S strain is pathogenic (disease-causing) and has a capsule outside its cell wall. As a result, it has a smooth appearance under the microscope. Griffith injected the live R strain into mice and they survived. In another experiment, when he injected mice with the heat-killed S strain, they also survived. In a third set of experiments, a mixture of live R strain and heat-killed S strain were injected into mice, and to his surprise the mice died. Upon isolating the live bacteria from the dead mouse, only the S strain of bacteria was recovered. When this isolated S strain was injected into fresh mice, the mice died. Griffith concluded that something had passed from the heat-killed S strain into the live R strain and transformed it into the pathogenic S strain, and he called this the transforming principle ( [link] ). These experiments are now famously known as Griffith's transformation experiments. Two strains of S. pneumoniae were used in Griffith s transformation experiments. The R strain is non-pathogenic. The S strain is pathogenic and causes death. When Griffith injected a mouse with the heat-killed S strain and a live R strain, the mouse died. The S strain was recovered from the dead mouse. Thus, Griffith concluded that something had passed from the heat-killed S strain to the R strain, transforming the R strain into S strain in the process. (credit "living mouse": modification of work by NIH; credit "dead mouse": modification of work by Sarah Marriage) 

Scientists Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) were interested in exploring this transforming principle further. They isolated the S strain from the dead mice and isolated the proteins and nucleic acids, namely RNA and DNA, as these were possible candidates for the molecule of heredity. They conducted a systematic elimination study. They used enzymes that specifically degraded each component and then used each mixture separately to transform the R strain. They found that when DNA was degraded, the resulting mixture was no longer able to transform the bacteria, whereas all of the other combinations were able to transform the bacteria. This led them to conclude that DNA was the transforming principle. 

Forensic Scientists and DNA Analysis DNA evidence was used for the first time to solve an immigration case. The story started with a teenage boy returning to London from Ghana to be with his mother. Immigration authorities at the airport were suspicious of him, thinking that he was traveling on a forged passport. After much persuasion, he was allowed to go live with his mother, but the immigration authorities did not drop the case against him. All types of evidence, including photographs, were provided to the authorities, but deportation proceedings were started nevertheless. Around the same time, Dr. Alec Jeffreys of Leicester University in the United Kingdom had invented a technique known as DNA fingerprinting. The immigration authorities approached Dr. Jeffreys for help. He took DNA samples from the mother and three of her children, plus an unrelated mother, and compared the samples with the boy s DNA. Because the biological father was not in the picture, DNA from the three children was compared with the boy s DNA. He found a match in the boy s DNA for both the mother and his three siblings. He concluded that the boy was indeed the mother s son. 

Forensic scientists analyze many items, including documents, handwriting, firearms, and biological samples. They analyze the DNA content of hair, semen, saliva, and blood, and compare it with a database of DNA profiles of known criminals. Analysis includes DNA isolation, sequencing, and sequence analysis; most forensic DNA analysis involves polymerase chain reaction (PCR) amplification of short tandem repeat (STR) loci and electrophoresis to determine the length of the PCR-amplified fragment. Only mitochondrial DNA is sequenced for forensics. Forensic scientists are expected to appear at court hearings to present their findings. They are usually employed in crime labs of city and state government agencies. Geneticists experimenting with DNA techniques also work for scientific and research organizations, pharmaceutical industries, and college and university labs. Students wishing to pursue a career as a forensic scientist should have at least a bachelor's degree in chemistry, biology, or physics, and preferably some experience working in a laboratory. Activity DNA Necklace. 

1) Using a molecular modeling kit (or an online virtual kit such as jmol), create a model of each of the 4 nucleotides in DNA, based on structural diagrams found in this chapter or elsewhere online. 

2) Identify where each nucleotide hydrogen-bonds with its complementary base. Add these bonds to secure the two pairs of nucleotides together. How does the hydrogen bonding differ between the two pairs of complementary bases? 

3) Now look at a structural diagram of a complete DNA molecule. Based on the diagram, connect your two pairs of nucleotides together along your DNA s sugar-phosphate backbone (depending on your model kit, you may have to first disconnect the hydrogen bonds between the complementary bases). Which atoms and molecules did you have to remove and add to create the sugar-phosphate backbone? Think About It 

Explain why radioactive sulfur and phosphorus were used to label T2 bacteriophages in the Hershey-Chase experiments. How did the results of these experiments contribute to the identification of DNA as the genetic material? 

The activity is an application of Learning Objective 4.1 and Science Practice 7.1 because students are examining the spatial relationships among the components of a DNA strand and explaining the connections between the sequence and subcomponents of the nucleotides. 

An expanded lab investigation for DNA, involving restriction enzyme analysis, is available from the College Board's AP Biology Investigative Labs: An Inquiry-Based Approach in Investigation 9 . 

1) Group size is dependent on the availability of molecular model kits. Please note that extra carbon and hydrogen bonds are likely needed for students to make all 4 nucleotides. Groups could also be assigned to make one of the two pairs of nucleotides, after which the groups can combine the molecules into DNA in step 3. Jmol is available for download here . 

2) Note: some molecular model kits have special bonds to use for hydrogen bonds. If these bonds are not used, the students may not be able to connect the nucleotides together. Sample answer: One notable difference is that thymine and adenine bond with two hydrogen bonds while cytosine and guanine bond using three hydrogen bonds. 

3) To bond two nucleotides along the sugar-phosphate backbone of DNA, we removed one H from carbon 3 of deoxyribose. We then bonded carbon 3 to one of the single-bonded O atoms on the phosphate ion. Next, we removed the OH group from the CH 2 group on the deoxyribose. The carbon on this CH 2 group was then bonded to the other single-bonded O on the phosphate ion. 

The Think About It question is an application of Learning Objective 3.2 and Science Practice 4.1 because students are asked to justify that the Hershey-Chase experiments supported the identification of DNA as the carrier of genetic information. It is also an application of Learning Objective 3.1 and Science Practice 6.5 because students will evaluate researchers claims that DNA is found in cells and is the primary source of heritable information. Answer: Hershey and Chase used radioactive sulfur because sulfur is not found in DNA but is present in T2 s protein coat. They used radioactive phosphorus because phosphorus is not found in protein but is present in DNA. When they observed the infected bacterial cells they found them to contain radioactive phosphorus but no radioactive sulfur. Therefore, Hershey and Chase knew that the DNA was the infectious agent and, thus, the transmitter of genetic information. 

Experiments conducted by Martha Chase and Alfred Hershey in 1952 provided confirmatory evidence that DNA was the genetic material and not proteins. Chase and Hershey were studying a bacteriophage, which is a virus that infects bacteria. Viruses typically have a simple structure: a protein coat, called the capsid, and a nucleic acid core that contains the genetic material, either DNA or RNA. The bacteriophage infects the host bacterial cell by attaching to its surface, and then it injects its nucleic acids inside the cell. The phage DNA makes multiple copies of itself using the host machinery, and eventually the host cell bursts, releasing a large number of bacteriophages. Hershey and Chase labeled one batch of phage with radioactive sulfur, 35 S, to label the protein coat. Another batch of phage were labeled with radioactive phosphorus, 32 P. Because phosphorous is found in DNA, but not protein, the DNA and not the protein would be tagged with radioactive phosphorus. 

Each batch of phage was allowed to infect the cells separately. After infection, the phage bacterial suspension was put in a blender, which caused the phage coat to be detached from the host cell. The phage and bacterial suspension was spun down in a centrifuge. The heavier bacterial cells settled down and formed a pellet, whereas the lighter phage particles stayed in the supernatant. In the tube that contained phage labeled with 35 S, the supernatant contained the radioactively labeled phage, whereas no radioactivity was detected in the pellet. In the tube that contained the phage labeled with 32 P, the radioactivity was detected in the pellet that contained the heavier bacterial cells, and no radioactivity was detected in the supernatant. Hershey and Chase concluded that it was the phage DNA that was injected into the cell and carried information to produce more phage particles, thus providing evidence that DNA was the genetic material and not proteins ( [link] ). In Hershey and Chase's experiments, bacteria were infected with phage radiolabeled with either 35 S, which labels protein, or 32 P, which labels DNA. Only 32 P entered the bacterial cells, indicating that DNA is the genetic material. 

Around this same time, Austrian biochemist Erwin Chargaff examined the content of DNA in different species and found that the amounts of adenine, thymine, guanine, and cytosine were not found in equal quantities, and that it varied from species to species, but not between individuals of the same species. He found that the amount of adenine equals the amount of thymine, and the amount of cytosine equals the amount of guanine, or A = T and G = C. This is also known as Chargaff s rules. This finding proved immensely useful when Watson and Crick were getting ready to propose their DNA double helix model. Section Summary 

DNA was first isolated from white blood cells by Friedrich Miescher, who called it nuclein because it was isolated from nuclei. Frederick Griffith's experiments with strains of Streptococcus pneumoniae provided the first hint that DNA may be the transforming principle. Avery, MacLeod, and McCarty proved that DNA is required for the transformation of bacteria. Later experiments by Hershey and Chase using bacteriophage T2 proved that DNA is the genetic material. Chargaff found that the ratio of A = T and C = G, and that the percentage content of A, T, G, and C is different for different species. Review Questions 

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[link] Glossary transformation process in which external DNA is taken up by a cellDNA Structure and Sequencing DNA Structure and Sequencing 

In this section, you will explore the following questions: What is the molecular structure of DNA? What is the Sanger method of DNA sequencing? What is an application of DNA sequencing? What are the similarities and differences between eukaryotic and prokaryotic DNA? Connection for AP Courses 

The currently accepted model of the structure of DNA was proposed in 1953 by Watson and Crick, who made their model after seeing a photograph of DNA that Franklin had taken using X-ray crystallography. The photo showed the molecule s double-helix shape and dimensions. The two strands that make up the double helix are complementary and anti-parallel in nature. That is, one strand runs in the 5' to 3' direction, whereas the complementary strand runs in the 3' to 5' direction. (The significance of directionality will be important when we explore how DNA copies itself.) DNA is a polymer of nucleotides that consists of deoxyribose sugar, a phosphate group, and one of four nitrogenous bases A, T, C, and G with a purine always pairing with a pyrimidine (as Chargaff found). The genetic language of DNA is found in sequences of the nucleotides. During cell division each daughter cell receives a copy of DNA in a process called replication. In the years since the discovery of the structure of DNA, many technologies, including DNA sequencing, have been developed that enable us to better understand DNA and its role in our genomes. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven science practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA to support the claim that DNA is the primary source of heritable information. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question. Learning Objective 3.2 The student is able to justify the selection of data from historical investigations that support the claim that DNA is the source of heritable information. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.5 The student can justify the claim that humans can manipulate heritable information by identifying at least two commonly used technologies. 

Franklin s X-ray diffraction pictures helped lead to the discovery of the structure of DNA, but Watson and Crick did not mention Franklin in their seminal 1953 paper, which can be found here . This paper includes annotations that help place the work in historical context. Students might be interested to learn how Watson and Crick discovered the structure of DNA. Details can be found at this PBS website . If possible, find a copy of the announcement of the discovery as it appeared in The New York Times . The wording is interesting and the significance of the discovery is understated. 

The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group ( [link] ). The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T). Each nucleotide is made up of a sugar, a phosphate group, and a nitrogenous base. The sugar is deoxyribose in DNA and ribose in RNA. 

The nucleotides combine with each other by covalent bonds known as phosphodiester bonds or linkages. The purines have a double ring structure with a six-membered ring fused to a five-membered ring. Pyrimidines are smaller in size; they have a single six-membered ring structure. The carbon atoms of the five-carbon sugar are numbered 1', 2', 3', 4', and 5' (1' is read as one prime ). The phosphate residue is attached to the hydroxyl group of the 5' carbon of one sugar of one nucleotide and the hydroxyl group of the 3' carbon of the sugar of the next nucleotide, thereby forming a 5'-3' phosphodiester bond. 

In the 1950s, Francis Crick and James Watson worked together to determine the structure of DNA at the University of Cambridge, England. Other scientists like Linus Pauling and Maurice Wilkins were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. In Wilkins lab, researcher Rosalind Franklin was using X-ray diffraction methods to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule on the basis of Franklin's data because Crick had also studied X-ray diffraction ( [link] ). In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously. The work of pioneering scientists (a) James Watson, Francis Crick, and Maclyn McCarty led to our present day understanding of DNA. Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure. (credit a: modification of work by Marjorie McCarty, Public Library of Science) 

Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. Base pairing takes place between a purine and pyrimidine; namely, A pairs with T and G pairs with C. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds and cytosine and guanine form three hydrogen bonds. The two strands are anti-parallel in nature; that is, the 3' end of one strand faces the 5' end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. Each base pair is separated from the other base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, ten base pairs are present per turn of the helix. The diameter of the DNA double helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves ( [link] ). DNA has (a) a double helix structure and (b) phosphodiester bonds. The (c) major and minor grooves are binding sites for DNA binding proteins during processes such as transcription (the copying of RNA from DNA) and replication. Activity 

Read Watson and Crick s original Nature article, Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid, How did Watson and Crick s model build on the findings of Rosalind Franklin? How did their model of DNA build on the findings of Hershey and Chase, and others, showing that DNA can encode and pass information on to the next generation? Think About It 

Watson and Crick s work determined the structure of DNA. However, it was still relatively unknown how DNA encoded information into genes. Select one modern form of biotechnology and research its basic methods online. Examples include gene sequencing, DNA fingerprinting, PCR (polymerase chain reaction), genetically-modified food, etc. Briefly describe your chosen technology, and what benefits it provides us. Then describe how Watson and Crick s findings were vital to the development of your chosen technology. 

The activity is an application of Learning Objective 3.1 and Science Practice 6.5 because students are analyzing Watson and Crick s model of DNA relative to the findings of other DNA researchers who determined that DNA is the molecule of heredity. The activity is also an application of Learning Objective 3.2 and Science Practice 4.1 because students are analyzing the historic published results of Watson and Crick and selecting evidence that Watson and Crick used to create their model of DNA and further show that DNA is the molecule of heredity. Possible answer: Watson and Crick s model built on Franklin s findings that DNA has the structure of a double helix. The finding that DNA can pass information on to the next generation by Hershey and Chase was further evidenced by Watson and Crick s model, which showed that DNA could encode information using the sequence of its four nucleotides. 

The Think About It question is an application of Learning Objective 3.5 and Science Practice 6.4 because students are researching the methods by which humans can manipulate heritable information and describing how those methods were based on the scientific theories and models of Watson and Crick. Possible answer: PCR allows us to make many copies of DNA for research or other applications. PCR involves separating out the two strands of DNA and adding nucleotides to the specific regions one wishes to amplify. Attaching nucleotide primers allows one to create many copies of only the desired sequences of the DNA. The ability to separate DNA and amplify select regions depends on the knowledge of nucleotide bonding within the DNA molecule described in the Watson and Crick model. DNA Sequencing Techniques 

Until the 1990s, the sequencing of DNA (reading the sequence of DNA) was a relatively expensive and long process. Using radiolabeled nucleotides also compounded the problem through safety concerns. With currently available technology and automated machines, the process is cheap, safer, and can be completed in a matter of hours. Fred Sanger developed the sequencing method used for the human genome sequencing project, which is widely used today ( [link] ). 

Visit this site to watch a video explaining the DNA sequence reading technique that resulted from Sanger s work. 

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The method is known as the dideoxy chain termination method. The sequencing method is based on the use of chain terminators, the dideoxynucleotides (ddNTPs). The dideoxynucleotides, or ddNTPSs, differ from the deoxynucleotides by the lack of a free 3' OH group on the five-carbon sugar. If a ddNTP is added to a growing a DNA strand, the chain is not extended any further because the free 3' OH group needed to add another nucleotide is not available. By using a predetermined ratio of deoxyribonucleotides to dideoxynucleotides, it is possible to generate DNA fragments of different sizes. In Frederick Sanger's dideoxy chain termination method, dye-labeled dideoxynucleotides are used to generate DNA fragments that terminate at different points. The DNA is separated by capillary electrophoresis on the basis of size, and from the order of fragments formed, the DNA sequence can be read. The DNA sequence readout is shown on an electropherogram that is generated by a laser scanner. 

The DNA sample to be sequenced is denatured or separated into two strands by heating it to high temperatures. The DNA is divided into four tubes in which a primer, DNA polymerase, and all four nucleotides (A, T, G, and C) are added. In addition to each of the four tubes, limited quantities of one of the four dideoxynucleotides are added to each tube respectively. The tubes are labeled as A, T, G, and C according to the ddNTP added. For detection purposes, each of the four dideoxynucleotides carries a different fluorescent label. Chain elongation continues until a fluorescent dideoxy nucleotide is incorporated, after which no further elongation takes place. After the reaction is over, electrophoresis is performed. Even a difference in length of a single base can be detected. The sequence is read from a laser scanner. For his work on DNA sequencing, Sanger received a Nobel Prize in chemistry in 1980. 

Sanger s genome sequencing has led to a race to sequence human genomes at a rapid speed and low cost, often referred to as the $1000 in one day sequence. Learn more by selecting the Sequencing at Speed animation here . 

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Gel electrophoresis is a technique used to separate DNA fragments of different sizes. Usually the gel is made of a chemical called agarose. Agarose powder is added to a buffer and heated. After cooling, the gel solution is poured into a casting tray. Once the gel has solidified, the DNA is loaded on the gel and electric current is applied. The DNA has a net negative charge and moves from the negative electrode toward the positive electrode. The electric current is applied for sufficient time to let the DNA separate according to size; the smallest fragments will be farthest from the well (where the DNA was loaded), and the heavier molecular weight fragments will be closest to the well. Once the DNA is separated, the gel is stained with a DNA-specific dye for viewing it ( [link] ). DNA can be separated on the basis of size using gel electrophoresis. (credit: James Jacob, Tompkins Cortland Community College) 

Neanderthal Genome: How Are We Related? The first draft sequence of the Neanderthal genome was recently published by Richard E. Green et al. in 2010. 1 Neanderthals are the closest ancestors of present-day humans. They were known to have lived in Europe and Western Asia before they disappeared from fossil records approximately 30,000 years ago. Green s team studied almost 40,000-year-old fossil remains that were selected from sites across the world. Extremely sophisticated means of sample preparation and DNA sequencing were employed because of the fragile nature of the bones and heavy microbial contamination. In their study, the scientists were able to sequence some four billion base pairs. The Neanderthal sequence was compared with that of present-day humans from across the world. After comparing the sequences, the researchers found that the Neanderthal genome had 2 to 3 percent greater similarity to people living outside Africa than to people in Africa. While current theories have suggested that all present-day humans can be traced to a small ancestral population in Africa, the data from the Neanderthal genome may contradict this view. Green and his colleagues also discovered DNA segments among people in Europe and Asia that are more similar to Neanderthal sequences than to other contemporary human sequences. Another interesting observation was that Neanderthals are as closely related to people from Papua New Guinea as to those from China or France. This is surprising because Neanderthal fossil remains have been located only in Europe and West Asia. Most likely, genetic exchange took place between Neanderthals and modern humans as modern humans emerged out of Africa, before the divergence of Europeans, East Asians, and Papua New Guineans. 

Several genes seem to have undergone changes from Neanderthals during the evolution of present-day humans. These genes are involved in cranial structure, metabolism, skin morphology, and cognitive development. One of the genes that is of particular interest is RUNX2 , which is different in modern day humans and Neanderthals. This gene is responsible for the prominent frontal bone, bell-shaped rib cage, and dental differences seen in Neanderthals. It is speculated that an evolutionary change in RUNX2 was important in the origin of modern-day humans, and this affected the cranium and the upper body. 

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Watch Svante P bo s talk explaining the Neanderthal genome research at the 2011 annual TED (Technology, Entertainment, Design) conference. 

[link] DNA Packaging in Cells 

When comparing prokaryotic cells to eukaryotic cells, prokaryotes are much simpler than eukaryotes in many of their features ( [link] ). Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid. 

A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid. 

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The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling; other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure. 

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus ( [link] ). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the beads on a string structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage, the chromosomes are at their most compact, are approximately 700 nm in width, and are found in association with scaffold proteins. 

In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted. These figures illustrate the compaction of the eukaryotic chromosome. Section Summary 

The currently accepted model of the double-helix structure of DNA was proposed by Watson and Crick. Some of the salient features are that the two strands that make up the double helix are complementary and anti-parallel in nature. Deoxyribose sugars and phosphates form the backbone of the structure, and the nitrogenous bases are stacked inside. The diameter of the double helix, 2 nm, is uniform throughout. A purine always pairs with a pyrimidine; A pairs with T, and G pairs with C. One turn of the helix has ten base pairs. During cell division, each daughter cell receives a copy of the DNA by a process known as DNA replication. Prokaryotes are much simpler than eukaryotes in many of their features. Most prokaryotes contain a single, circular chromosome. In general, eukaryotic chromosomes contain a linear DNA molecule packaged into nucleosomes, and have two distinct regions that can be distinguished by staining, reflecting different states of packaging and compaction. Review Questions 

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Richard E. Green et al., A Draft Sequence of the Neandertal Genome, Science 328 (2010): 710-22. Glossary electrophoresis technique used to separate DNA fragments according to sizeBasics of DNA Replication Basics of DNA Replication 

In this section, you will explore the following questions: How does the structure of DNA provide for the process of replication? How did the Meselson and Stahl experiments support the semi-conservative nature of replication? Connection for AP Courses 

The Watson and Crick model suggested a way in which DNA could be replicated during cell division. Basically, the two strands unwind and separate where the hydrogen bonds connect the nucleotides. Each parental strand then serves as a template for a new, complementary daughter strand. Replication is said to be semi-conservative because the original information encoded in each parental strand is conserved (kept) in the daughter molecules. Thus, a newly replicated molecule of DNA consists of one old strand and one new strand. Meselson and Stahl used density differences in nitrogen isotopes to investigate replication, and their experiments supported the semi-conservative model. However, the process of replication is more complex than their model s simple description. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 and Big Idea 4 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.3 The student is able to describe representations and models that illustrate how genetic information is copied for transmission between generations. 

Before the Meselson and Stahl experiment in 1958, scientists did not know how chromosomes replicated. Watson and Crick had suggested that replication was semi-conservative, but other scientists favored one of two other hypotheses, shown in [link] . The Meselson and Stahl experiment can be confusing. Take time to walk students through the process. 

Take some time to trace a mythical family tree, assume no recombination over time and illustrate how a chromosome from a distant ancestor might have ended up in a modern-day person. 

The elucidation of the structure of the double helix provided a hint as to how DNA divides and makes copies of itself. This model suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. What was not clear was how the replication took place. There were three models suggested ( [link] ): conservative, semi-conservative, and dispersive. The three suggested models of DNA replication. Grey indicates the original DNA strands, and blue indicates newly synthesized DNA. 

In conservative replication, the parental DNA remains together, and the newly formed daughter strands are together. The semi-conservative method suggests that each of the two parental DNA strands act as a template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or old strand and one new strand. In the dispersive model, both copies of DNA have double-stranded segments of parental DNA and newly synthesized DNA interspersed. 

Meselson and Stahl were interested in understanding how DNA replicates. They grew E. coli for several generations in a medium containing a heavy isotope of nitrogen ( 15 N) that gets incorporated into nitrogenous bases, and eventually into the DNA ( [link] ). Meselson and Stahl experimented with E. coli grown first in heavy nitrogen ( 15 N) then in 14 N. DNA grown in 15 N (red band) is heavier than DNA grown in 14 N (orange band), and sediments to a lower level in cesium chloride solution in an ultracentrifuge. When DNA grown in 15 N is switched to media containing 14 N, after one round of cell division the DNA sediments halfway between the 15 N and 14 N levels, indicating that it now contains fifty percent 14 N. In subsequent cell divisions, an increasing amount of DNA contains 14 N only. This data supports the semi-conservative replication model. (credit: modification of work by Mariana Ruiz Villareal) 

The E. coli culture was then shifted into medium containing 14 N and allowed to grow for one generation. The cells were harvested and the DNA was isolated. The DNA was centrifuged at high speeds in an ultracentrifuge. Some cells were allowed to grow for one more life cycle in 14 N and spun again. During the density gradient centrifugation, the DNA is loaded into a gradient (typically a salt such as cesium chloride or sucrose) and spun at high speeds of 50,000 to 60,000 rpm. Under these circumstances, the DNA will form a band according to its density in the gradient. DNA grown in 15 N will band at a higher density position than that grown in 14 N. Meselson and Stahl noted that after one generation of growth in 14 N after they had been shifted from 15 N, the single band observed was intermediate in position in between DNA of cells grown exclusively in 15 N and 14 N. This suggested either a semi-conservative or dispersive mode of replication. The DNA harvested from cells grown for two generations in 14 N formed two bands: one DNA band was at the intermediate position between 15 N and 14 N, and the other corresponded to the band of 14 N DNA. These results could only be explained if DNA replicates in a semi-conservative manner. Therefore, the other two modes were ruled out. 

During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or old strand. When two daughter DNA copies are formed, they have the same sequence and are divided equally into the two daughter cells. 

Click through this tutorial on DNA replication. 

[link] Activity 

Design (but do not implement) an experiment to test the three models of DNA replication. Summarize the results you would expect if each of the three models of DNA replication were correct. Assume you have access in a laboratory to the following: an experimental organism such as E. coli , an unlimited variety of isotopes, test tube and centrifuge, and organic growth media. 

This activity is an application of Learning Objective 3.3 and Science Practice 1.2 because by designing an experiment, students are describing the three models that were proposed to illustrate how genetic information is copied. Section Summary 

The model for DNA replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. In conservative replication, the parental DNA is conserved, and the daughter DNA is newly synthesized. The semi-conservative method suggests that each of the two parental DNA strands acts as template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or old strand and one new strand. The dispersive mode suggested that the two copies of the DNA would have segments of parental DNA and newly synthesized DNA. Review Questions 

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[link]DNA Replication in Prokaryotes DNA Replication in Prokaryotes 

In this section, you will explore the following questions: How is DNA replicated in prokaryotes, and what are the roles of the leading and lagging strands and Okazaki fragments in the process? What is the role of DNA polymerase and other enzymes and proteins in supporting replication? Connection for AP Courses 

As was stated previously, DNA replication is more complex than simply unzipping the double helix and making new complementary strands. Replication in prokaryotes starts from a sequence of nucleotides on the chromosome called the origin of replication the point at which the DNA opens up or unzips. The enzyme helicase opens up the DNA at the point where hydrogen bonds connect the strands, resulting in the formation of a Y-shaped replication fork. Single-strand binding proteins keep the fork open. The enzyme primase synthesizes RNA primers to initiate DNA synthesis by DNA polymerase, which can add nucleotides only in the 5' to 3' direction. DNA polymerase recognizes the 3'-OH end as its landing site; thus, polymerase reads the template strand in the 3' to 5' direction and builds the complementary DNA polymer in the 5' to 3' direction. One strand called the leading strand is synthesized continuously in the direction of the replication fork (the direction in which helicase is separating the two strands), with polymerase adding new nucleotides one-by-one. However, replication of the other strand called the lagging strand occurs in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. (Think of the activities on the lagging strand as analogous to trying to walk on a moving sidewalk that is moving in the opposite direction.) The RNA primers are replaced by DNA nucleotides, and ligase seals the DNA, creating phosphodiester bonds between the 3'-OH of one end and the 5'-phosphate of the other strand. The replicated DNA molecules now consist of one original template strand and one newly synthesized strand. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.3 The student is able to describe representations and models that illustrate how genetic information is copied for transmission between generations. 

Use the ten steps summarizing the process of DNA replication listed just prior to [link] in the text as an outline for discussing DNA replication in prokaryotes. 

DNA replication has been extremely well studied in prokaryotes primarily because of the small size of the genome and the mutants that are available. E. coli has 4.6 million base pairs in a single circular chromosome and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle in both directions. This means that approximately 1000 nucleotides are added per second. The process is quite rapid and occurs without many mistakes. 

DNA replication employs a large number of proteins and enzymes, each of which plays a critical role during the process. One of the key players is the enzyme DNA polymerase, also known as DNA pol, which adds nucleotides one by one to the growing DNA chain that are complementary to the template strand. The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the growing chain. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. It is now known that DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair. 

How does the replication machinery know where to begin? It turns out that there are specific nucleotide sequences called origins of replication where replication begins. In E. coli, which has a single origin of replication on its one chromosome (as do most prokaryotes), it is approximately 245 base pairs long and is rich in AT sequences. The origin of replication is recognized by certain proteins that bind to this site. An enzyme called helicase unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. ATP hydrolysis is required for this process. As the DNA opens up, Y-shaped structures called replication forks are formed. Two replication forks are formed at the origin of replication and these get extended bi- directionally as replication proceeds. Single-strand binding proteins coat the single strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix. DNA polymerase is able to add nucleotides only in the 5' to 3' direction (a new DNA strand can be only extended in this direction). It also requires a free 3'-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide. This essentially means that it cannot add nucleotides if a free 3'-OH group is not available. Then how does it add the first nucleotide? The problem is solved with the help of a primer that provides the free 3'-OH end. Another enzyme, RNA primase , synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA. Because this sequence primes the DNA synthesis, it is appropriately called the primer . DNA polymerase can now extend this RNA primer, adding nucleotides one by one that are complementary to the template strand ( [link] ). 

A replication fork is formed when helicase separates the DNA strands at the origin of replication. The DNA tends to become more highly coiled ahead of the replication fork. Topoisomerase breaks and reforms DNA s phosphate backbone ahead of the replication fork, thereby relieving the pressure that results from this supercoiling. Single-strand binding proteins bind to the single-stranded DNA to prevent the helix from re-forming. Primase synthesizes an RNA primer. DNA polymerase III uses this primer to synthesize the daughter DNA strand. On the leading strand, DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches called Okazaki fragments. DNA polymerase I replaces the RNA primer with DNA. DNA ligase seals the gaps between the Okazaki fragments, joining the fragments into a single DNA molecule. (credit: modification of work by Mariana Ruiz Villareal) 

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The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5' to 3' direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5' to 3' direction and the other is oriented in the 3' to 5' direction. One strand, which is complementary to the 3' to 5' parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand . The other strand, complementary to the 5' to 3' parental DNA, is extended away from the replication fork, in small fragments known as Okazaki fragments , each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the lagging strand . 

The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. A protein called the sliding clamp holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. Topoisomerase prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the exonuclease activity of DNA pol I, and the gaps are filled in by deoxyribonucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA ligase that catalyzes the formation of phosphodiester linkage between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment. 

Once the chromosome has been completely replicated, the two DNA copies move into two different cells during cell division. The process of DNA replication can be summarized as follows: DNA unwinds at the origin of replication. Helicase opens up the DNA-forming replication forks; these are extended bidirectionally. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA. Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling. Primase synthesizes RNA primers complementary to the DNA strand. DNA polymerase starts adding nucleotides to the 3'-OH end of the primer. Elongation of both the lagging and the leading strand continues. RNA primers are removed by exonuclease activity. Gaps are filled by DNA pol by adding dNTPs. The gap between the two DNA fragments is sealed by DNA ligase, which helps in the formation of phosphodiester bonds. 



[link] summarizes the enzymes involved in prokaryotic DNA replication and the functions of each. Prokaryotic DNA Replication: Enzymes and Their Functions Enzyme/protein Specific Function DNA pol I Exonuclease activity removes RNA primer and replaces with newly synthesized DNA DNA pol II Repair function DNA pol III Main enzyme that adds nucleotides in the 5'-3' direction Helicase Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases Ligase Seals the gaps between the Okazaki fragments to create one continuous DNA strand Primase Synthesizes RNA primers needed to start replication Sliding Clamp Helps to hold the DNA polymerase in place when nucleotides are being added Topoisomerase Helps relieve the stress on DNA when unwinding by causing breaks and then resealing the DNA Single-strand binding proteins (SSB) Binds to single-stranded DNA to avoid DNA rewinding back. 

Review the full process of DNA replication here . 

[link] Activity 

Use the model of DNA you constructed in Section 14.2 to demonstrate the process of replication in prokaryotes, showing how the activities differ on the leading and lagging strands. You need to add to your model by including enzymes and other proteins involved in the replication process. Think About It 

You isolate a DNA strand in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely mutated? 

The activity is an application of Learning Objective 3.3 and Science Practice 1.2 because students are describing the process of replication using a model of DNA. 

The Think About It question is an application of Learning Objective 3.3 and Science Practice 1.2 because students are describing the role of a particular enzyme in the process of DNA replication. Answer: The enzyme likely to be mutated is DNA ligase, which seals the gaps between the Okazaki fragments. Section Summary 

Replication in prokaryotes starts from a sequence found on the chromosome called the origin of replication the point at which the DNA opens up. Helicase opens up the DNA double helix, resulting in the formation of the replication fork. Single-strand binding proteins bind to the single-stranded DNA near the replication fork to keep the fork open. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides only in the 5' to 3' direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase, which creates phosphodiester bonds between the 3'-OH of one end and the 5' phosphate of the other strand. Review Questions 

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[link] Glossary helicase during replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds lagging strand during replication, the strand that is replicated in short fragments and away from the replication fork leading strand strand that is synthesized continuously in the 5'-3' direction which is synthesized in the direction of the replication fork ligase enzyme that catalyzes the formation of a phosphodiester linkage between the 3' OH and 5' phosphate ends of the DNA Okazaki fragment DNA fragment that is synthesized in short stretches on the lagging strand primase enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand primer short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides replication fork Y-shaped structure formed during initiation of replication single-strand binding protein during replication, protein that binds to the single-stranded DNA; this helps in keeping the two strands of DNA apart so that they may serve as templates sliding clamp ring-shaped protein that holds the DNA pol on the DNA strand topoisomerase enzyme that causes underwinding or overwinding of DNA when DNA replication is taking placeDNA Replication in Eukaryotes DNA Replication in Eukaryotes 

In this section, you will explore the following questions: What are the similarities and differences between DNA replication in eukaryotes and prokaryotes? What is the role of telomerase in DNA replication? Connection for AP Courses 

Concepts and examples described in this section are not in scope for AP. However, the roles of telomeres and telomerase in aging and cancer are informative and build on your knowledge of DNA replication in prokaryotes. 

Contrast eukaryotic DNA replication with prokaryotic replication. [link] is useful. Obtain illustrations of the process in eukaryotic cells that allow students to view the details. 

Combine these topics in a discussion of telomeres, aging, and cancer. Students might think that telomere length explains differences in life spans among different animals, such as humans and dogs. Explain that this might be a tempting conclusion, but some long-lived species, such as humans, have shorter telomeres than mice, which live only a few years. 

Eukaryotic genomes are much more complex and larger in size than prokaryotic genomes. The human genome has three billion base pairs per haploid set of chromosomes, and 6 billion base pairs are replicated during the S phase of the cell cycle. There are multiple origins of replication on the eukaryotic chromosome; humans can have up to 100,000 origins of replication. The rate of replication is approximately 100 nucleotides per second, much slower than prokaryotic replication. In yeast, which is a eukaryote, special sequences known as Autonomously Replicating Sequences (ARS) are found on the chromosomes. These are equivalent to the origin of replication in E. coli . 

The number of DNA polymerases in eukaryotes is much more than prokaryotes: 14 are known, of which five are known to have major roles during replication and have been well studied. They are known as pol , pol , pol , pol , and pol . 

The essential steps of replication are the same as in prokaryotes. Before replication can start, the DNA has to be made available as template. Eukaryotic DNA is bound to basic proteins known as histones to form structures called nucleosomes. The chromatin (the complex between DNA and proteins) may undergo some chemical modifications, so that the DNA may be able to slide off the proteins or be accessible to the enzymes of the DNA replication machinery. At the origin of replication, a pre-replication complex is made with other initiator proteins. Other proteins are then recruited to start the replication process ( [link] ). 

A helicase using the energy from ATP hydrolysis opens up the DNA helix. Replication forks are formed at each replication origin as the DNA unwinds. The opening of the double helix causes over-winding, or supercoiling, in the DNA ahead of the replication fork. These are resolved with the action of topoisomerases. Primers are formed by the enzyme primase, and using the primer, DNA pol can start synthesis. While the leading strand is continuously synthesized by the enzyme pol , the lagging strand is synthesized by pol . A sliding clamp protein known as PCNA (Proliferating Cell Nuclear Antigen) holds the DNA pol in place so that it does not slide off the DNA. RNase H removes the RNA primer, which is then replaced with DNA nucleotides. The Okazaki fragments in the lagging strand are joined together after the replacement of the RNA primers with DNA. The gaps that remain are sealed by DNA ligase, which forms the phosphodiester bond. Telomere Replication 

Unlike prokaryotic chromosomes, eukaryotic chromosomes are linear. As you ve learned, the enzyme DNA pol can add nucleotides only in the 5' to 3' direction. In the leading strand, synthesis continues until the end of the chromosome is reached. On the lagging strand, DNA is synthesized in short stretches, each of which is initiated by a separate primer. When the replication fork reaches the end of the linear chromosome, there is no place for a primer to be made for the DNA fragment to be copied at the end of the chromosome. These ends thus remain unpaired, and over time these ends may get progressively shorter as cells continue to divide. 

The ends of the linear chromosomes are known as telomeres , which have repetitive sequences that code for no particular gene. In a way, these telomeres protect the genes from getting deleted as cells continue to divide. In humans, a six base pair sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the enzyme telomerase ( [link] ) helped in the understanding of how chromosome ends are maintained. The telomerase enzyme contains a catalytic part and a built-in RNA template. It attaches to the end of the chromosome, and complementary bases to the RNA template are added on the 3' end of the DNA strand. Once the 3' end of the lagging strand template is sufficiently elongated, DNA polymerase can add the nucleotides complementary to the ends of the chromosomes. Thus, the ends of the chromosomes are replicated. The ends of linear chromosomes are maintained by the action of the telomerase enzyme. 

Telomerase is typically active in germ cells and adult stem cells. It is not active in adult somatic cells. For her discovery of telomerase and its action, Elizabeth Blackburn ( [link] ) received the Nobel Prize for Medicine and Physiology in 2009. Elizabeth Blackburn, 2009 Nobel Laureate, is the scientist who discovered how telomerase works. (credit: US Embassy Sweden) Telomerase and Aging 

Cells that undergo cell division continue to have their telomeres shortened because most somatic cells do not make telomerase. This essentially means that telomere shortening is associated with aging. With the advent of modern medicine, preventative health care, and healthier lifestyles, the human life span has increased, and there is an increasing demand for people to look younger and have a better quality of life as they grow older. 

In 2010, scientists found that telomerase can reverse some age-related conditions in mice. This may have potential in regenerative medicine. 1 Telomerase-deficient mice were used in these studies; these mice have tissue atrophy, stem cell depletion, organ system failure, and impaired tissue injury responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed neurodegeneration, and improved the function of the testes, spleen, and intestines. Thus, telomere reactivation may have potential for treating age-related diseases in humans. 

Cancer is characterized by uncontrolled cell division of abnormal cells. The cells accumulate mutations, proliferate uncontrollably, and can migrate to different parts of the body through a process called metastasis. Scientists have observed that cancerous cells have considerably shortened telomeres and that telomerase is active in these cells. Interestingly, only after the telomeres were shortened in the cancer cells did the telomerase become active. If the action of telomerase in these cells can be inhibited by drugs during cancer therapy, then the cancerous cells could potentially be stopped from further division. Difference between Prokaryotic and Eukaryotic Replication Property Prokaryotes Eukaryotes Origin of replication Single Multiple Rate of replication 1000 nucleotides/s 50 to 100 nucleotides/s DNA polymerase types 5 14 Telomerase Not present Present RNA primer removal DNA pol I RNase H Strand elongation DNA pol III Pol , pol Sliding clamp Sliding clamp PCNA Section Summary 

Replication in eukaryotes starts at multiple origins of replication. The mechanism is quite similar to prokaryotes. A primer is required to initiate synthesis, which is then extended by DNA polymerase as it adds nucleotides one by one to the growing chain. The leading strand is synthesized continuously, whereas the lagging strand is synthesized in short stretches called Okazaki fragments. The RNA primers are replaced with DNA nucleotides; the DNA remains one continuous strand by linking the DNA fragments with DNA ligase. The ends of the chromosomes pose a problem as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected. Review Questions 

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[link] Footnotes 1 Jaskelioff et al., Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice, Nature 469 (2011): 102-7. Glossary telomerase enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends telomere DNA at the end of linear chromosomesDNA Repair DNA Repair 

In this section, you will explore the following questions: What are different types of mutations in DNA and the significance of mutations? What are examples of mechanisms that repair mutations in DNA? Connection for AP Courses 

DNA polymerase is an efficient enzyme but it can make mistakes while adding nucleotides during replication. It edits the DNA by proofreading every newly added base. An incorrect base is removed and replaced by the correct base. If a base remains mismatched, special repair enzymes can often recognize the wrongly incorporated base, excise it from the DNA, and replace it with the correct base. Most mistakes are corrected, but if they are not they may result in a mutation, which is defined as a permanent change in a DNA sequence. A mutation can be passed to daughter cells through DNA replication and cell division. There are several types of DNA mutations, including substitution, deletion, insertion, and translocation. Mutations in repair genes may lead to serious consequences, such as cancer. Mutations can be induced by environmental factors, such as UV radiation, or they can occur spontaneously. (We will explore the effects of mutation in more detail in a later chapter. Remember that mutations are not always detrimental. They can be beneficial, too. Changes in DNA increase genetic variation the foundation of evolution by natural selection.) 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.C.1 Changes in genotype can result in changes in phenotype. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 3.24 The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection. Essential Knowledge 3.C.1 Changes in genotype can result in changes in phenotype. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.25 The student can create a visual representation to illustrate how changes in a DNA nucleotide sequence can result in a change in the polypeptide produced. Essential Knowledge 3.C.2 Biological systems have multiple processes that increase genetic variation. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 3.28 The student is able to construct an explanation of the multiple processes that increase variation within a population. 

Emphasize that mistakes in replication occur on a regular basis and that most are repaired or are not significant. Use Images to illustrate the effects of different types of mutations. 

Have the class research specific mutations that cause different diseases. Ask the questions: Where are the mutations? How often do they occur? Why are these mistakes not corrected? Can they be corrected through gene therapy? 

Ask the class if it is possible that a silent mutation might be a benefit to the individual or species at a later time. 

DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare cases, mistakes are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or defective. 

Most of the mistakes during DNA replication are promptly corrected by DNA polymerase by proofreading the base that has been just added ( [link] ). In proofreading , the DNA pol reads the newly added base before adding the next one, so a correction can be made. The polymerase checks whether the newly added base has paired correctly with the base in the template strand. If it is the right base, the next nucleotide is added. If an incorrect base has been added, the enzyme makes a cut at the phosphodiester bond and releases the wrong nucleotide. This is performed by the exonuclease action of DNA pol III. Once the incorrect nucleotide has been removed, a new one will be added again. Proofreading by DNA polymerase corrects errors during replication. 

Some errors are not corrected during replication, but are instead corrected after replication is completed; this type of repair is known as mismatch repair ( [link] ). The enzymes recognize the incorrectly added nucleotide and excise it; this is then replaced by the correct base. If this remains uncorrected, it may lead to more permanent damage. How do mismatch repair enzymes recognize which of the two bases is the incorrect one? In E. coli , after replication, the nitrogenous base adenine acquires a methyl group; the parental DNA strand will have methyl groups, whereas the newly synthesized strand lacks them. Thus, DNA polymerase is able to remove the wrongly incorporated bases from the newly synthesized, non-methylated strand. In eukaryotes, the mechanism is not very well understood, but it is believed to involve recognition of unsealed nicks in the new strand, as well as a short-term continuing association of some of the replication proteins with the new daughter strand after replication has completed. In mismatch repair, the incorrectly added base is detected after replication. The mismatch repair proteins detect this base and remove it from the newly synthesized strand by nuclease action. The gap is now filled with the correctly paired base. 

In another type of repair mechanism, nucleotide excision repair , enzymes replace incorrect bases by making a cut on both the 3' and 5' ends of the incorrect base ( [link] ). The segment of DNA is removed and replaced with the correctly paired nucleotides by the action of DNA pol. Once the bases are filled in, the remaining gap is sealed with a phosphodiester linkage catalyzed by DNA ligase. This repair mechanism is often employed when UV exposure causes the formation of pyrimidine dimers. Nucleotide excision repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced. 

A well-studied example of mistakes not being corrected is seen in people suffering from xeroderma pigmentosa ( [link] ). Affected individuals have skin that is highly sensitive to UV rays from the sun. When individuals are exposed to UV, pyrimidine dimers, especially those of thymine, are formed; people with xeroderma pigmentosa are not able to repair the damage. These are not repaired because of a defect in the nucleotide excision repair enzymes, whereas in normal individuals, the thymine dimers are excised and the defect is corrected. The thymine dimers distort the structure of the DNA double helix, and this may cause problems during DNA replication. People with xeroderma pigmentosa may have a higher risk of contracting skin cancer than those who dont have the condition. Xeroderma pigmentosa is a condition in which thymine dimerization from exposure to UV is not repaired. Exposure to sunlight results in skin lesions. (credit: James Halpern et al.) 

Errors during DNA replication are not the only reason why mutations arise in DNA. Mutations , variations in the nucleotide sequence of a genome, can also occur because of damage to DNA. Such mutations may be of two types: induced or spontaneous. Induced mutations are those that result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent. Spontaneous mutations occur without any exposure to any environmental agent; they are a result of natural reactions taking place within the body. 

Mutations may have a wide range of effects. Some mutations are not expressed; these are known as silent mutations . Point mutations are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. These can be of two types, either transitions or transversions. Transition substitution refers to a purine or pyrimidine being replaced by a base of the same kind; for example, a purine such as adenine may be replaced by the purine guanine. Transversion substitution refers to a purine being replaced by a pyrimidine, or vice versa; for example, cytosine, a pyrimidine, is replaced by adenine, a purine. Mutations can also be the result of the addition of a base, known as an insertion, or the removal of a base, also known as deletion. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome; this is also known as translocation. These mutation types are shown in [link] . 

Sometimes a nucleotide is overlooked by the DNA repair system for no known reason. This malignant melanoma is the result of DNA not undergoing repair after too much UV exposure. 

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Mutations can lead to changes in the protein sequence encoded by the DNA. 

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Mutations in repair genes have been known to cause cancer. Many mutated repair genes have been implicated in certain forms of pancreatic cancer, colon cancer, and colorectal cancer. Mutations can affect either somatic cells or germ cells. If many mutations accumulate in a somatic cell, they may lead to problems such as the uncontrolled cell division observed in cancer. If a mutation takes place in germ cells, the mutation will be passed on to the next generation, as in the case of hemophilia and xeroderma pigmentosa. Think About It 

Infertility can sometimes be explained by chromosome translocations. Explain how chromosome translocations can cause infertility. Are there times when a chromosome translocation might not result in infertility? 

The Think About It question is an application of Learning Objective 3.28 and Science Practice 6.2 because students are asked to explain a phenomenon that increases genetic variation. Answer If a chromosome translocation occurs in a germ cell it could affect the function of genes required for the formation of reproductive cells. If severe enough, the mutation could give rise to infertility. A translocation in a germ cell that does not affect genes required for sex cell formation would likely not affect fertility. Neither would a translocation that occurs in a somatic cell. Section Summary 

DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then a new base is added. Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base. In yet another type of repair, nucleotide excision repair, the incorrect base is removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of DNA polymerase. The ends of the newly synthesized fragment are attached to the rest of the DNA using DNA ligase, which creates a phosphodiester bond. 

Most mistakes are corrected, and if they are not, they may result in a mutation defined as a permanent change in the DNA sequence. Mutations can be of many types, such as substitution, deletion, insertion, and translocation. Mutations in repair genes may lead to serious consequences such as cancer. Mutations can be induced or may occur spontaneously. Review Questions 

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[link] Glossary induced mutation mutation that results from exposure to chemicals or environmental agents mutation variation in the nucleotide sequence of a genome mismatch repair type of repair mechanism in which mismatched bases are removed after replication nucleotide excision repair type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed proofreading function of DNA pol in which it reads the newly added base before adding the next one point mutation mutation that affects a single base silent mutation mutation that is not expressed spontaneous mutation mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent transition substitution when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine transversion substitution when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purineIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Genes, which are carried on (a) chromosomes, are linearly organized instructions for making the RNA and protein molecules that are necessary for all of processes of life. The (b) interleukin-2 protein and (c) alpha-2u-globulin protein are just two examples of the array of different molecular structures that are encoded by genes. (credit chromosome: National Human Genome Research Institute; credit interleukin-2 : Ramin Herati/Created from PDB 1M47 and rendered with Pymol; credit alpha-2u-globulin : Darren Logan/rendered with AISMIG) 

The definition of gene has progressed from being an abstract unit of heredity in Mendel s time to our current concept of a tangible molecular entity capable of replication, expression, and mutation ( [link] ). Currently, we can perform tests for many genetic diseases, but these tests create ethical and legal issues. For example, would you want to be tested for a debilitating genetic disease if there was the possibility insurance companies could use that information to deny you coverage? Fortunately, the Genetic Information Nondiscrimination Act of 2008 protects American citizens from discrimination from both insurance companies and employers based on genetic information. More information about policy, legal, and ethical issues in genetic research can be found here . 

Introduce students to the Human Genome Project. The project was started in the late 80 s when sequencing was both costly and time consuming. The entire sequence of the human genome was announced in 2003. By then, both the expense and time required for sequencing had dropped considerably. The information can easily be stored and disseminated. As can be expected, with the advent of new technology come moral questions that society must ask. 

Ask students if they would like their genomes to be sequenced. What would they gain by such knowledge? Have them consider who would versus who should have access to that information. Have students balance the benefits of being aware of a predisposition to a certain condition to the risk of having employment or health insurance denied. For some diseases, it is possible with the information on hand to modify one s lifestyle and increase screening for early detection of the condition. What happens if there are no cures, as is the case for Huntington s disease? This is the context of the Genetic Information Nondiscrimination Act. To learn more about it, read this summary .The Genetic Code The Genetic Code 

In this section, you will explore the following questions: What is the Central Dogma of protein synthesis? What is the genetic code, and how does nucleotide sequence prescribe the amino acid and polypeptide sequence? Connection for AP Courses 

Since the rediscovery of Mendel s work in the 1900s, scientists have learned much about how the genetic blueprints stored in DNA are capable of replication, expression, and mutation. Just as the 26 letters of the English alphabet can be arranged into what seems to be a limitless number of words, with new ones added to the dictionary every year, the four nucleotides of DNA A, T, C, and G can generate sequences of DNA called genes that specify tens of thousands of polymers of amino acids. In turn, these sequences can be transcribed into mRNA and translated into proteins which orchestrate nearly every function of the cell. The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). But how do genes located on a chromosome ultimately produce a polypeptide that can result in a physical phenotype such as hair or eye color or a disease like cystic fibrosis or hemophilia? 

The Central Dogma describes the normal flow of genetic information from DNA to mRNA to protein: DNA in genes specify sequences of mRNA which, in turn, specify amino acid sequences in proteins. The process requires two steps, transcription and translation. During transcription, genes are used to make messenger RNA (mRNA). In turn, the mRNA is used to direct the synthesis of proteins during the process of translation. Translation also requires two other types of RNA: transfer RNA (tRNA) and ribosomal RNA (rRNA). The genetic code is a triplet code, with each RNA codon consisting of three consecutive nucleotides that specify one amino acid or the release of the newly formed polypeptide chain; for example, the mRNA codon CAU specifies the amino acid histidine. The code is degenerate; that is, some amino acids are specified by more than one codon, like synonyms you study in your English class (different word, same meaning). For example, CCU, CCC, CCA, and CCG are all codons for proline. It is important to remember the same genetic code is universal to almost all organisms on Earth. Small variations in codon assignment exist in mitochondria and some microorganisms. 

Deviations from the simple scheme of the central dogma are discovered as researchers explore gene expression with new technology. For example the human immunodeficiency virus (HIV) is a retrovirus which stores its genetic information in single stranded RNA molecules. Upon infection of a host cell, RNA is used as a template by the virally encoded enzyme, reverse transcriptase, to synthesize DNA. The viral DNA is later transcribed into mRNA and translated into proteins. Some RNA viruses such as the influenza virus never go through a DNA step. The RNA genome is replicated by an RNA dependent RNA polymerase which is virally encoded. 

The content presented in this section supports the Learning Objectives outlined in Big Idea 1 and Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives merge Essential Knowledge content with one or more of the seven Science Practices. These Learning Objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP Exam questions. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 3.1 The student can pose scientific questions. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Hereditable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structure and functions of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information. 

The Central Dogma has been validated by many experiments. The flow of information from DNA to mRNA to polypeptide is the common scheme in all cells, both prokaryotic and eukaryotic. The information in DNA is contained in the sequence of nitrogenous bases. Next question is, How is the sequence of the nitrogenous bases translated into amino acids? A combination of two out of the four letters gives 16 possible amino acids (4 2 = 16); for example, AA, or AC; but, there 20 amino acids. A combination of three bases gives 64 possible sets (4 3 = 64); for example, AAA or AAC. A combination of three bases in a row is a codon or triplets. This gives rise to more than enough combinations for the 20 common acids. Some amino acids are specified by a single codon, for example, methionine and tryptophan; others are encoded by up to six independent codons, for example, leucine. 

Although protein synthesis follows the same general scheme in prokaryotes and eukaryotes, the detailed mechanism of each can be quite different. The presence of the nuclear membrane adds a layer of complexity to the process. In prokaryotes, transcription and translation are tightly coupled. As soon as the 5'-end of a mRNA has been transcribed from the template strand of DNA, ribosomes can latch onto it and polypeptide synthesis begins. Eukaryotic cells use a more complex series of steps. The enzyme RNA polymerase forms the transcription initiation complex with many proteins called transcription factors. The product of transcription, mRNA undergoes several modifications that change its stability and facilitate export from the nucleus. These extra steps allow greater control over gene expression. Although prokaryotic mRNA is not generally modified, eukaryotic mRNA strands undergo the addition of a methyl-guanosine cap at the 5'-end and a poly-adenosine tail at the 3'- end, without which they may not exit the nucleus. The mRNA also undergoes splicing to remove introns , the non protein coding regions of the gene. Protein translation depends on the presence of ribosomes, mRNA, a full complement of tRNA molecules, many enzymes, and many protein factors. As the polypeptide is synthesized, it starts folding into its three-dimensional structure. Further modifications will ensure that the protein is fully functional and shipped to its destination. 

Ask the students what a dogma is. It will serve as an introduction to deviations from the Central Dogma. Viruses show numerous variations. The Human Immunodeficiency Virus (HIV) is a retrovirus. Its genome is encoded in RNA molecules which serve as a template for the synthesis of DNA by a virally encoded enzyme called reverse transcriptase. Point out that this enzyme, which is not found in humans, is the target of many anti-HIV medications. The flu virus carries non-coding strands of RNA molecules which are replicated in the host cell by a RNA-dependent RNA polymerase, an enzyme encoded in the viral genome. In the case of the flu virus, there is no DNA stage at all. The flow of information is RNA to RNA to proteins. Closer to home, the telomeres, the ends of the linear chromosomes in eukaryotes, are replicated by a special enzyme, a telomerase, which synthesizes DNA from an RNA template. 

Just as we transfer information using letters and numbers, the cell transfers information using molecules. Emphasize the similarities between writing and the genetic code. Tell the students that much of the vocabulary of molecular genetics is borrowed from editing: transcription, translation, proofreading, missense, nonsense, etc. 

Although the chapter does not use the term open reading frame, tie it to [link] . An open reading frame is a DNA sequence that follows a start codon and ends with a stop codon. A long open reading frame is likely to be a gene. 

Students confuse the vocabulary used to describe the Central Dogma. Copying information from DNA to RNA is transcription because the language is the same. Both are constructed using nucleotides. When a polypeptide is synthesized, the building blocks or letters have switched to amino acids. It is a translation. Although not quite identical, show students an example similar to the following: 

Dog to Dog (transcription) to Canis (translation) 

The first two words represent transcription. The letters are just copied. The last word has the same meaning, dog in Latin, but now the language is different. 

Consider using the word redundant to help explain the meaning of the word degenerate in this context. Students confuse the fact that the code is degenerate several codons can encode the same amino acid with the fact that the genetic code is universal, which means that the same codon, AUG as an example, is translated as methionine in all cells. The confusion arises from students learning the two concepts at the same time. Give examples of changes in the codons which result in the same amino acids. Although the gene sequence is different, the polypeptide is the same. Remind students that each codon specifies one amino acid, but the reverse is not true. Depending on the amino acid, more than one codon will translate to the same amino acid. 

Explain that many proteins of interest are synthesized in bacteria and yeast by inserting the genes for the proteins in the host expression systems. This is possible because the code is universal. If a gene coding for human insulin is inserted in the chromosomes of E. coli , the bacteria will synthesize human insulin. 

Give students examples of codons and ask them to find the matching amino acid. Bring to their attention that typographical errors are a great source of mutations. They should proofread their sequences carefully. 

The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters ( [link] ). Each amino acid is defined by a three-nucleotide sequence called the triplet codon. Different amino acids have different chemistries (such as acidic versus basic, or polar and nonpolar) and different structural constraints. Variation in amino acid sequence gives rise to enormous variation in protein structure and function. Structures of the 20 amino acids found in proteins are shown. Each amino acid is composed of an amino group ( N H 3 + N H 3 + ), a carboxyl group (COO - ), and a side chain (blue). The side chain may be nonpolar, polar, or charged, as well as large or small. It is the variety of amino acid side chains that gives rise to the incredible variation of protein structure and function. The Central Dogma: DNA Encodes RNA; RNA Encodes Protein 

The flow of genetic information in cells from DNA to mRNA to protein is described by the Central Dogma ( [link] ), which states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis, while keeping the DNA itself intact and protected. The copying of DNA to RNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every nucleotide read in the DNA strand. The translation to protein is a bit more complex because three mRNA nucleotides correspond to one amino acid in the polypeptide sequence. However, the translation to protein is still systematic and colinear , such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on. Instructions on DNA are transcribed onto messenger RNA. Ribosomes are able to read the genetic information inscribed on a strand of messenger RNA and use this information to string amino acids together into a protein. The Genetic Code Is Degenerate and Universal 

Given the different numbers of letters in the mRNA and protein alphabets, scientists theorized that combinations of nucleotides corresponded to single amino acids. Nucleotide doublets would not be sufficient to specify every amino acid because there are only 16 possible two-nucleotide combinations (4 2 ). In contrast, there are 64 possible nucleotide triplets (4 3 ), which is far more than the number of amino acids. Scientists theorized that amino acids were encoded by nucleotide triplets and that the genetic code was degenerate . In other words, a given amino acid could be encoded by more than one nucleotide triplet. This was later confirmed experimentally; Francis Crick and Sydney Brenner used the chemical mutagen proflavin to insert one, two, or three nucleotides into the gene of a virus. When one or two nucleotides were inserted, protein synthesis was completely abolished. When three nucleotides were inserted, the protein was synthesized and functional. This demonstrated that three nucleotides specify each amino acid. These nucleotide triplets are called codons . The insertion of one or two nucleotides completely changed the triplet reading frame , thereby altering the message for every subsequent amino acid ( [link] ). Though insertion of three nucleotides caused an extra amino acid to be inserted during translation, the integrity of the rest of the protein was maintained. The deletion of two nucleotides shifts the reading frame of an mRNA and changes the entire protein message, creating a nonfunctional protein or terminating protein synthesis altogether. 

Scientists painstakingly solved the genetic code by translating synthetic mRNAs in vitro and sequencing the proteins they specified ( [link] ). This figure shows the genetic code for translating each nucleotide triplet in mRNA into an amino acid or a termination signal in a nascent protein. (credit: modification of work by NIH) 

In addition to instructing the addition of a specific amino acid to a polypeptide chain, three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are called nonsense codons , or stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5' end of the mRNA. 

The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis. Conservation of codons means that a purified mRNA encoding the globin protein in horses could be transferred to a tulip cell, and the tulip would synthesize horse globin. That there is only one genetic code is powerful evidence that all of life on Earth shares a common origin, especially considering that there are about 10 84 possible combinations of 20 amino acids and 64 triplet codons. 

Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this site . 

[link] Think About It 

A strand of DNA has the nucleotide sequence 3' GCT GTC AAA TTC GAT 5'. What is the sequence of mRNA that is complementary to this DNA sequence? Using the chart of codons in the text, determine the sequence of amino acids which can be generated from this strand of DNA. How does degeneracy of the genetic code make cells less vulnerable to mutations? What is an advantage of degeneracy with respect to the negative impact of random mutations on natural selection and evolution? 

The first question is an application of Learning Objective 3.1 and Science Practice 6.5 because students are explaining how the language of DNA can be transcribed and translated into a sequence of amino acids . 

The second set of questions are an application of Learning Objective 1.15 and Science Practice 3.1 because students are asked to raise questions about the universal genetic code and the impact of its degeneracy on mutations. Answer 3' GCT GTC AAA TTC GAT 5' mRNA 5' CGA CAG UUU AAG CUA 3' ; peptide Arg Gln Phe Lys Leu 

Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations. Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid but have no effect or specify a similar amino acid, preventing the protein from being rendered completely nonfunctional. 

Which Has More DNA: A Kiwi or a Strawberry? Do you think that a kiwi or a strawberry has more DNA per fruit? (credit kiwi : "Kelbv"/Flickr; credit: strawberry : Alisdair McDiarmid) 

Question : Would a kiwifruit and strawberry that are approximately the same size ( [link] ) also have approximately the same amount of DNA? 

Background : Genes are carried on chromosomes and are made of DNA. All mammals are diploid, meaning they have two copies of each chromosome. However, not all plants are diploid. The common strawberry is octoploid (8 n ) and the cultivated kiwi is hexaploid (6 n ). Research the total number of chromosomes in the cells of each of these fruits and think about how this might correspond to the amount of DNA in these fruits cell nuclei. Read about the technique of DNA isolation to understand how each step in the isolation protocol helps liberate and precipitate DNA. 

Hypothesis : Hypothesize whether you would be able to detect a difference in DNA quantity from similarly sized strawberries and kiwis. Which fruit do you think would yield more DNA? 

Test your hypothesis : Isolate the DNA from a strawberry and a kiwi that are similarly sized. Perform the experiment in at least triplicate for each fruit. Prepare a bottle of DNA extraction buffer from 900 mL water, 50 mL dish detergent, and two teaspoons of table salt. Mix by inversion (cap it and turn it upside down a few times). Grind a strawberry and a kiwifruit by hand in a plastic bag, or using a mortar and pestle, or with a metal bowl and the end of a blunt instrument. Grind for at least two minutes per fruit. Add 10 mL of the DNA extraction buffer to each fruit, and mix well for at least one minute. Remove cellular debris by filtering each fruit mixture through cheesecloth or porous cloth and into a funnel placed in a test tube or an appropriate container. Pour ice-cold ethanol or isopropanol (rubbing alcohol) into the test tube. You should observe white, precipitated DNA. Gather the DNA from each fruit by winding it around separate glass rods. 

Record your observations : Because you are not quantitatively measuring DNA volume, you can record for each trial whether the two fruits produced the same or different amounts of DNA as observed by eye. If one or the other fruit produced noticeably more DNA, record this as well. Determine whether your observations are consistent with several pieces of each fruit. 

Analyze your data : Did you notice an obvious difference in the amount of DNA produced by each fruit? Were your results reproducible? 

Draw a conclusion : Given what you know about the number of chromosomes in each fruit, can you conclude that chromosome number necessarily correlates to DNA amount? Can you identify any drawbacks to this procedure? If you had access to a laboratory, how could you standardize your comparison and make it more quantitative? Section Summary 

The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Almost every species on the planet uses the same genetic code. Review Questions 

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[link] Glossary Central Dogma states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins codon three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation colinear in terms of RNA and protein, three units of RNA (nucleotides) specify one unit of protein (amino acid) in a consecutive fashion degeneracy (of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous nonsense codon one of the three mRNA codons that specifies termination of translation reading frame sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that proteinProkaryotic Transcription Prokaryotic Transcription 

In this section, you will explore the following questions: What are the steps, in order, in prokaryotic transcription? How and when is transcription terminated? Connection for AP Courses 

During transcription, the enzyme RNA polymerase moves along the DNA template, reading nucleotides in a 3 to 5 direction, with U pairing with A and C with G, and assembling the mRNA transcript in a 5 to 3 direction. In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template. Transcription continues until RNA polymerase reaches a stop or terminator sequence at the end of the gene. Termination frees the mRNA and often occurs by the formation of an mRNA hairpin. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information. 

Ask students to draw a timeline of the steps needed for transcription and add all the different components as specific shapes. Use different colors to label the promoter and the terminator sequences. 

Review the complementarity of nitrogenous bases and the stability of base pairing as a function of number of hydrogen bonds. The couple AT/AU is much less stable than CG; therefore promoter sequences will be rich in AT because it takes less energy to unzip DNA. 

Ask the students, How do you recognize the beginning of a sentence? They may answer that they see a period. Answer that some abbreviations are followed by a period. So the period is not enough. Upper case is not enough either. It is the combination of period followed by a space and an upper case which indicates the beginning of a sentence. In the same way consensus sequences, which indicate a promoter region where an RNA polymerase binds, contain several elements that are required for recognition. 

Use a diagram to illustrate rho-independent termination. The following drawing may clarify the text in the chapter. 

There can be more than one consensus sequence in a genome as there are several sigma factors that recognize different sequences. Clarify, if necessary, the role of the sigma factor and rho proteins. Students confuse transcription, termination, and stop codons. 

Ask students to diagram a generic gene and label the following regions in the correct sequence in the 5'-3' direction. The regions are given in the correct order here. Change the order when giving the exercise to the class: 

Sigma binding consensus sequence/TATA box 

Shine Dalgarno sequence (binding to ribosome) 

ATG (start codon for protein transcription) 

STOP codon (polypeptide termination) 

Terminator region 

Students have difficulty visualizing polycistronic messages. Explain that as long as there are stop codons in the message, the polypeptides will be released and ribosomes reattached at the following Shine-Dalgarno sequence. If one were to write out the structure of a polycistronic mRNA, it would be Shine-Dalgarno-AUG-------STOP---Shine-Dalgarno AUG-------STOP---Shine-Dalgarno AUG---STOP. 

The prokaryotes, which include bacteria and archaea, are mostly single-celled organisms that, by definition, lack membrane-bound nuclei and other organelles. A bacterial chromosome is a covalently closed circle that, unlike eukaryotic chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is called the nucleoid. In addition, prokaryotes often have abundant plasmids , which are shorter circular DNA molecules that may only contain one or a few genes. Plasmids can be transferred independently of the bacterial chromosome during cell division and often carry traits such as antibiotic resistance. 

Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a transcription bubble. Transcription always proceeds from the same DNA strand for each gene, which is called the template strand . The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand . The only difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides. In an RNA double helix, A can bind U via two hydrogen bonds, just as in A T pairing in a DNA double helix. 

The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the initiation site . Nucleotides preceding the initiation site are given negative numbers and are designated upstream . Conversely, nucleotides following the initiation site are denoted with + numbering and are called downstream nucleotides. Initiation of Transcription in Prokaryotes 

Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often covers more than one gene and produces polycistronic mRNAs that specify more than one protein. 

Our discussion here will exemplify transcription by describing this process in Escherichia coli , a well-studied bacterial species. Although some differences exist between transcription in E. coli and transcription in archaea, an understanding of E. coli transcription can be applied to virtually all bacterial species. Prokaryotic RNA Polymerase 

Prokaryotes use the same RNA polymerase to transcribe all of their genes. In E. coli , the polymerase is composed of five polypeptide subunits, two of which are identical. Four of these subunits, denoted , , , and ' comprise the polymerase core enzyme . These subunits assemble every time a gene is transcribed, and they disassemble once transcription is complete. Each subunit has a unique role; the two -subunits are necessary to assemble the polymerase on the DNA; the -subunit binds to the ribonucleoside triphosphate that will become part of the nascent recently born mRNA molecule; and the ' binds the DNA template strand. The fifth subunit, , is involved only in transcription initiation. It confers transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site. Without , the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein gibberish. The polymerase comprised of all five subunits is called the holoenzyme . Prokaryotic Promoters 

A promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although promoters vary among prokaryotic genomes, a few elements are conserved. At the -10 and -35 regions upstream of the initiation site, there are two promoter consensus sequences, or regions that are similar across all promoters and across various bacterial species ( [link] ). The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence, TTGACA, is recognized and bound by . Once this interaction is made, the subunits of the core enzyme bind to the site. The A T-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made. The transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10 nucleotides that are made and released. The subunit of prokaryotic RNA polymerase recognizes consensus sequences found in the promoter region upstream of the transcription start sight. The subunit dissociates from the polymerase after transcription has been initiated. 

View this MolecularMovies animation to see the first part of transcription and the base sequence repetition of the TATA box. 

[link] Elongation and Termination in Prokaryotes 

The transcription elongation phase begins with the release of the subunit from the polymerase. The dissociation of allows the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it ( [link] ). The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely. During elongation, the prokaryotic RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5' to 3' direction, and unwinds and rewinds the DNA as it is read. Prokaryotic Termination Signals 

Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble. 

Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C G nucleotides. The mRNA folds back on itself, and the complementary C G nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall as soon as it begins to transcribe a region rich in A T nucleotides. The complementary U A region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript. 

Upon termination, the process of transcription is complete. By the time termination occurs, the prokaryotic transcript would already have been used to begin synthesis of numerous copies of the encoded protein because these processes can occur concurrently. The unification of transcription, translation, and even mRNA degradation is possible because all of these processes occur in the same 5' to 3' direction, and because there is no membranous compartmentalization in the prokaryotic cell ( [link] ). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation. Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration in the bacterial cell. 

Visit this BioStudio animation to see the process of prokaryotic transcription. 

[link] Activity 

Working in small groups, use a model of DNA to demonstrate synthesis transcription of mRNA to other groups in your class. In your demonstration, be sure to distinguish the differences between DNA and RNA, the template and non-template strands of the DNA, the directionality of transcription, and the significance of promoters. Think About It 

If mRNA is complementary to the DNA template strand, and the DNA template strand is complementary to the DNA non-template strand, are the base sequences of mRNA and the DNA non-template strand ever identical? Justify your answer. 

The activity is an application of Learning Objective 3.1 and Science Practice 6.5 because students are using a model to explain the process of transcription and how both DNA and RNA are carriers of heritable information. This activity also is an application of Learning Objective 3.21 and Science Practice 1.4 because they are using the model to describe the role of promoters in the regulation of transcription. 

The Think About It question is an application of Learning Objective 3.1 and Science Practice 6.5 because students are using a model to explain the process of transcription as well as how both DNA and RNA are carriers of heritable information. Answer DNA is different from RNA in that T nucleotides in DNA are replaced with U nucleotides in RNA. Therefore, they could never be identical in base sequence. A gene would not lack T residues as the initiation codon is AUG for methionine. Section Summary 

In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and a protein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin. Review Questions 

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[link] Glossary consensus DNA sequence that is used by many species to perform the same or similar functions core enzyme prokaryotic RNA polymerase consisting of , , , and ' but missing ; this complex performs elongation downstream nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3' end relative to a site on the mRNA hairpin structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides holoenzyme prokaryotic RNA polymerase consisting of , , , ', and ; this complex is responsible for transcription initiation initiation site nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a +1 nontemplate strand strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA plasmid extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes promoter DNA sequence to which RNA polymerase and associated factors bind and initiate transcription Rho-dependent termination in prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template Rho-independent termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase TATA box conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription template strand strand of DNA that specifies the complementary mRNA molecule transcription bubble region of locally unwound DNA that allows for transcription of mRNA upstream nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNAEukaryotic Transcription Eukaryotic Transcription 

In this section, you will explore the following questions: What are the steps in eukaryotic transcription? What are the structural and functional similarities and differences among the three RNA polymerases? Connection for AP Courses 

As expected, transcription in eukaryotes is more complex than transcription in prokaryotes. First, transcription in eukaryotes involves one of three types of RNA polymerase, depending on the gene being transcribed. Second, the initiation of transcription involves the binding of several transcription factors to complex promoters which are usually located upstream of the gene being copied. Transcription factors can either activate or inhibit gene expression. Termination of transcription involves the RNA polymerases. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information. 

Ask students if they expect transcription to be different in eukaryotes. Ask students to explain their answers. Review the major difference between prokaryotes and eukaryotes, the presence of the nucleus. 

Explain that the process follows the same general order, but there are major differences. The initiation of transcription in eukaryotes is more complicated. Polycistronic mRNAs exist in eukaryotes although they are very rare. Remind students, if applicable, that they have encountered nuclear transcription factors when you studied cell signaling. Point out the useful role of -amanitin in differentiating between RNA polymerases. Remind students that the final product of a gene can be an RNA molecule, for example an rRNA molecule, or a polypeptide. 

Ask students to prepare a timeline of transcription in eukaryotes and compare it to their timeline of transcription in prokaryotes. Teach students a simple way to remember which are the intr ons ( in the tr ash) and which are the ex ons ( ex pressed). 

RNA polymerases in prokaryotes and eukaryotes have the same general functions; however, they are different enzymes. The numbering of RNA polymerases in eukaryotes does not reflect the order of activity. Pol II is the best studied polymerase, most likely because it transcribes mRNA. 

Ribosome assembly takes place in the nucleolus which means that the ribosomal proteins are synthesized in the cytoplasm and re-enter the nucleus. 

Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most important difference between prokaryotes and eukaryotes is the latter s membrane-bound nucleus and organelles. With the genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its mRNA from degrading before it is translated. Eukaryotes also employ three different polymerases that each transcribe a different subset of genes. Eukaryotic mRNAs are usually monogenic, meaning that they specify a single protein. Initiation of Transcription in Eukaryotes 

Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase. The Three Eukaryotic RNA Polymerases 

The features of eukaryotic mRNA synthesis are markedly more complex those of prokaryotes. Instead of a single polymerase comprising five subunits, the eukaryotes have three polymerases that are each made up of 10 subunits or more. Each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template. 

RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes ( [link] ). The rRNA molecules are considered structural RNAs because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are essential to the process of translation. RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule. The S designation applies to Svedberg units, a nonadditive value that characterizes the speed at which a particle sediments during centrifugation. Locations, Products, and Sensitivities of the Three Eukaryotic RNA Polymerases RNA Polymerase Cellular Compartment Product of Transcription -Amanitin Sensitivity I Nucleolus All rRNAs except 5S rRNA Insensitive II Nucleus All protein-coding nuclear pre-mRNAs Extremely sensitive III Nucleus 5S rRNA, tRNAs, and small nuclear RNAs Moderately sensitive 

RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-mRNAs undergo extensive processing after transcription but before translation. For clarity, this module s discussion of transcription and translation in eukaryotes will use the term mRNAs to describe only the mature, processed molecules that are ready to be translated. RNA polymerase II is responsible for transcribing the overwhelming majority of eukaryotic genes. 

RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre- RNAs . The tRNAs have a critical role in translation; they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs have a variety of functions, including splicing pre-mRNAs and regulating transcription factors. 

A scientist characterizing a new gene can determine which polymerase transcribes it by testing whether the gene is expressed in the presence of a particular mushroom poison, -amanitin ( [link] ). Interestingly, -amanitin produced by Amanita phalloides , the Death Cap mushroom, affects the three polymerases very differently. RNA polymerase I is completely insensitive to -amanitin, meaning that the polymerase can transcribe DNA in vitro in the presence of this poison. In contrast, RNA polymerase II is extremely sensitive to -amanitin, and RNA polymerase III is moderately sensitive. Knowing the transcribing polymerase can clue a researcher into the general function of the gene being studied. Because RNA polymerase II transcribes the vast majority of genes, we will focus on this polymerase in our subsequent discussions about eukaryotic transcription factors and promoters. Structure of an RNA Polymerase II Promoter 

Eukaryotic promoters are much larger and more complex than prokaryotic promoters, but both have a TATA box. For example, in the mouse thymidine kinase gene, the TATA box is located at approximately -30 relative to the initiation (+1) site ( [link] ). For this gene, the exact TATA box sequence is TATAAAA, as read in the 5' to 3' direction on the nontemplate strand. This sequence is not identical to the E. coli TATA box, but it conserves the A T rich element. The thermostability of A T bonds is low and this helps the DNA template to locally unwind in preparation for transcription. A generalized promoter of a gene transcribed by RNA polymerase II is shown. Transcription factors recognize the promoter. RNA polymerase II then binds and forms the transcription initiation complex. 

Eukaryotic mRNA contains introns that must be spliced out. A 5' cap and 3' poly-A tail are also added. 

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The mouse genome includes one gene and two pseudogenes for cytoplasmic thymidine kinase. Pseudogenes are genes that have lost their protein-coding ability or are no longer expressed by the cell. These pseudogenes are copied from mRNA and incorporated into the chromosome. For example, the mouse thymidine kinase promoter also has a conserved CAAT box (GGCCAATCT) at approximately -80. This sequence is essential and is involved in binding transcription factors. Further upstream of the TATA box, eukaryotic promoters may also contain one or more GC-rich boxes (GGCG) or octamer boxes (ATTTGCAT). These elements bind cellular factors that increase the efficiency of transcription initiation and are often identified in more active genes that are constantly being expressed by the cell. Transcription Factors for RNA Polymerase II 

The complexity of eukaryotic transcription does not end with the polymerases and promoters. An army of basal transcription factors, enhancers, and silencers also help to regulate the frequency with which pre-mRNA is synthesized from a gene. Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed. Basal transcription factors are crucial in the formation of a preinitiation complex on the DNA template that subsequently recruits RNA polymerase II for transcription initiation. 

The names of the basal transcription factors begin with TFII (this is the transcription factor for RNA polymerase II) and are specified with the letters A J. The transcription factors systematically fall into place on the DNA template, with each one further stabilizing the preinitiation complex and contributing to the recruitment of RNA polymerase II. 

The processes of bringing RNA polymerases I and III to the DNA template involve slightly less complex collections of transcription factors, but the general theme is the same. Eukaryotic transcription is a tightly regulated process that requires a variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs that it needs for protein synthesis. 

During human embryonic development, a transcription factor encoded by the SRY gene starts a chain of events, causing the embryo to develop male sex characteristics. This gene is on the Y chromosome in humans and many other mammals. A deletion or mutation of the SRY gene can cause the human embryo to not develop into a male even though the individual has an XY genotype, a condition called Swyer syndrome. The SYR gene of the Y chromosome produces proteins that lead to the expression of primary sex characteristics, as shown. 

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The Evolution of Promoters The evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters and other gene regulatory sequences may evolve as well. For instance, consider a gene that, over many generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell needs to synthesize in abundance for a certain function. If this is the case, it would be beneficial to the cell for that gene s promoter to recruit transcription factors more efficiently and increase gene expression. 

Scientists examining the evolution of promoter sequences have reported varying results. In part, this is because it is difficult to infer exactly where a eukaryotic promoter begins and ends. Some promoters occur within genes; others are located very far upstream, or even downstream, of the genes they are regulating. However, when researchers limited their examination to human core promoter sequences that were defined experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even faster than protein-coding genes. 

It is still unclear how promoter evolution might correspond to the evolution of humans or other higher organisms. However, the evolution of a promoter to effectively make more or less of a given gene product is an intriguing alternative to the evolution of the genes themselves. 1 

[link] Promoter Structures for RNA Polymerases I and III 

In eukaryotes, the conserved promoter elements differ for genes transcribed by RNA polymerases I, II, and III. RNA polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105 upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves. Eukaryotic Elongation and Termination 

Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5' to 3' direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination. 

Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin. The DNA is tightly packaged around charged histone proteins at repeated intervals. These DNA histone complexes, collectively called nucleosomes, are regularly spaced and include 146 nucleotides of DNA wound around eight histones like thread around a spool. 

For polynucleotide synthesis to occur, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. This is accomplished by a special protein complex called FACT , which stands for facilitates chromatin transcription. This complex pulls histones away from the DNA template as the polymerase moves along it. Once the pre-mRNA is synthesized, the FACT complex replaces the histones to recreate the nucleosomes. 

The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,000 2,000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing. On the other hand, RNA polymerases I and III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is recognized by a termination protein. The process of termination in RNA polymerase III involves an mRNA hairpin similar to rho-independent termination of transcription in prokaryotes. Section Summary 

Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing. Review Questions 

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[link] Footnotes 1 H Liang et al., Fast evolution of core promoters in primate genomes, Molecular Biology and Evolution 25 (2008): 1239 44. Glossary CAAT box (GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors FACT complex that facilitates chromatin transcription by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by GC-rich box (GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter Octamer box (ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter preinitiation complex cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template small nuclear RNA molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factorsRNA Processing in Eukaryotes RNA Processing in Eukaryotes 

In this section, you will explore the following questions: What are the steps in eukaryotic transcription? What are the structural and functional similarities and differences among the three RNA polymerases? Connection for AP Courses 

Scientists discovered a strand of mRNA translated into a sequence of amino acids (polypeptide) shorter than the mRNA molecule transcribed from DNA. Before the information in eukaryotic mRNA is translated into protein, it is modified or edited in several ways. A 5 methylguanosine (or GTP) cap and a 3 poly-A tail are added to protect mature mRNA from degradation and allow its export from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected. Exons can be reconnected in different sequences, a phenomenon referred to as alternative gene splicing, which allows a single eukaryotic gene to code for different proteins. (We will explore the significance of alternative gene splicing in more detail in other chapters.) 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Hereditable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information. 

Have students work in groups of 4 5 and ask them to prepare models of RNA molecules undergoing processing. Supply scissors, glue, large sheets of white paper, and colored construction paper to differentiate the components of RNA molecules, exons and introns, and the other molecules such as transcription factors and enzymes associated with the process. Emphasize the importance of the order of the steps. Ask students to specify whether these steps happen in the nucleus or in the cytoplasm. 

Ask students which mRNAs would they expect to be stable and which mRNAs should have short half-lives. Proteins that control growth and cell cycles are associated with short-lived RNAs. The globin mRNAs which encode the protein parts of hemoglobin are unusually stable. Synthesis of globin continues in red blood cells without the nucleus being present. 

Explain that introns and exons vary in number and length. Mention that not all exons will be included in the final polypeptide and that there is alternative splicing which allows cells to produce different proteins using the same gene. 

After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. Eukaryotic (and prokaryotic) tRNAs and rRNAs also undergo processing before they can function as components in the protein synthesis machinery. mRNA Processing 

The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. The additional steps involved in eukaryotic mRNA maturation create a molecule with a much longer half-life than a prokaryotic mRNA. Eukaryotic mRNAs last for several hours, whereas the typical E. coli mRNA lasts no more than five seconds. 

Pre-mRNAs are first coated in RNA-stabilizing proteins; these protect the pre-mRNA from degradation while it is processed and exported out of the nucleus. The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5' and 3' ends of the molecule, and the removal of intervening sequences that do not specify the appropriate amino acids. In rare cases, the mRNA transcript can be edited after it is transcribed. 

RNA Editing in Trypanosomes The trypanosomes are a group of protozoa that include the pathogen Trypanosoma brucei , which causes sleeping sickness in humans ( [link] ). Trypanosomes, and virtually all other eukaryotes, have organelles called mitochondria that supply the cell with chemical energy. Mitochondria are organelles that express their own DNA and are believed to be the remnants of a symbiotic relationship between a eukaryote and an engulfed prokaryote. The mitochondrial DNA of trypanosomes exhibit an interesting exception to The Central Dogma: their pre-mRNAs do not have the correct information to specify a functional protein. Usually, this is because the mRNA is missing several U nucleotides. The cell performs an additional RNA processing step called RNA editing to remedy this. Trypanosoma brucei is the causative agent of sleeping sickness in humans. The mRNAs of this pathogen must be modified by the addition of nucleotides before protein synthesis can occur. (credit: modification of work by Torsten Ochsenreiter) 

Other genes in the mitochondrial genome encode 40- to 80-nucleotide guide RNAs. One or more of these molecules interacts by complementary base pairing with some of the nucleotides in the pre-mRNA transcript. However, the guide RNA has more A nucleotides than the pre-mRNA has U nucleotides to bind with. In these regions, the guide RNA loops out. The 3' ends of guide RNAs have a long poly-U tail, and these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. This process is entirely mediated by RNA molecules. That is, guide RNAs rather than proteins serve as the catalysts in RNA editing. 

RNA editing is not just a phenomenon of trypanosomes. In the mitochondria of some plants, almost all pre-mRNAs are edited. RNA editing has also been identified in mammals such as rats, rabbits, and even humans. What could be the evolutionary reason for this additional step in pre-mRNA processing? One possibility is that the mitochondria, being remnants of ancient prokaryotes, have an equally ancient RNA-based method for regulating gene expression. In support of this hypothesis, edits made to pre-mRNAs differ depending on cellular conditions. Although speculative, the process of RNA editing may be a holdover from a primordial time when RNA molecules, instead of proteins, were responsible for catalyzing reactions. 

[link] 5' Capping 

While the pre-mRNA is still being synthesized, a 7-methylguanosine cap is added to the 5' end of the growing transcript by a phosphate linkage. This moiety (functional group) protects the nascent mRNA from degradation. In addition, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes. 3' Poly-A Tail 

Once elongation is complete, the pre-mRNA is cleaved by an endonuclease between an AAUAAA consensus sequence and a GU-rich sequence, leaving the AAUAAA sequence on the pre-mRNA. An enzyme called poly-A polymerase then adds a string of approximately 200 A residues, called the poly-A tail . This modification further protects the pre-mRNA from degradation and signals the export of the cellular factors that the transcript needs to the cytoplasm. Pre-mRNA Splicing 

Eukaryotic genes are composed of exons , which correspond to protein-coding sequences ( ex- on signifies that they are ex pressed), and int ervening sequences called introns ( int- ron denotes their int ervening role), which may be involved in gene regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins. 

The discovery of introns came as a surprise to researchers in the 1970s who expected that pre-mRNAs would specify protein sequences without further processing, as they had observed in prokaryotes. The genes of higher eukaryotes very often contain one or more introns. These regions may correspond to regulatory sequences; however, the biological significance of having many introns or having very long introns in a gene is unclear. It is possible that introns slow down gene expression because it takes longer to transcribe pre-mRNAs with lots of introns. Alternatively, introns may be nonfunctional sequence remnants left over from the fusion of ancient genes throughout evolution. This is supported by the fact that separate exons often encode separate protein subunits or domains. For the most part, the sequences of introns can be mutated without ultimately affecting the protein product. 

All of a pre-mRNA s introns must be completely and precisely removed before protein synthesis. If the process errs by even a single nucleotide, the reading frame of the rejoined exons would shift, and the resulting protein would be dysfunctional. The process of removing introns and reconnecting exons is called splicing ( [link] ). Introns are removed and degraded while the pre-mRNA is still in the nucleus. Splicing occurs by a sequence-specific mechanism that ensures introns will be removed and exons rejoined with the accuracy and precision of a single nucleotide. The splicing of pre-mRNAs is conducted by complexes of proteins and RNA molecules called spliceosomes. 

Pre-mRNA splicing involves the precise removal of introns from the primary RNA transcript. The splicing process is catalyzed by protein complexes called spliceosomes that are composed of proteins and RNA molecules called snRNAs. Spliceosomes recognize sequences at the 5' and 3' end of the intron. 

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Note that more than 70 individual introns can be present, and each has to undergo the process of splicing in addition to 5' capping and the addition of a poly-A tail just to generate a single, translatable mRNA molecule. 

See how introns are removed during RNA splicing at this website . 

[link] Processing of tRNAs and rRNAs 

The tRNAs and rRNAs are structural molecules that have roles in protein synthesis; however, these RNAs are not themselves translated. Pre-rRNAs are transcribed, processed, and assembled into ribosomes in the nucleolus. Pre-tRNAs are transcribed and processed in the nucleus and then released into the cytoplasm where they are linked to free amino acids for protein synthesis. 

Most of the tRNAs and rRNAs in eukaryotes and prokaryotes are first transcribed as a long precursor molecule that spans multiple rRNAs or tRNAs. Enzymes then cleave the precursors into subunits corresponding to each structural RNA. Some of the bases of pre-rRNAs are methylated; that is, a CH 3 moiety (methyl functional group) is added for stability. Pre-tRNA molecules also undergo methylation. As with pre-mRNAs, subunit excision occurs in eukaryotic pre-RNAs destined to become tRNAs or rRNAs. 

Mature rRNAs make up approximately 50 percent of each ribosome. Some of a ribosome s RNA molecules are purely structural, whereas others have catalytic or binding activities. Mature tRNAs take on a three-dimensional structure through intramolecular hydrogen bonding to position the amino acid binding site at one end and the anticodon at the other end ( [link] ). The anticodon is a three-nucleotide sequence in a tRNA that interacts with an mRNA codon through complementary base pairing. This is a space-filling model of a tRNA molecule that adds the amino acid phenylalanine to a growing polypeptide chain. The anticodon AAG binds the Codon UUC on the mRNA. The amino acid phenylalanine is attached to the other end of the tRNA. Section Summary 

Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5' capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized. Review Questions 

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[link] Glossary 7-methylguanosine cap modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation anticodon three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon exon sequence present in protein-coding mRNA after completion of pre-mRNA splicing intron non protein-coding intervening sequences that are spliced from mRNA during processing poly-A tail modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus RNA editing direct alteration of one or more nucleotides in an mRNA that has already been synthesized splicing process of removing introns and reconnecting exons in a pre-mRNARibosomes and Protein Synthesis Ribosomes and Protein Synthesis 

In this section, you will explore the following questions: What are the different sequential steps in protein synthesis? What is the role of ribosomes in protein synthesis? Connection for AP Courses 

After the information in the gene has been transcribed to mRNA, it is ready to be translated to polypeptide. The players in translation include the mRNA template, ribosomes, tRNA molecules, amino acids, and various enzymes. Ribosomes consist of small and large subunits of protein and rRNA which bind with mRNA; many ribosomes can move along the same mRNA at a time. Translation begins at the initiating AUG on mRNA, specifying methionine, the first amino acid in any polypeptide. Each amino acid is carried to the ribosome by attaching to a specific molecule of tRNA. A tRNA molecule often is depicted as a cloverleaf, with an anticodon on one end, and the amino acid attachment site at the other. Amino-acid charging enzymes ensure that the correct amino acid is attached to the correct tRNA. The anticodons on tRNA are complementary to the codons on mRNA; for example, the anticodon AAA on tRNA corresponds to TTT on mRNA. Sequential amino acids are linked by peptide bonds. The mRNA is translated, elongating the polypeptide, until a STOP or nonsense codon is reached. When this happens, a release factor dissociates the components and frees the new polypeptide. Folding of the protein occurs during and after translation. Once a polypeptide is synthesized, its role as a protein is established, such as determining a physical phenotype of an organism. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Hereditable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 3.4 The student is able to describe representations and models illustrating how genetic information is translated into polypeptides. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression. 

Create models of protein synthesis with the following items: Pipe cleaners for RNA linking several units to represent mRNA and twisting some to represent tRNAs Cotton puff balls or other supplies to represent ribosomes Colored beads to represent amino acids and nucleotides 

Ask students what specific challenges must face amino-acyl tRNA synthetases. The enzymes must recognize the anticodon, the amino acid that matches that anticodon, and the tRNA acceptor site. 

Ask students to compare and contrast TATA boxes and Kozak s sequences. Both are based on consensus sequences. TATA boxes are associated with promoters and Kozak s sequences with binding of the ribosomes. 

The RNA in the ribosomes catalyze the formation of the peptide bond. This is a good example of a ribozyme, an RNA molecule that acts as an enzyme. Students may have heard that all enzymes are proteins. This is an opportunity to clarify the point. The enzyme involved in the splicing of introns is another example of RNA with catalytic properties. 

The synthesis of proteins consumes more of a cell s energy than any other metabolic process. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform virtually every function of a cell. The process of translation, or protein synthesis, involves the decoding of an mRNA message into a polypeptide product. Amino acids are covalently strung together by interlinking peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000. Each individual amino acid has an amino group (NH 2 ) and a carboxyl (COOH) group. Polypeptides are formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid ( [link] ). This reaction is catalyzed by ribosomes and generates one water molecule. A peptide bond links the carboxyl end of one amino acid with the amino end of another, expelling one water molecule. For simplicity in this image, only the functional groups involved in the peptide bond are shown. The R and R' designations refer to the rest of each amino acid structure. The Protein Synthesis Machinery 

In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of rRNAs and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors. 

Click through the steps of this PBS interactive to see protein synthesis in action. 

[link] Ribosomes 

Even before an mRNA is translated, a cell must invest energy to build each of its ribosomes. In E. coli , there are between 10,000 and 70,000 ribosomes present in each cell at any given time. A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the synthesis and assembly of rRNAs. 

Ribosomes exist in the cytoplasm in prokaryotes and in the cytoplasm and rough endoplasmic reticulum in eukaryotes. Mitochondria and chloroplasts also have their own ribosomes in the matrix and stroma, which look more similar to prokaryotic ribosomes (and have similar drug sensitivities) than the ribosomes just outside their outer membranes in the cytoplasm. Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation. In E. coli , the small subunit is described as 30S, and the large subunit is 50S, for a total of 70S (recall that Svedberg units are not additive). Mammalian ribosomes have a small 40S subunit and a large 60S subunit, for a total of 80S. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially binds tRNAs. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction: reading the mRNA from 5' to 3' and synthesizing the polypeptide from the N terminus to the C terminus. The complete mRNA/poly-ribosome structure is called a polysome . tRNAs 

The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. Depending on the species, 40 to 60 types of tRNAs exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that actually translate the language of RNA into the language of proteins. 

Of the 64 possible mRNA codons or triplet combinations of A, U, G, and C three specify the termination of protein synthesis and 61 specify the addition of amino acids to the polypeptide chain. Of these 61, one codon (AUG) also encodes the initiation of translation. Each tRNA anticodon can base pair with one of the mRNA codons and add an amino acid or terminate translation, according to the genetic code. For instance, if the sequence CUA occurred on an mRNA template in the proper reading frame, it would bind a tRNA expressing the complementary sequence, GAU, which would be linked to the amino acid leucine. 

As the adaptor molecules of translation, it is surprising that tRNAs can fit so much specificity into such a small package. Consider that tRNAs need to interact with three factors: 1) they must be recognized by the correct aminoacyl synthetase (see below); 2) they must be recognized by ribosomes; and 3) they must bind to the correct sequence in mRNA. Aminoacyl tRNA Synthetases 

The process of pre-tRNA synthesis by RNA polymerase III only creates the RNA portion of the adaptor molecule. The corresponding amino acid must be added later, once the tRNA is processed and exported to the cytoplasm. Through the process of tRNA charging, each tRNA molecule is linked to its correct amino acid by a group of enzymes called aminoacyl tRNA synthetases . At least one type of aminoacyl tRNA synthetase exists for each of the 20 amino acids; the exact number of aminoacyl tRNA synthetases varies by species. These enzymes first bind and hydrolyze ATP to catalyze a high-energy bond between an amino acid and adenosine monophosphate (AMP); a pyrophosphate molecule is expelled in this reaction. The activated amino acid is then transferred to the tRNA, and AMP is released. The Mechanism of Protein Synthesis 

As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we ll explore how translation occurs in E. coli , a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation. Initiation of Translation 

Protein synthesis begins with the formation of an initiation complex. In E. coli , this complex involves the small 30S ribosome, the mRNA template, three initiation factors (IFs; IF-1, IF-2, and IF-3), and a special initiator tRNA , called t R N A f M e t t R N A f M e t . The initiator tRNA interacts with the start codon AUG (or rarely, GUG), links to a formylated methionine called fMet, and can also bind IF-2. Formylated methionine is inserted by f M e t t R N A f M e t f M e t t R N A f M e t at the beginning of every polypeptide chain synthesized by E. coli , but it is usually clipped off after translation is complete. When an in-frame AUG is encountered during translation elongation, a non-formylated methionine is inserted by a regular Met-tRNA Met . 

In E. coli mRNA, a sequence upstream of the first AUG codon, called the Shine-Dalgarno sequence (AGGAGG), interacts with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template. Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts as an energy source during translation both at the start of elongation and during the ribosome s translocation. 

In eukaryotes, a similar initiation complex forms, comprising mRNA, the 40S small ribosomal subunit, IFs, and nucleoside triphosphates (GTP and ATP). The charged initiator tRNA, called Met-tRNA i , does not bind fMet in eukaryotes, but is distinct from other Met-tRNAs in that it can bind IFs. 

Instead of depositing at the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 7-methylguanosine cap at the 5' end of the mRNA. A cap-binding protein (CBP) and several other IFs assist the movement of the ribosome to the 5' cap. Once at the cap, the initiation complex tracks along the mRNA in the 5' to 3' direction, searching for the AUG start codon. Many eukaryotic mRNAs are translated from the first AUG, but this is not always the case. According to Kozak s rules , the nucleotides around the AUG indicate whether it is the correct start codon. Kozak s rules state that the following consensus sequence must appear around the AUG of vertebrate genes: 5'-gccRccAUGG-3'. The R (for purine) indicates a site that can be either A or G, but cannot be C or U. Essentially, the closer the sequence is to this consensus, the higher the efficiency of translation. 

Once the appropriate AUG is identified, the other proteins and CBP dissociate, and the 60S subunit binds to the complex of Met-tRNA i , mRNA, and the 40S subunit. This step completes the initiation of translation in eukaryotes. Translation, Elongation, and Termination 

In prokaryotes and eukaryotes, the basics of elongation are the same, so we will review elongation from the perspective of E. coli . The 50S ribosomal subunit of E. coli consists of three compartments: the A (aminoacyl) site binds incoming charged aminoacyl tRNAs. The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids. There is one exception to this assembly line of tRNAs: in E. coli , f M e t t R N A f M e t f M e t t R N A f M e t is capable of entering the P site directly without first entering the A site. Similarly, the eukaryotic Met-tRNA i , with help from other proteins of the initiation complex, binds directly to the P site. In both cases, this creates an initiation complex with a free A site ready to accept the tRNA corresponding to the first codon after the AUG. 

During translation elongation, the mRNA template provides specificity. As the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured. If mRNA were not present in the elongation complex, the ribosome would bind tRNAs nonspecifically. 

Elongation proceeds with charged tRNAs entering the A site and then shifting to the P site followed by the E site with each single-codon step of the ribosome. Ribosomal steps are induced by conformational changes that advance the ribosome by three bases in the 3' direction. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes GTP. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by peptidyl transferase , an RNA-based enzyme that is integrated into the 50S ribosomal subunit. The energy for each peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The amino acid bound to the P-site tRNA is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled ( [link] ). Amazingly, the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid protein can be translated in just 10 seconds. 

Translation begins when an initiator tRNA anticodon recognizes a codon on mRNA. The large ribosomal subunit joins the small subunit, and a second tRNA is recruited. As the mRNA moves relative to the ribosome, the polypeptide chain is formed. Entry of a release factor into the A site terminates translation and the components dissociate. 

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Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with the A site, these nonsense codons are recognized by release factors in prokaryotes and eukaryotes that instruct peptidyl transferase to add a water molecule to the carboxyl end of the P-site amino acid. This reaction forces the P-site amino acid to detach from its tRNA, and the newly made protein is released. The small and large ribosomal subunits dissociate from the mRNA and from each other; they are recruited almost immediately into another translation initiation complex. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction. Protein Folding, Modification, and Targeting 

During and after translation, individual amino acids may be chemically modified, signal sequences may be appended, and the new protein folds into a distinct three-dimensional structure as a result of intramolecular interactions. A signal sequence is a short tail of amino acids that directs a protein to a specific cellular compartment. These sequences at the amino end or the carboxyl end of the protein can be thought of as the protein s train ticket to its ultimate destination. Other cellular factors recognize each signal sequence and help transport the protein from the cytoplasm to its correct compartment. For instance, a specific sequence at the amino terminus will direct a protein to the mitochondria or chloroplasts (in plants). Once the protein reaches its cellular destination, the signal sequence is usually clipped off. 

Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from aggregating during the complicated process of folding. Even if a protein is properly specified by its corresponding mRNA, it could take on a completely dysfunctional shape if abnormal temperature or pH conditions prevent it from folding correctly. Activity Working in a small group, create a simple board game to model the key steps of transcription and translation and have classmates spend ten minutes playing the game. Provided with incomplete or incorrect diagrams illustrating transcription and translation in prokaryotes, have students refine or revise the diagrams and share the edited versions with classmates for critical review. Think About It 

Many antibiotics inhibit protein synthesis. For example, tetracycline blocks the A site on the ribosome. What is the likely effect of tetracycline on protein synthesis? Using a chart of codons, transcribe and translate the following DNA sequence (non-template strand): 5 -ATGGCCGGTTATTAAGCA-3 . How can a single nucleotide change affect the protein produced from this sequence and its function? 

The activities are applications of Learning Objective 3.4 and Science Practice 1.2 because students model how genetic information in DNA is ultimately translated into protein. 

The first question is an application of Learning Objective 3.4 and Science Practice 1.2 because students are modeling how genetic information in DNA is ultimately translated into protein. 

The second question is an application of Learning Objective 3.6 and Science Practice 6.4 because provided with a DNA sequence, students are asked to transcribe and translate the sequence and make a prediction about the possible effect of a mutation on the protein produced. Answers: Tetracycline would directly affect tRNA binding to the ribosome. The mRNA would be: 5'-AUGGCCGGUUAUUAAGCA-3'. The protein would be: MAGY (methionine-alanine-glycine-tyrosine.) Even though there are six codons, the fifth codon corresponds to a stop, so the sixth codon would not be translated. Responses to the second part of the inquiry may vary, as it would be dependent upon which nucleotide was changed. For example, if the A in the first codon (AUG) was changed to C, no protein would result. Section Summary 

The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit forms on the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide steps of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation. Review Questions 

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[link] Glossary aminoacyl tRNA synthetase enzyme that charges tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid initiator tRNA in prokaryotes, called t R N A f M e t t R N A f M e t ; in eukaryotes, called tRNA i ; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain Kozak s rules determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5 -GCC( purine )CC AUG G -3 ; the bolded bases are most important peptidyl transferase RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds polysome mRNA molecule simultaneously being translated by many ribosomes all going in the same direction Shine-Dalgarno sequence (AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome signal sequence short tail of amino acids that directs a protein to a specific cellular compartment start codon AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionineIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" The genetic content of each somatic cell in an organism is the same, but not all genes are expressed in every cell. The control of which genes are expressed dictates whether a cell is (a) an eye cell or (b) a liver cell. It is the differential gene expression patterns that arise in different cells that give rise to (c) a complete organism. 

Most people know that regular exercise is important to maintain good health. It promotes cardiovascular health and helps to prevent obesity. Scientists have now discovered that long-term endurance training also changes how genes are expressed in muscle tissue. In a recent study, 23 healthy people each exercised one leg for 45 minutes four days a week while resting the other leg. After three months, muscles from participants legs were biopsied, and scientists analyzed the activity level of over 20,000 genes in the tissue samples. 

They found that for each participant the exercised leg had reduced inflammation and improved metabolism compared with the non-exercised leg. These differences were accompanied by changes in genes associated with metabolism and inflammation. However, the actual nucleotide sequences of the genes weren t changed. Instead, some genes were methylated, which simply means methyl groups were attached to certain nucleotides along the sequence. This, essentially, turned the genes off or otherwise changed how they were expressed. DNA methylation is an example of epigenetics, which is a process that alters genes without affecting the nucleotide sequence of the genes. The full research article can be found here . 

Before students begin this chapter, they should review these concepts: DNA and chromatin structure, transcription, and translation.Regulation of Gene Expression Regulation of Gene Expression 

In this section, you will explore the following question: How does prokaryotic gene regulation differ from eukaryotic gene regulation? Connection for AP Courses 

Structure and function in biology result from the presence of genetic information and the correct expression of this information. In the chapter on DNA structure and function, we explored how genes are translated into proteins, which in turn determine the nature of the cell. But how does a cell know when to turn on its DNA? With few exceptions, each cell in your body contains identical genetic information. If each cell has the same exact DNA make up, how is it that a liver cell differs from a nerve or muscle cell? 

As we will discover, although each cell shares the same genome and DNA sequence, each cell does not express exactly the same genes. Many factors determine when and how genes are expressed in a given cell. Even the type of chromosome a gene is located on, like whether it is a sex chromosome or not, can determine its expression pattern, as can mutations or changes in DNA sequence and other external factors. In prokaryotes, gene expression is regulated primarily at the level of transcription, when DNA is copied into RNA. However, eukaryotes have evolved regulatory mechanisms in gene expression at multiple levels. In all cases, regulation of gene expression determines the type and amount of protein produced in the cell. Errors in regulatory processes can result in many human diseases and conditions, including cancer. 

Gene expression regulation occurs at different points in prokaryotes and eukaryotes. Prokaryotic organisms express their entire genome in every cell, but not necessarily all at the same time. In general, a gene is expressed only when its specific protein product is needed. Remember that each cell in an organism carries the same DNA as every other cell. Yet cells of eukaryotic organisms each express a unique subset of DNA depending on cell type. To express a protein, DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, transcription and translation occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus, separate from the translation that occurs in the cytoplasm along ribosomes attached to endoplasmic reticulum. As stated above, gene expression in prokaryotes is regulated at the level of transcription, whereas in eukaryotes, gene expression is regulated at multiple levels, including the epigenetic (DNA), transcriptional, pre- and post-transcriptional, and translational levels. 

The science of epigenetics studies heritable changes in the genome that do not affect the underlying DNA gene sequences. 

The content presented in this section supports the learning objectives outlined in Big Idea 3 of the AP Biology Curriculum Framework. The AP learning objectives merge essential knowledge content with one or more of the seven science practices. These objectives provide a transparent foundation for the AP Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP exam questions. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.B Expression of genetic information involves cellular and molecular mechanisms. Essential Knowledge 3.B.1 Gene regulation results in differential gene expression, leading to cell specialization Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 3.18 The student is able to describe the connection between the regulation of gene expression and observed differences between different kinds of organisms. 

For a cell to function properly, necessary proteins must be synthesized at the proper time. All cells control or regulate the synthesis of proteins from information encoded in their DNA. The process of turning on a gene to produce RNA and protein is called gene expression . Whether in a simple unicellular organism or a complex multi-cellular organism, each cell controls when and how its genes are expressed. For this to occur, there must be a mechanism to control when a gene is expressed to make RNA and protein, how much of the protein is made, and when it is time to stop making that protein because it is no longer needed. 

The regulation of gene expression conserves energy and space. It would require a significant amount of energy for an organism to express every gene at all times, so it is more energy efficient to turn on the genes only when they are required. In addition, only expressing a subset of genes in each cell saves space because DNA must be unwound from its tightly coiled structure to transcribe and translate the DNA. Cells would have to be enormous if every protein were expressed in every cell all the time. 

The control of gene expression is extremely complex. Malfunctions in this process are detrimental to the cell and can lead to the development of many diseases, including cancer. 

Ask students what genes are present in the DNA in a muscle cell and skin cell. Ask them if the same genome is present in every cell in the body, how do the cells have different properties. For example, discuss red blood cells, which lose their nucleus during development. This video gives an overview of gene regulation in prokaryotes and eukaryotes. Prokaryotic versus Eukaryotic Gene Expression 

To understand how gene expression is regulated, we must first understand how a gene codes for a functional protein in a cell. The process occurs in both prokaryotic and eukaryotic cells, just in slightly different manners. 

Prokaryotic organisms are single-celled organisms that lack a cell nucleus, and their DNA therefore floats freely in the cell cytoplasm. To synthesize a protein, the processes of transcription and translation occur almost simultaneously. When the resulting protein is no longer needed, transcription stops. As a result, the primary method to control what type of protein and how much of each protein is expressed in a prokaryotic cell is the regulation of DNA transcription. All of the subsequent steps occur automatically. When more protein is required, more transcription occurs. Therefore, in prokaryotic cells, the control of gene expression is mostly at the transcriptional level. 

Eukaryotic cells, in contrast, have intracellular organelles that add to their complexity. In eukaryotic cells, the DNA is contained inside the cell s nucleus and there it is transcribed into RNA. The newly synthesized RNA is then transported out of the nucleus into the cytoplasm, where ribosomes translate the RNA into protein. The processes of transcription and translation are physically separated by the nuclear membrane; transcription occurs only within the nucleus, and translation occurs only outside the nucleus in the cytoplasm. The regulation of gene expression can occur at all stages of the process ( [link] ). Regulation may occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors ( epigenetic level), when the RNA is transcribed (transcriptional level), when the RNA is processed and exported to the cytoplasm after it is transcribed ( post-transcriptional level), when the RNA is translated into protein (translational level), or after the protein has been made ( post-translational level). Prokaryotic transcription and translation occur simultaneously in the cytoplasm, and regulation occurs at the transcriptional level. Eukaryotic gene expression is regulated during transcription and RNA processing, which take place in the nucleus, and during protein translation, which takes place in the cytoplasm. Further regulation may occur through post-translational modifications of proteins. 

The differences in the regulation of gene expression between prokaryotes and eukaryotes are summarized in [link] . The regulation of gene expression is discussed in detail in subsequent modules. Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms Prokaryotic organisms Eukaryotic organisms Lack nucleus Contain nucleus DNA is found in the cytoplasm DNA is confined to the nuclear compartment RNA transcription and protein formation occur almost simultaneously RNA transcription occurs prior to protein formation, and it takes place in the nucleus. Translation of RNA to protein occurs in the cytoplasm. Gene expression is regulated primarily at the transcriptional level Gene expression is regulated at many levels (epigenetic, transcriptional, nuclear shuttling, post-transcriptional, translational, and post-translational) Evolution of Gene Regulation 

Prokaryotic cells can only regulate gene expression by controlling the amount of transcription. As eukaryotic cells evolved, the complexity of the control of gene expression increased. For example, with the evolution of eukaryotic cells came compartmentalization of important cellular components and cellular processes. A nuclear region that contains the DNA was formed. Transcription and translation were physically separated into two different cellular compartments. It therefore became possible to control gene expression by regulating transcription in the nucleus, and also by controlling the RNA levels and protein translation present outside the nucleus. 

Some cellular processes arose from the need of the organism to defend itself. Cellular processes such as gene silencing developed to protect the cell from viral or parasitic infections. If the cell could quickly shut off gene expression for a short period of time, it would be able to survive an infection when other organisms could not. Therefore, the organism evolved a new process that helped it survive, and it was able to pass this new development to offspring. 

[link] Think About It 

How does controlling gene expression alter the overall protein level in the cell? 

The question is an application of Learning Objective 3.18 and Science Practice 7.1 because students are asked to describe the connection between genes, gene expression (i.e., transcription and translation), and how the production of different proteins can result in cell specialization and differences between organisms. Answer 

The cell controls which proteins are expressed and to what level each protein is expressed in the cell. Prokaryotic cells alter the transcription rate to turn genes on or off. This method will increase or decrease protein levels in response to what is needed by the cell. Eukaryotic cells change the accessibility (through epigenetic mechanisms), transcription, or translation of a gene. This will alter the amount of RNA and the lifespan of the RNA to alter the amount of protein that exists. Eukaryotic organisms are much more complex and can manipulate protein levels by changing many stages in the process. Section Summary 

While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is regulated only at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels. Review Questions 

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[link] Critical Thinking Questions 

[link] Test Prep for AP Courses 

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[link] Glossary epigenetic heritable changes that do not involve changes in the DNA sequence gene expression processes that control the turning on or turning off of a gene post-transcriptional control of gene expression after the RNA molecule has been created but before it is translated into protein post-translational control of gene expression after a protein has been createdProkaryotic Gene Regulation Prokaryotic Gene Regulation 

In this section, you will explore the following question: What are operons and what are the roles of activators, inducers, and repressors in regulating operons and gene expression? Connection for AP Courses 

The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. Simply stated, if a cell does not transcribe the DNA s message into mRNA, translation (protein synthesis), does not occur. Bacterial genes are often organized into common pathways or processes called operons for more coordinated regulation of expression. For example, in E. coli , genes responsible for lactose metabolism are located together on the bacterial chromosome. (The operon model includes several components, so when studying how the operon works, it is helpful to refer to a diagram of the model. See [link] and [link] .) The operon includes a regulatory gene that codes for a repressor protein that binds to the operator, which prevents RNA polymerase from transcribing the gene(s) of interest. An example of this is seen in the structural genes for lactose metabolism. However, if the repressor is inactivated, RNA polymerase binds to the promoter, and transcription of the structural genes occurs. 

There are three ways to control the transcription of an operon: inducible control, repressible control, and activator control. The lac operon is an example of inducible control because the presence of lactose turns on transcription of the genes for its own metabolism. The trp operon is an example of repressible control because it uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase. If tryptophan is not needed by the cell, the genes necessary to produce it are turned off. Activator control (typified by the action of Catabolite Activator Protein) increases the binding ability of RNA polymerase to the promoter. Certain genes are continually expressed via this regulatory mechanism. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.B Expression of genetic information involves cellular and molecular mechanisms. Essential Knowledge 3.B.1 Gene regulation results in differential gene expression, leading to cell specialization Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively Learning Objective 3.21 The student can use representations to describe how gene regulation influences cell products and function. Essential Knowledge 3.B.2 A variety of intercellular and intracellular signal transmissions mediate gene expression. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 3.23 The student can use representations to describe mechanisms of the regulation of gene expression. 

When discussing the operons with students, challenge them to think about what would happen if there were a gene mutation that disrupted the function of one of the proteins that controls transcription of the operon. For example, if the repressor protein in the lac operon has a mutation that prevents it from binding to lactose, then the repressor will remain bound to the operator and will prevent transcription of the operon even in the presence of lactose. This video describes two other examples of mutations in the lac operon. 

Introduce the regulation of transcription in the lac operon using visuals such as this video . 

The DNA of prokaryotes is organized into a circular chromosome supercoiled in the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks called operons . For example, all of the genes needed to use lactose as an energy source are coded next to each other in the lactose (or lac ) operon. 

In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers. Repressors are proteins that suppress transcription of a gene in response to an external stimulus, whereas activators are proteins that increase the transcription of a gene in response to an external stimulus. Finally, inducers are small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate. The trp Operon: A Repressor Operon 

Bacteria such as E. coli need amino acids to survive. Tryptophan is one such amino acid that E. coli can ingest from the environment. E. coli can also synthesize tryptophan using enzymes that are encoded by five genes. These five genes are next to each other in what is called the tryptophan ( trp ) operon ( [link] ). If tryptophan is present in the environment, then E. coli does not need to synthesize it and the switch controlling the activation of the genes in the trp operon is switched off. However, when tryptophan availability is low, the switch controlling the operon is turned on, transcription is initiated, the genes are expressed, and tryptophan is synthesized. The five genes that are needed to synthesize tryptophan in E. coli are located next to each other in the trp operon. When tryptophan is plentiful, two tryptophan molecules bind the repressor protein at the operator sequence. This physically blocks the RNA polymerase from transcribing the tryptophan genes. When tryptophan is absent, the repressor protein does not bind to the operator and the genes are transcribed. 

A DNA sequence that codes for proteins is referred to as the coding region. The five coding regions for the tryptophan biosynthesis enzymes are arranged sequentially on the chromosome in the operon. Just before the coding region is the transcriptional start site . This is the region of DNA to which RNA polymerase binds to initiate transcription. The promoter sequence is upstream of the transcriptional start site; each operon has a sequence within or near the promoter to which proteins (activators or repressors) can bind and regulate transcription. 

A DNA sequence called the operator sequence is encoded between the promoter region and the first trp coding gene. This operator contains the DNA code to which the repressor protein can bind. When tryptophan is present in the cell, two tryptophan molecules bind to the trp repressor, which changes shape to bind to the trp operator. Binding of the tryptophan repressor complex at the operator physically prevents the RNA polymerase from binding, and transcribing the downstream genes. 

When tryptophan is not present in the cell, the repressor by itself does not bind to the operator; therefore, the operon is active and tryptophan is synthesized. Because the repressor protein actively binds to the operator to keep the genes turned off, the trp operon is negatively regulated and the proteins that bind to the operator to silence trp expression are negative regulators . Link to Learning 

Watch this video to learn more about the trp operon. 

[link] Catabolite Activator Protein (CAP): An Activator Regulator 

Just as the trp operon is negatively regulated by tryptophan molecules, there are proteins that bind to the operator sequences that act as a positive regulator to turn genes on and activate them. For example, when glucose is scarce, E. coli bacteria can turn to other sugar sources for fuel. To do this, new genes to process these alternate genes must be transcribed. When glucose levels drop, cyclic AMP (cAMP) begins to accumulate in the cell. The cAMP molecule is a signaling molecule that is involved in glucose and energy metabolism in E. coli . When glucose levels decline in the cell, accumulating cAMP binds to the positive regulator catabolite activator protein (CAP) , a protein that binds to the promoters of operons that control the processing of alternative sugars. When cAMP binds to CAP, the complex binds to the promoter region of the genes that are needed to use the alternate sugar sources ( [link] ). In these operons, a CAP binding site is located upstream of the RNA polymerase binding site in the promoter. This increases the binding ability of RNA polymerase to the promoter region and the transcription of the genes. When glucose levels fall, E. coli may use other sugars for fuel but must transcribe new genes to do so. As glucose supplies become limited, cAMP levels increase. This cAMP binds to the CAP protein, a positive regulator that binds to an operator region upstream of the genes required to use other sugar sources. The lac Operon: An Inducer Operon 

The third type of gene regulation in prokaryotic cells occurs through inducible operons , which have proteins that bind to activate or repress transcription depending on the local environment and the needs of the cell. The lac operon is a typical inducible operon. As mentioned previously, E. coli is able to use other sugars as energy sources when glucose concentrations are low. To do so, the cAMP CAP protein complex serves as a positive regulator to induce transcription. One such sugar source is lactose. The lac operon encodes the genes necessary to acquire and process the lactose from the local environment. CAP binds to the operator sequence upstream of the promoter that initiates transcription of the lac operon. However, for the lac operon to be activated, two conditions must be met. First, the level of glucose must be very low or non-existent. Second, lactose must be present. Only when glucose is absent and lactose is present will the lac operon be transcribed ( [link] ). This makes sense for the cell, because it would be energetically wasteful to create the proteins to process lactose if glucose was plentiful or lactose was not available. 

Transcription of the lac operon is carefully regulated so that its expression only occurs when glucose is limited and lactose is present to serve as an alternative fuel source. 

[link] 

If glucose is absent, then CAP can bind to the operator sequence to activate transcription. If lactose is absent, then the repressor binds to the operator to prevent transcription. If either of these requirements is met, then transcription remains off. Only when both conditions are satisfied is the lac operon transcribed ( [link] ). Signals that Induce or Repress Transcription of the lac Operon Glucose CAP binds Lactose Repressor binds Transcription + - - + No + - + - Some - + - + No - + + - Yes 

Watch an animated tutorial about the workings of lac operon here. 

[link] Activity 

Modeling the Operon. Use construction paper or more elaborate materials, such as Styrofoam noodles, electrical tape, and Velcro tabs, to create a model of the lac and trp operons that include a regulator, promoter, operator, and structural genes. Then use the model to show how the presence of substrate, e.g., allolactose or tryptophan, can change the activity of the operons. As an extension of the activity, use the model to make predictions about the effects of mutations in any of the regions on gene expression. Think About It 

In E. coli , the trp operon is on by default, while the lac operon is off by default. Why do you think this is the case? 

The activity is an application of Learning Objectives 3.21 and 3.23 and Science Practice 1.4 because students are using a representation to describe how operons regulate gene expression in prokaryotes. In addition, students are applying Science Practice 6.4 because they will use the model to make predictions about gene regulation and expression. 

The question is an application of Learning Objectives 3.2 and 3.23 and Science Practice 1.4 because students are using the operon model of gene regulation in prokaryotes to describe an observed phenomenon. Answer 

Tryptophan is an amino acid necessary for making proteins, so the cell always needs to have some on hand. However, if plenty of tryptophan is present, it is wasteful to make more, and the expression of the trp genes is repressed. Lactose, a sugar found in milk, is not always available. Cells need not make the enzymes necessary to digest an energy source that is not available, so the lac operon is only turned on when lactose is present. Section Summary 

The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. There are three ways to control the transcription of an operon: repressive control, activator control, and inducible control. Repressive control, typified by the trp operon, uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase and the activation of transcription. Therefore, if tryptophan is not needed, the repressor is bound to the operator and transcription remains off. Activator control, typified by the action of CAP, increases the binding ability of RNA polymerase to the promoter when CAP is bound. In this case, low levels of glucose result in the binding of cAMP to CAP. CAP then binds the promoter, which allows RNA polymerase to bind to the promoter better. In the last example the lac operon two conditions must be met to initiate transcription. Glucose must not be present, and lactose must be available for the lac operon to be transcribed. If glucose is absent, CAP binds to the operator. If lactose is present, the repressor protein does not bind to its operator. Only when both conditions are met will RNA polymerase bind to the promoter to induce transcription. Review Questions 

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[link] Critical Thinking Questions 

[link] Test Prep for AP Courses 

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[link] Glossary activator protein that binds to prokaryotic operators to increase transcription catabolite activator protein (CAP) protein that complexes with cAMP to bind to the promoter sequences of operons that control sugar processing when glucose is not available inducible operon operon that can be activated or repressed depending on cellular needs and the surrounding environment lac operon operon in prokaryotic cells that encodes genes required for processing and intake of lactose negative regulator protein that prevents transcription operator region of DNA outside of the promoter region that binds activators or repressors that control gene expression in prokaryotic cells operon collection of genes involved in a pathway that are transcribed together as a single mRNA in prokaryotic cells positive regulator protein that increases transcription repressor protein that binds to the operator of prokaryotic genes to prevent transcription transcriptional start site site at which transcription begins trp operon series of genes necessary to synthesize tryptophan in prokaryotic cells tryptophan amino acid that can be synthesized by prokaryotic cells when necessaryEukaryotic Epigenetic Gene Regulation Eukaryotic Epigenetic Gene Regulation 

In this section, you will explore the following question: What is the science of epigenetics and how is this process regulated? Connection for AP Courses 

One reason that eukaryotic gene expression is more complex than prokaryotic gene expression is because the processes of transcription and translation are physically separated within the eukaryotic cell. Eukaryotic cells also package their genomes in a more sophisticated way compared with prokaryotic cells. Consequently, eukaryotic cells can regulate gene expression at multiple levels, beginning with control of access to DNA. Because genomic DNA is folded around histone proteins to create nucleosome complexes, nucleosomes physically regulate the access of proteins, such as transcription factors and enzymes, to the underlying DNA. Methylation of DNA and histones causes nucleosomes to pack tightly together, preventing transcription factors from binding to the DNA. Methylated nucleosomes contain DNA that is not expressed. On the other hand, histone acetylation results in loose packing of nucleosomes, allowing transcription factors to bind to DNA. Acetylated nucleosomes contain DNA that may be expressed. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.B Expression of genetic information involves cellular and molecular mechanisms. Essential Knowledge 3.B.1 Gene regulation results in differential gene expression, leading to cell specialization. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales Learning Objective 3.19 The student is able to describe the connection between the regulation of gene expression and observed differences between individuals in a population Epigenetic Control: Regulating Access to Genes within the Chromosome 

As stated earlier, one reason why eukaryotic gene expression is more complex than prokaryotic gene expression is because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Eukaryotic gene expression begins with control of access to the DNA. This form of regulation, called epigenetic regulation, occurs even before transcription is initiated. 

Introduce epigenetics and have students work on an epigenetics activity found on the University of Utah s website . 

The human genome encodes over 20,000 genes; each of the 23 pairs of human chromosomes encodes thousands of genes. The DNA in the nucleus is precisely wound, folded, and compacted into chromosomes so that it will fit into the nucleus. It is also organized so that specific segments can be accessed as needed by a specific cell type. 

The first level of organization, or packing, is the winding of DNA strands around histone proteins. Histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions ( [link] a ). Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string ( [link] b ). These beads (histone proteins) can move along the string (DNA) and change the structure of the molecule. DNA is folded around histone proteins to create (a) nucleosome complexes. These nucleosomes control the access of proteins to the underlying DNA. When viewed through an electron microscope (b), the nucleosomes look like beads on a string. (credit micrograph : modification of work by Chris Woodcock) 

If DNA encoding a specific gene is to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate transcription ( [link] ). Nucleosomes can move to open the chromosome structure to expose a segment of DNA, but do so in a very controlled manner. 

Nucleosomes can slide along DNA. When nucleosomes are spaced closely together (top), transcription factors cannot bind and gene expression is turned off. When the nucleosomes are spaced far apart (bottom), the DNA is exposed. Transcription factors can bind, allowing gene expression to occur. Modifications to the histones and DNA affect nucleosome spacing. 

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How the histone proteins move is dependent on signals found on both the histone proteins and on the DNA. These signals are tags added to histone proteins and DNA that tell the histones if a chromosomal region should be open or closed ( [link] depicts modifications to histone proteins and DNA). These tags are not permanent, but may be added or removed as needed. They are chemical modifications (phosphate, methyl, or acetyl groups) that are attached to specific amino acids in the protein or to the nucleotides of the DNA. The tags do not alter the DNA base sequence, but they do alter how tightly wound the DNA is around the histone proteins. DNA is a negatively charged molecule; therefore, changes in the charge of the histone will change how tightly wound the DNA molecule will be. When unmodified, the histone proteins have a large positive charge; by adding chemical modifications like acetyl groups, the charge becomes less positive. 

The DNA molecule itself can also be modified. This occurs within very specific regions called CpG islands. These are stretches with a high frequency of cytosine and guanine dinucleotide DNA pairs (CG) found in the promoter regions of genes. When this configuration exists, the cytosine member of the pair can be methylated (a methyl group is added). This modification changes how the DNA interacts with proteins, including the histone proteins that control access to the region. Highly methylated (hypermethylated) DNA regions with deacetylated histones are tightly coiled and transcriptionally inactive. Histone proteins and DNA nucleotides can be modified chemically. Modifications affect nucleosome spacing and gene expression. (credit: modification of work by NIH) 

This type of gene regulation is called epigenetic regulation. Epigenetic means around genetics. The changes that occur to the histone proteins and DNA do not alter the nucleotide sequence and are not permanent. Instead, these changes are temporary (although they often persist through multiple rounds of cell division) and alter the chromosomal structure (open or closed) as needed. A gene can be turned on or off depending upon the location and modifications to the histone proteins and DNA. If a gene is to be transcribed, the histone proteins and DNA are modified surrounding the chromosomal region encoding that gene. This opens the chromosomal region to allow access for RNA polymerase and other proteins, called transcription factors , to bind to the promoter region, located just upstream of the gene, and initiate transcription. If a gene is to remain turned off, or silenced, the histone proteins and DNA have different modifications that signal a closed chromosomal configuration. In this closed configuration, the RNA polymerase and transcription factors do not have access to the DNA and transcription cannot occur ( [link] ). Think About It 

In females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes will have on nucleosome packaging and, consequently, gene expression? 

The question is an application of Learning Objective 3.19 and Science Practice 7.1 because students are asked to describe how epigenetic changes to chromatin during development can result in differential gene expression and, consequently, differences among cells and organisms. Answer: The nucleosomes will pack more tightly together. 

View this video that describes how epigenetic regulation controls gene expression. 

[link] Section Summary 

In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription. Review Questions 

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[link] Critical Thinking Questions 

[link] Glossary transcription factor protein that binds to the DNA at the promoter or enhancer region and that influences transcription of a geneEukaryotic Transcription Gene Regulation Eukaryotic Transcription Gene Regulation 

In this section, you will explore the following question: What is the role of transcription factors, enhancers, and repressors in gene regulation? Connection for AP Courses 

To start transcription, general transcription factors must first bind to a specific area on the DNA called the TATA box and then recruit RNA polymerase to that location. In addition, other areas on the DNA called enhancer regions help augment transcription. Transcription factors can bind to enhancer regions to increase or prevent transcription. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.B Expression of genetic information involves cellular and molecular mechanisms. Essential Knowledge 3.B.1 Gene regulation results in differential gene expression, leading to cell specialization Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 3.18 The student is able to describe the connection between the regulation of gene expression and observed differences between different kinds of organisms Essential Knowledge 3.B.1 Gene regulation results in differential gene expression, leading to cell specialization Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales Learning Objective 3.19 The student is able to describe the connection between the regulation of gene expression and observed differences between individuals in a population Essential Knowledge 3.B.1 Gene regulation results in differential gene expression, leading to cell specialization. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices Learning Objective 3.20 The student is able to explain how the regulation of gene expression is essential for the processes and structures that support efficient cell function. Essential Knowledge 3.B.1 1 Gene regulation results in differential gene expression, leading to cell specialization. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 3.21 The student can use representations to describe how gene regulation influences cell products and function. 

Have students create a visual representation using colored paper that shows DNA transcription and the role of enhancers and repressors in transcription. 

Like prokaryotic cells, the transcription of genes in eukaryotes requires the actions of an RNA polymerase to bind to a sequence upstream of a gene to initiate transcription. However, unlike prokaryotic cells, the eukaryotic RNA polymerase requires other proteins, or transcription factors, to facilitate transcription initiation. Transcription factors are proteins that bind to the promoter sequence and other regulatory sequences to control the transcription of the target gene. RNA polymerase by itself cannot initiate transcription in eukaryotic cells. Transcription factors must bind to the promoter region first and recruit RNA polymerase to the site for transcription to be established. 

View the process of transcription the making of RNA from a DNA template at this site . 

[link] The Promoter and the Transcription Machinery 

Genes are organized to make the control of gene expression easier. The promoter region is immediately upstream of the coding sequence. This region can be short (only a few nucleotides in length) or quite long (hundreds of nucleotides long). The longer the promoter, the more available space for proteins to bind. This also adds more control to the transcription process. The length of the promoter is gene-specific and can differ dramatically between genes. Consequently, the level of control of gene expression can also differ quite dramatically between genes. The purpose of the promoter is to bind transcription factors that control the initiation of transcription. 

Within the promoter region, just upstream of the transcriptional start site, resides the TATA box. This box is simply a repeat of thymine and adenine dinucleotides (literally, TATA repeats). RNA polymerase binds to the transcription initiation complex, allowing transcription to occur. To initiate transcription, a transcription factor (TFIID) is the first to bind to the TATA box. Binding of TFIID recruits other transcription factors, including TFIIB, TFIIE, TFIIF, and TFIIH to the TATA box. Once this complex is assembled, RNA polymerase can bind to its upstream sequence. When bound along with the transcription factors, RNA polymerase is phosphorylated. This releases part of the protein from the DNA to activate the transcription initiation complex and places RNA polymerase in the correct orientation to begin transcription; DNA-bending protein brings the enhancer, which can be quite a distance from the gene, in contact with transcription factors and mediator proteins ( [link] ). An enhancer is a DNA sequence that promotes transcription. Each enhancer is made up of short DNA sequences called distal control elements. Activators bound to the distal control elements interact with mediator proteins and transcription factors. Two different genes may have the same promoter but different distal control elements, enabling differential gene expression. 

In addition to the general transcription factors, other transcription factors can bind to the promoter to regulate gene transcription. These transcription factors bind to the promoters of a specific set of genes. They are not general transcription factors that bind to every promoter complex, but are recruited to a specific sequence on the promoter of a specific gene. There are hundreds of transcription factors in a cell that each bind specifically to a particular DNA sequence motif. When transcription factors bind to the promoter just upstream of the encoded gene, it is referred to as a cis -acting element , because it is on the same chromosome just next to the gene. The region that a particular transcription factor binds to is called the transcription factor binding site . Transcription factors respond to environmental stimuli that cause the proteins to find their binding sites and initiate transcription of the gene that is needed. Enhancers and Transcription 

In some eukaryotic genes, there are regions that help increase or enhance transcription. These regions, called enhancers , are not necessarily close to the genes they enhance. They can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or may be thousands of nucleotides away. 

Enhancer regions are binding sequences, or sites, for transcription factors. When a DNA-bending protein binds, the shape of the DNA changes ( [link] ). This shape change allows for the interaction of the activators bound to the enhancers with the transcription factors bound to the promoter region and the RNA polymerase. Whereas DNA is generally depicted as a straight line in two dimensions, it is actually a three-dimensional object. Therefore, a nucleotide sequence thousands of nucleotides away can fold over and interact with a specific promoter. Turning Genes Off: Transcriptional Repressors 

Like prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription. Transcriptional repressors can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors. Think About It 

How can cells in a multicellular eukaryotic organism be of different types given that they all share the same genome? 

The question is an application of Learning Objective 3.18 and Science Practice 7.1 and Learning Objective 3.21 and Science Practice 1.4 because students are asked to explain how the regulation of gene expression with the same genome influences cell morphology, function, and products (i.e., cell differentiation/specialization). Answer: Even though the genome within each cell of an organism is the same, when and whether those genes are expressed is controlled by many factors, including transcription factors, enhancers, repressors, and environmental stimuli. This results in different genes being expressed in different cells and allows cells to differentiate and specialize. Section Summary 

To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors to cis -acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription. Review Questions 

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[link] Critical Thinking Questions 

[link] Test Prep for AP Courses 

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[link] Glossary cis -acting element transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it enhancer segment of DNA that is upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence the transcription of a specific gene trans -acting element transcription factor binding site found outside the promoter or on another chromosome that influences the transcription of a particular gene transcription factor binding site sequence of DNA to which a transcription factor bindsEukaryotic Post-transcriptional Gene Regulation Eukaryotic Post-transcriptional Gene Regulation 

In this section, you will explore the following question: How is gene expression controlled through post-transcriptional modifications of RNA molecules? Connection for AP Courses 

Post-transcriptional regulation can occur at any stage after transcription. One important post-transcriptional mechanism is RNA splicing. After RNA is transcribed, it is often modified to create a mature RNA that is ready to be translated. As we studied in previous chapters, processing messenger RNA involves the removal of introns that do not code for protein. Spliceosomes remove the introns and ligate the exons together, often in different sequences than their original order on the newly transcribed (immature) messenger RNA. A GTP cap is added to the 5 -end and a poly-A tail is added to the 3 -end. This mature messenger RNA then leaves the nucleus and enters the cytoplasm. Once in the cytoplasm, the length of time the messenger RNA resides there before being degraded a characteristic lifespan or shelf-life of the molecule called RNA stability can be altered to control the amount of protein that is synthesized. RNA stability is controlled by several factors, including microRNAs (miRNA or RNAi, RNA interference); miRNAs always decrease stability and promote decay of messenger RNA. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.5 The student can evaluate alternative scientific explanations. Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, RNA are the primary source of heritable information. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression. 

Introduce mRNA modifications using videos such as this one about 5'caps and 3'poly-A tails. 

Students may not realize that splicing occurs with variation, not all introns are excised in exactly the same way all of the time. Differential splicing produces different protein products. This one introduces RNA splicing. 

RNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized. RNA Splicing, the First Stage of Post-transcriptional Control 

In eukaryotic cells, the RNA transcript often contains regions, called introns, that are removed prior to translation. The regions of RNA that code for protein are called exons ( [link] ). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing. Pre-mRNA can be alternatively spliced to create different proteins. Alternative RNA Splicing 

In the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns, and sometimes exons, are removed from the transcript ( [link] ). This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells or at different stages of development. Alternative splicing is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70 percent of genes in humans are expressed as multiple proteins through alternative splicing. There are five basic modes of alternative splicing. 

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Visualize how mRNA splicing happens by watching the process in action in this video . 

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What is an evolutionary advantage of alternative gene splicing of introns during post-transcriptional modification of mRNA? 

The question is an application of Learning Objective 3.1 and Science Practice 6.5 and Learning Objective 3.6 and Science Practice 6.4 because students are asked to explain how alternative spicing, i.e., the rearranging on introns following transcription, affects the product(s) produced and why this splicing provides evolutionary advantage(s). Answer: Alternative splicing has many advantages including higher efficiency, because one DNA sequence (one gene) can code for a number of different proteins. It also allows for evolutionary flexibility: different protein isoforms with different functions can be formed through alternative splicing. Control of RNA Stability 

Before the mRNA leaves the nucleus, it is given two protective "caps" that prevent the end of the strand from degrading during its journey. The 5' cap , which is placed on the 5' end of the mRNA, is usually composed of a methylated guanosine triphosphate molecule (GTP). The poly-A tail , which is attached to the 3' end, is usually composed of a series of adenine nucleotides. Once the RNA is transported to the cytoplasm, the length of time that the RNA resides there can be controlled. Each RNA molecule has a defined lifespan and decays at a specific rate. This rate of decay can influence how much protein is in the cell. If the decay rate is increased, the RNA will not exist in the cytoplasm as long, shortening the time for translation to occur. Conversely, if the rate of decay is decreased, the RNA molecule will reside in the cytoplasm longer and more protein can be translated. This rate of decay is referred to as the RNA stability. If the RNA is stable, it will be detected for longer periods of time in the cytoplasm. 

Binding of proteins to the RNA can influence its stability. Proteins, called RNA-binding proteins , or RBPs, can bind to the regions of the RNA just upstream or downstream of the protein-coding region. These regions in the RNA that are not translated into protein are called the untranslated regions , or UTRs. They are not introns (those have been removed in the nucleus). Rather, these are regions that regulate mRNA localization, stability, and protein translation. The region just before the protein-coding region is called the 5' UTR , whereas the region after the coding region is called the 3' UTR ( [link] ). The binding of RBPs to these regions can increase or decrease the stability of an RNA molecule, depending on the specific RBP that binds. The protein-coding region of mRNA is flanked by 5' and 3' untranslated regions (UTRs). The presence of RNA-binding proteins at the 5' or 3' UTR influences the stability of the RNA molecule. RNA Stability and microRNAs 

In addition to RBPs that bind to and control (increase or decrease) RNA stability, other elements called microRNAs can bind to the RNA molecule. These microRNAs , or miRNAs, are short RNA molecules that are only 21 24 nucleotides in length. The miRNAs are made in the nucleus as longer pre-miRNAs. These pre-miRNAs are chopped into mature miRNAs by a protein called dicer . Like transcription factors and RBPs, mature miRNAs recognize a specific sequence and bind to the RNA; however, miRNAs also associate with a ribonucleoprotein complex called the RNA-induced silencing complex (RISC) . RISC binds along with the miRNA to degrade the target mRNA. Together, miRNAs and the RISC complex rapidly destroy the RNA molecule. Section Summary 

Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. The RNA stability can be increased, leading to longer residency time in the cytoplasm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly; however, miRNAs always decrease stability and promote decay. Review Questions 

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[link] Glossary 3' UTR 3' untranslated region; region just downstream of the protein-coding region in an RNA molecule that is not translated 5' cap a methylated guanosine triphosphate (GTP) molecule that is attached to the 5' end of a messenger RNA to protect the end from degradation 5' UTR 5' untranslated region; region just upstream of the protein-coding region in an RNA molecule that is not translated dicer enzyme that chops the pre-miRNA into the mature form of the miRNA microRNA (miRNA) small RNA molecules (approximately 21 nucleotides in length) that bind to RNA molecules to degrade them poly-A tail a series of adenine nucleotides that are attached to the 3' end of an mRNA to protect the end from degradation RNA-binding protein (RBP) protein that binds to the 3' or 5' UTR to increase or decrease the RNA stability RNA stability how long an RNA molecule will remain intact in the cytoplasm untranslated region segment of the RNA molecule that are not translated into protein. These regions lie before (upstream or 5') and after (downstream or 3') the protein-coding region RISC protein complex that binds along with the miRNA to the RNA to degrade itEukaryotic Translational and Post-translational Gene Regulation Eukaryotic Translational and Post-translational Gene Regulation 

In this section, you will explore the following question: What are different ways in which translational and post-translational control of gene expression take place? Connection for AP Courses 

Changing the status of the RNA or the protein itself can affect the amount of protein produced, the function of the protein, or how long the protein resides in the cell. Modifications such as phosphorylation and environmental stimuli can affect the stability and function of the protein. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 4 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 4 Biological systems interact, and these systems and their interactions possess complex properties. 

Enduring Understanding 4.A Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.3 Interactions between external stimuli and regulated gene expression result in specialization of cells, tissues and organs. Science Practice 1.3 The student can refine representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 4.7 The student is able to refine representations to illustrate how interactions between external stimuli and gene expression result in specialization of cells, tissues, and organs. 

Introduce the topic of post-translation gene regulation using visuals such as this video . 

After the RNA has been transported to the cytoplasm, it is translated into protein. Control of this process is largely dependent on the RNA molecule. As previously discussed, the stability of the RNA will have a large impact on its translation into a protein. As the stability changes, the amount of time that it is available for translation also changes. The Initiation Complex and Translation Rate 

Like transcription, translation is controlled by proteins that bind and initiate the process. In translation, the complex that assembles to start the process is referred to as the initiation complex . The first protein to bind to the RNA to initiate translation is the eukaryotic initiation factor-2 (eIF-2) . The eIF-2 protein is active when it binds to the high-energy molecule guanosine triphosphate (GTP) . GTP provides the energy to start the reaction by giving up a phosphate and becoming guanosine diphosphate (GDP) . The eIF-2 protein bound to GTP binds to the small 40S ribosomal subunit . When bound, the methionine initiator tRNA associates with the eIF-2/40S ribosome complex, bringing along with it the mRNA to be translated. At this point, when the initiator complex is assembled, the GTP is converted into GDP and energy is released. The phosphate and the eIF-2 protein are released from the complex and the large 60S ribosomal subunit binds to translate the RNA. The binding of eIF-2 to the RNA is controlled by phosphorylation. If eIF-2 is phosphorylated, it undergoes a conformational change and cannot bind to GTP. Therefore, the initiation complex cannot form properly and translation is impeded ( [link] ). When eIF-2 remains unphosphorylated, it binds the RNA and actively translates the protein. 

Gene expression can be controlled by factors that bind the translation initiation complex. 

[link] Chemical Modifications, Protein Activity, and Longevity 

Proteins can be chemically modified with the addition of groups including methyl, phosphate, acetyl, and ubiquitin groups. The addition or removal of these groups from proteins regulates their activity or the length of time they exist in the cell. Sometimes these modifications can regulate where a protein is found in the cell for example, in the nucleus, the cytoplasm, or attached to the plasma membrane. 

Chemical modifications occur in response to external stimuli such as stress, the lack of nutrients, heat, or ultraviolet light exposure. These changes can alter epigenetic accessibility, transcription, mRNA stability, or translation all resulting in changes in expression of various genes. This is an efficient way for the cell to rapidly change the levels of specific proteins in response to the environment. Because proteins are involved in every stage of gene regulation, the phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications). 

The addition of an ubiquitin group to a protein marks that protein for degradation. Ubiquitin acts like a flag indicating that the protein lifespan is complete. These proteins are moved to the proteasome , an organelle that functions to remove proteins, to be degraded ( [link] ). One way to control gene expression, therefore, is to alter the longevity of the protein. Proteins with ubiquitin tags are marked for degradation within the proteasome. Think About It 

How can environmental stimuli such as ultraviolet light exposure or nutrient deficiency modify gene expression? 

This question is an application of Learning Objective 4.7 and Science Practice 1.3 because, based on the student s knowledge of transcription and translation, the student is describing the means of translational control of gene expression. Answer: Proteins can be chemically modified with the addition of functional groups including methyl, phosphate, acetyl, and ubiquitin groups. The addition or removal of these groups from proteins regulates the protein activity or the length of time the proteins exist in the cell. Sometimes these modifications can regulate where a protein is found in the cell: in the nucleus or cytoplasm or attached to the plasma membrane, for example. Chemical modifications occur in response to external stimuli such as stressors including the lack of nutrients, increases in temperature, or exposure to ultraviolet light. These changes can alter epigenetic accessibility, transcription, mRNA stability, or translation all resulting in changes in expression of various genes. Section Summary 

Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein. Review Questions 

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[link] Glossary eukaryotic initiation factor-2 (eIF-2) protein that binds first to an mRNA to initiate translation guanine diphosphate (GDP) molecule that is left after the energy is used to start translation guanine triphosphate (GTP) energy-providing molecule that binds to eIF-2 and is needed for translation initiation complex protein complex containing eIF2-2 that starts translation large 60S ribosomal subunit second, larger ribosomal subunit that binds to the RNA to translate it into protein proteasome organelle that degrades proteins small 40S ribosomal subunit ribosomal subunit that binds to the RNA to translate it into proteinCancer and Gene Regulation Cancer and Gene Regulation 

In this section, you will explore the following questions: How can changes in gene expression cause cancer? How can changes to gene expression at different levels disrupt the cell cycle? Connection for AP Courses 

Cancer is a disease of altered gene expression that can occur at every level of control, including at the levels of DNA methylation, histone acetylation, and activation of transcription factors. By understanding how each stage of gene regulation works in normal cells, we can understand what goes wrong in diseased states. For example, changes in the activity of the tumor suppressor gene p53 can result in cancer. Phosphorylation and other protein modifications have also been implicated in cancer. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.B Expression of genetic information involves cellular and molecular mechanisms. Essential Knowledge 3.B.2 A variety of intercellular and intracellular signal transmissions mediate gene expression. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 3.22 The student is able to explain how signal pathways mediate gene expression, including how this process can affect protein production. Essential Knowledge 3.B.2 A variety of intercellular and intracellular signal transmissions mediate gene expression. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 3.23 The student can use representations to describe mechanisms of the regulation of gene expression. 

The normal role of the p53 protein is to arrest the cell cycle or to initiate apoptosis in response to stimuli such as DNA damage. 

Introduce the topic of cancer and gene regulation using visuals such as this video . 

Cancer is not a single disease but includes many different diseases. In cancer cells, mutations modify cell-cycle control and cells don t stop growing as they normally would. Mutations can also alter the growth rate or the progression of the cell through the cell cycle. One example of a gene modification that alters the growth rate is increased phosphorylation of cyclin B, a protein that controls the progression of a cell through the cell cycle and serves as a cell-cycle checkpoint protein. 

For cells to move through each phase of the cell cycle, the cell must pass through checkpoints. This ensures that the cell has properly completed the step and has not encountered any mutation that will alter its function. Many proteins, including cyclin B, control these checkpoints. The phosphorylation of cyclin B, a post-translational event, alters its function. As a result, cells can progress through the cell cycle unimpeded, even if mutations exist in the cell and its growth should be terminated. This post-translational change of cyclin B prevents it from controlling the cell cycle and contributes to the development of cancer. Cancer: Disease of Altered Gene Expression 

Cancer can be described as a disease of altered gene expression. There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell. A gene that is not normally expressed in that cell can be switched on and expressed at high levels. This can be the result of gene mutation or changes in gene regulation (epigenetic, transcription, post-transcription, translation, or post-translation). 

Changes in epigenetic regulation, transcription, RNA stability, protein translation, and post-translational control can be detected in cancer. While these changes don t occur simultaneously in one cancer, changes at each of these levels can be detected when observing cancer at different sites in different individuals. Therefore, changes in histone acetylation (epigenetic modification that leads to gene silencing), activation of transcription factors by phosphorylation, increased RNA stability, increased translational control, and protein modification can all be detected at some point in various cancer cells. Scientists are working to understand the common changes that give rise to certain types of cancer or how a modification might be exploited to destroy a tumor cell. Tumor Suppressor Genes, Oncogenes, and Cancer 

In normal cells, some genes function to prevent excess, inappropriate cell growth. These are tumor suppressor genes, which are active in normal cells to prevent uncontrolled cell growth. There are many tumor suppressor genes in cells. The most studied tumor suppressor gene is p53, which is mutated in over 50 percent of all cancer types. The p53 protein itself functions as a transcription factor. It can bind to sites in the promoters of genes to initiate transcription. Therefore, the mutation of p53 in cancer will dramatically alter the transcriptional activity of its target genes. 

Watch this animation to learn more about the use of p53 in fighting cancer. 

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Proto-oncogenes are positive cell-cycle regulators. When mutated, proto-oncogenes can become oncogenes and cause cancer. Overexpression of the oncogene can lead to uncontrolled cell growth. This is because oncogenes can alter transcriptional activity, stability, or protein translation of another gene that directly or indirectly controls cell growth. An example of an oncogene involved in cancer is a protein called myc. Myc is a transcription factor that is aberrantly activated in Burkett s Lymphoma, a cancer of the lymph system. Overexpression of myc transforms normal B cells into cancerous cells that continue to grow uncontrollably. High B-cell numbers can result in tumors that can interfere with normal bodily function. Patients with Burkett s lymphoma can develop tumors on their jaw or in their mouth that interfere with the ability to eat. Cancer and Epigenetic Alterations 

Silencing genes through epigenetic mechanisms is also very common in cancer cells. There are characteristic modifications to histone proteins and DNA that are associated with silenced genes. In cancer cells, the DNA in the promoter region of silenced genes is methylated on cytosine DNA residues in CpG islands. Histone proteins that surround that region lack the acetylation modification that is present when the genes are expressed in normal cells. This combination of DNA methylation and histone deacetylation (epigenetic modifications that lead to gene silencing) is commonly found in cancer. When these modifications occur, the gene present in that chromosomal region is silenced. Increasingly, scientists understand how epigenetic changes are altered in cancer. Because these changes are temporary and can be reversed for example, by preventing the action of the histone deacetylase protein that removes acetyl groups, or by DNA methyl transferase enzymes that add methyl groups to cytosines in DNA it is possible to design new drugs and new therapies to take advantage of the reversible nature of these processes. Indeed, many researchers are testing how a silenced gene can be switched back on in a cancer cell to help re-establish normal growth patterns. 

Genes involved in the development of many other illnesses, ranging from allergies to inflammation to autism, are thought to be regulated by epigenetic mechanisms. As our knowledge of how genes are controlled deepens, new ways to treat diseases like cancer will emerge. Cancer and Transcriptional Control 

Alterations in cells that give rise to cancer can affect the transcriptional control of gene expression. Mutations that activate transcription factors, such as increased phosphorylation, can increase the binding of a transcription factor to its binding site in a promoter. This could lead to increased transcriptional activation of that gene that results in modified cell growth. Alternatively, a mutation in the DNA of a promoter or enhancer region can increase the binding ability of a transcription factor. This could also lead to the increased transcription and aberrant gene expression that is seen in cancer cells. 

Researchers have been investigating how to control the transcriptional activation of gene expression in cancer. Identifying how a transcription factor binds, or a pathway that activates where a gene can be turned off, has led to new drugs and new ways to treat cancer. In breast cancer, for example, many proteins are overexpressed. This can lead to increased phosphorylation of key transcription factors that increase transcription. One such example is the overexpression of the epidermal growth factor receptor (EGFR) in a subset of breast cancers. The EGFR pathway activates many protein kinases that, in turn, activate many transcription factors that control genes involved in cell growth. New drugs that prevent the activation of EGFR have been developed and are used to treat these cancers. Cancer and Post-transcriptional Control 

Changes in the post-transcriptional control of a gene can also result in cancer. Recently, several groups of researchers have shown that specific cancers have altered expression of miRNAs. Because miRNAs bind to the 3' UTR of RNA molecules to degrade them, overexpression of these miRNAs could be detrimental to normal cellular activity. Too many miRNAs could dramatically decrease the RNA population leading to a decrease in protein expression. Several studies have demonstrated a change in the miRNA population in specific cancer types. It appears that the subset of miRNAs expressed in breast cancer cells is quite different from the subset expressed in lung cancer cells or even from normal breast cells. This suggests that alterations in miRNA activity can contribute to the growth of breast cancer cells. These types of studies also suggest that if some miRNAs are specifically expressed only in cancer cells, they could be potential drug targets. It would, therefore, be conceivable that new drugs that turn off miRNA expression in cancer could be an effective method to treat cancer. Cancer and Translational/Post-translational Control 

There are many examples of how translational or post-translational modifications of proteins arise in cancer. Modifications are found in cancer cells from the increased translation of a protein to changes in protein phosphorylation to alternative splice variants of a protein. An example of how the expression of an alternative form of a protein can have dramatically different outcomes is seen in colon cancer cells. The c-Flip protein, a protein involved in mediating the cell death pathway, comes in two forms: long (c-FLIPL) and short (c-FLIPS). Both forms appear to be involved in initiating controlled cell death mechanisms in normal cells. However, in colon cancer cells, expression of the long form results in increased cell growth instead of cell death. Clearly, the expression of the wrong protein dramatically alters cell function and contributes to the development of cancer. New Drugs to Combat Cancer: Targeted Therapies 

Scientists are using what is known about the regulation of gene expression in disease states, including cancer, to develop new ways to treat and prevent disease development. Many scientists are designing drugs on the basis of the gene expression patterns within individual tumors. This idea, that therapy and medicines can be tailored to an individual, has given rise to the field of personalized medicine. With an increased understanding of gene regulation and gene function, medicines can be designed to specifically target diseased cells without harming healthy cells. Some new medicines, called targeted therapies, have exploited the overexpression of a specific protein or the mutation of a gene to develop a new medication to treat disease. One such example is the use of anti-EGF receptor medications to treat the subset of breast cancer tumors that have very high levels of the EGF protein. Undoubtedly, more targeted therapies will be developed as scientists learn more about how gene expression changes can cause cancer. Clinical Trial Coordinator 

A clinical trial coordinator is the person managing the proceedings of the clinical trial. This job includes coordinating patient schedules and appointments, maintaining detailed notes, building the database to track patients (especially for long-term follow-up studies), ensuring proper documentation has been acquired and accepted, and working with the nurses and doctors to facilitate the trial and publication of the results. A clinical trial coordinator may have a science background, like a nursing degree, or other certification. People who have worked in science labs or in clinical offices are also qualified to become a clinical trial coordinator. These jobs are generally in hospitals; however, some clinics and doctor s offices also conduct clinical trials and may hire a coordinator. Think About It 

New drugs are being developed that decrease DNA methylation and prevent the removal of acetyl groups from histone proteins. Explain how these drugs could affect gene expression to help kill tumor cells. 

How can understanding the gene expression in a cancer cell tell you something about that specific form of cancer? 

The first question is an application of Learning Objective 3.22 and Science Practice 6.2 because students are asked to explain how altered gene expression can result in cancer and how drugs that target problems in signaling pathways can treat cancer. 

The second question is an application of Learning Objective 3.22 and Science Practice 6.2 and Learning Objective 3.23 and Science Practice 1.4 because students are explaining the connection between alterations in signaling pathways and alterations in gene expression, and how these changes can result in cancer. Answers: 

These drugs will keep the histone proteins and the DNA methylation patterns in the open chromosomal configuration so that transcription is feasible. If a gene is silenced in the cancer cell, these drugs could reverse the epigenetic configuration to re-express the gene. 

Understanding which genes are expressed in a cancer cell can help diagnose the specific form of cancer. It can also help identify treatment options for that patient. For example, if a breast cancer tumor expresses the epidermal growth factor receptor (EGFR) in high numbers, it might respond to specific anti-EGFR therapy. If this receptor is not expressed, then this cancer will not respond to anti-EGFR therapy. Section Summary 

Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer. Review Questions 

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[link] Glossary DNA methylation epigenetic modification that leads to gene silencing; commonly found in cancer cells histone acetylation epigenetic modification that leads to gene silencing; commonly found in cancer cells found in cancer cells myc oncogene that causes cancer in many cancer cellsIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" In genomics, the DNA of different organisms is compared, enabling scientists to create maps with which to navigate the DNA of different organisms. (credit "map": modification of photo by NASA) 

Some of the greatest accomplishments of biotechnology are in the fields of medicine and medical research. For example, intestinal failure due to missing or abnormal intestinal tissue is a frequent problem in premature babies. Intestinal problems are also common for people who have had parts of their small intestines removed for reasons , such as Crohn s Disease, cancer, and blockages. Complications from intestinal failure may include liver disease, bacterial overgrowth, dehydration, and malnutrition. 

Scientists have recently developed a way to engineer human intestines from human cells using mice. Using a mixture of healthy mouse and human intestinal cells and placing it on scaffolding in the abdominal cavity of immunocompromised mice, functional human intestinal cells grow within four weeks. This could be the breakthrough needed to help patients suffering from intestinal failure. More details about this exciting research can be found here . 

This chapter gives the instructor the opportunity to explore the developments in the areas of biotechnology and genomics for both the good and detriment of individuals and society. The newest developments will have exceeded the scope of this text and will need to be supplemented during the course.Biotechnology Biotechnology 

In this section, you will explore the following questions: What are examples of basic techniques used to manipulate genetic material (DNA and RNA)? What is the difference between molecular and reproductive cloning? What are examples of uses of biotechnology in medicine and agriculture? Connection for AP Courses 

Did you eat cereal for breakfast or tomatoes in your dinner salad? Do you know someone who has received gene therapy to treat a disease such as cancer? Should your school, health insurance provider, or employer have access to your genetic profile? Understanding how DNA works has allowed scientists to recombine DNA molecules, clone organisms, and produce mice that glow in the dark. We likely have eaten genetically modified foods and are familiar with how DNA analysis is used to solve crimes. Manipulation of DNA by humans has resulted in bacteria that can protect plants from insect pests and restore ecosystems. Biotechnologies also have been used to produce insulin, hormones, antibiotics, and medicine that dissolve blood clots. Comparative genomics yields new insights into relationships among species, and DNA sequences reveal our personal genetic make-up. However, manipulation of DNA comes with social and ethical responsibilities, raising questions about its appropriate uses. 

Nucleic acids can be isolated from cells for analysis by lysing cell membranes and enzymatically destroying all other macromolecules. Fragmented or whole chromosomes can be separated on the basis of size (base pair length) by gel electrophoresis. Short sequences of DNA or RNA can be amplified using the polymerase chain reaction (PCR). Recombinant DNA technology can combine DNA from different sources using bacterial plasmids or viruses as vectors to carry foreign genes into host cells, resulting in genetically modified organisms (GMOs). Transgenic bacteria, agricultural plants such as corn and rice, and farm animals produce protein products such as hormones and vaccines that benefit humans. (It is important to remind ourselves that recombinant technology is possible because the genetic code is universal, and the processes of transcription and translation are fundamentally the same in all organisms.) Cloning produces genetically identical copies of DNA, cells, or even entire organisms (reproductive cloning). Genetic testing identifies disease-causing genes, and gene therapy can be used to treat or cure an inheritable disease. However, questions emerge from these technologies including the safety of GMOs and privacy issues. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.5 The student can justify the claim that humans can manipulate heritable information by identifying an example of a commonly used technology. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.C.1 Changes in genotype can result in changes in phenotype. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 3.24 The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection. 

Begin the discussion with the ethical considerations, such as genetic modified foods, the availability of a genome to the government or insurance provider, or modifying a genome for therapy or the sex selection with embryos. These topics will be in the minds of students, so get them out in front and then get into the mechanics of the topic. 

Basic Techniques to Manipulate Genetic Material (DNA and RNA) Go through the process of DNA extraction in class as a demonstration. This would probably be the first time the students would have an opportunity to actually see DNA. Bring in a gel from gel electrophoresis and the results of Southern Blotting as illustrations of the techniques. This will help the discussion be a little more concrete. Be sure that students understand the different uses of the word clone, such as molecular cloning, cellular cloning, reproductive cloning. Emphasize that the word is neutral and does not automatically infer a negative process. Earlier discussions of the ethics of the subject should help to put it into context. 

Biotechnology is the use of biological agents for technological advancement. Biotechnology was used for breeding livestock and crops long before the scientific basis of these techniques was understood. Since the discovery of the structure of DNA in 1953, the field of biotechnology has grown rapidly through both academic research and private companies. The primary applications of this technology are in medicine (production of vaccines and antibiotics) and agriculture (genetic modification of crops, such as to increase yields). Biotechnology also has many industrial applications, such as fermentation, the treatment of oil spills, and the production of biofuels ( [link] ). Antibiotics are chemicals produced by fungi, bacteria, and other organisms that have antimicrobial properties. The first antibiotic discovered was penicillin. Antibiotics are now commercially produced and tested for their potential to inhibit bacterial growth. (credit "advertisement": modification of work by NIH; credit "test plate": modification of work by Don Stalons/CDC; scale-bar data from Matt Russell) Basic Techniques to Manipulate Genetic Material (DNA and RNA) 

To understand the basic techniques used to work with nucleic acids, remember that nucleic acids are macromolecules made of nucleotides (a sugar, a phosphate, and a nitrogenous base) linked by phosphodiester bonds. The phosphate groups on these molecules each have a net negative charge. An entire set of DNA molecules in the nucleus is called the genome. DNA has two complementary strands linked by hydrogen bonds between the paired bases. The two strands can be separated by exposure to high temperatures (DNA denaturation) and can be reannealed by cooling. The DNA can be replicated by the DNA polymerase enzyme. Unlike DNA, which is located in the nucleus of eukaryotic cells, RNA molecules leave the nucleus. The most common type of RNA that is analyzed is the messenger RNA (mRNA) because it represents the protein-coding genes that are actively expressed. However, RNA molecules present some other challenges to analysis, as they are often less stable than DNA. DNA and RNA Extraction 

To study or manipulate nucleic acids, the DNA or RNA must first be isolated or extracted from the cells. Various techniques are used to extract different types of DNA ( [link] ). Most nucleic acid extraction techniques involve steps to break open the cell and use enzymatic reactions to destroy all macromolecules that are not desired (such as degradation of unwanted molecules and separation from the DNA sample). Cells are broken using a lysis buffer (a solution which is mostly a detergent); lysis means to split. These enzymes break apart lipid molecules in the cell membranes and nuclear membranes. Macromolecules are inactivated using enzymes such as proteases that break down proteins, and ribonucleases (RNAses) that break down RNA. The DNA is then precipitated using alcohol. Human genomic DNA is usually visible as a gelatinous, white mass. The DNA samples can be stored frozen at 80 C for several years. This diagram shows the basic method used for extraction of DNA. 

RNA analysis is performed to study gene expression patterns in cells. RNA is naturally very unstable because RNAses are commonly present in nature and very difficult to inactivate. Similar to DNA, RNA extraction involves the use of various buffers and enzymes to inactivate macromolecules and preserve the RNA. Gel Electrophoresis 

Because nucleic acids are negatively charged ions at neutral or basic pH in an aqueous environment, they can be mobilized by an electric field. Gel electrophoresis is a technique used to separate molecules on the basis of size, using this charge. The nucleic acids can be separated as whole chromosomes or fragments. The nucleic acids are loaded into a slot near the negative electrode of a semisolid, porous gel matrix and pulled toward the positive electrode at the opposite end of the gel. Smaller molecules move through the pores in the gel faster than larger molecules; this difference in the rate of migration separates the fragments on the basis of size. There are molecular weight standard samples that can be run alongside the molecules to provide a size comparison. Nucleic acids in a gel matrix can be observed using various fluorescent or colored dyes. Distinct nucleic acid fragments appear as bands at specific distances from the top of the gel (the negative electrode end) on the basis of their size ( [link] ). A mixture of genomic DNA fragments of varying sizes appear as a long smear, whereas uncut genomic DNA is usually too large to run through the gel and forms a single large band at the top of the gel. Shown are DNA fragments from seven samples run on a gel, stained with a fluorescent dye, and viewed under UV light. (credit: James Jacob, Tompkins Cortland Community College) Amplification of Nucleic Acid Fragments by Polymerase Chain Reaction 

Although genomic DNA is visible to the naked eye when it is extracted in bulk, DNA analysis often requires focusing on one or more specific regions of the genome. Polymerase chain reaction ( PCR ) is a technique used to amplify specific regions of DNA for further analysis ( [link] ). PCR is used for many purposes in laboratories, such as the cloning of gene fragments to analyze genetic diseases, identification of contaminant foreign DNA in a sample, and the amplification of DNA for sequencing. More practical applications include the determination of paternity and detection of genetic diseases. Polymerase chain reaction, or PCR, is used to amplify a specific sequence of DNA. Primers short pieces of DNA complementary to each end of the target sequence are combined with genomic DNA, Taq polymerase, and deoxynucleotides. Taq polymerase is a DNA polymerase isolated from the thermostable bacterium Thermus aquaticus that is able to withstand the high temperatures used in PCR. Thermus aquaticus grows in the Lower Geyser Basin of Yellowstone National Park. Reverse transcriptase PCR (RT-PCR) is similar to PCR, but cDNA is made from an RNA template before PCR begins. 

DNA fragments can also be amplified from an RNA template in a process called reverse transcriptase PCR (RT-PCR) . The first step is to recreate the original DNA template strand (called cDNA) by applying DNA nucleotides to the mRNA. This process is called reverse transcription. This requires the presence of an enzyme called reverse transcriptase. After the cDNA is made, regular PCR can be used to amplify it. 

Deepen your understanding of the polymerase chain reaction by clicking through this interactive exercise . 

[link] Hybridization, Southern Blotting, and Northern Blotting 

Nucleic acid samples, such as fragmented genomic DNA and RNA extracts, can be probed for the presence of certain sequences. Short DNA fragments called probes are designed and labeled with radioactive or fluorescent dyes to aid detection. Gel electrophoresis separates the nucleic acid fragments according to their size. The fragments in the gel are then transferred onto a nylon membrane in a procedure called blotting ( [link] ). The nucleic acid fragments that are bound to the surface of the membrane can then be probed with specific radioactively or fluorescently labeled probe sequences. When DNA is transferred to a nylon membrane, the technique is called Southern blotting , and when RNA is transferred to a nylon membrane, it is called northern blotting . Southern blots are used to detect the presence of certain DNA sequences in a given genome, and northern blots are used to detect gene expression. Southern blotting is used to find a particular sequence in a sample of DNA. DNA fragments are separated on a gel, transferred to a nylon membrane, and incubated with a DNA probe complementary to the sequence of interest. Northern blotting is similar to Southern blotting, but RNA is run on the gel instead of DNA. In western blotting, proteins are run on a gel and detected using antibodies. Molecular Cloning 

In general, the word cloning means the creation of a perfect replica; however, in biology, the re-creation of a whole organism is referred to as reproductive cloning. Long before attempts were made to clone an entire organism, researchers learned how to reproduce desired regions or fragments of the genome, a process that is referred to as molecular cloning. 

Cloning small fragments of the genome allows for the manipulation and study of specific genes (and their protein products), or noncoding regions in isolation. A plasmid (also called a vector) is a small circular DNA molecule that replicates independently of the chromosomal DNA. In cloning, the plasmid molecules can be used to provide a "folder" in which to insert a desired DNA fragment. Plasmids are usually introduced into a bacterial host for proliferation. In the bacterial context, the fragment of DNA from the human genome (or the genome of another organism that is being studied) is referred to as foreign DNA , or a transgene, to differentiate it from the DNA of the bacterium, which is called the host DNA . 

Plasmids occur naturally in bacterial populations (such as Escherichia coli ) and have genes that can contribute favorable traits to the organism, such as antibiotic resistance (the ability to be unaffected by antibiotics). Plasmids have been repurposed and engineered as vectors for molecular cloning and the large-scale production of important reagents, such as insulin and human growth hormone. An important feature of plasmid vectors is the ease with which a foreign DNA fragment can be introduced via the multiple cloning site (MCS) . The MCS is a short DNA sequence containing multiple sites that can be cut with different commonly available restriction endonucleases. Restriction endonucleases recognize specific DNA sequences and cut them in a predictable manner; they are naturally produced by bacteria as a defense mechanism against foreign DNA. Many restriction endonucleases make staggered cuts in the two strands of DNA, such that the cut ends have a 2- or 4-base single-stranded overhang. Because these overhangs are capable of annealing with complementary overhangs, these are called sticky ends. Addition of an enzyme called DNA ligase permanently joins the DNA fragments via phosphodiester bonds. In this way, any DNA fragment generated by restriction endonuclease cleavage can be spliced between the two ends of a plasmid DNA that has been cut with the same restriction endonuclease ( [link] ). Recombinant DNA Molecules 

Plasmids with foreign DNA inserted into them are called recombinant DNA molecules because they are created artificially and do not occur in nature. They are also called chimeric molecules because the origin of different parts of the molecules can be traced back to different species of biological organisms or even to chemical synthesis. Proteins that are expressed from recombinant DNA molecules are called recombinant proteins . Not all recombinant plasmids are capable of expressing genes. The recombinant DNA may need to be moved into a different vector (or host) that is better designed for gene expression. Plasmids may also be engineered to express proteins only when stimulated by certain environmental factors, so that scientists can control the expression of the recombinant proteins. 

This diagram shows the steps involved in molecular cloning. 

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View an animation of recombination in cloning from the DNA Learning Center. 

[link] Activity 

Cloning can be used to quickly replicate crop plants that have advantageous genes, such as greater disease resistance or greater fruit production. However, cloning also produces crop plants that have little genetic variation. In a group, discuss the advantages and disadvantages of using clones as human food sources in an era where the Earth is undergoing a period of climate change. How well will cloned populations of crop plants be able to adapt to climate change, compared to non-clone crop plants? Then, defend your group s position against those of other groups in a classroom debate. Think About It 

How would a scientist introduce a gene for herbicide resistance into a plant, such as corn? 

Suggested group size for the activity is 3 6 students. Guide student groups to think about climate change as a natural selection pressure that will affect the success of the clones. By using crop plants with little genetic variation, there is little potential that these plants to withstand an environmental change such as rapid, human-induced global warming. 

The activity is an application of Learning Objective 3.5 and Science Practice 6.4 because students are discussing the justification for cloning crop plants and then predicting how climate change will act as a selection pressure on the clones. 

The Think About It question is an application of Learning Objective 3.5 and Science Practice 6.4 because the technique for introducing new genes into an organism is an example of how heritable information can be manipulated. 

An expanded lab investigation for biotechnology, involving performing a genetic transformation on E. coli , is available from the College Board s AP Biology Investigative Labs: An Inquiry-Based Approach in Investigation 8 . Answer: Alter a plant RNA virus to contain the gene for herbicide resistance. Use the virus as a vector to place the gene into appropriate plants. 

Genetic engineering is as old as farming. Discuss the efforts that were made by farmers to develop better crops before technology gave its assistance. Discuss how technology has increased the changes in crops worldwide. What is the evidence for possible benefits and possible hazards of the development of genetically modified crops (GMO s)? Cellular Cloning 

Unicellular organisms, such as bacteria and yeast, naturally produce clones of themselves when they replicate asexually by binary fission; this is known as cellular cloning . The nuclear DNA duplicates by the process of mitosis, which creates an exact replica of the genetic material. Reproductive Cloning 

Reproductive cloning is a method used to make a clone or an identical copy of an entire multicellular organism. Most multicellular organisms undergo reproduction by sexual means, which involves genetic hybridization of two individuals (parents), making it impossible for generation of an identical copy or a clone of either parent. Recent advances in biotechnology have made it possible to artificially induce asexual reproduction of mammals in the laboratory. 

Parthenogenesis, or virgin birth, occurs when an embryo grows and develops without the fertilization of the egg occurring; this is a form of asexual reproduction. An example of parthenogenesis occurs in species in which the female lays an egg and if the egg is fertilized, it is a diploid egg and the individual develops into a female; if the egg is not fertilized, it remains a haploid egg and develops into a male. The unfertilized egg is called a parthenogenic, or virgin, egg. Some insects and reptiles lay parthenogenic eggs that can develop into adults. 

Sexual reproduction requires two cells; when the haploid egg and sperm cells fuse, a diploid zygote results. The zygote nucleus contains the genetic information to produce a new individual. However, early embryonic development requires the cytoplasmic material contained in the egg cell. This idea forms the basis for reproductive cloning. Therefore, if the haploid nucleus of an egg cell is replaced with a diploid nucleus from the cell of any individual of the same species (called a donor), it will become a zygote that is genetically identical to the donor. Somatic cell nuclear transfer is the technique of transferring a diploid nucleus into an enucleated egg. It can be used for either therapeutic cloning or reproductive cloning. 

The first cloned animal was Dolly, a sheep who was born in 1996. The success rate of reproductive cloning at the time was very low. Dolly lived for seven years and died of respiratory complications ( [link] ). There is speculation that because the cell DNA belongs to an older individual, the age of the DNA may affect the life expectancy of a cloned individual. Since Dolly, several animals such as horses, bulls, and goats have been successfully cloned, although these individuals often exhibit facial, limb, and cardiac abnormalities. There have been attempts at producing cloned human embryos as sources of embryonic stem cells, sometimes referred to as cloning for therapeutic purposes. Therapeutic cloning produces stem cells to attempt to remedy detrimental diseases or defects (unlike reproductive cloning, which aims to reproduce an organism). Still, therapeutic cloning efforts have met with resistance because of bioethical considerations. 

Dolly the sheep was the first mammal to be cloned. To create Dolly, the nucleus was removed from a donor egg cell. The nucleus from a second sheep was then introduced into the cell, which was allowed to divide to the blastocyst stage before being implanted in a surrogate mother. (credit: modification of work by "Squidonius"/Wikimedia Commons) 

[link] Genetic Engineering 

Genetic engineering is the alteration of an organism s genotype using recombinant DNA technology to modify an organism s DNA to achieve desirable traits. The addition of foreign DNA in the form of recombinant DNA vectors generated by molecular cloning is the most common method of genetic engineering. The organism that receives the recombinant DNA is called a genetically modified organism (GMO). If the foreign DNA that is introduced comes from a different species, the host organism is called transgenic . Bacteria, plants, and animals have been genetically modified since the early 1970s for academic, medical, agricultural, and industrial purposes. In the US, GMOs such as Roundup-ready soybeans and borer-resistant corn are part of many common processed foods. Gene Targeting 

Although classical methods of studying the function of genes began with a given phenotype and determined the genetic basis of that phenotype, modern techniques allow researchers to start at the DNA sequence level and ask: "What does this gene or DNA element do?" This technique, called reverse genetics, has resulted in reversing the classic genetic methodology. This method would be similar to damaging a body part to determine its function. An insect that loses a wing cannot fly, which means that the function of the wing is flight. The classical genetic method would compare insects that cannot fly with insects that can fly, and observe that the non-flying insects have lost wings. Similarly, mutating or deleting genes provides researchers with clues about gene function. The methods used to disable gene function are collectively called gene targeting. Gene targeting is the use of recombinant DNA vectors to alter the expression of a particular gene, either by introducing mutations in a gene, or by eliminating the expression of a certain gene by deleting a part or all of the gene sequence from the genome of an organism. Biotechnology in Medicine and Agriculture 

It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our species, the genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes provides methods to treat the disease. Biotechnology in agriculture can enhance resistance to disease, pest, and environmental stress, and improve both crop yield and quality. Genetic Diagnosis and Gene Therapy 

The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by genetic testing . Depending on the inheritance patterns of a disease-causing gene, family members are advised to undergo genetic testing. For example, women diagnosed with breast cancer are usually advised to have a biopsy so that the medical team can determine the genetic basis of cancer development. Treatment plans are based on the findings of genetic tests that determine the type of cancer. If the cancer is caused by inherited gene mutations, other female relatives are also advised to undergo genetic testing and periodic screening for breast cancer. Genetic testing is also offered for fetuses (or embryos with in vitro fertilization) to determine the presence or absence of disease-causing genes in families with specific debilitating diseases. 

Gene therapy is a genetic engineering technique used to cure disease. In its simplest form, it involves the introduction of a good gene at a random location in the genome to aid the cure of a disease that is caused by a mutated gene. The good gene is usually introduced into diseased cells as part of a vector transmitted by a virus that can infect the host cell and deliver the foreign DNA ( [link] ). More advanced forms of gene therapy try to correct the mutation at the original site in the genome, such as is the case with treatment of severe combined immunodeficiency (SCID). Gene therapy using an adenovirus vector can be used to cure certain genetic diseases in which a person has a defective gene. (credit: NIH) Production of Vaccines, Antibiotics, and Hormones 

Traditional vaccination strategies use weakened or inactive forms of microorganisms to mount the initial immune response. Modern techniques use the genes of microorganisms cloned into vectors to mass produce the desired antigen. The antigen is then introduced into the body to stimulate the primary immune response and trigger immune memory. Genes cloned from the influenza virus have been used to combat the constantly changing strains of this virus. 

Antibiotics are a biotechnological product. They are naturally produced by microorganisms, such as fungi, to attain an advantage over bacterial populations. Antibiotics are produced on a large scale by cultivating and manipulating fungal cells. 

Recombinant DNA technology was used to produce large-scale quantities of human insulin in E. coli as early as 1978. Previously, it was only possible to treat diabetes with pig insulin, which caused allergic reactions in humans because of differences in the gene product. In addition, human growth hormone (HGH) is used to treat growth disorders in children. The HGH gene was cloned from a cDNA library and inserted into E. coli cells by cloning it into a bacterial vector. Transgenic Animals 

Although several recombinant proteins used in medicine are successfully produced in bacteria, some proteins require a eukaryotic animal host for proper processing. For this reason, the desired genes are cloned and expressed in animals, such as sheep, goats, chickens, and mice. Animals that have been modified to express recombinant DNA are called transgenic animals. Several human proteins are expressed in the milk of transgenic sheep and goats, and some are expressed in the eggs of chickens. Mice have been used extensively for expressing and studying the effects of recombinant genes and mutations. Transgenic Plants 

Manipulating the DNA of plants (i.e., creating GMOs) has helped to create desirable traits, such as disease resistance, herbicide and pesticide resistance, better nutritional value, and better shelf-life ( [link] ). Plants are the most important source of food for the human population. Farmers developed ways to select for plant varieties with desirable traits long before modern-day biotechnology practices were established. Corn, a major agricultural crop used to create products for a variety of industries, is often modified through plant biotechnology. (credit: Keith Weller, USDA) 

Plants that have received recombinant DNA from other species are called transgenic plants. Because they are not natural, transgenic plants and other GMOs are closely monitored by government agencies to ensure that they are fit for human consumption and do not endanger other plant and animal life. Because foreign genes can spread to other species in the environment, extensive testing is required to ensure ecological stability. Staples like corn, potatoes, and tomatoes were the first crop plants to be genetically engineered. Transformation of Plants Using Agrobacterium tumefaciens 

Gene transfer occurs naturally between species in microbial populations. Many viruses that cause human diseases, such as cancer, act by incorporating their DNA into the human genome. In plants, tumors caused by the bacterium Agrobacterium tumefaciens occur by transfer of DNA from the bacterium to the plant. Although the tumors do not kill the plants, they make the plants stunted and more susceptible to harsh environmental conditions. Many plants, such as walnuts, grapes, nut trees, and beets, are affected by A. tumefaciens . The artificial introduction of DNA into plant cells is more challenging than in animal cells because of the thick plant cell wall. 

Researchers used the natural transfer of DNA from Agrobacterium to a plant host to introduce DNA fragments of their choice into plant hosts. In nature, the disease-causing A. tumefaciens have a set of plasmids, called the Ti plasmids (tumor-inducing plasmids), that contain genes for the production of tumors in plants. DNA from the Ti plasmid integrates into the infected plant cell s genome. Researchers manipulate the Ti plasmids to remove the tumor-causing genes and insert the desired DNA fragment for transfer into the plant genome. The Ti plasmids carry antibiotic resistance genes to aid selection and can be propagated in E. coli cells as well. The Organic Insecticide Bacillus thuringiensis 

Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals during sporulation that are toxic to many insect species that affect plants. Bt toxin has to be ingested by insects for the toxin to be activated. Insects that have eaten Bt toxin stop feeding on the plants within a few hours. After the toxin is activated in the intestines of the insects, death occurs within a couple of days. Modern biotechnology has allowed plants to encode their own crystal Bt toxin that acts against insects. The crystal toxin genes have been cloned from Bt and introduced into plants. Bt toxin has been found to be safe for the environment, non-toxic to humans and other mammals, and is approved for use by organic farmers as a natural insecticide. Flavr Savr Tomato 

The first GM crop to be introduced into the market was the Flavr Savr Tomato produced in 1994. Antisense RNA technology was used to slow down the process of softening and rotting caused by fungal infections, which led to increased shelf life of the GM tomatoes. Additional genetic modification improved the flavor of this tomato. The Flavr Savr tomato did not successfully stay in the market because of problems maintaining and shipping the crop. Section Summary 

Nucleic acids can be isolated from cells for the purposes of further analysis by breaking open the cells and enzymatically destroying all other major macromolecules. Fragmented or whole chromosomes can be separated on the basis of size by gel electrophoresis. Short stretches of DNA or RNA can be amplified by PCR. Southern and northern blotting can be used to detect the presence of specific short sequences in a DNA or RNA sample. The term cloning may refer to cloning small DNA fragments (molecular cloning), cloning cell populations (cellular cloning), or cloning entire organisms (reproductive cloning). Genetic testing is performed to identify disease-causing genes, and gene therapy is used to cure an inheritable disease. 

Transgenic organisms possess DNA from a different species, usually generated by molecular cloning techniques. Vaccines, antibiotics, and hormones are examples of products obtained by recombinant DNA technology. Transgenic plants are usually created to improve characteristics of crop plants. Review Questions 

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[link] Glossary antibiotic resistance ability of an organism to be unaffected by the actions of an antibiotic biotechnology use of biological agents for technological advancement cellular cloning production of identical cell populations by binary fission clone exact replica foreign DNA DNA that belongs to a different species or DNA that is artificially synthesized gel electrophoresis technique used to separate molecules on the basis of size using electric charge gene targeting method for altering the sequence of a specific gene by introducing the modified version on a vector gene therapy technique used to cure inheritable diseases by replacing mutant genes with good genes genetic diagnosis diagnosis of the potential for disease development by analyzing disease-causing genes genetic engineering alteration of the genetic makeup of an organism genetic testing process of testing for the presence of disease-causing genes genetically modified organism (GMO) organism whose genome has been artificially changed host DNA DNA that is present in the genome of the organism of interest lysis buffer solution used to break the cell membrane and release cell contents molecular cloning cloning of DNA fragments multiple cloning site (MCS) site that can be recognized by multiple restriction endonucleases northern blotting transfer of RNA from a gel to a nylon membrane polymerase chain reaction (PCR) technique used to amplify DNA probe small DNA fragment used to determine if the complementary sequence is present in a DNA sample protease enzyme that breaks down proteins recombinant DNA combination of DNA fragments generated by molecular cloning that does not exist in nature; also known as a chimeric molecule recombinant protein protein product of a gene derived by molecular cloning reproductive cloning cloning of entire organisms restriction endonuclease enzyme that can recognize and cleave specific DNA sequences reverse genetics method of determining the function of a gene by starting with the gene itself instead of starting with the gene product reverse transcriptase PCR (RT-PCR) PCR technique that involves converting RNA to DNA by reverse transcriptase ribonuclease enzyme that breaks down RNA Southern blotting transfer of DNA from a gel to a nylon membrane Ti plasmid plasmid system derived from Agrobacterium tumifaciens that has been used by scientists to introduce foreign DNA into plant cells transgenic organism that receives DNA from a different speciesMapping Genomes Mapping Genomes 

In this section, you will explore the following questions: What is genomics? What is a genetic map? What is an example of a genomic mapping method? Connection for AP Courses 

Genome mapping is similar to solving a big, complicated puzzle with pieces of information collected from laboratories all over the world. Genetic maps provide an outline for the location of genes within a chromosome. Distances between genes and genetic markers are estimated on the basis of recombination (crossing over) frequencies during meiosis. The Human Genome Project helped researchers identify thousands of human genes and their protein products. Noncoding regions of DNA may be involved in regulating gene expression, and other sequences once considered junk may play an important role in genome evolution. Few differences exist between human DNA sequences and those of many other organisms. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. 

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 

Enduring Understanding 3.A Heritable information provides for continuity of life. Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.5 The student can justify the claim that humans can manipulate heritable information by identifying examples of commonly used technologies. Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 3.10 The student is able to represent the connection between meiosis and increased genetic diversity necessary for evolution. Essential Knowledge 3.A.3 The chromosomal basis of inheritance provides an understanding of the pattern of passage (transmission) of genes from parent to offspring. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. 

Mapping is the first step in examining the genome of an organism. Some of the techniques have been used for years while others were developed with the advances in technology. In addition to discussing the details of this subject, this may be a good time to discuss the genetic similarities between races of people and between humans and other organisms. A very good movie about this has been put out by PBS, here . Obtain examples of genetic and physical maps and cytogenetic maps for humans and other species to use in general teaching and in the discussions suggested above. 

Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. Genome mapping is the process of finding the locations of genes on each chromosome. The maps created by genome mapping are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that co-segregates (shows genetic linkage) with a specific trait. Early geneticists called this linkage analysis. Physical maps present the intimate details of smaller regions of the chromosomes (similar to a detailed road map). A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers. Both genetic linkage maps and physical maps are required to build a complete picture of the genome. Having a complete map of the genome makes it easier for researchers to study individual genes. Human genome maps help researchers in their efforts to identify human disease-causing genes related to illnesses like cancer, heart disease, and cystic fibrosis. Genome mapping can be used in a variety of other applications, such as using live microbes to clean up pollutants or even prevent pollution. Research involving plant genome mapping may lead to producing higher crop yields or developing plants that better adapt to climate change. Genetic Maps 

The study of genetic maps begins with linkage analysis , a procedure that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. The term linkage was used before the discovery of DNA. Early geneticists relied on the observation of phenotypic changes to understand the genotype of an organism. Shortly after Gregor Mendel (the father of modern genetics) proposed that traits were determined by what are now known as genes, other researchers observed that different traits were often inherited together, and thereby deduced that the genes were physically linked by being located on the same chromosome. The mapping of genes relative to each other based on linkage analysis led to the development of the first genetic maps. 

Observations that certain traits were always linked and certain others were not linked came from studying the offspring of crosses between parents with different traits. For example, in experiments performed on the garden pea, it was discovered that the color of the flower and shape of the plant s pollen were linked traits, and therefore the genes encoding these traits were in close proximity on the same chromosome. The exchange of DNA between homologous pairs of chromosomes is called genetic recombination , which occurs by the crossing over of DNA between homologous strands of DNA, such as nonsister chromatids. Linkage analysis involves studying the recombination frequency between any two genes. The greater the distance between two genes, the higher the chance that a recombination event will occur between them, and the higher the recombination frequency between them. Two possibilities for recombination between two nonsister chromatids during meiosis are shown in [link] . If the recombination frequency between two genes is less than 50 percent, they are said to be linked. Crossover may occur at different locations on the chromosome. Recombination between genes A and B is more frequent than recombination between genes B and C because genes A and B are farther apart; a crossover is therefore more likely to occur between them. 

The generation of genetic maps requires markers, just as a road map requires landmarks (such as rivers and mountains). Early genetic maps were based on the use of known genes as markers. More sophisticated markers, including those based on non-coding DNA, are now used to compare the genomes of individuals in a population. Although individuals of a given species are genetically similar, they are not identical; every individual has a unique set of traits. These minor differences in the genome between individuals in a population are useful for the purposes of genetic mapping. In general, a good genetic marker is a region on the chromosome that shows variability or polymorphism (multiple forms) in the population. 

Some genetic markers used in generating genetic maps are restriction fragment length polymorphisms (RFLP), variable number of tandem repeats (VNTRs), microsatellite polymorphisms , and the single nucleotide polymorphisms (SNPs). RFLPs (sometimes pronounced rif-lips ) are detected when the DNA of an individual is cut with a restriction endonuclease that recognizes specific sequences in the DNA to generate a series of DNA fragments, which are then analyzed by gel electrophoresis. The DNA of every individual will give rise to a unique pattern of bands when cut with a particular set of restriction endonucleases; this is sometimes referred to as an individual s DNA fingerprint. Certain regions of the chromosome that are subject to polymorphism will lead to the generation of the unique banding pattern. VNTRs are repeated sets of nucleotides present in the non-coding regions of DNA. Non-coding, or junk, DNA has no known biological function; however, research shows that much of this DNA is actually transcribed. While its function is uncertain, it is certainly active, and it may be involved in the regulation of coding genes. The number of repeats may vary in individual organisms of a population. Microsatellite polymorphisms are similar to VNTRs, but the repeat unit is very small. SNPs are variations in a single nucleotide. 

Because genetic maps rely completely on the natural process of recombination, mapping is affected by natural increases or decreases in the level of recombination in any given area of the genome. Some parts of the genome are recombination hotspots, whereas others do not show a propensity for recombination. For this reason, it is important to look at mapping information developed by multiple methods. Physical Maps 

A physical map provides detail of the actual physical distance between genetic markers, as well as the number of nucleotides. There are three methods used to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping. Cytogenetic mapping uses information obtained by microscopic analysis of stained sections of the chromosome ( [link] ). It is possible to determine the approximate distance between genetic markers using cytogenetic mapping, but not the exact distance (number of base pairs). Radiation hybrid mapping uses radiation, such as x-rays, to break the DNA into fragments. The amount of radiation can be adjusted to create smaller or larger fragments. This technique overcomes the limitation of genetic mapping and is not affected by increased or decreased recombination frequency. Sequence mapping resulted from DNA sequencing technology that allowed for the creation of detailed physical maps with distances measured in terms of the number of base pairs. The creation of genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped up the process of physical mapping. A genetic site used to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location. An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs. An EST is a short STS that is identified with cDNA libraries, while SSLPs are obtained from known genetic markers and provide a link between genetic maps and physical maps. A cytogenetic map shows the appearance of a chromosome after it is stained and examined under a microscope. (credit: National Human Genome Research Institute) Integration of Genetic and Physical Maps 

Genetic maps provide the outline and physical maps provide the details. It is easy to understand why both types of genome mapping techniques are important to show the big picture. Information obtained from each technique is used in combination to study the genome. Genomic mapping is being used with different model organisms that are used for research. Genome mapping is still an ongoing process, and as more advanced techniques are developed, more advances are expected. Genome mapping is similar to completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories all over the world is entered into central databases, such as GenBank at the National Center for Biotechnology Information (NCBI). Efforts are being made to make the information more easily accessible to researchers and the general public. Just as we use global positioning systems instead of paper maps to navigate through roadways, NCBI has created a genome viewer tool to simplify the data-mining process. 

How to Use a Genome Map Viewer 

Problem statement: Do the human, macaque, and mouse genomes contain common DNA sequences? 

Develop a hypothesis. 

To test the hypothesis, click this link . 

In Search box on the left panel, type any gene name or phenotypic characteristic, such as iris pigmentation (eye color). Select the species you want to study, and then press Enter. The genome map viewer will indicate which chromosome encodes the gene in your search. Click each hit in the genome viewer for more detailed information. This type of search is the most basic use of the genome viewer; it can also be used to compare sequences between species, as well as many other complicated tasks. 

Is the hypothesis correct? Why or why not? 

Online Mendelian Inheritance in Man (OMIM) is a searchable online catalog of human genes and genetic disorders. This website shows genome mapping information, and also details the history and research of each trait and disorder. Click this link to search for traits (such as handedness) and genetic disorders (such as diabetes). 

[link] Think About It 

Why is so much effort being poured into genome mapping applications? How could a genetic map of the human genome help find a treatment for genetically based cancers? 

The questions are applications of Learning Objectives 3.5 and Science Practice 6.4 because mapping the human genome and possibly altering it are examples of how humans can manipulate heritable information. 

Answer 

A genetic map of the human genome for multiple individuals could identify alleles of genes that are susceptible to agents that could cause cancer. The mapping could also identify allele variations that are resistant to changes that result in cancer, thereby offering the opportunity of genetic therapy for the disorders. Section Summary 

Genome mapping is similar to solving a big, complicated puzzle with pieces of information coming from laboratories all over the world. Genetic maps provide an outline for the location of genes within a genome, and they estimate the distance between genes and genetic markers on the basis of recombination frequencies during meiosis. Physical maps provide detailed information about the physical distance between the genes. The most detailed information is available through sequence mapping. Information from all mapping and sequencing sources is combined to study an entire genome. Review Questions 

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[link] Glossary cytogenetic mapping technique that uses a microscope to create a map from stained chromosomes expressed sequence tag (EST) short STS that is identified with cDNA genetic map outline of genes and their location on a chromosome genetic marker gene or sequence on a chromosome with a known location that is associated with a specific trait genetic recombination exchange of DNA between homologous pairs of chromosomes genome mapping process of finding the location of genes on each chromosome cDNA library collection of cloned cDNA sequences genomic library collection of cloned DNA which represents all of the sequences and fragments from a genome genomics study of entire genomes including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species linkage analysis procedure that analyzes the recombination of genes to determine if they are linked microsatellite polymorphism variation between individuals in the sequence and number of repeats of microsatellite DNA physical map representation of the physical distance between genes or genetic markers radiation hybrid mapping information obtained by fragmenting the chromosome with x-rays restriction fragment length polymorphism (RFLP) variation between individuals in the length of DNA fragments generated by restriction endonucleases sequence mapping mapping information obtained after DNA sequencing single nucleotide polymorphism (SNP) variation between individuals in a single nucleotide variable number of tandem repeats (VNTRs) variation in the number of tandem repeats between individuals in the populationWhole-Genome Sequencing Whole-Genome Sequencing 

In this section, you will explore the following questions: What are three types of gene sequencing? What is whole-genome sequencing? Connection for AP Courses 

Information presented in section is not in scope for AP . However, you can study information in the section as optional or illustrative material. 

With older techniques, identification of pathogenic bacteria is a time consuming process that may take days or weeks. Previously, identification of the tuberculosis bacteria can take up to six weeks. The development of DNA microarrays has enabled clinical laboratories to shorten that time to hours, with better specificity of the identification. This has provided physicians with the information they need to get patients on the most effective antibiotic therapy rapidly, providing better care and preventing the infectious agent from spreading to more hosts. 

Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by some diseases, and they are using whole-genome sequencing to get to the bottom of the problem. Whole-genome sequencing is a process that determines the DNA sequence of an entire genome. Whole-genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease. Several laboratories now provide services to sequence, analyze, and interpret entire genomes. 

For example, whole-exome sequencing is a lower-cost alternative to whole genome sequencing. In exome sequencing, only the coding, exon-producing regions of the DNA are sequenced. In 2010, whole-exome sequencing was used to save a young boy whose intestines had multiple mysterious abscesses. The child had several colon operations with no relief. Finally, whole-exome sequencing was performed, which revealed a defect in a pathway that controls apoptosis (programmed cell death). A bone-marrow transplant was used to overcome this genetic disorder, leading to a cure for the boy. He was the first person to be successfully treated based on a diagnosis made by whole-exome sequencing. Today, human genome sequencing is more readily available and can be completed in a day or two for about $1000. Strategies Used in Sequencing Projects 

The basic sequencing technique used in all modern day sequencing projects is the chain termination method (also known as the dideoxy method), which was developed by Fred Sanger in the 1970s. The chain termination method involves DNA replication of a single-stranded template with the use of a primer and a regular deoxynucleotide (dNTP), which is a monomer, or a single unit, of DNA. The primer and dNTP are mixed with a small proportion of fluorescently labeled dideoxynucleotides (ddNTPs). The ddNTPs are monomers that are missing a hydroxyl group ( OH) at the site at which another nucleotide usually attaches to form a chain ( [link] ). Each ddNTP is labeled with a different color of fluorophore. Every time a ddNTP is incorporated in the growing complementary strand, it terminates the process of DNA replication, which results in multiple short strands of replicated DNA that are each terminated at a different point during replication. When the reaction mixture is processed by gel electrophoresis after being separated into single strands, the multiple newly replicated DNA strands form a ladder because of the differing sizes. Because the ddNTPs are fluorescently labeled, each band on the gel reflects the size of the DNA strand and the ddNTP that terminated the reaction. The different colors of the fluorophore-labeled ddNTPs help identify the ddNTP incorporated at that position. Reading the gel on the basis of the color of each band on the ladder produces the sequence of the template strand ( [link] ). A dideoxynucleotide is similar in structure to a deoxynucleotide, but is missing the 3' hydroxyl group (indicated by the box). When a dideoxynucleotide is incorporated into a DNA strand, DNA synthesis stops. Frederick Sanger's dideoxy chain termination method is illustrated. Using dideoxynucleotides, the DNA fragment can be terminated at different points. The DNA is separated on the basis of size, and these bands, based on the size of the fragments, can be read. Early Strategies: Shotgun Sequencing and Pair-Wise End Sequencing 

In shotgun sequencing method, several copies of a DNA fragment are cut randomly into many smaller pieces (somewhat like what happens to a round shot cartridge when fired from a shotgun). All of the segments are then sequenced using the chain-sequencing method. Then, with the help of a computer, the fragments are analyzed to see where their sequences overlap. By matching up overlapping sequences at the end of each fragment, the entire DNA sequence can be reformed. A larger sequence that is assembled from overlapping shorter sequences is called a contig . As an analogy, consider that someone has four copies of a landscape photograph that you have never seen before and know nothing about how it should appear. The person then rips up each photograph with their hands, so that different size pieces are present from each copy. The person then mixes all of the pieces together and asks you to reconstruct the photograph. In one of the smaller pieces you see a mountain. In a larger piece, you see that the same mountain is behind a lake. A third fragment shows only the lake, but it reveals that there is a cabin on the shore of the lake. Therefore, from looking at the overlapping information in these three fragments, you know that the picture contains a mountain behind a lake that has a cabin on its shore. This is the principle behind reconstructing entire DNA sequences using shotgun sequencing. 

Originally, shotgun sequencing only analyzed one end of each fragment for overlaps. This was sufficient for sequencing small genomes. However, the desire to sequence larger genomes, such as that of a human, led to the development of double-barrel shotgun sequencing, more formally known as pairwise-end sequencing . In pairwise-end sequencing, both ends of each fragment are analyzed for overlap. Pairwise-end sequencing is, therefore, more cumbersome than shotgun sequencing, but it is easier to reconstruct the sequence because there is more available information. Next-generation Sequencing 

Since 2005, automated sequencing techniques used by laboratories are under the umbrella of next-generation sequencing , which is a group of automated techniques used for rapid DNA sequencing. These automated low-cost sequencers can generate sequences of hundreds of thousands or millions of short fragments (25 to 500 base pairs) in the span of one day. These sequencers use sophisticated software to get through the cumbersome process of putting all the fragments in order. 

Comparing Sequences A sequence alignment is an arrangement of proteins, DNA, or RNA; it is used to identify regions of similarity between cell types or species, which may indicate conservation of function or structures. Sequence alignments may be used to construct phylogenetic trees. The following website uses a software program called BLAST (basic local alignment search tool) . 

Under Basic Blast, click Nucleotide Blast. Input the following sequence into the large "query sequence" box: ATTGCTTCGATTGCA. Below the box, locate the "Species" field and type "human" or "Homo sapiens". Then click BLAST to compare the inputted sequence against known sequences of the human genome. The result is that this sequence occurs in over a hundred places in the human genome. Scroll down below the graphic with the horizontal bars and you will see short description of each of the matching hits. Pick one of the hits near the top of the list and click on "Graphics". This will bring you to a page that shows where the sequence is found within the entire human genome. You can move the slider that looks like a green flag back and forth to view the sequences immediately around the selected gene. You can then return to your selected sequence by clicking the "ATG" button. 

[link] Use of Whole-Genome Sequences of Model Organisms 

The first genome to be completely sequenced was of a bacterial virus, the bacteriophage fx174 (5368 base pairs); this was accomplished by Fred Sanger using shotgun sequencing. Several other organelle and viral genomes were later sequenced. The first organism whose genome was sequenced was the bacterium Haemophilus influenzae ; this was accomplished by Craig Venter in the 1980s. Approximately 74 different laboratories collaborated on the sequencing of the genome of the yeast Saccharomyces cerevisiae , which began in 1989 and was completed in 1996, because it was 60 times bigger than any other genome that had been sequenced. By 1997, the genome sequences of two important model organisms were available: the bacterium Escherichia coli K12 and the yeast Saccharomyces cerevisiae . Genomes of other model organisms, such as the mouse Mus musculus , the fruit fly Drosophila melanogaster , the nematode Caenorhabditis. elegans , and humans Homo sapiens are now known. A lot of basic research is performed in model organisms because the information can be applied to genetically similar organisms. A model organism is a species that is studied as a model to understand the biological processes in other species represented by the model organism. Having entire genomes sequenced helps with the research efforts in these model organisms. The process of attaching biological information to gene sequences is called genome annotation . Annotation of gene sequences helps with basic experiments in molecular biology, such as designing PCR primers and RNA targets. 

Click through each step of genome sequencing at this site . 

[link] Uses of Genome Sequences 

DNA microarrays are methods used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences. Almost one million genotypic abnormalities can be discovered using microarrays, whereas whole-genome sequencing can provide information about all six billion base pairs in the human genome. Although the study of medical applications of genome sequencing is interesting, this discipline tends to dwell on abnormal gene function. Knowledge of the entire genome will allow future onset diseases and other genetic disorders to be discovered early, which will allow for more informed decisions to be made about lifestyle, medication, and having children. Genomics is still in its infancy, although someday it may become routine to use whole-genome sequencing to screen every newborn to detect genetic abnormalities. 

In addition to disease and medicine, genomics can contribute to the development of novel enzymes that convert biomass to biofuel, which results in higher crop and fuel production, and lower cost to the consumer. This knowledge should allow better methods of control over the microbes that are used in the production of biofuels. Genomics could also improve the methods used to monitor the impact of pollutants on ecosystems and help clean up environmental contaminants. Genomics has allowed for the development of agrochemicals and pharmaceuticals that could benefit medical science and agriculture. 

It sounds great to have all the knowledge we can get from whole-genome sequencing; however, humans have a responsibility to use this knowledge wisely. Otherwise, it could be easy to misuse the power of such knowledge, leading to discrimination based on a person's genetics, human genetic engineering, and other ethical concerns. This information could also lead to legal issues regarding health and privacy. Section Summary 

Whole-genome sequencing is the latest available resource to treat genetic diseases. Some doctors are using whole-genome sequencing to save lives. Genomics has many industrial applications including biofuel development, agriculture, pharmaceuticals, and pollution control. The basic principle of all modern-day sequencing strategies involves the chain termination method of sequencing. 

Although the human genome sequences provide key insights to medical professionals, researchers use whole-genome sequences of model organisms to better understand the genome of the species. Automation and the decreased cost of whole-genome sequencing may lead to personalized medicine in the future. Review Questions 

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[link] Glossary chain termination method method of DNA sequencing using labeled dideoxynucleotides to terminate DNA replication; it is also called the dideoxy method or the Sanger method contig larger sequence of DNA assembled from overlapping shorter sequences deoxynucleotide individual monomer (single unit) of DNA dideoxynucleotide individual monomer of DNA that is missing a hydroxyl group ( OH) DNA microarray method used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences genome annotation process of attaching biological information to gene sequences model organism species that is studied and used as a model to understand the biological processes in other species represented by the model organism next-generation sequencing group of automated techniques used for rapid DNA sequencing shotgun sequencing method used to sequence multiple DNA fragments to generate the sequence of a large piece of DNA whole-genome sequencing process that determines the DNA sequence of an entire genomeApplying Genomics Applying Genomics 

In this section, you will explore the following questions: What is pharmacogenomics? What is an example of a polygenic human disease? Connection for AP Courses 

Information presented in section is not in scope for AP . However, you can study information in the section as optional or illustrative material. 

Predicting Disease Risk at the Individual Level: 

Cancer, heart disease, and stroke account for a large number of health problems in developed countries. Genomics is a tool which allows physicians to predict who may be susceptible to particular cancers and what someone s risk of heart disease is. This is making adjustments in life style and important to prolonging life. 

Pharmacogenomics and Toxicogenomics: 

Assign the class the job of identifying drugs from the literature whose metabolism is susceptible to genetic variation in patients. Can pharmacogenomics benefit these patients? 

Microbial Genomics: Creation of New Biofuels, Mitochondrial Genomics, Genomics in Agriculture: 

Assign three groups from the class to investigate the following questions. What biofuels are on the market and what has their impact been on energy use? Why are mitochondrial genes examined in forensic cases, but not nuclear chromosomal material? What effects have agricultural applications of genomics had? 

The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to understand and find cures for diseases. Predicting Disease Risk at the Individual Level 

Predicting the risk of disease involves screening currently healthy individuals by genome analysis at the individual level. Intervention with lifestyle changes and drugs can be recommended before disease onset. However, this approach is most applicable when the problem resides within a single gene defect. Such defects only account for approximately 5 percent of diseases in developed countries. Most of the common diseases, such as heart disease, are multi-factored or polygenic , which is a phenotypic characteristic that involves two or more genes, and also involve environmental factors such as diet. In April 2010, scientists at Stanford University published the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford University, who had his genome sequenced); the analysis predicted his propensity to acquire various diseases. A risk assessment was performed to analyze Quake s percentage of risk for 55 different medical conditions. A rare genetic mutation was found, which showed him to be at risk for sudden heart attack. He was also predicted to have a 23 percent risk of developing prostate cancer and a 1.4 percent risk of developing Alzheimer s. The scientists used databases and several publications to analyze the genomic data. Even though genomic sequencing is becoming more affordable and analytical tools are becoming more reliable, ethical issues surrounding genomic analysis at a population level remain to be addressed. 

PCA3 is a gene that is expressed in prostate epithelial cells and overexpressed in cancerous cells. A high concentration of PCA3 in urine is indicative of prostate cancer. The PCA3 test is considered to be a better indicator of cancer than the more well know PSA test, which measures the level of PSA (prostate-specific antigen) in the blood. 

[link] Pharmacogenomics and Toxicogenomics 

Pharmacogenomics , also called toxicogenomics, involves evaluating the effectiveness and safety of drugs on the basis of information from an individual's genomic sequence. Genomic responses to drugs can be studied using experimental animals (such as laboratory rats or mice) or live cells in the laboratory before embarking on studies with humans. Studying changes in gene expression could provide information about the transcription profile in the presence of the drug, which can be used as an early indicator of the potential for toxic effects. For example, genes involved in cellular growth and controlled cell death, when disturbed, could lead to the growth of cancerous cells. Genome-wide studies can also help to find new genes involved in drug toxicity. Personal genome sequence information can be used to prescribe medications that will be most effective and least toxic on the basis of the individual patient s genotype. The gene signatures may not be completely accurate, but can be tested further before pathologic symptoms arise. Microbial Genomics: Metagenomics 

Traditionally, microbiology has been taught with the view that microorganisms are best studied under pure culture conditions, which involves isolating a single type of cell and culturing it in the laboratory. Because microorganisms can go through several generations in a matter of hours, their gene expression profiles adapt to the new laboratory environment very quickly. In addition, the vast majority of bacterial species resist being cultured in isolation. Most microorganisms do not live as isolated entities, but in microbial communities known as biofilms. For all of these reasons, pure culture is not always the best way to study microorganisms. Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment ( [link] ). Metagenomics involves isolating DNA from multiple species within an environmental niche. Microbial Genomics: Creation of New Biofuels 

Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria. The primary sources of fuel today are coal, oil, wood, and other plant products, such as ethanol. Although plants are renewable resources, there is still a need to find more alternative renewable sources of energy to meet our population s energy demands. The microbial world is one of the largest resources for genes that encode new enzymes and produce new organic compounds, and it remains largely untapped. Microorganisms are used to create products, such as enzymes that are used in research, antibiotics, and other anti-microbial mechanisms. Microbial genomics is helping to develop diagnostic tools, improved vaccines, new disease treatments, and advanced environmental cleanup techniques. Mitochondrial Genomics 

Mitochondria are intracellular organelles that contain their own DNA. Mitochondrial DNA mutates at a rapid rate and is often used to study evolutionary relationships. Another feature that makes studying the mitochondrial genome interesting is that the mitochondrial DNA in most multicellular organisms is passed on from the mother during the process of fertilization. For this reason, mitochondrial genomics is often used to trace genealogy. 

Information and clues obtained from DNA samples found at crime scenes have been used as evidence in court cases, and genetic markers have been used in forensic analysis. Genomic analysis has also become useful in this field. In 2001, the first use of genomics in forensics was published. It was a collaborative attempt between academic research institutions and the FBI to solve the mysterious cases of anthrax communicated via the US Postal Service. Using microbial genomics, researchers determined that a specific strain of anthrax was used in all the mailings. Genomics in Agriculture 

Genomics can reduce the trials and failures involved in scientific research to a certain extent, which could improve the quality and quantity of crop yields in agriculture. Linking traits to genes or gene signatures helps to improve crop breeding to generate hybrids with the most desirable qualities. Scientists use genomic data to identify desirable traits, and then transfer those traits to a different organism. Scientists are discovering how genomics can improve the quality and quantity of agricultural production. For example, scientists could use desirable traits to create a useful product or enhance an existing product, such as making a drought-sensitive crop more tolerant of the dry season. Section Summary 

Imagination is the only barrier to the applicability of genomics. Genomics is being applied to most fields of biology; it is being used for personalized medicine, prediction of disease risks at an individual level, the study of drug interactions before the conduct of clinical trials, and the study of microorganisms in the environment as opposed to the laboratory. It is also being applied to developments such as the generation of new biofuels, genealogical assessment using mitochondria, advances in forensic science, and improvements in agriculture. Review Questions 

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[link] Glossary metagenomics study of the collective genomes of multiple species that grow and interact in an environmental niche pharmacogenomics study of drug interactions with the genome or proteome; also called toxicogenomics polygenic phenotypic characteristic caused by two or more genes pure culture growth of a single type of cell in the laboratoryGenomics and Proteomics Genomics and Proteomics 

In this section, you will explore the following questions: What is a proteome? What is a protein signature and what is its relevance to cancer screening? Connection for AP Courses 

Information presented in section is not in scope for AP . However, you can study information in the section as optional or illustrative material. 

Cancer Proteomics: 

Connect this section to the previous one titled: Predicting Disease Risk at the Individual Level. Emphasize the importance of accurate testing and that there is always a number of false positives, meaning that the test is positive, but shouldn t be, and false negatives, meaning that the test should have been positive and wasn t. A test that can serve as a case study for this situation is the Prostate Specific Antigen (PSA) assay that has been used in conjunction with prostate cancer diagnosis. Research the current understanding and usefulness of the test as reflected in its characteristics of false positives and negatives. 

Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or because of direct impact on a specific protein. 

A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins. The study of the function of proteomes is called proteomics . Proteomics complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells of a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternately spliced (cut and pasted to create novel combinations and novel proteins) and many proteins are modified after translation by processes such as proteolytic cleavage, phosphorylation, glycosylation, and ubiquitination. There are also protein-protein interactions, which complicate the study of proteomes. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome. 

Metabolomics is related to genomics and proteomics. Metabolomics involves the study of small molecule metabolites found in an organism. The metabolome is the complete set of metabolites that are related to the genetic makeup of an organism. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all of the metabolites that are found in the tissues and fluids of living organisms. Basic Techniques in Protein Analysis 

The ultimate goal of proteomics is to identify or compare the proteins expressed from a given genome under specific conditions, study the interactions between the proteins, and use the information to predict cell behavior or develop drug targets. Just as the genome is analyzed using the basic technique of DNA sequencing, proteomics requires techniques for protein analysis. The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry. Mass spectrometry is used to identify and determine the characteristics of a molecule. Advances in spectrometry have allowed researchers to analyze very small samples of protein. X-ray crystallography, for example, enables scientists to determine the three-dimensional structure of a protein crystal at atomic resolution. Another protein imaging technique, nuclear magnetic resonance (NMR), uses the magnetic properties of atoms to determine the three-dimensional structure of proteins in aqueous solution. Protein microarrays have also been used to study interactions between proteins. Large-scale adaptations of the basic two-hybrid screen ( [link] ) have provided the basis for protein microarrays. Computer software is used to analyze the vast amount of data generated for proteomic analysis. 

Genomic- and proteomic-scale analyses are part of systems biology. Systems biology is the study of whole biological systems (genomes and proteomes) based on interactions within the system. The European Bioinformatics Institute and the Human Proteome Organization (HUPO) are developing and establishing effective tools to sort through the enormous pile of systems biology data. Because proteins are the direct products of genes and reflect activity at the genomic level, it is natural to use proteomes to compare the protein profiles of different cells to identify proteins and genes involved in disease processes. Most pharmaceutical drug trials target proteins. Information obtained from proteomics is being used to identify novel drugs and understand their mechanisms of action. Two-hybrid screening is used to determine whether two proteins interact. In this method, a transcription factor is split into a DNA-binding domain (BD) and an activator domain (AD). The binding domain is able to bind the promoter in the absence of the activator domain, but it does not turn on transcription. A protein called the bait is attached to the BD, and a protein called the prey is attached to the AD. Transcription occurs only if the prey catches the bait. 

The challenge of techniques used for proteomic analyses is the difficulty in detecting small quantities of proteins. Although mass spectrometry is good for detecting small amounts of proteins, variations in protein expression in diseased states can be difficult to discern. Proteins are naturally unstable molecules, which makes proteomic analysis much more difficult than genomic analysis. Cancer Proteomics 

Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker , whereas a set of proteins with altered expression levels is called a protein signature . For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids, such as sweat, blood, or urine, such that large-scale screenings can be performed in a non-invasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of protein biomarkers used in cancer detection are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells. Proteomics is also being used to develop individualized treatment plans, which involves the prediction of whether or not an individual will respond to specific drugs and the side effects that the individual may experience. Proteomics is also being used to predict the possibility of disease recurrence. 

The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The Clinical Proteomic Technologies for Cancer and the Early Detection Research Network are efforts to identify protein signatures specific to different types of cancers. The Biomedical Proteomics Program is designed to identify protein signatures and design effective therapies for cancer patients. Section Summary 

Proteomics is the study of the entire set of proteins expressed by a given type of cell under certain environmental conditions. In a multicellular organism, different cell types will have different proteomes, and these will vary with changes in the environment. Unlike a genome, a proteome is dynamic and in constant flux, which makes it both more complicated and more useful than the knowledge of genomes alone. 

Proteomics approaches rely on protein analysis; these techniques are constantly being upgraded. Proteomics has been used to study different types of cancer. Different biomarkers and protein signatures are being used to analyze each type of cancer. The future goal is to have a personalized treatment plan for each individual. Review Questions 

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[link] Glossary biomarker individual protein that is uniquely produced in a diseased state false negative incorrect test result that should have been positive metabolome complete set of metabolites which are related to the genetic makeup of an organism metabolomics study of small molecule metabolites found in an organism protein signature set of uniquely expressed proteins in the diseased state proteome entire set of proteins produced by a cell type proteomics study of the function of proteomes systems biology study of whole biological systems (genomes and proteomes) based on interactions within the systemIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" All organisms are products of evolution adapted to their environment. (a) Saguaro ( Carnegiea gigantea ) can soak up 750 liters of water in a single rain storm, enabling these cacti to survive the dry conditions of the Sonora desert in Mexico and the Southwestern United States. (b) The Andean semiaquatic lizard ( Potamites montanicola ) discovered in Peru in 2010 lives between 1,570 to 2,100 meters in elevation, and, unlike most lizards, is nocturnal and swims. Scientists still do no know how these ectotherms, which rely on external sources of body heat, are able to move in the cold (10 to 15 C) temperatures of the Andean night. (credit a: modification of work by Gentry George, U.S. Fish and Wildlife Service; credit b: modification of work by Germ n Ch vez and Diego V squez, ZooKeys ) 

The field of biology is a diverse one that includes the study of organisms from the small and simple to the large and complex. From biological molecules to biomes, the one theme that remains consistent is evolution. All species of living organisms are descended from a common ancestor. Although it may seem that living things today stay much the same, this is not the case. Evolution is actually an ongoing process. Additionally, new species are discovered regularly. For example, scientists have used a method called fluorescent in situ hybridization, which uses fluorescent probes to locate specific genes on chromosomes, to discover a green sea slug that can perform photosynthesis just like a plant. 1 The slug obtains genes related to photosynthesis from the algae it eats through a process called horizontal gene transfer. In this process, genes can be transferred directly from one cell to another. The algal genes code for products that repair and maintain chloroplasts eaten by the slug. You can read more about it at this website . 

The ongoing process of evolution includes the repeated formation of new species (speciation), changes within species (anagenesis), and death of species (extinction). Patterns in shared morphological and biochemical traits, including shared DNA sequences, can be used in constructing a diagram that illustrates the biodiversity, taxonomic links, and evolutionary history of extinct and extant living things. Such diagrams are commonly called The Tree of Life. 

You may wish to share a tree of life diagram with students and use the diagram alongside facts about the rates of extinction (historically and currently) and species estimates versus species documentation to guide a discussion about evidence for evolution as an ongoing process. Ask students to discuss where in their daily lives they are aware of evidence of speciation, anagenesis, and extinction. Through discussion, elicit from students the importance of considering scale (both temporal and physical) when considering evidence of evolutionary change. Ideas and thoughts shared during this discussion may prove to be helpful reference points when students read about misconceptions of evolution later in the chapter. Footnotes 1 Biol. Bull. 227: 300 312. (December 2014)Understanding Evolution Understanding Evolution 

In this section, you will explore the following questions: How was the present-day theory of evolution developed? What is adaptation, and how does adaptation relate to natural selection? What are the differences between convergent and divergent evolution, and what are examples of each that support evolution by natural selection? What are examples of homologous and vestigial structures, and what evidence do these structures provide to support patterns of evolution? What are common misconceptions about the theory of evolution? Connection for AP Courses 

Millions of species, from bacteria to blueberries to baboons, currently call Earth their home, but these organisms evolved from different species. Furthermore, scientists estimate that several million more species will become extinct before they have been classified and studied. But why don t polar bears naturally inhabit deserts or rain forests, except, perhaps, in movies? Why do humans possess traits, such as opposable thumbs, that are unique to primates but not other mammals? How did observations of finches by Charles Darwin visiting the Galapagos Islands in the 1800s provide the foundation for our modern understanding of evolution? 

The theory of evolution as proposed by Darwin is the unifying theory of biology. The tenet that all life has evolved and diversified from a common ancestor is the foundation from which we approach all questions in biology. As we learned in our exploration of the structure and function of DNA, variations in individuals within a population occur through mutation, allowing more desirable traits to be passed to the next generation. Due to competition for resources and other environmental pressures, individuals possessing more favorable adaptive characteristics are more likely to survive and reproduce, passing those characteristics to the next generation with increased frequency. When environments change, what was once an unfavorable trait may become a favorable one. Organisms may evolve in response to their changing environment by the accumulation of favorable traits in succeeding generations. Thus, evolution by natural selection explains both the unity and diversity of life. 

Convergent evolution occurs when similar traits with the same function evolve in multiple species exposed to similar selection pressure, such as the wings of bats and insects. In divergent evolution , two species evolve in different directions from a common point, such as the forelimbs of humans, dogs, birds, and whales. Although Darwin s theory was revolutionary for its time because it contrasted with long-held ideas (for example, Lamarck proposed the inheritance of acquired characteristics ), evidence drawn from many scientific disciplines, including the fossil record, the existence of homologous and vestigial structures, mathematics, and DNA analysis supports evolution through natural selection. It is also important to understand that evolution continues to occur; for example, bacteria that evolve resistance to antibiotics or plants that become resistant to pesticides provide evidence for continuing change. 

Information presented and the examples highlighted in this section support concepts outlined in Big Idea 1 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.A Change in the genetic makeup of a population over time is evolution. Essential Knowledge 1.A.1 Natural selection is a major mechanism of evolution. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 1.9 The student is able to evaluate evidence provided by data from many scientific disciplines that support biological evolution. Essential Knowledge 1.A.2 Natural selection acts on phenotypic variations in populations. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 1.5 The student is able to connect evolutionary changes in a population over time to a change in the environment. Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Learning Objective 1.2 The student is able to evaluate evidence provided by data to qualitatively and quantitatively investigate the role of natural selection in evolution. Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 1.12 The student is able to connect scientific evidence from many scientific disciplines to support the modern concept of evolution. Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 5.2 The student can refine observations and measurements based on data analysis. Learning Objective 1.10 The student is able to refine evidence based on data from many scientific disciplines that support biological evolution. 

Enduring Understanding 1.C Life continues to evolve within a changing environment. Essential Knowledge 1.C.3 Populations of organisms continue to evolve. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 1.26 The student is able to evaluate given data sets that illustrate evolution as an ongoing processes. Essential Knowledge 1.C.3 Populations of organisms continue to evolve. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 1.25 The student is able to describe a model that represents evolution within a population. Essential Knowledge 1.C.3 Populations of organisms continue to evolve. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 1.4 The student is able to evaluate data-based evidence that describes evolutionary changes in the genetic makeup of a population over time. 

The chapter talks about embryology, so it might be important to mention Ernst Haeckel (1834 1919) and his famous principle "ontogeny recapitulates phylogeny." Please see this PBS website for more information. Charles Darwin and Natural Selection 

In the mid-nineteenth century, the actual mechanism for evolution was independently conceived of and described by two naturalists: Charles Darwin and Alfred Russel Wallace. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle , including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin s journey, like Wallace s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Gal pagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Gal pagos Islands comprised several species with a unique beak shape ( [link] ). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the mainland of South America. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that the varied beaks of each finch helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey. Darwin observed that beak shape varies among finch species. He postulated that the beak of an ancestral species had adapted over time to equip the finches to acquire different food sources. 

Wallace and Darwin both observed similar patterns in other organisms and they independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection , also known as survival of the fittest, is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits; this leads to evolutionary change. 

For example, a population of giant tortoises found in the Galapagos Archipelago was observed by Darwin to have longer necks than those that lived on other islands with dry lowlands. These tortoises were selected because they could reach more leaves and access more food than those with short necks. In times of drought when fewer leaves would be available, those that could reach more leaves had a better chance to eat and survive than those that couldn t reach the food source. Consequently, long-necked tortoises would be more likely to be reproductively successful and pass the long-necked trait to their offspring. Over time, only long-necked tortoises would be present in the population. 

Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, most characteristics of organisms are inherited, or passed from parent to offspring. Although no one, including Darwin and Wallace, knew how this happened at the time, it was a common understanding. Second, more offspring are produced than are able to survive, so resources for survival and reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is competition for those resources in each generation. Both Darwin and Wallace s understanding of this principle came from reading an essay by the economist Thomas Malthus who discussed this principle in relation to human populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Darwin and Wallace reasoned that offspring with inherited characteristics which allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called descent with modification. Ultimately, natural selection leads to greater adaptation of the population to its local environment; it is the only mechanism known for adaptive evolution. 

Papers by Darwin and Wallace ( [link] ) presenting the idea of natural selection were read together in 1858 before the Linnean Society in London. The following year Darwin s book, On the Origin of Species, was published. His book outlined in considerable detail his arguments for evolution by natural selection. Both (a) Charles Darwin and (b) Alfred Wallace wrote scientific papers on natural selection that were presented together before the Linnean Society in 1858. 

Demonstrations of evolution by natural selection are time consuming and difficult to obtain. One of the best examples has been demonstrated in the very birds that helped to inspire Darwin s theory: the Gal pagos finches. Peter and Rosemary Grant and their colleagues have studied Gal pagos finch populations every year since 1976 and have provided important demonstrations of natural selection. The Grants found changes from one generation to the next in the distribution of beak shapes with the medium ground finch on the Gal pagos island of Daphne Major. The birds have inherited variation in the bill shape with some birds having wide deep bills and others having thinner bills. During a period in which rainfall was higher than normal because of an El Ni o, the large hard seeds that large-billed birds ate were reduced in number; however, there was an abundance of the small soft seeds which the small-billed birds ate. Therefore, survival and reproduction were much better in the following years for the small-billed birds. In the years following this El Ni o, the Grants measured beak sizes in the population and found that the average bill size was smaller. Since bill size is an inherited trait, parents with smaller bills had more offspring and the size of bills had evolved to be smaller. As conditions improved in 1987 and larger seeds became more available, the trend toward smaller average bill size ceased. Career Connection 

Field Biologist Many people hike, explore caves, scuba dive, or climb mountains for recreation. People often participate in these activities hoping to see wildlife. Experiencing the outdoors can be incredibly enjoyable and invigorating. What if your job was to be outside in the wilderness? Field biologists by definition work outdoors in the field. The term field in this case refers to any location outdoors, even under water. A field biologist typically focuses research on a certain species, group of organisms, or a single habitat ( [link] ). A field biologist tranquilizes a polar bear for study. (credit: Karen Rhode) 

One objective of many field biologists includes discovering new species that have never been recorded. Not only do such findings expand our understanding of the natural world, but they also lead to important innovations in fields such as medicine and agriculture. Plant and microbial species, in particular, can reveal new medicinal and nutritive knowledge. Other organisms can play key roles in ecosystems or be considered rare and in need of protection. When discovered, these important species can be used as evidence for environmental regulations and laws. Processes and Patterns of Evolution 

Natural selection can only take place if there is variation , or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons such as an individual being taller because of better nutrition rather than different genes. 

Genetic diversity in a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in DNA, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes on the phenotype. A mutation can affect the phenotype of the organism in a way that gives it reduced fitness lower likelihood of survival or fewer offspring. Alternatively, a mutation may produce a phenotype with a beneficial effect on fitness. And, many mutations will also have no effect on the fitness of the phenotype; these are called neutral mutations. Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their phenotype, from a small effect to a great effect. Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring. 

A heritable trait that helps the survival and reproduction of an organism in its present environment is called an adaptation . Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the fit of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards thick fur is an adaptation for living in the cold. The cheetahs fast speed is an adaptation for catching prey. 

Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed, and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions. 

The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators ( [link] ). Flowering plants evolved from a common ancestor. Notice that the (a) dense blazing star ( Liatrus spicata ) and the (b) purple coneflower ( Echinacea purpurea ) vary in appearance, yet both share a similar basic morphology. (credit a: modification of work by Drew Avery; credit b: modification of work by Cory Zanker) 

In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have structures we refer to as wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry. The two species came to the same function, flying, but did so separately from each other. 

These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change. Evidence of Evolution 

The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species , to identifying patterns in nature that were consistent with evolution, and since Darwin, our understanding has become clearer and broader. Fossils 

Fossils provide solid evidence that organisms from the past are not the same as those found today, and fossils show a progression of evolution. Scientists determine the age of fossils and categorize them from all over the world to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years ( [link] ). For example, scientists have recovered highly detailed records showing the evolution of humans and horses. In this (a) display, fossil hominids are arranged from oldest (bottom) to newest (top). As hominids evolved, the shape of the skull changed. An artist s rendition of (b) extinct species of the genus Equus reveals that these ancient species resembled the modern horse ( Equus ferus ) but varied in size. Anatomy and Embryology 

Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in the appendages of a human, dog, bird, and whale all share the same overall construction ( [link] ) resulting from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures . The similar construction of these appendages indicates that these organisms share a common ancestor. 

Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past common ancestor. These unused structures without function are called vestigial structures . Examples of vestigial structures include wings on flightless birds, leaves on some cacti, and hind leg bones in whales. Link to Learning 

Visit this interactive site to guess which bones structures are homologous and which are analogous, and see examples of evolutionary adaptations to illustrate these concepts. 

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Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan, living in the arctic region have been selected for seasonal white phenotypes during winter to blend with the snow and ice ( [link] ab ). These similarities occur not because of common ancestry, but because of similar selection pressures the benefits of not being seen by predators. The white winter coat of the (a) arctic fox and the (b) ptarmigan s plumage are adaptations to their environments. (credit a: modification of work by Keith Morehouse) 

Embryology, the study of the development of the anatomy of an organism to its adult form, also provides evidence of relatedness between now widely divergent groups of organisms. Mutational tweaking in the embryo can have such magnified consequences in the adult that embryo formation tends to be conserved. As a result, structures that are absent in some groups often appear in their embryonic forms and disappear by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups but are maintained in adult forms of aquatic groups such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by the time of birth. Biogeography 

The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of members of the plant family Proteaceae in Australia, southern Africa, and South America, for example, is best explained by their presence prior to the southern supercontinent Gondwana breaking up. 

The great diversification of marsupials in Australia and the absence of other mammals reflect Australia s long isolation. Australia has an abundance of endemic species species found nowhere else which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Gal pagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands. Molecular Biology 

Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material and in the near universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences exactly the pattern that would be expected from descent and diversification from a common ancestor. 

DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplication events that allow the free modification of one copy by mutation, selection, or drift (changes in a population s gene pool resulting from chance), while the second copy continues to produce a functional protein. Misconceptions of Evolution 

Although the theory of evolution generated some controversy when it was first proposed, it was almost universally accepted by biologists, particularly younger biologists, within 20 years after publication of On the Origin of Species . Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound. Link to Learning 

This site addresses some of the main misconceptions associated with the theory of evolution. 

[link] Evolution Is Just a Theory 

Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word theory with the way scientists use the word. In science, a theory is understood to be a body of thoroughly tested and verified explanations for a set of observations of the natural world. Scientists have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes understood facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists. In contrast, a theory in common vernacular is a word meaning a guess or suggested explanation; this meaning is more akin to the scientific concept of hypothesis. When critics of evolution say evolution is just a theory, they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization. Individuals Evolve 

Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, obviously, but this is called development and involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium-ground finches in the Gal pagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time and then measures the average bill size in the population several years later, this average value will be different as a result of evolution. Although some individuals may survive from the first time to the second, they will still have the same bill size; however, there will be many new individuals that contribute to the shift in average bill size. Evolution Explains the Origin of Life 

It is a common misunderstanding that evolution includes an explanation of life s origins. Conversely, some of the theory s critics believe that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, and presumably it just occurred once. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages would immediately become food for existing living things. 

However, once a mechanism of inheritance was in place in the form of a molecule like DNA either within a cell or pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers. So while evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties. Organisms Evolve on Purpose 

Statements such as organisms evolve in response to a change in an environment are quite common, but such statements can lead to two types of misunderstandings. First, the statement must not be understood to mean that individual organisms evolve. The statement is shorthand for a population evolves in response to a changing environment. However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and therefore producing proportionately more offspring than other phenotypes. This results in change in the population if the characteristics are genetically determined. 

It is also important to understand that the variation that natural selection works on is already in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select a population of bacteria that are resistant to antibiotics. The resistance, which is caused by a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, likely at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic. 

In a larger sense, evolution is not goal directed. Species do not become better over time; they simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no goal of making faster, bigger, more complex, or even smarter species, despite the commonness of this kind of language in popular discourse. What characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly changing in a non-directional way. What trait is fit in one environment at one time may well be fatal at some point in the future. This holds equally well for a species of insect as it does the human species. Activity 

Using information from a book or online resource such as Jonathan Weiner s The Beak of the Finch , explain how contemporary evidence drawn from multiple scientific disciplines supports the observations of Charles Darwin regarding evolution by natural selection. Then, in small groups or as a whole class discussion or debate, present an argument to dispel misconceptions about evolution and how it works. Lab Investigation 

AP Biology Investigative Labs: Inquiry-Based, Investigation 8: Biotechnology: Bacterial Transformation . You will explore how genetic engineering techniques can be used to manipulate heritable information by inserting plasmids into bacterial cells. Think About It 

What selection pressures may affect the survival and reproduction of a group of pea seeds scattered by a person along the ground? The activity is an application of all of the AP Learning Objectives and Science Practices listed above because students are constructing an argument based on scientific evidence and data that support Darwin s model of evolution through natural selection. The lab investigation is an application of AP Learning Objective 1.2 and Science Practices 2.2 and 5.3, Learning Objective 1.4 and Science Practice 5.3, and Learning Objective 1.26 and Science Practice 5.3 because students are performing experiments and collecting and analyzing data to confirm that the development of resistance to antibiotics by bacteria is an example of evolution by natural selection and that evolution continues to occur. (Note: This lab investigation also connects to concepts studied in the Biotechnology chapter and is a link between genetic variation and evolution.) The Think About It question is an application of Learning Objective 1.25 and Science Practice 1.2 because students are describing a model that represents evolution within a population. Think About It sample answer: The survival and reproduction of the pea seeds would likely face selection pressure imposed by the fertility of the ground on which they land, how often the ground is disturbed (such as by people walking on it), and the amount of water and light the plants receive. Biointeractive activities, such as that found at [link] contain more evolution activities that generate population statistics which students can analyze. Section Summary 

Evolution is the process of adaptation through mutation which allows more desirable characteristics to be passed to the next generation. Over time, organisms evolve more characteristics that are beneficial to their survival. For living organisms to adapt and change to environmental pressures, genetic variation must be present. With genetic variation, individuals have differences in form and function that allow some to survive certain conditions better than others. These organisms pass their favorable traits to their offspring. Eventually, environments change, and what was once a desirable, advantageous trait may become an undesirable trait and organisms may further evolve. Evolution may be convergent with similar traits evolving in multiple species or divergent with diverse traits evolving in multiple species that came from a common ancestor. Evidence of evolution can be observed by means of DNA code and the fossil record, and also by the existence of homologous and vestigial structures. Review Questions 

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[link] Glossary adaptation heritable trait or behavior in an organism that aids in its survival and reproduction in its present environment convergent evolution process by which groups of organisms independently evolve to similar forms divergent evolution process by which groups of organisms evolve in diverse directions from a common point homologous structures parallel structures in diverse organisms that have a common ancestor natural selection reproduction of individuals with favorable genetic traits that survive environmental change because of those traits, leading to evolutionary change variation genetic differences among individuals in a population vestigial structure physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a distant ancestor acquired characteristics modifications caused by an individual s environment that can be inherited by its offspring theory of evolution explains how populations change over time and how life diversifies the origin of speciesFormation of New Species Formation of New Species 

In this section, you will explore the following questions: What defines a species, and how can different species be distinguished from each other? How does genetic variation lead to speciation? What is the role of pre-zygotic and post-zygotic reproductive barriers in speciation? What is the difference between allopatric speciation and sympatric speciation? How does adaptive radiation explain the diversification? Connection for AP Courses 

Speciation explains the diversity of organisms that inhabit the Earth. Although all life shares various genetic similarities, only certain organisms combine genetic information by sexual reproduction and produce viable and fertile offspring that, in turn, can successfully reproduce. Scientists call such organisms members of a biological species. As we will study in later, changes in allele frequencies within a population over generations result in microevolution. However, macroevolution leads to the evolution of new species when populations diverge from a common ancestor and, for one reason or another, become reproductively isolated from the original population. 

Speciation occurs along two main pathways: geographic separation ( allopatric speciation ) and through mechanisms that occur within a shared habitat ( sympatric speciation ). In both cases, populations become reproductively isolated. When populations become geographically isolated, the free-flow of alleles is prevented. Over time and because of different selective pressures the populations diverge and become genetically independent species. Prezygotic barriers block reproduction prior to formation of a zygote, whereas postzygotic barriers block reproduction after fertilization occurs. Obviously, if two populations are separated by a vast ocean, they will not come in contact with each other to reproduce. However, if speciation has occurred, even when brought back together, they will retain their species identity. There are many examples of this in nature, including Darwin s finches, northern and Mexican spotted owls, and Hawaiian honeycreeper. Adaptive radiation occurs when a single ancestral species gives rise to many new species. This may occur, for example, when new habitats become available. It can also be seen historically in the rise of mammals following the extinction of dinosaurs. Other examples of prezygotic isolating mechanisms include mating seasons and unique courtship behaviors. Sometimes mating occurs between two different species, resulting in a hybrid such as the mule, which is a cross between a horse and a donkey. However, most hybrids are inviable or sterile. 

Sympatric speciation does not require a geographic barrier and explains how many different species can inhabit the same area. One form of sympatric speciation begins with a serious chromosomal error during cell division. As you recall from our exploration of meiosis, sometimes errors occur in the separation of chromosomes or chromatids, resulting in gametes with extra chromosomes ( polyploidy ). This type of speciation is more common in plants than in animals, though some examples in animals exist. For example, two groups of cichlid fish in Africa s Lake Victoria, which have distinct morphologies and diets, may be in the early stage of sympatric speciation without polyploidy, as genetic differences arise between the two groups. 

Information presented and the examples highlighted in this section support concepts outlined in Big Idea 1 and Big Idea 3 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.C Life continues to evolve within a changing environment. Essential Knowledge 1.C.1 Speciation and extinction have occurred throughout the Earth s history. Science Practice 5.1 The student can analyze data to identify patterns or relationships. Learning Objective 1.20 The student is able to analyze data related to questions of speciation and extinction throughout the Earth s history. Essential Knowledge 1.C.1 Speciation and extinction have occurred throughout the Earth s Science Practice 4.2 The student can design a plan for collecting data to answer a particular scientific question. Learning Objective 1.21 The student is able to design a plan for collecting data to investigate the scientific claim that speciation and extinction have occurred throughout the Earth s history. Essential Knowledge 1.C.2 Speciation may occur when two populations become reproductively isolated from each other. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 1.22 The student is able to use data from a real or simulated population(s), based on graphs or models of types of selection, to predict what will happen to the population in the future. Essential Knowledge 1.C.2 Speciation may occur when two populations become reproductively isolated from each other. Science Practice 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question. Learning Objective 1.23 The student is able to justify the selection of data that address questions related to reproductive isolation and speciation. Essential Knowledge 1.C.2 Speciation may occur when two populations become reproductively isolated from each other. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 1.24 The student is able to describe speciation in an isolated population and connect it to change in gene frequency, change in environment, natural selection, and/or genetic drift. 

Big Idea 3 Living systems store, retrieve, transmit, and respond to information essential to life processes. 

Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.C.1 Changes in genotype can result in changes in phenotype. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 3.24 The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection. Essential Knowledge 3.C.1 Changes in genotype can result in changes in phenotype. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 3.26 The student is able to explain the connection between genetic variations in organisms and phenotypic variations in populations. 

The word species means kind in Latin. In daily life, we commonly distinguish between kinds of organisms strictly by using the criteria of appearance. Differentiating between kinds of organisms on the basis of bodily form (or morphology) is, of course, both a useful and practical thing to do. As it turns out, it is also largely in line with other means (physiological traits, biochemical patterns, and DNA sequences) of biological differentiation. 

The definition of species as a group of individuals whose members have the potential to interbreed and produce viable, fertile offspring is known as the biological species concept . Inherent in this concept of species as populations of reproductively compatible individuals is the related concept of speciation as dependent on reproductive isolation. While this definition of species depends on ideas of separateness, other definitions depend on ideas of unity. For example, the ecological species concept defines species as a set of organisms adapted to a singular niche. In the phylogenetic species concept , a species is defined as the smallest cluster of individuals within which there is a pattern of ancestry and descent. 

You may wish to ask students to research and report on different species concepts. Have students compare and contrast the different definitions. Through discussion, elicit which definitions are useful, and in what kinds of situations, and which are less useful, and in what kinds of situations. You might ask questions such as: Which definition or definitions is useful for identifying asexual species? Which definition or definitions is useful for identifying asexual and sexual species? Why might different definitions work in different environments, for different types of organisms, or at different junctures of individuals lives? Species and the Ability to Reproduce 

A species is a group of individual organisms that interbreed and produce fertile, viable offspring. According to this definition, one species is distinguished from another when, in nature, it is not possible for matings between individuals from each species to produce fertile offspring. 

Members of the same species share both external and internal characteristics, which develop from their DNA. The closer relationship two organisms share, the more DNA they have in common, just like people and their families. People s DNA is likely to be more like their father or mother s DNA than their cousin or grandparent s DNA. Organisms of the same species have the highest level of DNA alignment and therefore share characteristics and behaviors that lead to successful reproduction. 

Species appearance can be misleading in suggesting an ability or inability to mate. For example, even though domestic dogs ( Canis lupus familiaris ) display phenotypic differences, such as size, build, and coat, most dogs can interbreed and produce viable puppies that can mature and sexually reproduce ( [link] ). The (a) poodle and (b) cocker spaniel can reproduce to produce a breed known as (c) the cockapoo. (credit a: modification of work by Sally Eller, Tom Reese; credit b: modification of work by Jeremy McWilliams; credit c: modification of work by Kathleen Conklin) 

In other cases, individuals may appear similar although they are not members of the same species. For example, even though bald eagles ( Haliaeetus leucocephalus ) and African fish eagles ( Haliaeetus vocifer ) are both birds and eagles, each belongs to a separate species group ( [link] ). If humans were to artificially intervene and fertilize the egg of a bald eagle with the sperm of an African fish eagle and a chick did hatch, that offspring, called a hybrid (a cross between two species), would probably be infertile unable to successfully reproduce after it reached maturity. Different species may have different genes that are active in development; therefore, it may not be possible to develop a viable offspring with two different sets of directions. Thus, even though hybridization may take place, the two species still remain separate. The (a) African fish eagle is similar in appearance to the (b) bald eagle, but the two birds are members of different species. (credit a: modification of work by Nigel Wedge; credit b: modification of work by U.S. Fish and Wildlife Service) 

Populations of species share a gene pool: a collection of all the variants of genes in the species. Again, the basis to any changes in a group or population of organisms must be genetic for this is the only way to share and pass on traits. When variations occur within a species, they can only be passed to the next generation along two main pathways: asexual reproduction or sexual reproduction. The change will be passed on asexually simply if the reproducing cell possesses the changed trait. For the changed trait to be passed on by sexual reproduction, a gamete, such as a sperm or egg cell, must possess the changed trait. In other words, sexually-reproducing organisms can experience several genetic changes in their body cells, but if these changes do not occur in a sperm or egg cell, the changed trait will never reach the next generation. Only heritable traits can evolve. Therefore, reproduction plays a paramount role for genetic change to take root in a population or species. In short, organisms must be able to reproduce with each other to pass new traits to offspring. 

Until recently, these three species of short-tailed pythons, Python curtus, Python brongersmai (middle), and Python breitensteini were considered one species. However, due to the different locations in which they are found, they have become three distinct species. 

[link] Speciation 

The biological definition of species, which works for sexually reproducing organisms, is a group of actually or potentially interbreeding individuals. There are exceptions to this rule. Many species are similar enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. In fact, the presence in nature of hybrids between similar species suggests that they may have descended from a single interbreeding species, and the speciation process may not yet be complete. 

Given the extraordinary diversity of life on the planet there must be mechanisms for speciation : the formation of two species from one original species. Darwin envisioned this process as a branching event and diagrammed the process in the only illustration found in On the Origin of Species ( [link] a ). Compare this illustration to the diagram of elephant evolution ( [link] b ), which shows that as one species changes over time, it branches to form more than one new species, repeatedly, as long as the population survives or until the organism becomes extinct. The only illustration in Darwin's On the Origin of Species is (a) a diagram showing speciation events leading to biological diversity. The diagram shows similarities to phylogenetic charts that are drawn today to illustrate the relationships of species. (b) Modern elephants evolved from the Palaeomastodon , a species that lived in Egypt 35 50 million years ago. 

For speciation to occur, two new populations must be formed from one original population and they must evolve in such a way that it becomes impossible for individuals from the two new populations to interbreed. Biologists have proposed mechanisms by which this could occur that fall into two broad categories. Allopatric speciation (allo- = "other"; -patric = "homeland") involves geographic separation of populations from a parent species and subsequent evolution. Sympatric speciation (sym- = "same"; -patric = "homeland") involves speciation occurring within a parent species remaining in one location. 

Biologists think of speciation events as the splitting of one ancestral species into two descendant species. There is no reason why there might not be more than two species formed at one time except that it is less likely and multiple events can be conceptualized as single splits occurring close in time. Allopatric Speciation 

A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When populations become geographically discontinuous, that free-flow of alleles is prevented. When that separation lasts for a period of time, the two populations are able to evolve along different trajectories. Thus, their allele frequencies at numerous genetic loci gradually become more and more different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors for the two populations will differ causing natural selection to favor divergent adaptations in each group. 

Isolation of populations leading to allopatric speciation can occur in a variety of ways: a river forming a new branch, erosion forming a new valley, a group of organisms traveling to a new location without the ability to return, or seeds floating over the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the biology of the organism and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances are, individuals from each population would fly back and forth continuing gene flow. However, if two rodent populations became divided by the formation of a new lake, continued gene flow would be unlikely; therefore, speciation would be more likely. 

Biologists group allopatric processes into two categories: dispersal and vicariance. Dispersal is when a few members of a species move to a new geographical area, and vicariance is when a natural situation arises to physically divide organisms. 

Scientists have documented numerous cases of allopatric speciation taking place. For example, along the west coast of the United States, two separate sub-species of spotted owls exist. The northern spotted owl has genetic and phenotypic differences from its close relative: the Mexican spotted owl, which lives in the south ( [link] ). The northern spotted owl and the Mexican spotted owl inhabit geographically separate locations with different climates and ecosystems. The owl is an example of allopatric speciation. (credit "northern spotted owl": modification of work by John and Karen Hollingsworth; credit "Mexican spotted owl": modification of work by Bill Radke) 

Additionally, scientists have found that the farther the distance between two groups that once were the same species, the more likely it is that speciation will occur. This seems logical because as the distance increases, the various environmental factors would likely have less in common than locations in close proximity. Consider the two owls: in the north, the climate is cooler than in the south; the types of organisms in each ecosystem differ, as do their behaviors and habits; also, the hunting habits and prey choices of the southern owls vary from the northern owls. These variances can lead to evolved differences in the owls, and speciation likely will occur. Adaptive Radiation 

In some cases, a population of one species disperses throughout an area, and each population finds a distinct niche or isolated habitat. Over time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species. This is called adaptive radiation because many adaptations evolve from a single point of origin; thus, causing the species to radiate into several new ones. Island archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island which leads to geographical isolation for many organisms. The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single species, called the founder species, numerous species have evolved, including the six shown in [link] . The honeycreeper birds illustrate adaptive radiation. From one original species of bird, multiple others evolved, each with its own distinctive characteristics. 

Notice the differences in the species beaks in [link] . Evolution in response to natural selection based on specific food sources in each new habitat led to evolution of a different beak suited to the specific food source. The seed-eating bird has a thicker, stronger beak which is suited to break hard nuts. The nectar-eating birds have long beaks to dip into flowers to reach the nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and impaling insects. Darwin s finches are another example of adaptive radiation in an archipelago. Link to Learning 

Click through this interactive site to see how island birds evolved in evolutionary increments from 5 million years ago to today. 

[link] Sympatric Speciation 

Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same habitat? The answer is yes. The process of speciation within the same space is called sympatric speciation; the prefix sym means same, so sympatric means same homeland in contrast to allopatric meaning other homeland. A number of mechanisms for sympatric speciation have been proposed and studied. 

One form of sympatric speciation can begin with a serious chromosomal error during cell division. In a normal cell division event chromosomes replicate, pair up, and then separate so that each new cell has the same number of chromosomes. However, sometimes the pairs separate and the end cell product has too many or too few individual chromosomes in a condition called aneuploidy ( [link] ). Visual Connection Aneuploidy results when the gametes have too many or too few chromosomes due to nondisjunction during meiosis. In the example shown here, the resulting offspring will have 2 n +1 or 2 n -1 chromosomes 

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Polyploidy is a condition in which a cell or organism has an extra set, or sets, of chromosomes. Scientists have identified two main types of polyploidy that can lead to reproductive isolation of an individual in the polyploidy state. Reproductive isolation is the inability to interbreed. In some cases, a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy ( [link] ). The prefix auto- means self, so the term means multiple chromosomes from one s own species. Polyploidy results from an error in meiosis in which all of the chromosomes move into one cell instead of separating. Autopolyploidy results when mitosis is not followed by cytokinesis. 

For example, if a plant species with 2 n = 6 produces autopolyploid gametes that are also diploid (2 n = 6, when they should be n = 3), the gametes now have twice as many chromosomes as they should have. These new gametes will be incompatible with the normal gametes produced by this plant species. However, they could either self-pollinate or reproduce with other autopolyploid plants with gametes having the same diploid number. In this way, sympatric speciation can occur quickly by forming offspring with 4 n called a tetraploid. These individuals would immediately be able to reproduce only with those of this new kind and not those of the ancestral species. 

The other form of polyploidy occurs when individuals of two different species reproduce to form a viable offspring called an allopolyploid . The prefix allo- means other (recall from allopatric): therefore, an allopolyploid occurs when gametes from two different species combine. [link] illustrates one possible way an allopolyploid can form. Notice how it takes two generations, or two reproductive acts, before the viable fertile hybrid results. Alloploidy results when two species mate to produce viable offspring. In the example shown, a normal gamete from one species fuses with a polyploidy gamete from another. Two matings are necessary to produce viable offspring. 

The cultivated forms of wheat, cotton, and tobacco plants are all allopolyploids. Although polyploidy occurs occasionally in animals, it takes place most commonly in plants. (Animals with any of the types of chromosomal aberrations described here are unlikely to survive and produce normal offspring.) Scientists have discovered more than half of all plant species studied relate back to a species evolved through polyploidy. With such a high rate of polyploidy in plants, some scientists hypothesize that this mechanism takes place more as an adaptation than as an error. Activity 

Create a visual representation such as a diagram with annotation to explain how island chains provide ideal conditions for allopatric speciation and adaptive radiation to occur. Then design a plan for collecting data to support the claim that speciation has occurred. Think About It Two species of fish had recently undergone sympatric speciation. The males of each species had a different coloring through which the females could identify and choose a partner from her own species. After some time, pollution made the lake so cloudy that it was hard for females to distinguish colors. What might take place in this situation? In a lake where most fish of a single species exhibit colorful stripes, a few individual animals have muted colors. The local fisherman receives a large order to catch the most colorful fish for a local aquarium store. The fisherman casts wide nets across the lake to catch a large number of the fish. He then keeps the colorful fish for the aquarium and throws back the dull colored fish. How will this single event change the make-up of the fish population? This activity is an application of AP Learning Objective 1.21 and Science Practice 4.2 because students are designing a plan to support the claim that islands provide the ideal conditions for allopatric speciation and adaptive radiation. The first Think About It question is an application of AP Learning Objective 1.22 and Science Practice 6.4 because students are making a prediction based on observations and a model of natural selection. Students also address questions relating to reproductive isolation and speciation (Learning Objective 1.23 and Science Practice 4.1). In the case of the first Think About It question, the females will likely attempt to breed with members of both species. However, because the two species can no longer interbreed, only females that mate with males of the same species will have offspring. This may eventually drive the evolution of other distinguishing traits, such as chemical signals, so that females can better identify males of their own species. The second Think About It question is an application of AP Learning Objective 1.24 and Science Practice 6.4 because students are making a prediction based on observations and a model of natural selection. In the second Think About It question, the gene frequency here will be modified as a consequence of a random event which drastically changes the composition of the population and is an example of genetic drift and the bottle-neck effect. The fish in the lake represent an isolated population on which genetic drift will act rapidly. Reproductive Isolation 

Given enough time, the genetic and phenotypic divergence between populations will affect characters that influence reproduction: if individuals of the two populations were to be brought together, mating would be less likely, but if mating occurred, offspring would be non-viable or infertile. Many types of diverging characters may affect the reproductive isolation (the inability to interbreed) of the two populations. 

Reproductive isolation can take place in a variety of ways. Scientists organize them into two groups: prezygotic barriers and postzygotic barriers. Recall that a zygote is a fertilized egg: the first cell of the development of an organism that reproduces sexually. Therefore, a prezygotic barrier is a mechanism that blocks reproduction from taking place; this includes barriers that prevent fertilization when organisms attempt reproduction. A postzygotic barrier occurs after zygote formation; this includes organisms that don t survive the embryonic stage and those that are born sterile. 

Some types of prezygotic barriers prevent reproduction entirely. Many organisms only reproduce at certain times of the year, often just annually. Differences in breeding schedules, called temporal isolation , can act as a form of reproductive isolation. For example, two species of frogs inhabit the same area, but one reproduces from January to March, whereas the other reproduces from March to May ( [link] ). These two related frog species exhibit temporal reproductive isolation. (a) Rana aurora breeds earlier in the year than (b) Rana boylii . (credit a: modification of work by Mark R. Jennings, USFWS; credit b: modification of work by Alessandro Catenazzi) 

In some cases, populations of a species move or are moved to a new habitat and take up residence in a place that no longer overlaps with the other populations of the same species. This situation is called habitat isolation . Reproduction with the parent species ceases, and a new group exists that is now reproductively and genetically independent. For example, a cricket population that was divided after a flood could no longer interact with each other. Over time, the forces of natural selection, mutation, and genetic drift will likely result in the divergence of the two groups ( [link] ). Speciation can occur when two populations occupy different habitats. The habitats need not be far apart. The cricket (a) Gryllus pennsylvanicus prefers sandy soil, and the cricket (b) Gryllus firmus prefers loamy soil. The two species can live in close proximity, but because of their different soil preferences, they became genetically isolated. 

Behavioral isolation occurs when the presence or absence of a specific behavior prevents reproduction from taking place. For example, male fireflies use specific light patterns to attract females. Various species of fireflies display their lights differently. If a male of one species tried to attract the female of another, she would not recognize the light pattern and would not mate with the male. 

Other prezygotic barriers work when differences in their gamete cells (eggs and sperm) prevent fertilization from taking place; this is called a gametic barrier . Similarly, in some cases closely related organisms try to mate, but their reproductive structures simply do not fit together. For example, damselfly males and females of different species have differently shaped reproductive organs. If one species tries to mate with another, their body parts simply do not fit together. ( [link] ). The shape of the male reproductive organ varies among male damselfly species, and is only compatible with the female of the same species. Reproductive organ incompatibility keeps each species reproductively isolated. 

In plants, certain structures aimed to attract one type of pollinator simultaneously prevent a different pollinator from accessing the pollen. The tunnel through which an animal must access nectar can vary widely in length and diameter, which prevents the plant from being cross-pollinated with a different species ( [link] ). Some flowers have evolved to attract certain pollinators. The (a) wide foxglove flower is adapted for pollination by bees, while the (b) long, tube-shaped trumpet creeper flower is adapted for pollination by humming birds. 

When fertilization takes place and a zygote forms, postzygotic barriers can prevent reproduction. Hybrid individuals in many cases cannot form normally in the womb and simply do not survive past the embryonic stages. This is called hybrid inviability because the hybrid organisms simply are not viable. In another postzygotic situation, reproduction leads to the birth and growth of a hybrid that is sterile and unable to reproduce offspring of their own; this is called hybrid sterility. Habitat Influence on Speciation 

Sympatric speciation may also take place in ways other than polyploidy. For example, consider a species of fish that lives in a lake. As the population grows, competition for food also grows. Under pressure to find food, suppose that a group of these fish had the genetic flexibility to discover and feed off another resource that was unused by the other fish. What if this new food source was found at a different depth of the lake? Over time, those feeding on the second food source would interact more with each other than the other fish; therefore, they would breed together as well. Offspring of these fish would likely behave as their parents: feeding and living in the same area and keeping separate from the original population. If this group of fish continued to remain separate from the first population, eventually sympatric speciation might occur as more genetic differences accumulated between them. 

This scenario does play out in nature, as do others that lead to reproductive isolation. One such place is Lake Victoria in Africa, famous for its sympatric speciation of cichlid fish. Researchers have found hundreds of sympatric speciation events in these fish, which have not only happened in great number, but also over a short period of time. [link] shows this type of speciation among a cichlid fish population in Nicaragua. In this locale, two types of cichlids live in the same geographic location but have come to have different morphologies that allow them to eat various food sources. Cichlid fish from Lake Apoyeque, Nicaragua, show evidence of sympatric speciation. Lake Apoyeque, a crater lake, is 1800 years old, but genetic evidence indicates that the lake was populated only 100 years ago by a single population of cichlid fish. Nevertheless, two populations with distinct morphologies and diets now exist in the lake, and scientists believe these populations may be in an early stage of speciation. Section Summary 

Speciation occurs along two main pathways: geographic separation (allopatric speciation) and through mechanisms that occur within a shared habitat (sympatric speciation). Both pathways isolate a population reproductively in some form. Mechanisms of reproductive isolation act as barriers between closely related species, enabling them to diverge and exist as genetically independent species. Prezygotic barriers block reproduction prior to formation of a zygote, whereas postzygotic barriers block reproduction after fertilization occurs. For a new species to develop, something must cause a breach in the reproductive barriers. Sympatric speciation can occur through errors in meiosis that form gametes with extra chromosomes (polyploidy). Autopolyploidy occurs within a single species, whereas allopolyploidy occurs between closely related species. Review Questions 

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[link] Glossary adaptive radiation speciation when one species radiates out to form several other species allopatric speciation speciation that occurs via geographic separation allopolyploid polyploidy formed between two related, but separate species aneuploidy condition of a cell having an extra chromosome or missing a chromosome for its species autopolyploid polyploidy formed within a single species behavioral isolation type of reproductive isolation that occurs when a specific behavior or lack of one prevents reproduction from taking place dispersal allopatric speciation that occurs when a few members of a species move to a new geographical area gametic barrier prezygotic barrier occurring when closely related individuals of different species mate, but differences in their gamete cells (eggs and sperm) prevent fertilization from taking place habitat isolation reproductive isolation resulting when populations of a species move or are moved to a new habitat, taking up residence in a place that no longer overlaps with the other populations of the same species hybrid offspring of two closely related individuals, not of the same species postzygotic barrier reproductive isolation mechanism that occurs after zygote formation prezygotic barrier reproductive isolation mechanism that occurs before zygote formation reproductive isolation situation that occurs when a species is reproductively independent from other species; this may be brought about by behavior, location, or reproductive barriers speciation formation of a new species species group of populations that interbreed and produce fertile offspring sympatric speciation speciation that occurs in the same geographic space temporal isolation differences in breeding schedules that can act as a form of prezygotic barrier leading to reproductive isolation vicariance allopatric speciation that occurs when something in the environment separates organisms of the same species into separate groups polyploidy gametes with extra chromosomesReconnection and Rates of Speciation Reconnection and Rates of Speciation 

In this section, you will explore the following questions: What are the pathways of species evolution in hybrid zones? What are the two major theories on rates of speciation? Connection for AP Courses 

Speciation can both occur gradually over time in small steps or in bursts of change known as punctuated equilibrium. With punctuated equilibrium, a species may remain unchanged for long periods of time. The primary influencing factor on changes in speciation rate is environmental change. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 1 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.C Life continues to evolve within a changing environment. Essential Knowledge 1.C.1 Speciation and extinction have occurred throughout Earth s history. Science Practice 5.1 The student can analyze data to identify patterns or relationships. Learning Objective 1.20 The student is able to analyze data related to questions of speciation and extinction throughout the Earth s history. 

Hybrid zones provide scientists with spaces from which to research the factors that cause reproductive isolation, and thus, speciation. The spatial patterns of hybrid zones reveal much about these factors and allow for inferences to be made about the number and degree of obstacles to gene flow as well as the number and types of contacts between species. 

You may wish to identify for students examples of hybrid zones, or encourage them to research zones for themselves. Pose questions to students about why hybrid zones might be viewed a natural experiments in which to study the process of speciation. Encourage them to compare and contrast the information they find about different hybrid zones. Have them consider what questions they might ask about the species in the zones and what information they might expect to gain from asking them. 

Speciation occurs over a span of evolutionary time, so when a new species arises, there is a transition period during which the closely related species continue to interact. Reconnection 

After speciation, two species may continue interacting indefinitely or even recombine. Individual organisms will mate with any nearby individual who they are capable of breeding with. An area where two closely related species continue to interact and reproduce, forming hybrids, is called a hybrid zone . Over time, the hybrid zone may change depending on the fitness of the hybrids and the reproductive barriers ( [link] ). If the hybrids are less fit than the parents, reinforcement of speciation occurs, and the species continue to diverge until they can no longer mate and produce viable offspring. If reproductive barriers weaken, fusion occurs and the two species become one. Barriers remain the same if hybrids are fit and reproductive: stability may occur and hybridization continues. Visual Connection After speciation has occurred, the two separate but closely related species may continue to produce offspring in an area called the hybrid zone. Reinforcement, fusion, or stability may result, depending on reproductive barriers and the relative fitness of the hybrids. 

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Hybrids can be either less fit than the parents, more fit, or about the same. Usually hybrids tend to be less fit; therefore, such reproduction diminishes over time, nudging the two species to diverge further in a process called reinforcement . This term is used because the low success of the hybrids reinforces the original speciation. If the hybrids are as fit or more fit than the parents, the two species may fuse back into one species ( [link] ). Scientists have also observed that sometimes two species will remain separate but also continue to interact to produce some hybrid individuals; this is classified as stability because no real net change is taking place. Varying Rates of Speciation 

Scientists around the world study speciation, documenting observations both of living organisms and those found in the fossil record. As their ideas take shape and as research reveals new details about how life evolves, they develop models to help explain rates of speciation. In terms of how quickly speciation occurs, two patterns are currently observed: gradual speciation model and punctuated equilibrium model. 

In the gradual speciation model , species diverge gradually over time in small steps. In the punctuated equilibrium model, a new species undergoes changes quickly from the parent species, and then remains largely unchanged for long periods of time afterward ( [link] ). This early change model is called punctuated equilibrium, because it begins with a punctuated or periodic change and then remains in balance afterward. While punctuated equilibrium suggests a faster tempo, it does not necessarily exclude gradualism. Visual Connection In (a) gradual speciation, species diverge at a slow, steady pace as traits change incrementally. In (b) punctuated equilibrium, species diverge quickly and then remain unchanged for long periods of time. 

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The primary influencing factor on changes in speciation rate is environmental conditions. Under some conditions, selection occurs quickly or radically. Consider a species of snails that had been living with the same basic form for many thousands of years. Layers of their fossils would appear similar for a long time. When a change in the environment takes place such as a drop in the water level a small number of organisms are separated from the rest in a brief period of time, essentially forming one large and one tiny population. The tiny population faces new environmental conditions. Because its gene pool quickly became so small, any variation that surfaces and that aids in surviving the new conditions becomes the predominant form. Link to Learning 

Visit this website to continue the speciation story of the snails. 

[link] Section Summary 

Speciation is not a precise division: overlap between closely related species can occur in areas called hybrid zones. Organisms reproduce with other similar organisms. The fitness of these hybrid offspring can affect the evolutionary path of the two species. Scientists propose two models for the rate of speciation: one model illustrates how a species can change slowly over time; the other model demonstrates how change can occur quickly from a parent generation to a new species. Both models continue to follow the patterns of natural selection. Review Questions 

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[link] Glossary gradual speciation model model that shows how species diverge gradually over time in small steps hybrid zone area where two closely related species continue to interact and reproduce, forming hybrids punctuated equilibrium model for rapid speciation that can occur when an event causes a small portion of a population to be cut off from the rest of the population reinforcement continued speciation divergence between two related species due to low fitness of hybrids between themIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" Living things may be single-celled or complex, multicellular organisms. They may be plants, animals, fungi, bacteria, or archaea. This diversity results from evolution. (credit "wolf": modification of work by Gary Kramer; credit "coral": modification of work by William Harrigan, NOAA; credit "river": modification of work by Vojt ch Dost l; credit "fish" modification of work by Christian Mehlf hrer; credit "mushroom": modification of work by Cory Zanker; credit "tree": modification of work by Joseph Kranak; credit "bee": modification of work by Cory Zanker) 

Evolutionary medicine is an emerging field that applies evolutionary theory to modern medicine. Rather than just seeking answers to how illness occurs, evolutionary medicine also asks why illness occurs. This approach to medicine has led to many important advances. For example, endogenous retroviruses (ERVs) are pieces of retroviruses that began invading mammalian genomes over 100 million years ago. While studying why smaller mammals tend to get cancer more frequently than larger mammals, scientists discovered that larger mammals have had fewer ERVs invade their genome. Because retroviral integration is associated with cancer, results from this research suggest the possibility that larger mammals are able to control EVR replication until they reach post-reproductive age. 1 More on this research can be found on the PLOS Pathogens website . Footnotes 1 Katzourakis A, Magiorkinis G, Lim AG, Gupta S, Belshaw R, et al. (2014) Larger Mammalian Body Size Leads to Lower Retroviral Activity. PLoS Pathog10(7): e1004214. doi: 10.1371/journal.ppat.1004214Population Evolution Population Evolution 

In this section, you will explore the following questions: What is population genetics and how is population genetics a synthesis of Mendelian inheritance and Darwinian evolution? What is the Hardy Weinberg principle, and how can it be applied to microevolution? 

The mechanisms of inheritance, or genetics, were not understood at the time Charles Darwin and Alfred Russel Wallace were developing their idea of natural selection. This lack of understanding was a stumbling block to understanding many aspects of evolution. In fact, the predominant (and incorrect) genetic theory of the time, blending inheritance, made it difficult to understand how natural selection might operate. Darwin and Wallace were unaware of the genetics work by Austrian monk Gregor Mendel, which was published in 1866, not long after publication of Darwin's book, On the Origin of Species . Mendel s work was rediscovered in the early twentieth century at which time geneticists were rapidly coming to an understanding of the basics of inheritance. Initially, the newly discovered particulate nature of genes made it difficult for biologists to understand how gradual evolution could occur. But over the next few decades genetics and evolution were integrated in what became known as the modern synthesis the coherent understanding of the relationship between natural selection and genetics that took shape by the 1940s and is generally accepted today. In sum, the modern synthesis describes how evolutionary processes, such as natural selection, can affect a population s genetic makeup, and, in turn, how this can result in the gradual evolution of populations and species. The theory also connects this change of a population over time, called microevolution , with the processes that gave rise to new species and higher taxonomic groups with widely divergent characters, called macroevolution . Connection for AP Courses 

Population genetics studies microevolution by measuring changes in a population s allele frequencies over time. (Remember that we studied genotypes and allele frequencies when we explored inheritance patterns proposed by Mendel.) For example, scientists examining allele frequencies in a pesticide resistance gene in mosquitoes at Equatorial Guinea found that the frequency of one resistance allele was 6.3%, while a second resistance allele s frequency was 74.6%, and the non-resistance allele s frequency was 19.0%. These three frequencies add up to 100%. 1 A population s gene pool is the sum of all the alleles. If these frequencies do not change over time, the population is said to be in Hardy Weinberg principle of equilibrium a stable, non-evolving state. However, if a phenotype is favored by natural selection, allele frequencies can change. If this is the case, the population is evolving. Sometimes allele frequencies within a population change randomly with no advantage to the population over existing allele frequencies. This phenomenon is called genetic drift . An event that initiates an allele frequency change in an isolated part of the population, which is not typical of the original population, is called the founder effect . In Population Genetics , we will explore how natural selection, random drift, and founder effects can lead to significant changes in the genome of a population. 

Hardy Weinberg equilibrium reflects a state of constancy in a population s gene pool. In other words, allele frequencies remain stable from generation to generation if certain conditions are met: no mutations, no gene flow, random mating, no genetic drift, and no selection. Because these conditions are rarely met, allele frequencies are typically changing, reflecting evolution. The Hardy Weinberg principle is represented by the mathematical equation p 2 + 2pq + q 2 = 1 , where p represents the frequency of the dominant allele and q represents the frequency of the recessive allele. Deviations from Hardy Weinberg equilibrium allow us to measure microevolutionary shifts in a population when one or more of the Hardy Weinberg parameters change. For example, if we go back to the study of the frequencies of alleles in a pesticide resistance gene, after an area was treated with pesticides for two years, the resistance alleles increased to 11.1% and 83.3%, respectively, while the non-resistance allele decreased to 5.6%. This indicates that microevolution was occurring. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 1 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1: The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.A Change in the genetic makeup of a population over time is evolution. Essential Knowledge 1.A.1 Natural selection is a major mechanism of evolution. Science Practice 1.5 The student can re-express key elements of natural phenomena across multiple representations in the domain. Science Practice 1.1 The student is able to convert a data set from a table of numbers that reflect a change in the genetic makeup of a population over time and to apply mathematical methods and conceptual understandings to investigate the cause(s) and effect(s) of this change. Essential Knowledge 1.A.1 Natural selection is a major mechanism of evolution. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Learning Objective 1.2 The student is able to evaluate evidence provided by data to qualitatively and quantitatively investigate the role of natural selection in evolution. Essential Knowledge 1.A.1 Natural selection is a major mechanism of evolution. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 1.3 The student is able to apply mathematical methods to data from a real or simulated population to predict what will happen to the population in the future. 

A good video tutorial by Bozeman on Hardy Weinberg can be found here . 

Evolution and Flu Vaccines Every fall, the media starts reporting on flu vaccinations and potential outbreaks. Scientists, health experts, and institutions determine recommendations for different parts of the population, predict optimal production and inoculation schedules, create vaccines, and set up clinics to provide inoculations. You may think of the annual flu shot as a lot of media hype, an important health protection, or just a briefly uncomfortable prick in your arm. But do you think of it in terms of evolution? 

The media hype of annual flu shots is scientifically grounded in our understanding of evolution. Each year, scientists across the globe strive to predict the flu strains that they anticipate being most widespread and harmful in the coming year. This knowledge is based in how flu strains have evolved over time and over the past few flu seasons. Scientists then work to create the most effective vaccine to combat those selected strains. Hundreds of millions of doses are produced in a short period in order to provide vaccinations to key populations at the optimal time. 

Because viruses, like the flu, evolve very quickly (especially in evolutionary time), this poses quite a challenge. Viruses mutate and replicate at a fast rate, so the vaccine developed to protect against last year s flu strain may not provide the protection needed against the coming year s strain. Evolution of these viruses means continued adaptions to ensure survival, including adaptations to survive previous vaccines. 

[link] Population Genetics 

Recall that a gene for a particular character may have several alleles, or variants, that code for different traits associated with that character. For example, in the ABO blood type system in humans, three alleles determine the particular blood-type protein on the surface of red blood cells. Each individual in a population of diploid organisms can only carry two alleles for a particular gene, but more than two may be present in the individuals that make up the population. Mendel followed alleles as they were inherited from parent to offspring. In the early twentieth century, biologists in a field of study known as population genetics began to study how selective forces change a population through changes in allele and genotypic frequencies. 

The allele frequency (or gene frequency) is the proportion of a specific allele within a population, relative to all other alleles of that gene that are present in the population. Until now we have discussed evolution as a change in the characteristics of a population of organisms, but behind that phenotypic change is genetic change. In population genetics, the term evolution is defined as a change in the frequency of an allele in a population. Using the ABO blood type system as an example, the frequency of one of the alleles, I A , is the number of copies of that allele divided by all the copies of the ABO gene in the population. For example, a study in Jordan 2 found a frequency of I A to be 26.1 percent. The I B and I 0 alleles made up 13.4 percent and 60.5 percent of the alleles respectively, and all of the frequencies added up to 100 percent. A change in this frequency over time would constitute evolution in the population. 

The allele frequency within a given population can change depending on environmental factors; therefore, certain alleles become more widespread than others during the process of natural selection. Natural selection can alter the population s genetic makeup; for example, if a given allele confers a phenotype that allows an individual to better survive or have more offspring. Because many of those offspring will also carry the beneficial allele, and often the corresponding phenotype, they will have more offspring of their own that also carry the allele, thus, perpetuating the cycle. Over time, the allele will spread throughout the population. Some alleles will quickly become fixed in this way, meaning that every individual of the population will carry the allele, while detrimental mutations may be swiftly eliminated if derived from a dominant allele from the gene pool. The gene pool is the sum of all the alleles in a population. 

Sometimes, allele frequencies within a population change randomly with no advantage to the population over existing allele frequencies. This phenomenon is called genetic drift. Natural selection and genetic drift usually occur simultaneously in populations and are not isolated events. It is hard to determine which process dominates because it is often nearly impossible to determine the cause of change in allele frequencies at each occurrence. An event that initiates an allele frequency change in an isolated part of the population, which is not typical of the original population, is called the founder effect. Natural selection, random drift, and founder effects can lead to significant changes in the genome of a population. Hardy Weinberg Principle of Equilibrium 

In the early twentieth century, English mathematician Godfrey Hardy and German physician Wilhelm Weinberg stated the principle of equilibrium to describe the genetic makeup of a population. The theory, which later became known as the Hardy Weinberg principle of equilibrium, states that a population s allele and genotype frequencies are inherently stable unless some kind of evolutionary force is acting upon the population, neither the allele nor the genotypic frequencies would change. The Hardy Weinberg principle assumes conditions with no mutations, migration, emigration, or selective pressure for or against genotype, plus an infinite population; while no population can satisfy those conditions, the principle offers a useful model against which to compare real population changes. 

Working under this theory, population geneticists represent different alleles as different variables in their mathematical models. The variable p, for example, typically represents the frequency of the dominant allele, say Y for the trait of yellow in Mendel's peas. The variable q represents the frequency of the recessive allele, in this case y, that confers the color green. If these are the only two possible alleles for a given locus in the population, p + q = 1. In other words, all the p alleles and all the q alleles make up all of the alleles for that locus that are found in the population. 

But what ultimately interests most biologists is not the frequencies of different alleles, but the frequencies of the resulting genotypes, known as the population s genetic structure , from which scientists can surmise the distribution of phenotypes. If the phenotype is observed, only the genotype of the homozygous recessive alleles can be known; the calculations provide an estimate of the remaining genotypes. Since each individual carries two alleles per gene, if the allele frequencies (p and q) are known, predicting the frequencies of these genotypes is a simple mathematical calculation to determine the probability of getting these genotypes if two alleles are drawn at random from the gene pool. So in the above scenario, an individual pea plant could be pp (YY), and thus produce yellow peas; pq (Yy), also yellow; or qq (yy), and thus producing green peas ( [link] ). In other words, the frequency of pp individuals is simply p 2 ; the frequency of pq individuals is 2pq; and the frequency of qq individuals is q 2 . And, again, if p and q are the only two possible alleles for a given trait in the population, these genotypes frequencies will sum to one: p 2 + 2pq + q 2 = 1. 

When populations are in the Hardy Weinberg equilibrium, the allelic frequency is stable from generation to generation and the distribution of alleles can be determined from the Hardy Weinberg equation. If the allelic frequency measured in the field differs from the predicted value, scientists can make inferences about what evolutionary forces are at play. 

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In theory, if a population is at equilibrium that is, there are no evolutionary forces acting upon it generation after generation would have the same gene pool and genetic structure, and these equations would all hold true all of the time. Of course, even Hardy and Weinberg recognized that no natural population is immune to evolution. Populations in nature are constantly changing in genetic makeup due to drift, mutation, possibly migration, and selection. As a result, the only way to determine the exact distribution of phenotypes in a population is to go out and count them. But the Hardy Weinberg principle gives scientists a mathematical baseline of a non-evolving population to which they can compare evolving populations and thereby infer what evolutionary forces might be at play. If the frequencies of alleles or genotypes deviate from the value expected from the Hardy Weinberg equation, then the population is evolving. 

Use this online calculator to determine the genetic structure of a population. 

[link] Lab Investigation 

AP Biology Investigative Labs: Inquiry-Based Approach, Investigation 2: Mathematical Modeling: Hardy Weinberg . In this lab investigation, you apply the Hardy Weinberg equation and create a spreadsheet to study changes in allele frequencies in a population and to examine possible causes for these changes. Think About It 

Imagine you are trying to determine if a population of flowers is undergoing microevolution. You suspect there is selection pressure on the color of the flower because bees seem to cluster around red flowers more often than blue flowers. In a separate experiment, you discover that blue flower color is dominant to red flower color. In a field, you count 600 blue flowers and 200 red flowers. Based on the H-W equation, what are the expected allele frequencies for flower color? 

Two years later, you revisit the same field and discover that out of 1,000 flowers, 650 are blue. Use the H W equation to determine if the population of flowers is undergoing evolution. This lab investigation is an application of AP Learning Objective 1.1 and Science Practices 1.5 and 2.2, Learning Objective 1.2 and Science Practices 2.2 and 5.3, and Learning Objective 1.3 and Science Practice 2.2 because students are analyzing data sets and applying the Hardy Weinberg equation to calculate allele frequencies and determine if a population if evolving based on changes in allele frequencies. For additional interactive programs and tutorials to aid students in understanding allelles, go to this website . Think About It Answers: In the first example, 200 out of 800 flowers had the recessive homozygous phenotype. The q2=0.25 and thus the frequency of q = 0.5. Since p + q = 1, the frequency of p is also 0.5. In the second example, using the same math, the frequency of p is 0.57 and q is 0.43, so it is clear that the allelic frequencies are changing and that the populations is indeed undergoing natural selection. The Think About It questions are applications of AP Learning Objective 1.1 and Science Practices 1.5 and 2.2, Learning Objective 1.2 and Science Practices 2.2 and 5.3, and Learning Objective 1.3 and Science Practice 2.2 because students are applying the Hardy Weinberg equation to data sets and using calculated allele frequencies to determine if a population is evolving. Section Summary 

The modern synthesis of evolutionary theory grew out of the cohesion of Darwin s, Wallace s, and Mendel s thoughts on evolution and heredity, along with the more modern study of population genetics. It describes the evolution of populations and species, from small-scale changes among individuals to large-scale changes over paleontological time periods. To understand how organisms evolve, scientists can track populations allele frequencies over time. If they differ from generation to generation, scientists can conclude that the population is not in Hardy Weinberg equilibrium, and is thus evolving. Review Questions 

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[link] Footnotes 1 Reddy, M. R., Godoy, A., Dion, K., Matias, A., Callender, K., Kiszewski, A. E., Slotman, M. A. (2013). Insecticide Resistance Allele Frequencies in Anopheles gambiae before and after Anti-Vector Interventions in Continental Equatorial Guinea. The American Journal of Tropical Medicine and Hygiene, 88 (5), 897 907. doi:10.4269/ajtmh.12-0467 2 Sahar S. Hanania, Dhia S. Hassawi, and Nidal M. Irshaid, Allele Frequency and Molecular Genotypes of ABO Blood Group System in a Jordanian Population, Journal of Medical Sciences 7 (2007): 51-58, doi:10.3923/jms.2007.51.58. Glossary allele frequency (also, gene frequency) rate at which a specific allele appears within a population founder effect event that initiates an allele frequency change in part of the population, which is not typical of the original population gene pool all of the alleles carried by all of the individuals in the population genetic structure distribution of the different possible genotypes in a population macroevolution broader scale evolutionary changes seen over paleontological time microevolution changes in a population s genetic structure modern synthesis overarching evolutionary paradigm that took shape by the 1940s and is generally accepted today population genetics study of how selective forces change the allele frequencies in a population over time Hardy Weinberg principle of equilibrium a stable, non-evolving state of a population in which allelic frequencies are stable over time genotype frequency the proportion of a specific genotype in a population relative to all other genotypes for those genes that are present in the populationPopulation Genetics Population Genetics 

In this section, you will explore the following questions: What are the different types of variation in a population? Why can only heritable variation be acted upon by natural selection? How can genetic drift, the bottleneck effect, and the founder effect influence allele frequencies in a population? How can gene flow, mutation, nonrandom mating, and environmental variance affect allele frequencies in a population? Connection for AP Courses 

Take a look at your classmates. Individuals of a population often display different phenotypes, or express different alleles of a particular gene. These differences are called polymorphisms . The distribution of phenotypes among individuals, known as population variation , is influenced by several factors, including the population s genetic structure and the environment ( [link] ). Understanding the sources of phenotypic variation is important for determining how a population will evolve in response to different evolutionary pressures. Only those variations that are encoded in an individual s genes can be passed to its offspring and be a target of natural selection. The distribution of phenotypes in this litter of kittens illustrates population variation. (credit: Pieter Lanser) 

As you learn in the chapter that discusses the evolution and origin of species, natural selection works by selecting for phenotypes and the alleles that determine them that confer beneficial traits or behaviors. Deleterious qualities are selected against. Genetic drift stems from the chance occurrence that some individuals have more offspring than others and, thus, will pass on more of their genes to the next generation. Small and isolated populations are more susceptible to genetic drift. Natural events, such as wildfires or hurricanes, can magnify genetic drift when a large portion of the population is killed. Because a fire does not distinguish between the genotypes of various organisms, no particular genotype survives the fire better than another. Therefore, the genetic structure of the surviving population may be very different from the genetic structure of the original population. This is called the bottleneck effect. Another scenario in which populations might experience a strong influence of genetic drift occurs when some portion of the population leaves to start a new population in a new location or gets separated by a physical barrier of some kind. In this situation, those individuals are unlikely to be representative of the entire population, a phenomenon called the founder effect. Both the bottleneck effect and the founder effect reduce genetic variation within a population and genetic variation is the basis for natural selection. When individuals leave or join a population, they carry their alleles with them, resulting in changes in the population s allele frequencies. Allele frequencies also can change due to mutation in DNA and when individuals do not randomly mate with others; when an individual selects a mate based on phenotype, the genotype is also selected. In summary, any of these conditions can result in deviations from the Hardy Weinberg equilibrium and lead to the microevolution of a population. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 1 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1: The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.A Change in the genetic makeup of a population over time is evolution. Essential Knowledge 1.A.1 Natural selection is a major mechanism of evolution. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Learning Objective 1.2 The student is able to evaluate evidence provided by data to qualitatively and quantitatively investigate the role of natural selection in evolution. Essential Knowledge 1.A.2 Natural selection acts on phenotypic variations in populations. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 1.3 The student is able to apply mathematical methods to data from a real or simulated population to predict what will happen to the population in the future. Essential Knowledge 1.A.2 Natural selection acts on phenotypic variations in populations. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 1.4 The student is able to evaluate data-based evidence that describes evolutionary changes in the genetic makeup of a population over time. Essential Knowledge 1.A.3 Evolutionary change is also driven by random processes. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective 1.8 The student is able to make predictions about the effects of genetic drift, migration, and artificial selection on the genetic makeup of a population. Essential Knowledge 1.A.3 Evolutionary change is also driven by random processes. Science Practice 1.4 The student can use representatives and models to analyze situations or solve problems qualitatively and quantitatively. Science Practice 2.1 The student can justify the selection of a mathematical routine to solve problems. Learning Objective 1.6 The student is able to use data from mathematical models based on the Hardy Weinberg equilibrium to analyze genetic drift and the effects of selection in the evolution of specific populations. Essential Knowledge 1.A.3 Evolutionary change is also driven by random processes. Science Practice 2.1 The student can justify the selection of a mathematical routine to solve problems. Learning Objective 1.7 The student is able to justify data from mathematical models based on the Hardy Weinberg equilibrium to analyze genetic drift and the effects of selection in the evolution of specific populations. 

Another online example of genetic drift can be found at this website . Genetic Variance 

Natural selection and some of the other evolutionary forces can only act on heritable traits, namely an organism s genetic code. Because alleles are passed from parent to offspring, those that confer beneficial traits or behaviors may be selected for, while deleterious alleles may be selected against. Acquired traits, for the most part, are not heritable. For example, if an athlete works out in the gym every day, building up muscle strength, the athlete s offspring will not necessarily grow up to be a body builder. If there is a genetic basis for the ability to run fast, on the other hand, this may be passed to a child. 

Before Darwinian evolution became the prevailing theory of the field, French naturalist Jean-Baptiste Lamarck theorized that acquired traits could, in fact, be inherited; while this hypothesis has largely been unsupported, scientists have recently begun to realize that Lamarck was not completely wrong. Visit this site to learn more. 

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Heritability is the fraction of phenotype variation that can be attributed to genetic differences, or genetic variance, among individuals in a population. The greater the hereditability of a population s phenotypic variation, the more susceptible it is to the evolutionary forces that act on heritable variation. 

The diversity of alleles and genotypes within a population is called genetic variance . When scientists are involved in the breeding of a species, such as with animals in zoos and nature preserves, they try to increase a population s genetic variance to preserve as much of the phenotypic diversity as they can. This also helps reduce the risks associated with inbreeding , the mating of closely related individuals, which can have the undesirable effect of bringing together deleterious recessive mutations that can cause abnormalities and susceptibility to disease. For example, a disease that is caused by a rare, recessive allele might exist in a population, but it will only manifest itself when an individual carries two copies of the allele. Because the allele is rare in a normal, healthy population with unrestricted habitat, the chance that two carriers will mate is low, and even then, only 25 percent of their offspring will inherit the disease allele from both parents. While it is likely to happen at some point, it will not happen frequently enough for natural selection to be able to swiftly eliminate the allele from the population, and as a result, the allele will be maintained at low levels in the gene pool. However, if a family of carriers begins to interbreed with each other, this will dramatically increase the likelihood of two carriers mating and eventually producing diseased offspring, a phenomenon known as inbreeding depression . 

Changes in allele frequencies that are identified in a population can shed light on how it is evolving. In addition to natural selection, there are other evolutionary forces that could be in play: genetic drift, gene flow, mutation, nonrandom mating, and environmental variances. Genetic Drift 

The theory of natural selection stems from the observation that some individuals in a population are more likely to survive longer and have more offspring than others; thus, they will pass on more of their genes to the next generation. A big, powerful male gorilla, for example, is much more likely than a smaller, weaker one to become the population s silverback, the pack s leader who mates far more than the other males of the group. The pack leader will father more offspring, who share half of his genes, and are likely to also grow bigger and stronger like their father. Over time, the genes for bigger size will increase in frequency in the population, and the population will, as a result, grow larger on average. That is, this would occur if this particular selection pressure , or driving selective force, were the only one acting on the population. In other examples, better camouflage or a stronger resistance to drought might pose a selection pressure. 

Another way a population s allele and genotype frequencies can change is genetic drift ( [link] ), which is simply the effect of chance. By chance, some individuals will have more offspring than others not due to an advantage conferred by some genetically-encoded trait, but just because one male happened to be in the right place at the right time (when the receptive female walked by) or because the other one happened to be in the wrong place at the wrong time (when a fox was hunting). 

Genetic drift in a population can lead to the elimination of an allele from a population by chance. In this example, rabbits with the brown coat color allele ( B ) are dominant over rabbits with the white coat color allele ( b ). In the first generation, the two alleles occur with equal frequency in the population, resulting in p and q values of .5. Only half of the individuals reproduce, resulting in a second generation with p and q values of .7 and .3, respectively. Only two individuals in the second generation reproduce, and by chance these individuals are homozygous dominant for brown coat color. As a result, in the third generation the recessive b allele is lost. 

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Small populations are more susceptible to the forces of genetic drift. Large populations, on the other hand, are buffered against the effects of chance. If one individual of a population of 10 individuals happens to die at a young age before it leaves any offspring to the next generation, all of its genes 1/10 of the population s gene pool will be suddenly lost. In a population of 100, that s only 1 percent of the overall gene pool; therefore, it is much less impactful on the population s genetic structure. 

Go to this site to watch an animation of random sampling and genetic drift in action. 

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Genetic drift can also be magnified by natural events, such as a natural disaster that kills at random a large portion of the population. Known as the bottleneck effect, it results in a large portion of the genome suddenly being wiped out ( [link] ). In one fell swoop, the genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population. A chance event or catastrophe can reduce the genetic variability within a population. 

Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population leaves to start a new population in a new location or if a population gets divided by a physical barrier of some kind. In this situation, those individuals are unlikely to be representative of the entire population, which results in the founder effect. The founder effect occurs when the genetic structure changes to match that of the new population s founding fathers and mothers. The founder effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners but rare in most other populations. This is likely due to the fact that a higher-than-normal proportion of the founding colonists carried these mutations. As a result, the population expresses unusually high incidences of Huntington s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause blood marrow and congenital abnormalities even cancer. 1 

Watch this short video to learn more about the founder and bottleneck effects. 

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Testing the Bottleneck Effect 

Question: How do natural disasters affect the genetic structure of a population? 

Background: When much of a population is suddenly wiped out by an earthquake or hurricane, the individuals that survive the event are usually a random sampling of the original group. As a result, the genetic makeup of the population can change dramatically. This phenomenon is known as the bottleneck effect. 

Hypothesis: Repeated natural disasters will yield different population genetic structures; therefore, each time this experiment is run, the results will vary. 

Test the hypothesis: Count out the original population using different colored beads. For example, red, blue, and yellow beads might represent red, blue, and yellow individuals. After recording the number of each individual in the original population, place them all in a bottle with a narrow neck that will only allow a few beads out at a time. Then, pour 1/3 of the bottle s contents into a bowl. This represents the surviving individuals after a natural disaster kills a majority of the population. Count the number of the different colored beads in the bowl, and record it. Then, place all of the beads back in the bottle and repeat the experiment four more times. 

Analyze the data: Compare the five populations that resulted from the experiment. Do the populations all contain the same number of different colored beads, or do they vary? Remember, these populations all came from the same exact parent population. 

Form a conclusion: Most likely, the five resulting populations will differ quite dramatically. This is because natural disasters are not selective they kill and spare individuals at random. Now think about how this might affect a real population. What happens when a hurricane hits the Mississippi Gulf Coast? How do the seabirds that live on the beach fare? Gene Flow 

Another important evolutionary force is gene flow : the flow of alleles in and out of a population due to the migration of individuals or gametes ( [link] ). While some populations are fairly stable, others experience more flux. Many plants, for example, send their pollen far and wide, by wind or by bird, to pollinate other populations of the same species some distance away. Even a population that may initially appear to be stable, such as a pride of lions, can experience its fair share of immigration and emigration as developing males leave their mothers to seek out a new pride with genetically unrelated females. This variable flow of individuals in and out of the group not only changes the gene structure of the population, but it can also introduce new genetic variation to populations in different geological locations and habitats. 

Gene flow can occur when an individual travels from one geographic location to another. Mutation 

Mutations are changes to an organism s DNA and are an important driver of diversity in populations. Species evolve because of the accumulation of mutations that occur over time. The appearance of new mutations is the most common way to introduce novel genotypic and phenotypic variance. Some mutations are unfavorable or harmful and are quickly eliminated from the population by natural selection. Others are beneficial and will spread through the population. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. Some mutations do not do anything and can linger, unaffected by natural selection, in the genome. Some can have a dramatic effect on a gene and the resulting phenotype. Nonrandom Mating 

If individuals nonrandomly mate with their peers, the result can be a changing population. There are many reasons nonrandom mating occurs. One reason is simple mate choice; for example, female peahens may prefer peacocks with bigger, brighter tails. Traits that lead to more matings for an individual become selected for by natural selection. One common form of mate choice, called assortative mating , is an individual s preference to mate with partners who are phenotypically similar to themselves. 

Another cause of nonrandom mating is physical location. This is especially true in large populations spread over large geographic distances where not all individuals will have equal access to one another. Some might be miles apart through woods or over rough terrain, while others might live immediately nearby. Environmental Variance 

Genes are not the only players involved in determining population variation. Phenotypes are also influenced by other factors, such as the environment ( [link] ). For example, sun exposure is an environmental factor, as a person who spends more time in the sun will likely have darker skin than a person who spends most of their time indoors (assuming both people had similarly-colored skin to start with). Some major characteristics, such as gender, are determined by the environment for some species. For example, some turtles and other reptiles have temperature-dependent sex determination (TSD). TSD means that individuals develop into males if their eggs are incubated within a certain temperature range, or females at a different temperature range. The sex of the American alligator ( Alligator mississippiensis ) is determined by the temperature at which the eggs are incubated. Eggs incubated at 30 C produce females, and eggs incubated at 33 C produce males. (credit: Steve Hillebrand, USFWS) 

Geographic separation between populations can lead to differences in the phenotypic variation between those populations. Such geographical variation is seen between most populations and can be significant. One type of geographic variation, called a cline , can be seen as populations of a given species vary gradually across an ecological gradient. Species of warm-blooded animals, for example, tend to have larger bodies in the cooler climates closer to the earth s poles, allowing them to better conserve heat. This is considered a latitudinal cline. Alternatively, flowering plants tend to bloom at different times depending on where they are along the slope of a mountain, known as an altitudinal cline. 

If there is gene flow between the populations, the individuals will likely show gradual differences in phenotype along the cline. Restricted gene flow, on the other hand, can lead to abrupt differences, even speciation. Lab Investigation 

AP Biology Investigative Labs: Inquiry-Based Approach, Investigation 1: Artificial Selection . Using Wisconsin Fast Plants, you explore evolution by conducting an artificial selection investigation to increase or decrease genetic variation in a population and then determine if extreme selection can change the expression of a quantitative trait. Think About It Do you think genetic drift would happen more quickly on an island or on the mainland? Provide reasoning for your answer. Consider the population of red and blue flowers you analyzed in Section 1 to determine if they were undergoing microevolution. Recall that you counted 600 blue flowers and 200 red flowers. Imagine that you return four years after your initial visit, and the flowers at the site have been split into two different populations by a newly formed river, which isolates the two populations. In the population 1, you counted 125 blue flowers and 10 red flowers. In the population 2, you counted 450 blue flowers and 300 red flowers. Did genetic drift or natural selection likely cause these change in allele frequencies in population 1? What about population 2? Explain how you know for each population. The lab investigation is an application of AP Learning Objective 1.8 and Science Practice 6.4 because students are investigating the effect(s) of artificial selection on the genetic makeup of a population. The first Think About It question is an application AP Learning Objective 1.8 and Science Practice 6.4 because students are making a prediction about the effect of genetic drift on the genetic makeup of a population, and the factors that influence the effects of genetic drift. First think about it question answer: Genetic drift is more likely on an island because of the founder effect. New island populations are often started by specific individuals of an original population, carrying gene frequencies different from those of the parent population. This causes genetic drift. Second Think About It Answers: In the first visit, it was determined that 200 out of 800 flowers had the recessive homozygous phenotype. Therefore, q 2 =0.25 and q = 0.5. For the first population, 10 out of 135 flowers were red. Therefore, q = 0.27. If bees were selecting for red flowers, the frequency of red flowers should increase, not decrease. Therefore, this evolutionary change in population 1 was likely caused by genetic drift. In the second population, 300 out of 750 flowers were red. Therefore, q=0.63 and p=0.37. This indicates that the frequency of the recessive allele q, which causes red coloration, is increasing, and is consistent with the hypothesis that red flowers are being selected for by bees. The second Think About It questions are applications AP Learning Objective 1.6 and Science Practices 1.4 and 2.1, and Learning Objective 1.7 and Science Practice 2.1, because students are using data sets that require the use of the Hardy Weinberg equation to justify if genetic drift or selection is involved in the evolution of specific populations. Section Summary 

Both genetic and environmental factors can cause phenotypic variation in a population. Different alleles can confer different phenotypes, and different environments can also cause individuals to look or act differently. Only those differences encoded in an individual s genes, however, can be passed to its offspring and, thus, be a target of natural selection. Natural selection works by selecting for alleles that confer beneficial traits or behaviors, while selecting against those for deleterious qualities. Genetic drift stems from the chance occurrence that some individuals in the germ line have more offspring than others. When individuals leave or join the population, allele frequencies can change as a result of gene flow. Mutations to an individual s DNA may introduce new variation into a population. Allele frequencies can also be altered when individuals do not randomly mate with others in the group. Review Questions 

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[link] Footnotes 1 A. J. Tipping et al., Molecular and Genealogical Evidence for a Founder Effect in Fanconi Anemia Families of the Afrikaner Population of South Africa, PNAS 98, no. 10 (2001): 5734-5739, doi: 10.1073/pnas.091402398. Glossary assortative mating when individuals tend to mate with those who are phenotypically similar to themselves bottleneck effect magnification of genetic drift as a result of natural events or catastrophes cline gradual geographic variation across an ecological gradient gene flow flow of alleles in and out of a population due to the migration of individuals or gametes genetic drift effect of chance on a population s gene pool genetic variance diversity of alleles and genotypes in a population geographical variation differences in the phenotypic variation between populations that are separated geographically heritability fraction of population variation that can be attributed to its genetic variance inbreeding mating of closely related individuals inbreeding depression increase in abnormalities and disease in inbreeding populations nonrandom mating changes in a population s gene pool due to mate choice or other forces that cause individuals to mate with certain phenotypes more than others polymorphisms variations in phenotype within individuals of a population population variation distribution of phenotypes in a population selective pressure environmental factor that causes one phenotype to be better than anotherAdaptive Evolution Adaptive Evolution 

In this section, you will explore the following questions: What are different ways in which natural selection can shape populations? How can these different forces lead to different outcomes in terms of population variation? Connections for AP Courses 

As we have learned, natural selection acts on the level of the individual, selecting those with a higher overall fitness (reproductive success) compared to the rest of the population. In other words, natural selection favors the most adaptive variation for a given environment. If the fit phenotypes are evolving in a stable environment, natural selection results in stabilizing selection , resulting in an overall decrease in the population s variation. However, if environmental conditions change, directional selection shifts a population s variance toward a new and more favorable phenotype. Diversifying selection results in increased variance by selecting for two or more distinct phenotypes. 

Sexual selection results when one sex has more reproductive success than the other; as a result, males and females experience different selective pressures, which often lead to distinct phenotypic differences, or sexual dimorphisms , between the two. For example, male birds often exhibit more colorful plumage than female birds of the same species. 

What is most important to recognize is that there is no perfect organism. Natural selection acts on existing variations in the population; it does not create anything from scratch. Although natural selection selects the fittest individuals, other forces of evolution, including genetic drift and gene flow, often introduce deleterious alleles to the population s gene pool. Evolution has no purpose; it is simply the sum of various forces that influence the genetic and phenotypic variation of a population. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 1 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.A. Natural selection is a major mechanism of evolution Essential Knowledge 1.A.1 Natural selection is a major mechanism of evolution. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 1.2 The student is able to evaluate evidence provided by data to qualitatively and quantitatively investigate the role of natural selection in evolution. Essential Knowledge 1.A.2 Natural selection acts on phenotypic variations in populations. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 1.5 The student is able to connect evolutionary changes in a population over time to a change in the environment. 

Natural selection only acts on the population s heritable traits: selecting for beneficial alleles and thus increasing their frequency in the population, while selecting against deleterious alleles and thereby decreasing their frequency a process known as adaptive evolution . Natural selection does not act on individual alleles, however, but on entire organisms. An individual may carry a very beneficial genotype with a resulting phenotype that, for example, increases the ability to reproduce (fecundity), but if that same individual also carries an allele that results in a fatal childhood disease, that fecundity phenotype will not be passed on to the next generation because the individual will not live to reach reproductive age. Natural selection acts at the level of the individual; it selects for individuals with greater contributions to the gene pool of the next generation, known as an organism s evolutionary (Darwinian) fitness . 

Fitness is often quantifiable and is measured by scientists in the field. However, it is not the absolute fitness of an individual that counts, but rather how it compares to the other organisms in the population. This concept, called relative fitness , allows researchers to determine which individuals are contributing additional offspring to the next generation, and thus, how the population might evolve. 

There are several ways selection can affect population variation: stabilizing selection, directional selection, diversifying selection, frequency-dependent selection, and sexual selection. As natural selection influences the allele frequencies in a population, individuals can either become more or less genetically similar and the phenotypes displayed can become more similar or more disparate. Stabilizing Selection 

If natural selection favors an average phenotype, selecting against extreme variation, the population will undergo stabilizing selection ( [link] ). In a population of mice that live in the woods, for example, natural selection is likely to favor individuals that best blend in with the forest floor and are less likely to be spotted by predators. Assuming the ground is a fairly consistent shade of brown, those mice whose fur is most closely matched to that color will be most likely to survive and reproduce, passing on their genes for their brown coat. Mice that carry alleles that make them a bit lighter or a bit darker will stand out against the ground and be more likely to fall victim to predation. As a result of this selection, the population s genetic variance will decrease. Directional Selection 

When the environment changes, populations will often undergo directional selection ( [link] ), which selects for phenotypes at one end of the spectrum of existing variation. A classic example of this type of selection is the evolution of the peppered moth in eighteenth- and nineteenth-century England. Prior to the Industrial Revolution, the moths were predominately light in color, which allowed them to blend in with the light-colored trees and lichens in their environment. But as soot began spewing from factories, the trees became darkened, and the light-colored moths became easier for predatory birds to spot. Over time, the frequency of the melanic form of the moth increased because they had a higher survival rate in habitats affected by air pollution because their darker coloration blended with the sooty trees. Similarly, the hypothetical mouse population may evolve to take on a different coloration if something were to cause the forest floor where they live to change color. The result of this type of selection is a shift in the population s genetic variance toward the new, fit phenotype. 

In science, sometimes things are believed to be true, and then new information comes to light that changes our understanding. The story of the peppered moth is an example: the facts behind the selection toward darker moths have recently been called into question. Read this article to learn more. 

[link] Diversifying Selection 

Sometimes two or more distinct phenotypes can each have their advantages and be selected for by natural selection, while the intermediate phenotypes are, on average, less fit. Known as diversifying selection ( [link] ), this is seen in many populations of animals that have multiple male forms. Large, dominant alpha males obtain mates by brute force, while small males can sneak in for furtive copulations with the females in an alpha male s territory. In this case, both the alpha males and the sneaking males will be selected for, but medium-sized males, which can t overtake the alpha males and are too big to sneak copulations, are selected against. Diversifying selection can also occur when environmental changes favor individuals on either end of the phenotypic spectrum. Imagine a population of mice living at the beach where there is light-colored sand interspersed with patches of tall grass. In this scenario, light-colored mice that blend in with the sand would be favored, as well as dark-colored mice that can hide in the grass. Medium-colored mice, on the other hand, would not blend in with either the grass or the sand, and would thus be more likely to be eaten by predators. The result of this type of selection is increased genetic variance as the population becomes more diverse. Different types of natural selection can impact the distribution of phenotypes within a population. In (a) stabilizing selection, an average phenotype is favored. In (b) directional selection, a change in the environment shifts the spectrum of phenotypes observed. In (c) diversifying selection, two or more extreme phenotypes are selected for, while the average phenotype is selected against. 

[link] Frequency-dependent Selection 

Another type of selection, called frequency-dependent selection , favors phenotypes that are either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection). An interesting example of this type of selection is seen in a unique group of lizards of the Pacific Northwest. Male common side-blotched lizards come in three throat-color patterns: orange, blue, and yellow. Each of these forms has a different reproductive strategy: orange males are the strongest and can fight other males for access to their females; blue males are medium-sized and form strong pair bonds with their mates; and yellow males ( [link] ) are the smallest, and look a bit like females, which allows them to sneak copulations. Like a game of rock-paper-scissors, orange beats blue, blue beats yellow, and yellow beats orange in the competition for females. That is, the big, strong orange males can fight off the blue males to mate with the blue s pair-bonded females, the blue males are successful at guarding their mates against yellow sneaker males, and the yellow males can sneak copulations from the potential mates of the large, polygynous orange males. A yellow-throated side-blotched lizard is smaller than either the blue-throated or orange-throated males and appears a bit like the females of the species, allowing it to sneak copulations. (credit: tinyfroglet /Flickr) 

In this scenario, orange males will be favored by natural selection when the population is dominated by blue males, blue males will thrive when the population is mostly yellow males, and yellow males will be selected for when orange males are the most populous. As a result, populations of side-blotched lizards cycle in the distribution of these phenotypes in one generation, orange might be predominant, and then yellow males will begin to rise in frequency. Once yellow males make up a majority of the population, blue males will be selected for. Finally, when blue males become common, orange males will once again be favored. 

Negative frequency-dependent selection serves to increase the population s genetic variance by selecting for rare phenotypes, whereas positive frequency-dependent selection usually decreases genetic variance by selecting for common phenotypes. Sexual Selection 

Males and females of certain species are often quite different from one another in ways beyond the reproductive organs. Males are often larger, for example, and display many elaborate colors and adornments, like the peacock s tail, while females tend to be smaller and duller in decoration. Such differences are known as sexual dimorphisms ( [link] ), which arise from the fact that in many populations, particularly animal populations, there is more variance in the reproductive success of the males than there is of the females. That is, some males often the bigger, stronger, or more decorated males get the vast majority of the total matings, while others receive none. This can occur because the males are better at fighting off other males, or because females will choose to mate with the bigger or more decorated males. In either case, this variation in reproductive success generates a strong selection pressure among males to get those matings, resulting in the evolution of bigger body size and elaborate ornaments to get the females attention. Females, on the other hand, tend to get a handful of selected matings; therefore, they are more likely to select more desirable males. 

Sexual dimorphism varies widely among species, of course, and some species are even sex-role reversed. In such cases, females tend to have a greater variance in their reproductive success than males and are correspondingly selected for the bigger body size and elaborate traits usually characteristic of males. Sexual dimorphism is observed in (a) peacocks and peahens, (b) Argiope appensa spiders (the female spider is the large one), and in (c) wood ducks. (credit spiders : modification of work by Sanba38 /Wikimedia Commons; credit duck : modification of work by Kevin Cole) 

The selection pressures on males and females to obtain matings is known as sexual selection; it can result in the development of secondary sexual characteristics that do not benefit the individual s likelihood of survival but help to maximize its reproductive success. Sexual selection can be so strong that it selects for traits that are actually detrimental to the individual s survival. Think, once again, about the peacock s tail. While it is beautiful and the male with the largest, most colorful tail is more likely to win the female, it is not the most practical appendage. In addition to being more visible to predators, it makes the males slower in their attempted escapes. There is some evidence that this risk, in fact, is why females like the big tails in the first place. The speculation is that large tails carry risk, and only the best males survive that risk: the bigger the tail, the more fit the male. This idea is known as the handicap principle . 

The good genes hypothesis states that males develop these impressive ornaments to show off their efficient metabolism or their ability to fight disease. Females then choose males with the most impressive traits because it signals their genetic superiority, which they will then pass on to their offspring. Though it might be argued that females should not be picky because it will likely reduce their number of offspring, if better males father more fit offspring, it may be beneficial. Fewer, healthier offspring may increase the chances of survival more than many, weaker offspring. Link to Learning 

In 1915, biologist Ronald Fisher proposed another model of sexual selection: the Fisherian runaway model , which suggests that selection of certain traits is a result of sexual preference. 

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In both the handicap principle and the good genes hypothesis, the trait is said to be an honest signal of the males quality, thus giving females a way to find the fittest mates males that will pass the best genes to their offspring. No Perfect Organism 

Natural selection is a driving force in evolution and can generate populations that are better adapted to survive and successfully reproduce in their environments. But natural selection cannot produce the perfect organism. Natural selection can only select on existing variation in the population; it does not create anything from scratch. Thus, it is limited by a population s existing genetic variance and whatever new alleles arise through mutation and gene flow. 

Natural selection is also limited because it works at the level of individuals, not alleles, and some alleles are linked due to their physical proximity in the genome, making them more likely to be passed on together (linkage disequilibrium). Any given individual may carry some beneficial alleles and some unfavorable alleles. It is the net effect of these alleles, or the organism s fitness, upon which natural selection can act. As a result, good alleles can be lost if they are carried by individuals that also have several overwhelmingly bad alleles; likewise, bad alleles can be kept if they are carried by individuals that have enough good alleles to result in an overall fitness benefit. 

Furthermore, natural selection can be constrained by the relationships between different polymorphisms. One morph may confer a higher fitness than another, but may not increase in frequency due to the fact that going from the less beneficial to the more beneficial trait would require going through a less beneficial phenotype. Think back to the mice that live at the beach. Some are light-colored and blend in with the sand, while others are dark and blend in with the patches of grass. The dark-colored mice may be, overall, more fit than the light-colored mice, and at first glance, one might expect the light-colored mice be selected for a darker coloration. But remember that the intermediate phenotype, a medium-colored coat, is very bad for the mice they cannot blend in with either the sand or the grass and are more likely to be eaten by predators. As a result, the light-colored mice would not be selected for a dark coloration because those individuals that began moving in that direction (began being selected for a darker coat) would be less fit than those that stayed light. 

Finally, it is important to understand that not all evolution is adaptive. While natural selection selects the fittest individuals and often results in a more fit population overall, other forces of evolution, including genetic drift and gene flow, often do the opposite: introducing deleterious alleles to the population s gene pool. Evolution has no purpose it is not changing a population into a preconceived ideal. It is simply the sum of the various forces described in this chapter and how they influence the genetic and phenotypic variance of a population. Think About It 

In recent years, factories have been cleaner, and less soot is released into the environment. What impact do you think this has had on the distribution of moth color in the population? This question is an application of AP Learning Objective 1.2 and Science Practices 2.2 and 5.3 and Learning Objective 1.5 and Science Practice 7.1 because, based on evidence, students are connecting evolutionary changes in a population by natural selection to environmental change. To further enrich this activity, use the peppered moth simulator located here . Additional information on the controversial nature of Kettlewell s findings can be found at the following sites: The Panda s Thumb The Peppered Moth An Update Fine Tuning The Peppered Moth Paradigm With less soot in the environment, tree bark tends to be lighter in color. This change is a selective advantage for light-colored moths, which will be camouflaged from predators. Darker moths, on the other hand, will have a selective disadvantage based on their color contrast with the lighter bark, making them stand out visually to predators. Thus, the percentage of light-colored moths will increase while the percentage of dark-colored moths will decrease. Section Summary 

Because natural selection acts to increase the frequency of beneficial alleles and traits while decreasing the frequency of deleterious qualities, it is adaptive evolution. Natural selection acts at the level of the individual, selecting for those that have a higher overall fitness compared to the rest of the population. If the fit phenotypes are those that are similar, natural selection will result in stabilizing selection, and an overall decrease in the population s variation. Directional selection works to shift a population s variance toward a new, fit phenotype, as environmental conditions change. In contrast, diversifying selection results in increased genetic variance by selecting for two or more distinct phenotypes. 

Other types of selection include frequency-dependent selection, in which individuals with either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection) are selected for. Finally, sexual selection results from the fact that one sex has more variance in the reproductive success than the other. As a result, males and females experience different selective pressures, which can often lead to the evolution of phenotypic differences, or sexual dimorphisms, between the two. Review Questions 

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[link] Glossary adaptive evolution increase in frequency of beneficial alleles and decrease in deleterious alleles due to selection directional selection selection that favors phenotypes at one end of the spectrum of existing variation diversifying selection selection that favors two or more distinct phenotypes evolutionary fitness (also, Darwinian fitness) individual s ability to survive and reproduce fitness measure of successful reproduction, the passing on alleles to the next generation frequency-dependent selection selection that favors phenotypes that are either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection) good genes hypothesis theory of sexual selection that argues individuals develop impressive ornaments to show off their efficient metabolism or ability to fight disease handicap principle theory of sexual selection that argues only the fittest individuals can afford costly traits honest signal trait that gives a truthful impression of an individual s fitness relative fitness individual s ability to survive and reproduce relative to the rest of the population sexual dimorphism phenotypic difference between the males and females of a population stabilizing selection selection that favors average phenotypesIntroduction Introduction class="introduction" class="summary" title="Chapter Summary" class="ost-reading-discard ost-chapter-review review" title="Review Questions" class="ost-reading-discard ost-chapter-review critical-thinking" title="Critical Thinking Questions" class="ost-chapter-review ost-reading-discard ap-test-prep" title="Test Prep for AP sup #174; /sup Courses" The life of a bee is very different from the life of a flower, but the two organisms are related. Both are members of the domain Eukarya and have cells containing many similar organelles, genes, and proteins. (credit: modification of work by John Beetham) 

This bee and Echinacea flower ( [link] ) could not look more different, yet they are related, as are all living organisms on Earth. By following pathways of similarities and changes both visible and genetic scientists seek to map the evolutionary past of how life developed from single-celled organisms to the tremendous variety of creatures that have germinated, crawled, floated, swam, flown, and walked on this planet. 

New species are discovered with frequent regularity, but it s not too common to discover a new large mammal. However, that s what scientists did in Australia when they named a new species of cetacean the Australian humpback dolphin, Souse sahulensis . The dolphin had originally been classified as another closely related species, but a closer look at its coloration, skeletal structure, habitat, and DNA determined that it was in fact a separate species. 

For more information, read the research article yourself.Organizing Life on Earth Organizing Life on Earth 

In this section, you will explore the following questions: Why do scientists need a comprehensive classification system to study living organisms? What are the different levels of the taxonomic classification system? How are systematics and taxonomy related to phylogeny? What are the components and purpose of a phylogenetic tree? Connection for AP Courses 

In prior chapters we explored how all organisms on Earth, extant and extinct, evolved from common ancestry. Supporting this claim are core features and processes, such as a common genetic code and metabolic pathways, which evolved billions of years ago and are widely distributed among organisms living today. The evolutionary history and relationship of an organism or a group of organisms is called phylogeny . Scientists often construct phylogenetic trees based on evidence drawn from multiple disciplines to illustrate evolutionary pathways and connections among organisms. 

Scientists historically organized Earth s millions of species into a hierarchical taxonomic classification system from the most inclusive category to the most specific: domain, kingdom, phylum, class, order, family, genus, and species. The traditional five-kingdom system that you might have studied in middle school was expanded (and reorganized) to include three domains: Bacteria, Archaea, and Eukarya, with prokaryotes divided between Bacteria or Archaea depending on their molecular genetic machinery, and protists, fungi, plants, and animals grouped in Eukarya. Today, however, phylogenetic trees provide more specific information about evolutionary history and relationships among organisms. (For the purpose of AP , you do not have to memorize the taxonomic levels. However, it is important to reiterate that taxonomy is a tool to organize the millions of organisms on Earth, similar to how items in a grocery store or mall shop are organized into different departments. Like new products, organisms are often shifted among their taxonomic groups!) 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 1 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1 The process of evolution drives and diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 3.1 The student can pose scientific questions. Learning Objective 1.14 The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insight into the history of life on Earth. Essential Knowledge 1.B.1 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 6.1 The student can justify claims with evidence. Learning Objective 1.16 The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Essential Knowledge 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. Science Practice 3.1 The student can pose scientific questions. Learning Objective 1.17 The student is able to pose scientific questions about a group of organisms whose relatedness is described by a phylogenetic tree or cladogram. Phylogenetic Trees 

Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a tree of life can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms ( [link] ). 

Unlike a taxonomic classification diagram, a phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted , which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains Bacteria, Archaea, and Eukarya diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees don t show a common ancestor but do show relationships among species. Both of these phylogenetic trees shows the relationship of the three domains of life Bacteria, Archaea, and Eukarya but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba) 

In a rooted tree, the branching indicates evolutionary relationships ( [link] ). The point where a split occurs, called a branch point , represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon . When two lineages stem from the same branch point, they are called sister taxa . A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other. The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy. 

The diagrams above can serve as a pathway to understanding evolutionary history. The pathway can be traced from the origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the "trunk" of the tree, one can discover that species' ancestors, as well as where lineages share a common ancestry. In addition, the tree can be used to study entire groups of organisms. 

Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point was rotated and the taxon order changed, this would not alter the information because the evolution of each taxon from the branch point was independent of the other. 

Many disciplines within the study of biology contribute to understanding how past and present life evolved over time; these disciplines together contribute to building, updating, and maintaining the tree of life. Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics . Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of an organism; since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned. Limitations of Phylogenetic Trees 

It may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in [link] shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits. This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share. 

Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, the length of a branch does not typically mean more time passed, nor does a short branch mean less time passed unless specified on the diagram. For example, in [link] , the tree does not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. Again using [link] , the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a part of the greater whole, and like a real tree, it does not grow in only one direction after a new branch develops. So, for the organisms in [link] , just because a vertebral column evolved does not mean that invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more phenotypically similar to each other than to a close relative. Link to Learning 

Head to this website to see interactive exercises that allow you to explore the evolutionary relationships among species. 

[link] Think About It 

How does a phylogenetic tree relate to the passing of time? What other questions about the evolutionary history of an organism and its relatedness to other organisms can a phylogenetic tree answer? This question is an application of AP Learning Objective 1.14 and Science Practice 3.1 and Learning Objective 1.17 and Science Practice 3.1 because students must pose questions about evolutionary history before they can answer them. Phylogenetic trees approximate the passing of time by the lengths of their branches. Longer branches mean that more time has passed since the organisms shared a common ancestor. Thus, a phylogenetic tree not only shows evolutionary relationships among organisms, but also how long ago the divergence from the common ancestor occurred. The Levels of Classification 

Taxonomy (which literally means arrangement law ) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. This organization from larger to smaller, more specific categories is called a hierarchical system. 

The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called a domain: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom . After kingdoms, the subsequent categories of increasing specificity are: phylum , class , order , family , genus , and species ( [link] ). The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog, Canis lupus familiaris , is a subspecies of Canis lupus , which also includes the wolf and dingo. (credit dog : modification of work by Janneke Vreugdenhil) 

The kingdom Animalia stems from the Eukarya domain. For the common dog, the classification levels would be as shown in [link] . Therefore, the full name of an organism technically has eight terms. For the dog, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus . Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, in what is called binomial nomenclature . Therefore, the scientific name of the dog is Canis lupus . The name at each level is also called a taxon . In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the familiaris in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are considered separate subspecies due to geographic or behavioral isolation or other factors. 

[link] shows how the levels move toward specificity with other organisms. Notice how the dog shares a domain with the widest diversity of organisms, including plants and butterflies. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists classified organisms using characteristics, but as DNA technology developed, more precise phylogenies have been determined. Visual Connection At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. (credit plant : modification of work by "berduchwal"/Flickr; credit insect : modification of work by Jon Sullivan; credit fish : modification of work by Christian Mehlf hrer; credit rabbit : modification of work by Aidan Wojtas; credit cat : modification of work by Jonathan Lidbeck; credit fox : modification of work by Kevin Bacher, NPS; credit jackal : modification of work by Thomas A. Hermann, NBII, USGS; credit wolf : modification of work by Robert Dewar; credit dog : modification of work by "digital_image_fan"/Flickr) 

[link] Link to Learning 

Visit this website to classify three organisms bear, orchid, and sea cucumber from kingdom to species. To launch the game, under Classifying Life, click the picture of the bear or the Launch Interactive button. 

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Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, changes and updates must be made as new discoveries occur. Recall that phylogenetic trees are hypotheses and are modified as data becomes available. In addition, classification historically has focused on grouping organisms mainly by shared characteristics and does not necessarily illustrate how the various groups relate to each other from an evolutionary perspective. For example, despite the fact that a hippopotamus resembles a pig more than a whale, the hippopotamus may be the closest living relative of the whale. Section Summary 

Scientists continually gain new information that helps understand the evolutionary history of life on Earth. Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence, scientists attempt to map the evolutionary pathways of all life on Earth. Historically, organisms were organized into a taxonomic classification system. However, today many scientists build phylogenetic trees to illustrate evolutionary relationships. Review Questions 

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[link] Glossary basal taxon branch on a phylogenetic tree that has not diverged significantly from the root ancestor binomial nomenclature system of two-part scientific names for an organism, which includes genus and species names branch point node on a phylogenetic tree where a single lineage splits into distinct new ones class division of phylum in the taxonomic classification system family division of order in the taxonomic classification system genus division of family in the taxonomic classification system; the first part of the binomial scientific name kingdom division of domain in the taxonomic classification system order division of class in the taxonomic classification system phylogenetic tree diagram used to reflect the evolutionary relationships among organisms or groups of organisms phylogeny evolutionary history and relationship of an organism or group of organisms phylum (plural: phyla) division of kingdom in the taxonomic classification system polytomy branch on a phylogenetic tree with more than two groups or taxa rooted single ancestral lineage on a phylogenetic tree to which all organisms represented in the diagram relate sister taxa two lineages that diverged from the same branch point systematics field of organizing and classifying organisms based on evolutionary relationships taxon (plural: taxa) single level in the taxonomic classification system taxonomy science of classifying organisms taxonomic classification system hierarchical system of classifying organisms, including the classification of domain, kingdom, phylum, class, order, family, genus, and speciesDetermining Evolutionary Relationships Determining Evolutionary Relationships What is the difference between homologous and analogous traits? How are these traits used when determining evolutionary relatedness? What is cladistics? How does a cladogram differ from a phylogenetic tree? What is parsimony? Connection for AP Courses 

To build phylogenetic trees, scientists must collect accurate information that allows them to make evolutionary connections among organisms. Using morphological and molecular data, scientists identify both homologous and analogous characteristics and genes. (In a prior chapter we explored the differences between homologous and analogous traits and how they relate to convergent and divergent evolution.) Similarities among organisms stem either from shared ancestral history (homologies) or from separate evolutionary paths (analogies). Cladograms are constructed by using shared derived traits to distinguish different groups of species from one another. For example, lizards, rabbits and humans all descended from a common ancestor that had an amniotic egg; thus, lizards, rabbits, and humans all belong to the same clade. Vertebrata is a larger clade that also includes fish, lamprey, and lancelets. The closer two species or groups are located to each on a phylogenetic tree or cladogram, they more recently they shared a common ancestor. With the influx of new information, scientists can revise phylogenetic trees; for example, computer programs, such as one called BLAST, which helps determine relatedness using DNA sequencing. Typically, a phylogenetic tree is constructed with the simplest explanation of evolutionary history (maximum parsimony ) and the fewest number of evolutionary steps. 

Understanding phylogeny extends far beyond understanding the evolutionary history of species on Earth. For botanists, phylogeny acts as a guide to discovering new plants that can be used to make food, medicine, and clothing. For doctors, phylogenies provide information about the origin of diseases and how to treat them, for example, HIV/AIDS. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 1 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1 The process of evolution drives the diversity and unity of life. 

Enduring Understanding 1.A Change in the genetic makeup of a population over time is evolution. Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 1.9 The student is able to evaluate evidence provided by data from many scientific disciplines that support biological evolution. Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 5.2 The student can refine observations and measurements based on data analysis. Learning Objective 1.10 The student is able to refine evidence based on data from many scientific disciplines that support biological evolution. Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 4.2 The student can design a plan for collecting data to answer a particular scientific question. Learning Objective 1.11 The student is able to design a plan to answer scientific questions regarding how organisms have changed over time using information from morphology, biochemistry, and geology. Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 1.12 The student is able to connect scientific evidence from many scientific disciplines to support the modern concept of evolution. Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Science Practice 2.1 The student can justify the selection of a mathematical routine to solve problems. Learning Objective 1.13 The student is able to construct and/or justify mathematical models, diagrams or simulations that represent processes of biological evolution. 

Big Idea 1 The process of evolution drives and diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 3.1 The student can pose scientific questions. Learning Objective 1.14 The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insight into the history of life on Earth. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 6.1 The student can justify claims with evidence. Learning Objective 1.16 The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Essential Knowledge 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. Science Practice 3.1 The student can pose scientific questions. Learning Objective 1.17 The student is able to pose scientific questions about a group of organisms whose relatedness is described by a phylogenetic tree or cladogram. Essential Knowledge 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective 1.18 The student is able to evaluate evidence provided by a data set in conjunction with a phylogenetic tree or simple cladogram to determine evolutionary history and speciation. Essential Knowledge 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Science Practice 2.1 The student can justify the selection of a mathematical routine to solve problems. Learning Objective 1.19 The student is able to create a phylogenetic tree or simple cladogram that correctly represents evolutionary history and speciation from a provided data set. Two Options for Similarities 

In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures; they stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures ( [link] ). Bat and bird wings are homologous structures, indicating that bats and birds share a common evolutionary past. (credit a: modification of work by Steve Hillebrand, USFWS; credit b: modification of work by U.S. DOI BLM) 

Notice it is not simply a single bone, but rather a grouping of several bones arranged in a similar way. The more complex the feature, the more likely any kind of overlap is due to a common evolutionary past. Imagine two people from different countries both inventing a car with all the same parts and in exactly the same arrangement without any previous or shared knowledge. That outcome would be highly improbable. However, if two people both invented a hammer, it would be reasonable to conclude that both could have the original idea without the help of the other. The same relationship between complexity and shared evolutionary history is true for homologous structures in organisms. Misleading Appearances 

Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. Similarly, unrelated organisms may be distantly related, but appear very much alike. This usually happens because both organisms were in common adaptations that evolved within similar environmental conditions. When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. These are called analogous structures ( [link] ). 

Similar traits can be either homologous or analogous. Homologous structures share a similar embryonic origin; analogous organs have a similar function. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm. These structures are not analogous. The wings of a butterfly and the wings of a bird are analogous but not homologous. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied. The (c) wing of a honeybee is similar in shape to a (b) bird wing and (a) bat wing, and it serves the same function. However, the honeybee wing is not composed of bones and has a distinctly different structure and embryonic origin. These wing types (insect versus bat and bird) illustrate an analogy similar structures that do not share an evolutionary history. (credit a: modification of work by Steve Hillebrand, USFWS; credit b: modification of work by U.S. DOI BLM; credit c: modification of work by Jon Sullivan) Link to Learning 

This website has several examples to show how appearances can be misleading in understanding the phylogenetic relationships of organisms. 

[link] Molecular Comparisons 

With the advancement of DNA technology, the area of molecular systematics , which describes the use of information on the molecular level including DNA analysis, has blossomed. New computer programs not only confirm many earlier classified organisms, but also uncover previously made errors. As with physical characteristics, even the DNA sequence can be tricky to read in some cases. For some situations, two very closely related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated. 

Sometimes two segments of DNA code in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships, and, ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny. Evolution Connection 

Why Does Phylogeny Matter? Evolutionary biologists could list many reasons why understanding phylogeny is important to everyday life in human society. For botanists, phylogeny acts as a guide to discovering new plants that can be used to benefit people. Think of all the ways humans use plants food, medicine, and clothing are a few examples. If a plant contains a compound that is effective in treating cancer, scientists might want to examine all of the relatives of that plant for other useful drugs. 

A research team in China identified a segment of DNA thought to be common to some medicinal plants in the family Fabaceae (the legume family) and worked to identify which species had this segment ( [link] ). After testing plant species in this family, the team found a DNA marker (a known location on a chromosome that enabled them to identify the species) present. Then, using the DNA to uncover phylogenetic relationships, the team could identify whether a newly discovered plant was in this family and assess its potential medicinal properties. Dalbergia sissoo (D. sissoo) is in the Fabaceae, or legume family. Scientists found that D. sissoo shares a DNA marker with species within the Fabaceae family that have antifungal properties. Subsequently, D. sissoo was shown to have fungicidal activity, supporting the idea that DNA markers can be used to screen for plants with potential medicinal properties. 

[link] Building Phylogenetic Trees 

How do scientists construct phylogenetic trees? After the homologous and analogous traits are sorted, scientists often organize the homologous traits using a system called cladistics . This system sorts organisms into clades: groups of organisms that descended from a single ancestor. For example, in [link] , all of the organisms in the orange region evolved from a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group . Clades must include all of the descendants from a branch point. Visual Connection Lizards, rabbits, and humans all descend from a common ancestor that had an amniotic egg. Thus, lizards, rabbits, and humans all belong to the clade Amniota. Vertebrata is a larger clade that also includes fish and lamprey. 

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Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the organisms in the clade or monophyletic group stem from a single point on the tree. This can be remembered because monophyletic breaks down into mono, meaning one, and phyletic, meaning evolutionary relationship. [link] shows various examples of clades. Notice how each clade comes from a single point, whereas the non-clade groups show branches that do not share a single point. Visual Connection All the organisms within a clade stem from a single point on the tree. A clade may contain multiple groups, as in the case of animals, fungi and plants, or a single group, as in the case of flagellates. Groups that diverge at a different branch point, or that do not include all groups in a single branch point, are not considered clades. 

[link] Shared Characteristics 

Organisms evolve from common ancestors and then diversify. Scientists use the phrase descent with modification because even though related organisms have many of the same characteristics and genetic codes, changes occur. This pattern repeats over and over as one goes through the phylogenetic tree of life: A change in the genetic makeup of an organism leads to a new trait which becomes prevalent in the group. Many organisms descend from this point and have this trait. New variations continue to arise: some are adaptive and persist, leading to new traits. With new traits, a new branch point is determined (go back to step 1 and repeat). 

If a characteristic is found in the ancestor of a group, it is considered a shared ancestral character because all of the organisms in the taxon or clade have that trait. The vertebrate in [link] is a shared ancestral character. Now consider the amniotic egg characteristic in the same figure. Only some of the organisms in [link] have this trait, and to those that do, it is called a shared derived character because this trait derived at some point but does not include all of the ancestors in the tree. 

The tricky aspect to shared ancestral and shared derived characters is the fact that these terms are relative. The same trait can be considered one or the other depending on the particular diagram being used. Returning to [link] , note that the amniotic egg is a shared ancestral character for the Amniota clade, while having hair is a shared derived character for some organisms in this group. These terms help scientists distinguish between clades in the building of phylogenetic trees. Choosing the Right Relationships 

Imagine being the person responsible for organizing all of the items in a department store properly an overwhelming task. Organizing the evolutionary relationships of all life on Earth proves much more difficult: scientists must span enormous blocks of time and work with information from long-extinct organisms. Trying to decipher the proper connections, especially given the presence of homologies and analogies, makes the task of building an accurate tree of life extraordinarily difficult. Add to that the advancement of DNA technology, which now provides large quantities of genetic sequences to be used and analyzed. Taxonomy is a subjective discipline: many organisms have more than one connection to each other, so each taxonomist will decide the order of connections. 

To aid in the tremendous task of describing phylogenies accurately, scientists often use a concept called maximum parsimony, which means that events occurred in the simplest, most obvious way. For example, if a group of people entered a forest preserve to go hiking, based on the principle of maximum parsimony, one could predict that most of the people would hike on established trails rather than forge new ones. 

For scientists deciphering evolutionary pathways, the same idea is used: the pathway of evolution probably includes the fewest major events that coincide with the evidence at hand. Starting with all of the homologous traits in a group of organisms, scientists look for the most obvious and simple order of evolutionary events that led to the occurrence of those traits. Link to Learning 

Head to this website to learn how maximum parsimony is used to create phylogenetic trees. 

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These tools and concepts are only a few of the strategies scientists use to tackle the task of revealing the evolutionary history of life on Earth. Recently, newer technologies have uncovered surprising discoveries with unexpected relationships, such as the fact that people seem to be more closely related to fungi than fungi are to plants. Sound unbelievable? As the information about DNA sequences grows, scientists will become closer to mapping the evolutionary history of all life on Earth. Activity 

Using a data set provided by your teacher or other sources, construct a phylogenetic tree or cladogram to reflect the evolutionary history among a group of organisms based on shared characteristics. Then share the phylogenetic tree or cladogram with peers for review and revision. Lab Investigation 

AP Biology Investigative Labs: Inquiry-Based Approach, Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST . Students will learn to use a common tool, BLAST, to compare several genes from different organisms and then use this information to construct a cladogram to determine evolutionary relatedness among species. Then students will use BLAST to track a gene(s) of choice through several species. Bioinformatics has many applications, including understanding genetic disease. Think About It 

Why must scientists distinguish between homologous and analogous characteristics before building phylogenetic trees? Do more closely related organisms share homologous or analogous traits? Which type of trait is used to support convergent or divergent evolution? This activity is an application of AP Learning Objective 1.19 and Science Practice 1.1, Learning Objective 1.18 and Science Practice 5.3, and Learning Objective 1.7 and Science Practice 1.3 because 1) students are asked to create a phylogenetic tree or cladogram based on evidence provided by a data set; 2) student s diagram should raise questions about the evolutionary history of the group; and 3) evolutionary history is subject to revision based on interpretation and new evidence. This lab investigation is an application of several AP Learning Objectives and Science Practices described above (Learning Objectives 1.11, 1.16, 1.17, and 1.18) because students will use BLAST to determine evolutionary relatedness among species based on molecular evidence/DNA sequences and then construct a cladogram based on that information. The Think About It question is an application of AP Learning Objective 1.17 and Science Practice 3.1 because students must distinguish between homologous and analogous characteristics when constructing phylogenetic trees. Only homologous traits are considered in establishing evolutionary relationships, because they are evidence of evolutionary change. Closely related organisms will share homologous traits, whereas analogous traits are often shared by only distantly related organisms. The study of convergent and divergent evolution also relies on the analysis of analogous and homologous traits. Section Summary 

To build phylogenetic trees, scientists must collect accurate information that allows them to make evolutionary connections between organisms. Using morphologic and molecular data, scientists work to identify homologous characteristics and genes. Similarities between organisms can stem either from shared evolutionary history (homologies) or from separate evolutionary paths (analogies). Newer technologies can be used to help distinguish homologies from analogies. After homologous information is identified, scientists use cladistics to organize these events as a means to determine an evolutionary timeline. Scientists apply the concept of maximum parsimony, which states that the order of events probably occurred in the most obvious and simple way with the least amount of steps. For evolutionary events, this would be the path with the least number of major divergences that correlate with the evidence. Review Questions 

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[link] Glossary analogy (also, homoplasy) characteristic that is similar between organisms by convergent evolution, not due to the same evolutionary path cladistics system used to organize homologous traits to describe phylogenies maximum parsimony applying the simplest, most obvious way with the least number of steps molecular systematics technique using molecular evidence to identify phylogenetic relationships monophyletic group (also, clade) organisms that share a single ancestor shared ancestral character describes a characteristic on a phylogenetic tree that is shared by all organisms on the tree shared derived character describes a characteristic on a phylogenetic tree that is shared only by a certain clade of organisms cladograms visual representations of evolutionary relationships between organisms parsimony the simplest, most straightforward way of constructing phylogenetic and evolutionary relationships between organismsPerspectives on the Phylogenetic Tree Perspectives on the Phylogenetic Tree 

In this section, you will explore the following questions: What is horizontal gene transfer and its significance in constructing phylogenetic trees? How do prokaryotes and eukaryotes transfer genes horizontally? What are other models of phylogenetic relationships and how do they differ from the original phylogenetic tree concept? Connection for AP Courses 

Newer technologies have uncovered surprising discoveries with unexpected relationships among organisms, such as the fact that humans seems to be more closely related to fungi than fungi are to plants. (Think about that the next time you see a mushroom). As the information about DNA sequences grows, scientists will become closer to mapping a more accurate evolutionary history of all life on Earth. 

What makes phylogeny difficult, especially among prokaryotes, is the transfer of genes horizontally ( horizontal gene transfer , or HGT ) between unrelated species. Like mutations, HGT introduces genetic variation into the bacterial population. This passing of genes between species adds a layer of complexity to understanding relatedness. 

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP Biology Curriculum Framework. The AP Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP Biology course, an inquiry-based laboratory experience, instructional activities, and AP exam questions. A learning objective merges required content with one or more of the seven science practices. 

Big Idea 1 The process of evolution drives and diversity and unity of life. 

Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 3.1 The student can pose scientific questions. Learning Objective 1.14 The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insight into the history of life on Earth. Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms. 

Big Idea 3 

Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation. Essential Knowledge 3.C.2 Biological systems have multiple processes that increase genetic variation. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective 3.27 The student is able to construct an explanation of processes that increase variation within a population. 

The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community. 

Many phylogenetic trees have been shown as models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 ( [link] a ), which served as a pattern for subsequent studies for more than a century. The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak ( [link] b ). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community. The (a) concept of the tree of life goes back to an 1837 sketch by Charles Darwin. Like an (b) oak tree, the tree of life has a single trunk and many branches. (credit b: modification of work by "Amada44"/Wikimedia Commons) Limitations to the Classic Model 

Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonally. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. The concept of genes being transferred between unrelated species was not considered as a possibility until relatively recently. Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. HGT has been shown to be an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships. 

The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance the evolution of the first eukaryotic cell, without which humans could not have come into existence. Horizontal Gene Transfer 

Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress. As the phenomenon is investigated more thoroughly, it may be revealed to be more common. Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation, which is the raw material for the process of natural selection. These transfers may occur between any two species that share an intimate relationship ( [link] ). Summary of Mechanisms of Prokaryotic and Eukaryotic HGT Mechanism Mode of Transmission Example Prokaryotes transformation DNA uptake many prokaryotes transduction bacteriophage (virus) bacteria conjugation pilus many prokaryotes gene transfer agents phage-like particles purple non-sulfur bacteria Eukaryotes from food organisms unknown aphid jumping genes transposons rice and millet plants epiphytes/parasites unknown yew tree fungi from viral infections HGT in Prokaryotes 

The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the Endosymbiont Theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species. 

The fact that genes are transferred among common bacteria is well known to microbiology students. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms: Transformation: naked DNA is taken up by a bacteria Transduction: genes are transferred using a virus Conjugation: the use a hollow tube called a pilus to transfer genes between organisms 

More recently, a fourth mechanism of gene transfer between prokaryotes has been discovered. Small, virus-like particles called gene transfer agents (GTAs) transfer random genomic segments from one species of prokaryote to another. GTAs have been shown to be responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. The first GTA was characterized in 1974 using purple, non-sulfur bacteria. These GTAs, which are thought to be bacteriophages that lost the ability to reproduce on their own, carry random pieces of DNA from one organism to another. The ability of GTAs to act with high frequency has been demonstrated in controlled studies using marine bacteria. Gene transfer events in marine prokaryotes, either by GTAs or by viruses, have been estimated to be as high as 10 13 per year in the Mediterranean Sea alone. GTAs and viruses are thought to be efficient HGT vehicles with a major impact on prokaryotic evolution. 

As a consequence of this modern DNA analysis, the idea that eukaryotes evolved directly from Archaea has fallen out of favor. While eukaryotes share many features that are absent in bacteria, such as the TATA box (found in the promoter region of many genes), the discovery that some eukaryotic genes were more homologous with bacterial DNA than Archaea DNA made this idea less tenable. Furthermore, the fusion of genomes from Archaea and Bacteria by endosymbiosis has been proposed as the ultimate event in eukaryotic evolution. HGT in Eukaryotes 

Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes. After all, prokaryotes are but single cells exposed directly to their environment, whereas the sex cells of multicellular organisms are usually sequestered in protected parts of the body. It follows from this idea that the gene transfers between multicellular eukaryotes should be more difficult. Indeed, it is thought that this process is rarer in eukaryotes and has a much smaller evolutionary impact than in prokaryotes. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species, and it is possible that more examples will be discovered in the future. 

In plants, gene transfer has been observed in species that cannot cross-pollinate by normal means. Transposons or jumping genes have been shown to transfer between rice and millet plant species. Furthermore, fungal species feeding on yew trees, from which the anti-cancer drug TAXOL is derived from the bark, have acquired the ability to make taxol themselves, a clear example of gene transfer. 

In animals, a particularly interesting example of HGT occurs within the aphid species ( [link] ). Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, and they serve a variety of functions in animals, who obtain these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color ( [link] ). (a) Red aphids get their color from red carotenoid pigment. Genes necessary to make this pigment are present in certain fungi, and scientists speculate that aphids acquired these genes through HGT after consuming fungi for food. If genes for making carotenoids are inactivated by mutation, the aphids revert back to (b) their green color. Red coloration makes the aphids a lot more conspicuous to predators, but evidence suggests that red aphids are more resistant to insecticides than green ones. Thus, red aphids may be more fit to survive in some environments than green ones. (credit a: modification of work by Benny Mazur; credit b: modification of work by Mick Talbot) 

Barbara McClintock (1902 1992) discovered transposons while working on maize genetics. 

[link] Genome Fusion and the Evolution of Eukaryotes 

Scientists believe the ultimate in HGT occurs through genome fusion between different species of prokaryotes when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the flagellum of the sperm fails to enter the egg. 

Within the past decade, the process of genome fusion by endosymbiosis has been proposed by James Lake of the UCLA/NASA Astrobiology Institute to be responsible for the evolution of the first eukaryotic cells ( [link] a ). Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event, such as Lake has proposed, would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis. 

More recent work by Lake ( [link] b ) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, indeed resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of the endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. Lake s work is not without skepticism, and the ideas are still debated within the biological science community. In addition to Lake s hypothesis, there are several other competing theories as to the origin of eukaryotes. How did the eukaryotic nucleus evolve? One theory is that the prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes. The theory that mitochondria and chloroplasts are endosymbiotic in origin is now widely accepted. More controversial is the proposal that (a) the eukaryotic nucleus resulted from the fusion of archaeal and bacterial genomes, and that (b) Gram-negative bacteria, which have two membranes, resulted from the fusion of Archaea and Gram-positive bacteria, each of which has a single membrane. 

The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first ( [link] a ), followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis proposes that mitochondria were first established in a prokaryotic host ( [link] b ), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity ( [link] c ). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data. Three alternate hypotheses of eukaryotic and prokaryotic evolution are (a) the nucleus-first hypothesis, (b) the mitochondrion-first hypothesis, and (c) the eukaryote-first hypothesis. Web and Network Models 

The recognition of the importance of HGT, especially in the evolution of prokaryotes, has caused some to propose abandoning the classic tree of life model. In 1999, W. Ford Doolittle proposed a phylogenetic model that resembles a web or a network more than a tree. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. As shown in [link] a , some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts. This model is often called the web of life . In an effort to save the tree analogy, some have proposed using the Ficus tree ( [link] b ) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT. In the (a) phylogenetic model proposed by W. Ford Doolittle, the tree of life arose from a community of ancestral cells, has multiple trunks, and has connections between branches where horizontal gene transfer has occurred. Visually, this concept is better represented by (b) the multi-trunked Ficus than by the single trunk of the oak similar to the tree drawn by Darwin [link] . (credit b: modification of work by "psyberartist"/Flickr) Ring of Life Models 

Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure, the so-called ring of life ( [link] ); a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Lake, again using the conditioned reconstruction algorithm, proposes a ring-like model in which species of all three domains Archaea, Bacteria, and Eukarya evolved from a single pool of gene-swapping prokaryotes. His laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model. According to the ring of life phylogenetic model, the three domains of life evolved from a pool of primitive prokaryotes. 

In summary, the tree of life model proposed by Darwin must be modified to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that all attempts should be made to discover some modification of the tree model to allow it to accurately fit his data, and only the inability to do so will sway people toward his ring proposal. 

This doesn t mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life. A consequence of the new thinking about phylogenetic models is the idea that Darwin s original conception of the phylogenetic tree is too simple, but made sense based on what was known at the time. However, the search for a more useful model moves on: each model serving as hypotheses to be tested with the possibility of developing new models. This is how science advances. These models are used as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data being analyzed. Section Summary 

The phylogenetic tree, first used by Darwin, is the classic tree of life model describing phylogenetic relationships among species, and the most common model used today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings. Review Questions 

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[link] Glossary eukaryote-first hypothesis proposal that prokaryotes evolved from eukaryotes gene transfer agent (GTA) bacteriophage-like particle that transfers random genomic segments from one species of prokaryote to another genome fusion fusion of two prokaryotic genomes, presumably by endosymbiosis horizontal gene transfer (HGT) (also, lateral gene transfer) transfer of genes between unrelated species mitochondria-first hypothesis proposal that prokaryotes acquired a mitochondrion first, followed by nuclear development nucleus-first hypothesis proposal that prokaryotes acquired a nucleus first, and then the mitochondrion ring of life phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes web of life phylogenetic model that attempts to incorporate the effects of horizontal gene transfer on evolution

Introduction Introduction class="summary" title="Section Summary" class="key-equations" title="Key Equations" class="concept" title="Concept Items" class="critical-thinking" title="Critical Thinking Items" class="problem" title="Problems" class="performance" title="Performance Task" class="multiple-choice" title="Multiple Choice" class="short-answer" title="Short Answer" class="extended-response" title="Extended Response" A plane slows down as it comes in for landing in St. Maarten. Its acceleration is in the opposite direction of its velocity. (credit: Steve Conry, Flickr) 

Ask the students to give definitions of acceleration. Dispel any misconceptions such as, acceleration means very high speed or going faster. Emphasize that acceleration does not just indicate speeding up; acceleration can also include slowing down or changing direction. Explain that acceleration is the change in either the magnitude or direction of velocity, or both. Have the students list the objects in the opening image that are moving. Then ask which are definitely accelerating and which might be accelerating. Review the use of + and signs as they relate to acceleration and velocity. Explain that, when studying motion, these symbols are often used to indicate the direction of motion. The + symbol typically represents motion that is to the right or upward, whereas typically represents motion that is to the left or downward. 

You may have heard the term accelerator , referring to the gas pedal in a car. When the gas pedal is pushed down, the flow of gasoline to the engine increases, which increases the car s velocity . Pushing on the gas pedal results in acceleration because the velocity of the car increases, and acceleration is defined as a change in velocity. You need two quantities to define velocity: a speed and a direction. Changing either of these quantities (or both together) changes the velocity. You may be surprised to learn that pushing on the brake pedal or turning the steering wheel also causes acceleration. The first reduces the speed and so changes the velocity, and the second changes the direction and so also changes the velocity. 

In fact, any change in velocity whether positive, negative, directional, or any combination of these is an acceleration . The plane in the picture is accelerating because its velocity is decreasing as it prepares to land. To begin our study of acceleration, we need to have a clear understanding of what it means. 

Before students begin this chapter, it is useful to review the following concepts: Significant figures: demonstrate how to obtain the proper number of significant figures when adding and multiplying. Scientific notation and how it expresses significant figures. Converting units: demonstrate how to convert from km/h to m/s. Show how units cancel in calculations. Calculating average: demonstrate how to calculate the average of two numbers. Commonly used terms: explain that constant means unchanging, so constant acceleration refers to acceleration that is not changing in time. Explain that initial means starting or beginning, so the initial time is the time at which the action of interest begins. Explain that an object that is not moving is often described in physics as being at rest. Review conventions of coordinate systems. Review kinematics concepts introduced earlier: vectors, displacement, velocity, speed.Acceleration Acceleration Section Learning Objectives 

By the end of this section, you will be able to: Explain acceleration and determine the direction and magnitude of acceleration in one dimension. Analyze motion in one dimension using kinematic equations and graphic representations. 

The Learning Objectives in this section will help your students master the following TEKS: (4A) : Generate and interpret graphs and charts describing different types of motion, including the use of real-time technology such as motion detectors or photogates. (4B) : Describe and analyze motion in one dimension using equations with the concepts of distance, displacement, speed, average velocity, instantaneous velocity, and acceleration. Section Key Terms average acceleration instantaneous acceleration negative acceleration 

[BL] [OL] Begin a general discussion about acceleration and deceleration. Ask for examples of both. Explain that deceleration is not used in physics because acceleration can be positive or negative. Lead the students to their topics of interest, such as motor vehicles or sports. Explain that the capital Greek letter delta always means final minus initial and that the net change may be zero, positive, or negative. 

[AL] See how much students remember about vectors. What does a vector arrow represent? Ask them to name some quantities that are vectors and some that are scalars. Defining Acceleration 

Throughout this chapter we will use the following terms: time , displacement , velocity , and acceleration . Recall that each of these terms has a designated variable and SI unit of measurement as follows: Time : t , measured in seconds (s) Displacement : d , measured in meters (m) Velocity : v , measured in meters per second (m/s) Acceleration : a , measured in meters per second per second (m/s 2 , also called meters per second squared) Also note: means change in. The subscript 0 refers to an initial value (sometimes subscript i is used to refer to initial value). The subscript f refers to final value. A bar over a symbol, such as a a , means average. 

[BL] Review the definitions of the terms: time , displacement , velocity , and acceleration . Point out that the variables commonly used to represent these quantities are the first letters of the corresponding term. 

[OL] Verify that the students know the SI units in which time, displacement, velocity, and acceleration are expressed. Note that these are some of the seven base units of the metric system. Explain that converting to base units is a good first step when calculating these quantities. Explain the meaning of seconds squared in the denominator of the units of acceleration. 

[AL] Review all the base units of the metric system. Explain how these units are interrelated. For example, show how the length is defined by time. 

[BL] [OL] Use the equation a = v t = v f v 0 t f t 0 a = v t = v f v 0 t f t 0 to emphasize the relationship between and the subscripts f and 0. Distinguish between constant and variable acceleration. There could be confusion here, especially in the case of increasing acceleration. Be sure students understand that the word deceleration is not used in physics and that acceleration can be positive or negative. 

[AL] See if students can use the concept of acceleration to understand confusing statements such as a decrease in the rate of increase. For example, use the concept of acceleration to analyze the statement the rate of increase in the cost of health care is decreasing. If the increase in the cost is defined as positive, then the acceleration in the cost of health care would be negative. 

[OL] The arrow for acceleration that points opposite to the arrow for velocity a may be confusing. Explain that it points in the direction opposite the velocity because it is the velocity is getting smaller (i.e., the velocity arrow is getting shorter). 

Acceleration is the change in velocity divided by a period of time during which the change occurs. The SI units of velocity are m/s and the SI units for time are s, so the SI units for acceleration are m/s 2 . Average acceleration is given by a = v t = v f v 0 t f t 0 a = v t = v f v 0 t f t 0 

Average acceleration is distinguished from instantaneous acceleration , which is acceleration at a specific instant in time. The magnitude of acceleration is often not constant over time. For example, runners in a race accelerate at a greater rate in the first second of a race than during the following seconds. You do not need to know all the instantaneous acceleration at all times to calculate average acceleration. All you need to know is the change in velocity (i.e., the final velocity minus the initial velocity) and the change in time (i.e., the final time minus the initial time), as shown in the formula. Note that the average acceleration can be positive, negative, or zero. A negative acceleration is simply an acceleration in the negative direction. 

Keep in mind that, although acceleration points in the same direction as the change in velocity, it is not always in the direction of the velocity itself. When an object slows down, its acceleration is opposite to the direction of its velocity. In everyday language, this is called deceleration, but in physics, it is acceleration (whose direction happens to be opposite that of the velocity). For now, let us assume that motion to the right along the x -axis is positive and motion to the left is negative. 

[link] shows a car with positive acceleration in (a) and negative acceleration in (b). The arrows represent vectors showing the direction and magnitude of velocity and acceleration. The car is speeding up in (a) and slowing down in (b). 

Velocity and acceleration are both vector quantities . Recall that vectors have both magnitude and direction. An object travelling at a constant velocity therefore having no acceleration does accelerate if it changes direction. This is why turning the steering wheel of a moving car makes the car accelerate: its velocity changes direction. The Moving Man 

With this animation, you can produce both variations of acceleration and velocity shown in [link] , plus a few more. Vary the velocity and acceleration by sliding the red and green markers along the scales. Keeping the velocity marker near zero will make the effect of acceleration more obvious. Try changing acceleration from positive to negative while the man is moving. We will come back to this animation and look at the Charts view when we study graphical representation of motion. Click here for the simulation 

Have students use a very low setting for velocity and acceleration because it is easier to see how the motion changes. Show them how setting velocity as positive and acceleration as negative creates the motion that resembles that of an object thrown into the air. 

[link] Calculating Average Acceleration 

Look back at the equation for average acceleration. You can see that the calculation of average acceleration involves three values: change in time, t ; change in velocity, v ; and acceleration, a . 

Change in time is often stated as a time interval, and change in velocity can often be calculated by subtracting the initial velocity from the final velocity. Average acceleration is then simply change in velocity divided by change in time. Before you begin calculating, be sure that all distances and times have been converted to meters and seconds. Look at these examples of acceleration of a subway train. 

[BL] [OL] Before beginning the calculations, verify that students understand the equation for acceleration. Do they understand what it means when quantities have a plus or minus sign? Do they understand the units for each variable? An Accelerating Subway Train 

A subway train accelerates from rest to 30.0 km/h in 20.0 s. What is the average acceleration during that time interval? Strategy 

Start by making a simple sketch: 

This problem involves four steps: Convert to units of meters and seconds. Determine the change in velocity. Determine the change in time. Use these values to calculate the average acceleration. Solution Identify the knowns. Be sure to read the problem for given information, which may not look like numbers. When the problem states that the train starts from rest, you can write down that the initial velocity is 0 m/s. Therefore: v 0 = 0; v f = 30.0 km/h; and t = 20.0 s 

Convert the units: 30.0 km h 10 3 m 1 km 1 h 3600 s = 8.333 m s 30.0 km h 10 3 m 1 km 1 h 3600 s = 8.333 m s Calculate change in velocity, v = v f v 0 = 8.333 m/s 0 = + 8.333 m/s v = v f v 0 = 8.333 m/s 0 = + 8.333 m/s , where the plus sign means the change in velocity is to the right. 

We know t , so all we have to do is insert the known values into the formula for average acceleration: a = v t = 8.333 m/s 20.0 s = + 0.417 m s 2 a = v t = 8.333 m/s 20.0 s = + 0.417 m s 2 Discussion 

The plus sign in the answer means that acceleration is to the right. This is a reasonable conclusion because the train starts from rest and ends up with a velocity directed to the right (i.e., positive). So acceleration is in the same direction as the change in velocity, as it should be. 

Note that extra digits were carried along and rounding off to the correct number of significant figures, 3, was not done until the final answer was calculated. An Accelerating Subway Train 

Now, suppose that, at the end of its trip, the train slows to a stop in 8.00 s from a speed of 30.0 km/h. What is its average acceleration during this time? Strategy 

Again, make a simple sketch: 

In this case, the train is decelerating and its acceleration is negative because it is pointing to the left. As in the previous example, we must find the change in velocity and the change in time, then solve for acceleration. Solution Identify the knowns: v 0 = 30.0 km/h; v f = 0; t = 8.00 s. Convert the units: From the first problem, we know that 30.0 km/h = 8.333 m/s. Calculate change in velocity, v = v f v 0 = 0 8.333 m/s = 8.333 m/s v = v f v 0 = 0 8.333 m/s = 8.333 m/s , where the minus sign means that the change in velocity points to the left. 

We know t = 8.00 s, so all we have to do is insert the known values into the equation for average acceleration: a = v t = 8.333 m/s 8.00 s = 1.04 m s 2 a = v t = 8.333 m/s 8.00 s = 1.04 m s 2 Discussion 

The minus sign indicates that acceleration is to the left. This is reasonable because the train initially has a positive velocity in this problem, and a negative acceleration would reduce the velocity. Again, acceleration is in the same direction as the change in velocity, which is negative in this case. This acceleration can be called a deceleration because it has a direction opposite to the velocity. 

Help students see the relationship between the direction of the vector arrows and the plus and minus signs. Explain that one indication of the sign for acceleration is that it is in the direction opposite that of the velocity. Also point out that correctly identifying the initial and final speeds will result in the correct sign for acceleration. It is easier to get plus and minus signs correct if you always assume that motion is away from 0 and toward positive values on the x axis. This way v always starts off being positive and points to the right. If speed is increasing, then acceleration is positive and also points to the right. If speed is decreasing, then acceleration is negative and points to the left. It is a good idea to carry two extra significant figures from step-to-step when making calculations. Do not round off with each step. When you arrive at the final answer, apply the rules of significant figures for the operations you carried out and round to the correct number of digits. Sometimes this will make your answer slightly more accurate. Practice Problems 

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[link] Acceleration 

This video shows the basic calculation of acceleration and some useful unit conversions. 

Ask students to note the explanation of units and the identification of the vector quantities. Tell them the calculations demonstrated in the video are fairly straightforward and that the definitions given for displacement, elapsed time, velocity, and acceleration should be clear. 

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[link] Measure the Acceleration of a Bicycle on a Slope 

In this lab you will take measurements to determine if the acceleration of a moving bicycle is constant. If the acceleration is constant, then the following relationships hold: v = d t = v 0 + v f 2 v = d t = v 0 + v f 2 If v 0 = 0 v 0 = 0 , then v f = 2 v v f = 2 v and a = v f t a = v f t . 

You will work in pairs to measure and record data for a bicycle coasting down an incline on a uniform, gentle slope. The data will consist of distances traveled and elapsed times. Find an open area to minimize the risk of injury during this lab. stopwatch measuring tape bicycle Find a gentle, paved slope, such as an incline on a bike path. The more gentle the slope, the more accurate your data is likely to be. Mark uniform distances along the slope, such as 5 m, 10 m, etc. Determine the following roles: the bike rider, the timer, and the recorder. The recorder should create a data table to collect the distance and time data. Have the rider at the starting point at rest on the bike. When the timer calls Start, the timer starts the stopwatch and the rider begins coasting down the slope on the bike without pedaling. Have the timer call out the elapsed times as the bike passes each marked point. The recorder should record the times in the data table. It may be necessary to repeat the process to practice roles and make necessary adjustments. Once acceptable data has been recorded, switch roles. Repeat Steps 3 5 to collect a second set of data. Switch roles again to collect a third set of data. Calculate average acceleration for each set of distance-time data. If your result for a a is not the same for different pairs of v and t , then acceleration is not constant. Interpret your results. 

Explain that two factors that could prevent uniform acceleration are (i) friction between the tires and the pavement and in the bicycle axles, and (ii) air resistance. Discuss methods for minimizing these factors (e.g., selecting a smooth surface for the bike to coast, greasing the axels, etc.). Explain that friction will only decrease acceleration, but air resistance to a tail wind would increase acceleration. Discuss why it would be difficult to study constant acceleration if students were to pedal the bicycle. Note that the given kinematic equation that is valid for constant acceleration, which is presented at the start of the Snap Lab!, will be presented in further detail in the following section. 

Prior to the lab, investigate appropriate areas around the school that have gentle, uniform slopes. Should the number of bicycles be limited, consider conducting the lab as a whole class or in larger clusters. Ensure that the planned paths of student groups not cross and that there is adequate space for riders to stop without risk of injury. 

[link] Check Your Understanding 

Use these questions to assess student achievement of the section s Learning Objectives. If students are struggling with a specific objective, these questions will help identify which and direct students to the relevant content. 

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[link] Section Summary Acceleration is the rate of change of velocity and may be negative or positive. Average acceleration is expressed in m/s 2 and, in one dimension, can be calculated by using a = v t = v f v 0 t f t o a = v t = v f v 0 t f t o Key Equations Average acceleration a = v t = v f v 0 t f t o a = v t = v f v 0 t f t o Concept Items 

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[link] Glossary average acceleration change in velocity divided by the time interval over which it changed instantaneous acceleration rate of change of velocity at a specific instant in time negative acceleration acceleration in the negative directionRepresenting Acceleration with Equations and Graphs Representing Acceleration with Equations and Graphs Section Learning Objectives 

By the end of this section, you will be able to: Explain the kinematic equations related to acceleration and illustrate them with graphs. Apply the kinematic equations and related graphs to problems involving acceleration. 

The Learning Objectives in this section will help your students master the following TEKS: (4A) : Generate and interpret graphs and charts describing different types of motion, including the use of real-time technology such as motion detectors or photogates. (4B) : Describe and analyze motion in one dimension using equations with the concepts of distance, displacement, speed, average velocity, instantaneous velocity, and acceleration. Section Key Terms acceleration due to gravity kinematic equations uniform acceleration 

[BL] Briefly review displacement, time, velocity, and acceleration; their variables, and their units. 

[OL] [AL] Explain that this section introduces five equations that allow us to solve a wider range of problems than just finding acceleration from time and velocity. Review graphical analysis, including axes, algebraic signs, how to designate points on a coordinate plane, i.e., ( x , y ), slopes and intercepts. Explain that these equations can also be represented graphically. How the Kinematic Equations are Related to Acceleration 

We are studying concepts related to motion: time, displacement, velocity , and especially acceleration. We are only concerned with motion in one dimension. The kinematic equations apply to conditions of constant acceleration and show how these concepts are related. Constant acceleration is acceleration that does not change over time. The first kinematic equation relates displacement d , average velocity v v , and time t . 

d = d 0 + v t the initial displacement d 0 is often 0, in which case the equation can be written as v = d t d = d 0 + v t the initial displacement d 0 is often 0, in which case the equation can be written as v = d t 

This equation says that average velocity is displacement per unit time. We will express velocity in meters per second. If we graph displacement versus time, as in [link] , the slope will be the velocity. Whenever a rate, such as velocity, is represented graphically, time is usually taken to be the independent variable and is plotted along the x axis. The slope of displacement versus time is velocity. 

Another expression for average velocity v v is simply the initial velocity plus the final velocity divided by two: v = v 0 + v f 2 v = v 0 + v f 2 

Now we come to our main concern of this chapter; namely, the kinematic equations that describe motion with constant acceleration. Acceleration is the rate at which velocity increases, so velocity at any point equals initial velocity plus acceleration multiplied by time: v = v 0 + a t Also , if we start from rest ( v 0 = 0 ), we can write a = v t v = v 0 + a t Also , if we start from rest ( v 0 = 0 ), we can write a = v t 

Note that Equation 3 does not have displacement in it. Therefore, if you do not know the displacement and are not trying to solve for a displacement, this equation might be a good one to use. 

Equation 3 is represented by the graph in [link] . The slope of velocity versus time is acceleration. 

The fourth kinematic equation shows how displacement is related to acceleration. d = d 0 + v 0 t + 1 2 a t 2 d = d 0 + v 0 t + 1 2 a t 2 

When starting at the origin, d 0 = 0 d 0 = 0 and, when starting from rest, v 0 = 0 v 0 = 0 , in which case the equation can be written as a = 2 d t 2 a = 2 d t 2 

This equation tells us that, for constant acceleration, the slope of a plot of 2 d versus t 2 is acceleration, as shown in [link] . When acceleration is constant, the slope of 2 d versus t 2 gives the acceleration. 

The final kinematic equation relates velocity, acceleration, and displacement: v 2 = v 0 2 + 2 a ( d d 0 ) v 2 = v 0 2 + 2 a ( d d 0 ) 

This equation is useful to when we do not know (or need to know) the time. 

When starting from rest, Equation 6 simplifies to: a = v 2 2 d a = v 2 2 d 

According to this equation, a graph of velocity squared versus twice the displacement will have a slope equal to acceleration. 

Note that, in reality, knowns and unknowns will vary. Sometimes you will want to rearrange a kinematic equation so that the knowns are the values on the axes and the unknown is the slope. Sometimes the intercept will not be at the origin (0, 0). This will happen when v 0 or d 0 is not 0. This will be the case when the object of interest is already in motion or the motion begins at some point other than at the origin of the coordinate system. 

[BL] Be sure everyone is completely comfortable with the idea that velocity is displacement divided by the time during which the displacement occurs. Use everyday examples. 

[OL] Remind students that they studied velocity in early chapters. Relate the simplified equation v = d t v = d t to a graph of displacement versus time. Point out the of the plot starts at (0,0) because the initial velocity is zero. Pick a segment on the graph and explain how finding the slope at this segment. Explain that [link] would show a straight line if velocity were changing; that is, if the object were accelerating. Show how the graph would change for both negative and positive acceleration. 

[OL] Build on the understanding of velocity to introduce acceleration. Contrast constant velocity with changing velocity. Use everyday examples from transportation, sports, or amusement park rides. Explain that [link] represents constant acceleration because it is a straight line. Give examples of increasing, decreasing, and constant acceleration and explain how each affects the shape of plots of velocity versus time. 

[OL] [AL] Ask students why all three of the plots are straight lines. Refer to the graph of 2 d vs t 2 and explain why this is a straight line whereas d vs t would be nonlinear. The Moving Man (Part 2) 

Look at the Moving Man video again and this time watch the Charts view. Again, vary the velocity and acceleration by sliding the red and green markers along the scales. Keeping the velocity marker near zero will make the effect of acceleration more obvious. Observe how the graphs of position, velocity, and acceleration vary with time. Note which are linear plots and which are not. Click here for the simulation 

Ask the students to click the Charts option and adjust the settings for the animation to reproduce the plots found in [link] and [link] . 

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The kinematic equations are applicable when you have constant acceleration. d = d 0 + v t d = d 0 + v t , or v = d t v = d t when d 0 = 0. v = v 0 + v f 2 v = v 0 + v f 2 v = v 0 + a t v = v 0 + a t , or a = v t a = v t when v 0 = 0. d = d 0 + v 0 t + 1 2 a t 2 d = d 0 + v 0 t + 1 2 a t 2 , or a = 2 d t 2 a = 2 d t 2 when d 0 = 0 and v 0 = 0. v 2 = v 0 2 + 2 a ( d d 0 ) v 2 = v 0 2 + 2 a ( d d 0 ) , or a = 2 d t 2 a = 2 d t 2 when d 0 = 0 and v 0 = 0. 

[OL] Go through the algebra to show how the kinematic equations can be simplified when some of the values are zero. Note that any motion starting or ending in a motionless state will simplify the equations. Applying Kinematic Equations to Situations of Constant Acceleration 

Problem-solving skills are essential to success in a science and in life in general. The ability to apply broad physical principles, which are often represented by equations, to specific situations is a very powerful form of knowledge. It is much more powerful than memorizing a list of facts. Analytical skills and problem-solving abilities can be applied to new situations, whereas a list of facts cannot be made long enough to contain every possible circumstance. Such analytical skills will be developed by solving problems in this text and will be useful for understanding physics and science in general throughout your life. Problem-Solving Steps 

While no single step-by-step method works for every problem, the following general procedures facilitate problem solving and make the answers more meaningful. A certain amount of creativity and insight are required as well. Examine the situation to determine which physical principles are involved. It is vital to draw a simple sketch at the outset. Decide which direction is positive and note that on your sketch. Identify the knowns: make a list of what information is given or can be inferred from the problem statement. Remember, not all given information will be in the form of a number with units in the problem. If something starts from rest, we know the initial velocity is zero. If something stops, we know the final velocity is zero Identify the unknowns: decide exactly what needs to be determined in the problem. Find an equation or set of equations that can help you solve the problem. Your list of knowns and unknowns can help here. For example, if time is not needed or not given, Equation 6, which does not include time, could be useful. Insert the knowns along with their units into the appropriate equation and obtain numerical solutions complete with units. This step produces the numerical answer; it also provides a check on units that can help you find errors. If the units of the answer are incorrect, then an error has been made. Check the answer to see if it is reasonable: does it make sense? This final step is extremely important because the goal of physics is to accurately describe nature. To see if the answer is reasonable, check its magnitude, its sign, and its units. Are the significant figures correct? Summary of Problem Solving Determine the knowns and unknowns. Find an equation that expresses the unknown in terms of the knowns. More than one unknown means more than one equation is needed. Solve the equation or equations. Be sure units and significant figures are correct. Check whether the answer is reasonable. 

[BL] [OL] [AL] Consider starting with the simplified summary of problem solving and then expand it to the more wordy description above. Stress that this is not a strict recipe that can solve all problems. Applying analytical skills is still required. If the preliminary analysis is correct and the knowns and unknowns are correctly sorted, the rest should go be correct. Try applying the method to some non-mathematical everyday problems. Ask for suggestions. Drag Racing Smoke rises from the tires of a dragster at the beginning of a drag race. (credit: Lt. Col. William Thurmond. Photo courtesy of U.S. Army.) 

The object of the sport of drag racing is acceleration. Period! The races take place from a standing start on a straight one-quarter-mile (402 m) track. Usually two cars race side by side, and the winner is the driver who gets the car past the quarter-mile point first. At the finish line, the cars may be going more than 300 miles per hour (134 m/s). The driver then deploys a parachute to bring the car to a stop because it is unsafe to brake at such high speeds. The cars, called dragsters, are capable of accelerating at 26 m/s 2 . By comparison, a typical sports car that is available to the general public can accelerate at about 5 m/s 2 . 

Several measurements are taken during each drag race: Reaction time is the time between the starting signal and when the front of the car crosses the starting line. Elapsed time is the time from when the vehicle crosses the starting line to when it crosses the finish line. The record is a little over 3 s. Speed is the average speed during the last 20 m before the finish line. The record is a little under 400 mph. 

The video shows a race between two dragsters powered by jet engines. The actual race lasts about four seconds and is near the end of the video . [link] 

Explain the direction and magnitude of acceleration and velocity vectors before and after the braking chute is deployed. Explain that mile is 440 yards. If any students are on the track team, you might ask them to describe this distance. Compare record times for this track event to 4 seconds. 

[link] Acceleration of a Dragster 

The time it takes for a dragster to cross the finish line is unknown. The dragster accelerates from rest at 26 m/s 2 for a quarter mile (0.250 mi). What is the final velocity of the dragster? Strategy 

The equation v 2 = v 0 2 + 2 a ( d d 0 ) v 2 = v 0 2 + 2 a ( d d 0 ) is ideally suited to this task because it gives the velocity from acceleration and displacement, without involving the time. Solution Convert miles to meters: ( 0.250 mi ) 1609 m 1 mi = 402 m ( 0.250 mi ) 1609 m 1 mi = 402 m Identify the known values. We know that v 0 = 0 since the dragster starts from rest, and we know that the distance traveled, d d 0 is 402 m. Finally, the acceleration is constant at a = 26.0 m/s 2 . Insert the knowns into the equation v 2 = v 0 2 + 2 a ( d d 0 ) v 2 = v 0 2 + 2 a ( d d 0 ) and solve for v : v 2 = 0 + 2 ( 26.0 m s 2 ) ( 402 m ) = 2.09 10 4 m 2 s 2 v 2 = 0 + 2 ( 26.0 m s 2 ) ( 402 m ) = 2.09 10 4 m 2 s 2 

Taking the square root gives us: v = 2.09 10 4 m 2 s 2 = 145 m s v = 2.09 10 4 m 2 s 2 = 145 m s Discussion 

145 m/s is about 522 km/hour or about 324 mi/h, but even this breakneck speed is short of the record for the quarter mile. Also, note that a square root has two values. We took the positive value because we know that the velocity must be in the same direction as the acceleration for the answer to make physical sense. 

An examination of the equation v 2 = v 0 2 + 2 a ( d d 0 ) v 2 = v 0 2 + 2 a ( d d 0 ) can produce further insights into the general relationships among physical quantities: The final velocity depends on the magnitude of the acceleration and the distance over which it applies. For a given acceleration, a car that is going twice as fast does not stop in twice the distance it goes much further before it stops. (This is why, for example, we have reduced speed zones near schools.) 

[OL] Work through the problem-solving steps with the student: What is the goal? What is known and unknown? Which equation expresses the unknown in terms of the knowns? Solve for the unknown. Insert known values. Calculate. Checking that answer is reasonable and has the correct units, sign, and significant figures. 

Repeat for the second sample problem. 

[AL] Initiate a discussion on variation in gravity. Compare gravity on Earth to gravity on the Moon. Explain the difference between g and constants that are the same everywhere in the universe, such as the speed of light. Practice Problems 

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[link] Constant Acceleration 

In many cases, acceleration is not uniform because the force acting on the accelerating object is not constant over time. A situation that gives constant acceleration is the acceleration of falling objects. When air resistance is not a factor, all objects near Earth s surface fall with an acceleration of about 9.80 m/s 2 . Although this value decreases slightly with increasing altitude, it may be assumed to be essentially constant. The value of 9.80 m/s 2 is labeled g and is referred to as acceleration due to gravity . Gravity is the force that causes nonsupported objects to accelerate downward (or, more precisely, toward the center of Earth). The magnitude of this force is called the weight of the object and is given by mg where m is the mass of the object (in kg). In places other than on Earth, such as the moon or on other planets, g is not 9.80 m/s 2 but takes on other values. When using g for the acceleration a in a kinematic equation, it is usually given a negative sign because the acceleration due to gravity is downward. Effects of Rapid Acceleration Astronauts train using G Force Simulators. (credit: NASA) 

When in a vehicle that accelerates rapidly, you experience a force on your entire body that accelerates your body. You feel this force in automobiles and slightly more on amusement park rides. For example, when you ride in a car that turns, the car applies a force on your body to make you accelerate in the direction in which the car is turning. If enough force is applied, you will accelerate at 9.80 m/s 2 . This is the same as the acceleration due to gravity, so this force is called one G. 

One G is the force required to accelerate an object at the acceleration due to gravity at Earth s surface. Thus, one G for a paper cup is much less than one G for an elephant, because the elephant is much more massive and so requires a greater force to make it accelerate at 9.80 m/s 2 . For a person, a G of about 4 is so strong that his or her face will distort as the bones accelerate forward through the loose flesh. Other symptoms at extremely high Gs include changes in vision, loss of consciousness, and even death. The space shuttle produces about 3 Gs during takeoff and reentry. Some roller coasters and dragsters produce forces of around 4 Gs for their occupants. A fighter jet can produce up to 12 Gs during a sharp turn. 

Astronauts and fighter pilots must undergo G-force training in simulators. The video shows the experience of several people undergoing this training. 

People such as astronauts who work with G forces must also be trained to experience zero G also called free fall or weightlessness which can cause queasiness. NASA has an aircraft that allows it occupants to experience about 25 s of free fall. The aircraft is nicknamed the Vomit Comet. 

Mention that, later in this course, students will encounter some interesting concepts related to gravity and acceleration when studying the general theory of relativity. In part, the theory is based on the idea that gravity cannot be distinguished from acceleration, either experientially or mathematically. When in an upward-bound elevator, can you really tell whether you are accelerating or whether gravity has suddenly become stronger? 

[link] Falling Objects 

A person standing on the edge of a high cliff throws a rock straight up with an initial velocity v 0 of 13 m/s. 

(a) Calculate the position and velocity of the rock at 1.00, 2.00, and 3.00 seconds after it is thrown. Ignore the effect of air resistance. Strategy 

Sketch the initial velocity and acceleration vectors and the axes. Initial conditions for rock thrown straight up. 

List the knowns: time t = 1.00 s, 2.00 s, and 3.00 s; initial velocity v 0 = 13 m/s; acceleration a = g = 9.80 m/s 2 ; position y 0 = 0 m. 

List the unknowns: y 1 , y 2 , and y 3 ; v 1 , v 2 , and v 3 (where 1, 2, 3 refer to times 1.00 s, 2.00 s, and 3.00 s). 

Choose the equations: 

d = d 0 + v 0 t + 1 2 a t 2 d = d 0 + v 0 t + 1 2 a t 2 becomes y = y 0 + v 0 t 1 2 g t 2 y = y 0 + v 0 t 1 2 g t 2 

v = v 0 + a t v = v 0 + a t becomes v = v 0 + g t v = v 0 + g t 

These equations describe the unknowns in terms of knowns only. Solution 

y 1 = 0 + ( 13.0 m/s ) ( 1.00 s ) + ( 9.80 m/s 2 ) ( 1.00 s ) 2 2 = 8.10 m y 2 = 0 + ( 13.0 m/s ) ( 2.00 s ) + ( 9.80 m/s 2 ) ( 2.00 s ) 2 2 = 6.40 m y 3 = 0 + ( 13.0 m/s ) ( 3.00 s ) + ( 9.80 m/s 2 ) ( 3.00 s ) 2 2 = 5.10 m v 1 = 13.0 m/s + ( 9.80 m/s 2 ) ( 1.00 s ) = 3.20 m/s v 2 = 13.0 m/s + ( 9.80 m/s 2 ) ( 2.00 s ) = 6.60 m/s v 3 = 13.0 m/s + ( 9.80 m/s 2 ) ( 3.00 s ) = 16.4 m/s y 1 = 0 + ( 13.0 m/s ) ( 1.00 s ) + ( 9.80 m/s 2 ) ( 1.00 s ) 2 2 = 8.10 m y 2 = 0 + ( 13.0 m/s ) ( 2.00 s ) + ( 9.80 m/s 2 ) ( 2.00 s ) 2 2 = 6.40 m y 3 = 0 + ( 13.0 m/s ) ( 3.00 s ) + ( 9.80 m/s 2 ) ( 3.00 s ) 2 2 = 5.10 m v 1 = 13.0 m/s + ( 9.80 m/s 2 ) ( 1.00 s ) = 3.20 m/s v 2 = 13.0 m/s + ( 9.80 m/s 2 ) ( 2.00 s ) = 6.60 m/s v 3 = 13.0 m/s + ( 9.80 m/s 2 ) ( 3.00 s ) = 16.4 m/s Discussion 

The first two positive values for y show that the rock is still above the edge of the cliff, and the third negative y value shows that it has passed the starting point and is below the cliff. Remember that we set up to be positive. Any position with a positive value is above the cliff, and any velocity with a positive value is an upward velocity. The first value for v is positive, so the rock is still on the way up. The second and third values for v are negative, so the rock is on its way down. 

(b) Make graphs of position versus time, velocity versus time, and acceleration versus time. Use increments of 0.5 s in your graphs. Strategy 

Time is customarily plotted on the x axis because it is the independent variable. Position versus time will not be linear, so calculate points for 0.50 s, 1.50 s, and 2.50 s. This will give a curve closer to the true, smooth shape. Solution 

The three graphs are shown in [link] . Discussion y vs. t does not represent the two-dimensional parabolic path of a trajectory. The path of the rock is straight up and straight down. The slope of a line tangent to the curve at any point on the curve equals the velocity at that point (i.e., the instantaneous velocity). Note that the v vs. t line crosses the vertical axis at the initial velocity and crosses the horizontal axis at the time when the rock changes direction and begin to fall back to Earth. This plot is linear because acceleration is constant. The a vs. t plot also shows that acceleration is constant; that is, it does not change with time. 

Prior to solving the problem, have students consider the following questions: What is the goal? What is known and unknown? Which equation expresses the unknown in terms of the knowns? 

After solving the problem, have students check that the answer is reasonable and has the correct units, sign, and significant figures. Practice Problems 

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[link] Check Your Understanding 

Use these questions to assess students achievement of the sections Learning Objectives. If students are struggling with a specific objective, the formative assessment will help identify which objective is the problem so that you can direct students to the relevant content. 

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[link] Section Summary The kinematic equations show how time, displacement, velocity, and acceleration are related for objects in motion. In general, kinematic problems can be solved by identifying the kinematic equation that expresses the unknown in terms of the knowns. Displacement, velocity, and acceleration may be displayed graphically versus time. Key Equations Average velocity d = d 0 + v t d = d 0 + v t , or v = d t v = d t when d 0 = 0. Average velocity v = v 0 + v f 2 v = v 0 + v f 2 Velocity v = v 0 + a t v = v 0 + a t , or when v 0 = 0. Displacement d = d 0 + v 0 t + 1 2 a t 2 d = d 0 + v 0 t + 1 2 a t 2 , or a = 2 d t 2 a = 2 d t 2 when d 0 = 0 and v 0 = 0. Acceleration v 2 = v 0 2 + 2 a ( d d 0 ) v 2 = v 0 2 + 2 a ( d d 0 ) , or a = v 2 2 d a = v 2 2 d when d 0 = 0 and v 0 = 0. Concept Items 

[link] Critical Thinking 

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[link] Performance Task 

Design an experiment to measure displacement and elapsed time. Use the data to calculate final velocity, average velocity, acceleration, and acceleration. Materials a small marble or ball bearing a garden hose a measuring tape a stopwatch or stopwatch software download a sloping driveway or lawn as long as the garden hose with a level area beyond 

(a) How would you use the garden hose, stopwatch, marble, measuring tape, and slope to measure displacement and elapsed time? (Hint: The marble is the accelerating object, and the length of the hose is total displacement.) 

(b) How would you use the displacement and time data to calculate velocity, average velocity, and acceleration? Which kinematic equations would you use? 

(c) How would you use the materials, the measured and calculated data, and the flat area below the slope to determine the negative acceleration? What would you measure, and which kinematic equation would you us? 

This performance task supports NGSS HS-PS2-1: Analyze data to support the claim that Newton s second law of motion describes the mathematical relationship among the net force on a macroscopic object, its mass, and its acceleration. 

Performance Task Rubric 

(a) Insert the marble (without a push) into the end of the hose at the top of the slope. With the stopwatch, measure the time, t , from when the marble was introduced at the top until it appears at the bottom. The length of the hose is displacement, x . 

(b) Use Equation 1 to calculate average velocity; use Equation 2 to calculate velocity; and use Equation 3 to calculate acceleration. 

(c) Measure the time from when the marble comes out of the hose until it stops to get t . You will not need x . Use the average v measurement from above for v 0 . The value of v is zero. Use Equation 3 to calculate deceleration. The sign of a will be minus. Test Prep Multiple Choice 

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[link] Glossary acceleration due to gravity acceleration of an object that is subject only to the force of gravity. Near Earth s surface this acceleration is 9.80 m/s 2 constant acceleration acceleration that does not change with respect to time kinematic equations the five equations that describe motion in terms of time, displacement, velocity, and accelerationIntroduction Introduction Force Newton s First Law of Motion: Inertia Newton s Second Law of Motion Newton s Third Law of Motion class="summary" title="Section Summary" class="key-equations" title="Key Equations" class="concept" title="Concept Items" class="critical-thinking" title="Critical Thinking Items" class="problem" title="Problems" class="performance" title="Performance Task" class="multiple-choice" title="Multiple Choice" class="short-answer" title="Short Answer" class="extended-response" title="Extended Response" 

Before students begin this chapter, they may wish to review the concepts of distance, displacement, speed, velocity, acceleration, scalars, vectors, representing vectors, units of acceleration, and acceleration due to gravity. Explain that an object that is not moving is often described in physics as being at rest. Newton s laws of motion describe the motion of the dolphin s path. (credit: Jin Jang) 

Point out that we come across motion in our everyday lives; for instance, a dolphin jumping out of water as shown in the photo. There are simple laws of physics that govern motion. These laws are universal; that is, they apply to every object in the universe. Much of the work done in describing motion was done by Sir Isaac Newton. This chapter is about motion, the causes of motion, and the universal laws of motion. 

Isaac Newton (1642 1727) was a natural philosopher; a great thinker who combined science and philosophy to try to explain the workings of nature on Earth and in the universe. His laws of motion were just one part of the monumental work that has made him legendary. The development of Newton s laws marks the transition from the Renaissance period of history to the modern era. This transition was characterized by a revolutionary change in the way people thought about the physical universe. Drawing upon earlier work by scientists Galileo Galilei and Johannes Kepler , Newton s laws of motion allowed motion on Earth and in space to be predicted mathematically. In this chapter you will learn about force as well as Newton s first, second, and third laws of motion.Force Force Section Learning Objectives 

By the end of this section, you will be able to: Differentiate between force, net force, and dynamics Draw a free-body diagram 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4C) : analyze and describe accelerated motion in two dimensions using equations, including projectile and circular examples (4E) : develop and interpret free-body diagrams 

[BL] [OL] Point out that objects at rest tend to stay at rest. A ball, for example, moves only when pushed or pulled. The action of pushing or pulling is the application of force. Force applied to an object changes its motion. 

[AL] Start a discussion about force and motion. Ask students what would happen if more than one force is applied to an object. Take a heavy object such as a desk for demonstration. Ask one student to push it from one side. Explain how force and motion work. Now ask a second student to push it in the opposite direction. Ask students why no motion occurs even though the first student applies the same amount of force. Introduce the concept of adding forces. Section Key Terms dynamics external force force free-body diagram net external force net force Defining Force and Dynamics 

[OL] Explain that the word dynamics comes from a Greek word meaning power. Also point out that the word dynamics is singular, like the word physics. 

[BL] [OL] You may want to introduce the terms system, external force, and internal force. 

[AL] Explain that both magnitude and direction must be considered when talking about forces. 

Demonstrate by using physical objects how different forces acting together can add if they act in the same direction or cancel if they act in opposite directions. Explain the terms acting on and being acted on. 

Force is the cause of motion, and motion draws our attention. Motion itself can be beautiful, such as a dolphin jumping out of the water, the flight of a bird, or the orbit of a satellite. The study of motion is called kinematics , but kinematics describes only the way objects move their velocity and their acceleration . Dynamics considers the forces that affect the motion of moving objects and systems . Newton s laws of motion are the foundation of dynamics. These laws describe the way objects speed up, slow down, stay in motion, and interact with other objects. They are also universal laws : they apply everywhere on Earth as well as in space. 

A force pushes or pulls an object. The object being moved by a force could be an inanimate object, such as a table, or an animate object, such as a person. The pushing or pulling may be done by a person, or even the gravitational pull of Earth. Forces have different magnitudes and directions; this means that some forces are stronger than others and can act in different directions. For example, a cannon exerts a strong force on the cannonball that is launched into the air. In contrast, a mosquito landing on your arm exerts only a small force on your arm. 

When multiple forces act on an object, the forces combine. Adding together all of the forces acting on an object gives the total force, or net force . An external force is a force that acts on an object within the system from outside the system. This type of force is different than an internal force, which acts between two objects that are both within the system. The net external force combines these two definitions; it is the total combined external force. We discuss further details about net force, external force, and net external force in the coming sections. 

In mathematical terms, two forces acting in opposite directions have opposite signs (positive or negative). By convention, the negative sign is assigned to movement to the left or downward. If two forces pushing in opposite directions are added together, the larger force will be somewhat canceled out by the smaller force pushing in the opposite direction. It is important to be consistent with your chosen coordinate system within a problem; for example, if negative values are assigned to the downward direction for velocity, then distance, force and acceleration should also be designated as negative in the downward direction. Free-body Diagrams and Examples of Forces 

[BL] Review vectors and how they are represented. Review vector addition. 

[AL] Ask students to give everyday examples of situations where multiple forces act together. Draw free-body diagrams for some of these situations. 

For our first example of force, consider an object hanging from a rope. This example gives us the opportunity to introduce a useful tool known as a free-body diagram . A free-body diagram represents the object being acted upon (that is, the free body) as a single point. Only the forces acting on the body (that is, external forces) are shown and are represented by vectors (which are drawn as arrows). These forces are the only ones shown because only external forces acting on the body affect its motion. We can ignore any internal forces within the body because they cancel each other out, as explained in the section on Newton's third law of motion. Free-body diagrams are very useful for analyzing forces acting on an object. An object of mass, m , is held up by the force of tension. 

[link] shows the force of tension in the rope acting in the upward direction, opposite the force of gravity. The forces are indicated in the free-body diagram by an arrow pointing up, representing tension, and another arrow pointing down, representing gravity. In a free-body diagram, the lengths of the arrows show the relative magnitude (or strength) of the forces. Because forces are vectors, they add just like other vectors. Notice that the two arrows have equal lengths in [link] which means that the forces of tension and weight are of equal magnitude. Because these forces of equal magnitude act in opposite directions, they are perfectly balanced, so they add together to give a net force of zero. 

Not all forces are as noticeable as when you push or pull on an object. Some forces act without physical contact, such as the pull of a magnet (in the case of magnetic force) or the gravitational pull of Earth (in the case of gravitational force). 

In the next three sections discussing Newton s laws of motion, we will learn about three specific types of forces: friction, the normal force , and the gravitational force . To analyze situations involving forces, we will create free-body diagrams to organize the framework of the mathematics for each individual situation. 

Correctly drawing and labeling a free-body diagram is an important first step for solving a problem. It will help you visualize the problem and correctly apply the mathematics to solve the problem. Section Summary Dynamics is the study of how forces affect the motion of objects and systems. Force is a push or pull that can be defined in terms of various standards. It is a vector and so has both magnitude and direction. External forces are any forces outside of a body that act on the body. A free-body diagram is a drawing of all external forces acting on a body. Check Your Understanding 

Use the questions in Check Your Understanding to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, the assessment through Check Your Understanding will help identify which objective is causing the problem and direct students to the relevant content. 

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[link] Glossary dynamics the study of how forces affect the motion of objects and systems external force a force acting on an object or system that originates outside of the object or system force a push or pull on an object with a specific magnitude and direction; can be represented by vectors; can be expressed as a multiple of a standard force free-body diagram a diagram showing all external forces acting on a body net external force the sum of all external forces acting on an object or system net force the sum of all forces acting on an object or systemNewton s First Law of Motion: Inertia Newton s First Law of Motion: Inertia Section Learning Objectives 

By the end of this section, you will be able to: Describe Newton s first law and friction Discuss the relationship between mass and inertia 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4D) : calculate the effect of forces on objects, including the law of inertia, the relationship between force and acceleration, and the nature of force pairs between objects 

Before students begin this section, it is useful to review the concepts of force, external force, net external force, and addition of forces. 

[BL] [OL] [AL] Ask students to speculate what happens to objects when they are set in motion. Do they remain in motion or stop after some time? Why? 

Students may believe that objects that are in motion tend to slow down and stop. Explain the concept of friction. Talk about objects in outer space, where there is no atmosphere and no gravity. Ask students to describe the motion of such objects. Section Key Terms friction inertia law of inertia mass Newton s first law of motion system Newton s First Law and Friction 

[BL] [OL] [AL] Discuss examples of Newton s First Law seen in everyday life. 

[BL] [OL] [AL] Talk about different pairs of surfaces and how each exhibits different levels of friction. Ask students to give examples of smooth and rough surfaces. Ask them where friction may be useful and where it may be undesirable. 

[OL] [AL] Ask students to give different examples of systems where multiple forces occur. Draw free-body diagrams for these. Include the force of friction. Emphasize the direction of the force of friction. 

Newton s first law of motion states that: A body at rest tends to remain at rest. A body in motion tends to remain in motion at constant velocity unless acted on by a net external force. (Recall that constant velocity means the body moves in a straight line and at a constant speed.) 

At first glance, this law may seem to contradict your everyday experience. You have probably noticed that a moving object will usually slow down and stop unless some effort is made to keep it moving. The key to understanding why, for example, a sliding box slows down (seemingly on its own) is to first understand that a net external force acts on the box to make the box slow down. Without this net external force, the box would continue to slide at a constant velocity (as stated in Newton s first law of motion). What force acts on the box to slow it down? It is called friction . Friction is an external force that acts opposite to the direction of motion (see [link] ). Think of it as a resistance to motion that slows things down. 

Consider an air hockey table. When the air is turned off, the puck slides only a short distance before friction slows it to a stop. However, when the air is turned on, it lifts the puck slightly, so that the puck experiences very little friction as it moves over the surface. With friction almost eliminated, the puck glides along with very little change in speed. On a frictionless surface, the puck would experience no net external force (ignoring air resistance, which is also a form of friction). Additionally, if we know enough about friction, we can accurately predict how quickly objects will slow down. 

Now let s think about another example. A man pushes a box across a floor at constant velocity by applying a force of +50 N. (The positive sign indicates that, by convention, the direction of motion is to the right.) What is the force of friction that opposes the motion? The force of friction must be 50 N. Why? According to Newton s first law of motion, any object moving at constant velocity has no net external force acting upon it, which means that the sum of the forces acting on the object must be zero. The mathematical way to say that no net external force acts on an object is F net = 0 F net = 0 or F = 0 F = 0 . So if the man applies +50 N of force, then the force of friction must be 50 N for the two forces to add up to zero (that is, for the two forces to cancel each other). Whenever you encounter the phrase at constant velocity, Newton s first law tells you that the net external force is zero. For a box sliding across a floor, friction acts in the direction opposite to the velocity. 

The force of friction depends on two factors: the coefficient of friction and the normal force . For any two surfaces that are in contact with one another, the coefficient of friction is a constant that depends on the nature of the surfaces. The normal force is the force exerted by a surface that pushes on an object in response to gravity pulling the object down. In equation form, the force of friction is f = N f = N 

where is the coefficient of friction and N is the normal force. (The coefficient of friction is discussed in more detail in another chapter, and the normal force is discussed in more detail in the section named Newton's Third Law of Motion, in this chapter.) 

Recall from the section on Force that a net external force acts from outside on the object of interest. A more precise definition is that it acts on the system of interest. A system is one or more objects that you choose to study. It is important to define the system at the beginning of a problem to figure out which forces are external and need to be considered and which are internal and can be ignored. 

For example, in [link] part (a), two children push a third child in a wagon at constant velocity. The system of interest is the wagon plus the small child, as shown in part (b) of the figure. The two children behind the wagon exert external forces on this system ( F 1, F 2). Friction f acting at the axles of the wheels and at the surface where the wheels touch the ground is another external force acting on the system. Two more external forces act on the system: the weight W of the system pulling down and the normal force N of the ground pushing up. Notice that the wagon is not accelerating vertically, so Newton s first law tells us that the normal force balances the weight. Because the wagon is moving forward at constant velocity, the force of friction must have the same strength as the sum of the forces applied by the two children. (a) The wagon and rider form a system that is acted on by external forces. (b)The two children pushing the wagon and child provide two external forces. Friction acting at the wheel axles and on the surface of the tires where they touch the ground provides an external force that acts against the direction of motion. The weight W and the normal force N from the ground are two more external forces acting on the system. All external forces are represented in the figure by arrows. All of the external forces acting on the system add together, but because the wagon moves at a constant velocity, all the forces must add up to zero. Mass and Inertia 

[BL] Review Newton s first law. Explain that the property of objects to maintain their state of motion is called inertia. 

[OL] [AL] Take two similar carts or trolleys with wheels. Place a heavy weight in one of them. Ask students which cart would require more force to change its state of motion. Ask students which would stay in motion longer if you were to set them in motion. Based on this discussion, have students speculate what inertia may depend on. 

[BL] [OL] Explain the concepts of mass and weight. Explain that these terms may be used interchangeably in everyday life but have different meanings in science. 

Inertia is the tendency for an object at rest to remain at rest, or for a moving object to remain in motion in a straight line with constant speed. This key property of objects was first described by Galileo. Later, Newton incorporated the concept of inertia into his first law, which is often referred to as the law of inertia . 

As we know from experience, some objects have more inertia than others. For example, changing the motion of a large truck is more difficult than changing the motion of a toy truck. In fact, the inertia of an object is proportional to the mass of the object. Mass is a measure of the amount of matter (or stuff ) in an object. The quantity or amount of matter in an object is determined by the number and types of atoms the object contains. Unlike weight (which changes if the gravitational force changes), mass does not depend on gravity. The mass of an object is the same on Earth, in orbit, or on the surface of the moon. In practice, it is very difficult to count and identify all of the atoms and molecules in an object, so mass is usually not determined this way. Instead, the mass of an object is determined by comparing it with the standard kilogram. Mass is therefore expressed in kilograms. 

In everyday language, people often use the terms weight and mass interchangeably but this is not correct. Weight is actually a force. (We cover this topic in more detail in section on Newton's Second Law of Motion.) Newton s First Law of Motion 

This video contrasts the way we thought about motion and force in the time before Galileo s concept of inertia and Newton s first law of motion with the way we understand force and motion now. 

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In this simulation, you will first explore net force by placing blue people on the left side of a tug of war rope and red people on the right side of the rope (by clicking people and dragging them with your mouse). Experiment with changing the number and size of people on each side to see how it affects the outcome of the match and the net force. Hit the Go! button to start the match, and the reset all button to start over. 

Next, click on the Friction tab. Try selecting different objects for the person to push. Slide the applied force button to the right to apply force to the right and to the left to apply force to the left. The force will continue to be applied as long as you hold down the button. See the arrow representing friction change in magnitude and direction, depending on how much force you apply. Try increasing or decreasing the friction force to see how this change affects the motion. Click here for the simulation 

[link] Section Summary Newton s first law states that a body at rest remains at rest or, if moving, remains in motion in a straight line at a constant speed unless acted on by a net external force. This law is also known as the law of inertia. Inertia is the tendency of an object at rest to remain at rest or, if moving, to remain in motion at constant velocity. Inertia is related to an object s mass. Friction is a force that opposes motion and causes an object or system to slow down. Mass is the quantity of matter in a substance. Key Equations Newton's first law of motion F net = 0 F net = 0 or F = 0 F = 0 

Use the questions in Check Your Understanding to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, the assessment through Check Your Understanding will help identify which objective is causing the problem and direct students to the relevant content. Check Your Understanding 

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[link] Glossary friction an external force that acts in the direction opposite to the direction of motion inertia the tendency of an object at rest to remain at rest, or for a moving object to remain in motion in a straight line and at constant speed law of inertia Newton s first law of motion: a body at rest remains at rest or, if in motion, remains in motion at a constant speed in a straight line unless acted on by a net external force; also known as the law of inertia mass the quantity of matter in a substance; measured in kilograms Newton s first law of motion a body at rest remains at rest or, if in motion, remains in motion at a constant speed in a straight line unless acted on by a net external force; also known as the law of inertia system one or more objects of interest for which only the forces acting on them from the outside are considered, but not the forces acting between them or inside of themNewton s Second Law of Motion Newton s Second Law of Motion Section Learning Objectives 

By the end of this section, you will be able to: Describe Newton s second law both verbally and mathematically Use Newton s second law to solve problems 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4D) : calculate the effect of forces on objects, including the law of inertia, the relationship between force and acceleration, and the nature of force pairs between objects 

Before beginning this section, review forces, acceleration, acceleration due to gravity (g), friction, inertia, and Newton s First Law. Section Key Terms freefall Newton s second law of motion weight Describing Newton s Second Law of Motion 

[BL] [OL] Review the concepts of inertia and Newton s first law. Explain that, according to Newton s First Law, a change in motion is caused by an external force. For instance, a ball that is pitched changes its speed and direction when it is hit by a bat. 

[BL] [OL] [AL] Write the equation for Newton s Second Law and show how it can be solved for all three variables, F , m , and a . Explain the practical implications for each case. Ask students how the other two variables would behave if one quantity is held constant. 

Students might confuse the terms equal and proportional. 

Newton s first law considered bodies at rest or bodies in motion at constant velocity . The other state of motion to consider is when an object is moving with a changing velocity, which means a change in the speed and/or the direction of motion. This type of motion is addressed by Newton s second law of motion , which states how force causes changes in motion. Newton s second law of motion is used to calculate what happens in situations involving forces and motion, and it shows the mathematical relationship between force, mass , and acceleration . Mathematically, the second law is most often written as F net = m a or F = m a F net = m a or F = m a 

where F net (or F ) is the net external force , m is the mass of the system, and a is the acceleration. Note that F net and F are the same because the net external force is the sum of all of the external forces acting on the system. 

First, what do we mean by a change in motion ? A change in motion is simply a change in velocity: the speed of an object can become slower or faster, the direction in which the object is moving can change, or both of these variables may change. A change in velocity means, by definition, that an acceleration has occurred. Newton s first law says that only a nonzero net external force can cause a change in motion, so a net external force must cause an acceleration. Note that acceleration can refer to slowing down or to speeding up. Acceleration can also refer to a change in the direction of motion with no change in speed, because acceleration is the change in velocity divided by the time it takes for that change to occur, and velocity is defined by speed and direction. 

From the equation F net = m a , F net = m a , we see that force is directly proportional to both mass and acceleration, which makes sense. To accelerate two objects from rest to the same velocity, you would expect more force to be required to accelerate the more massive object. Likewise, for two objects of the same mass, applying a greater force to one would accelerate it to a greater velocity. 

Now, let s rearrange Newton s second law to solve for acceleration. We get a = F net m or a = F m . a = F net m or a = F m . 

In this form, we can clearly see that acceleration is directly proportional to force, which we write as a F net , a F net , 

where the symbol means proportional to. 

This proportionality states mathematically what we just said in words acceleration is directly proportional to the net external force. When two variables are directly proportional to each other, then if one variable doubles, the other variable must double. Likewise, if one variable is reduced by half, the other variable must also be reduced by half. In general, when one variable is multiplied by a number, the other variable will also be multiplied by the same number. It seems reasonable that the acceleration of a system should be directly proportional to and in the same direction as the net external force acting on the system. An object experiences greater acceleration when acted on by a greater force. 

It is also clear from the equation a = F net / m a = F net / m that acceleration is inversely proportional to mass, which we write as a 1 m . a 1 m . 

Inversely proportional means that, if one variable is multiplied by a number, the other variable must be divided by the same number. Now, it also seems reasonable that acceleration should be inversely proportional to the mass of the system. In other words, the larger the mass (the inertia), the smaller the acceleration produced by a given force. This relationship is illustrated in [link] , which shows that a given net external force applied to a basketball produces a much greater acceleration than when applied to a car. The same force exerted on systems of different mass produces different accelerations. (a) A boy pushes a basketball to make a pass. The effect of gravity on the ball is ignored. (b) The same boy pushing with identical force on a stalled car produces a far smaller acceleration (friction is negligible). Note that the free-body diagrams for the ball and for the car are identical, which allows us to compare the two situations. Applying Newton s Second Law 

[BL] Review how to convert between units. 

[OL] [AL] Ask students to give examples of Newton s Second Law. 

Students might confuse weight, which is a force, and g , which is the acceleration due to gravity. 

[BL] [OL] [AL] Ask students if they think an astronaut weighs the same on the moon as they do on Earth. Talk about the difference between mass and weight. 

Before putting Newton s second law into action, it is important to consider units. The equation F net = m a F net = m a is used to define the units of force in terms of the three basic units of mass, length, and time (recall that acceleration has units of length divided by time squared). The SI unit of force is called the newton (abbreviated N) and is the force needed to accelerate a 1 kg system at the rate of 1 m/s2. That is, because F net = m a , F net = m a , we have 1 N = 1 kg 1 m/s 2 = 1 kg m s 2 1 N = 1 kg 1 m/s 2 = 1 kg m s 2 

One of the most important applications of Newton s second law is to calculate weight (also known as the gravitational force ), which is usually represented mathematically as W . When people talk about gravity , they don t always realize that it is an acceleration. When an object is dropped, it accelerates toward the center of Earth. Newton s second law states that the net external force acting on an object is responsible for the acceleration of the object. If air resistance is negligible, the net external force on a falling object is only the gravitational force (i.e., the weight of the object). 

Weight can be represented by a vector because it has a direction. Down is defined as the direction in which gravity pulls, so weight is normally considered a downward force. By using Newton s second law, we can figure out the equation for weight. 

Consider an object with mass m falling toward Earth. It experiences only the force of gravity (i.e. the gravitational force or weight), which is represented by W . Newton s second law states that F net = m a . F net = m a . Since the only force acting on the object is the gravitational force, we have F net = W . F net = W . We know that the acceleration of an object due to gravity is g , so we have a = g . a = g . Substituting these two expressions into Newton s second law gives W = m g W = m g 

This is the equation for weight the gravitational force on a mass m . On Earth, g = 9.80 m/s 2 , g = 9.80 m/s 2 , so the weight (disregarding for now the direction of the weight) of a 1.0 kg object on Earth is W = m g = (1 .0 kg)(9 .80 m/s 2 ) = 9.8 N W = m g = (1 .0 kg)(9 .80 m/s 2 ) = 9.8 N 

Although most of the world uses newtons as the unit of force, in the United States the most familiar unit of force is the pound (lb), where 1 N = 0.225 lb. 

Recall that, although gravity acts downward, it can be assigned a positive or negative value, depending on the positive direction in your chosen coordinate system. Be sure to take this into consideration when solving problems with weight. When the downward direction is taken to be negative, as is often the case, acceleration due to gravity becomes g = 9.8 m/s 2 . 

When the net external force on an object is its weight, we say that it is in freefall . In this case, the only force acting on the object is the force of gravity. On the surface of Earth, when objects fall downward toward Earth, they are never truly in freefall because there is always some upward force due to the air resistance that acts on the object (and there is also the buoyancy force of air, which is similar to the buoyancy force in water that keeps boats afloat). 

Gravity varies slightly over the surface of Earth, so that the weight of an object depends very slightly on its location on Earth. Weight varies dramatically away from Earth s surface. On the Moon, for example, the acceleration due to gravity is only 1.67 m/s 2 . Because weight depends on the force of gravity, a 1.0 kg mass weighs 9.8 N on Earth and only about 1.7 N on the Moon. 

It is important to remember that weight and mass are very different, although they are closely related. Mass is the quantity of matter (how much stuff ) in an object and does not vary, but weight is the gravitational force on an object and is proportional to the force of gravity. It is easy to confuse the two, because our experience is confined to Earth, and the weight of an object is essentially the same no matter where you are on Earth. Adding to the confusion, the terms mass and weight are often used interchangeably in everyday language; for example, our medical records often show our weight in kilograms, but never in the correct units of newtons. Mass and Weight 

Explain that, even though a scale gives a mass, it actually measures weight. Scales are calibrated to show the correct mass on Earth. They would give different results on the Moon, because the force of gravity is weaker on the Moon. 

In this activity you will use a scale to investigate mass and weight. 1 bathroom scale 1 table What do bathroom scales measure? When you stand on a bathroom scale, what happens to the scale? It depresses slightly. The scale contains springs that compress in proportion to your weight similar to rubber bands expanding when pulled. The springs provide a measure of your weight (provided you are not accelerating). This is a force in newtons (or pounds). In most countries, the measurement is now divided by 9.80 to give a reading in kilograms, which are units of mass. The scale detects weight but is calibrated to display mass. If you went to the Moon and stood on your scale, would it detect the same mass as it did on Earth? 

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Only net external force impacts the acceleration of an object. If more than one force acts on an object and you calculate the acceleration by using only one of these forces, you will not get the correct acceleration for the object. Newton s Second Law of Motion 

This video reviews Newton s second law of motion and how net external force and acceleration relate to one another and to mass. It also covers units of force, mass, and acceleration and goes over a worked example. 

[link] What Acceleration Can a Person Produce when Pushing a Lawn Mower? 

Suppose that the net external force (push minus friction) exerted on a lawn mower is 51 N parallel to the ground. The mass of the mower is 240 kg. What is its acceleration? Strategy 

Since F net and m are given, the acceleration can be calculated directly from Newton s second law: F net = m a . Solution 

Solving Newton s second law for the acceleration, we find that the magnitude of the acceleration, a , is a = F net m . a = F net m . Entering the given values for net external force and mass gives 

a = 51 N 240 kg a = 51 N 240 kg 

Inserting the units kg m/s 2 kg m/s 2 for N yields 

a = 51 kg m/s 2 240 kg = 0.21 m/s 2 a = 51 kg m/s 2 240 kg = 0.21 m/s 2 Discussion 

The acceleration is in the same direction as the net external force, which is parallel to the ground and to the right. There is no information given in this example about the individual external forces acting on the system, but we can say something about their relative magnitudes. For example, the force exerted by the person pushing the mower must be greater than the friction opposing the motion because we are given that the net external force is in the direction in which the person pushes. Also, the vertical forces must cancel if there is no acceleration in the vertical direction (the mower is moving only horizontally). The acceleration found is reasonable for a person pushing a mower; the mower s speed must increase by 0.21 m/s every second, which is possible. The time during which mower accelerates would not be very long because the person s top speed would soon be reached. At this point, the person could push a little less hard, because he only has to overcome friction. What Rocket Thrust Accelerates This Sled? 

Prior to manned space flights, rocket sleds were used to test aircraft, missile equipment, and physiological effects on humans at high accelerations. Rocket sleds consisted of a platform mounted on one or two rails and propelled by several rockets. Calculate the magnitude of force exerted by each rocket, called its thrust T , for the four-rocket propulsion system shown below. The sled s initial acceleration is 49 m/s 2 , 49 m/s 2 , the mass of the system is 2100 kg, and the force of friction opposing the motion is 650 N. Strategy 

The system of interest is the rocket sled. Although forces act vertically on the system, they must cancel because the system does not accelerate vertically. This leaves us with only horizontal forces to consider. We ll assign the direction to the right as the positive direction. See the free-body diagram in the figure. Solution 

We start with Newton s second law and look for ways to find the thrust T of the engines. Because all forces and acceleration are along a line, we need only consider the magnitudes of these quantities in the calculations. We begin with 

F net = m a , F net = m a , 

where F net F net is the net external force in the horizontal direction. We can see from the image above that the engine thrusts are in the same direction (which we call the positive direction), whereas friction opposes the thrust. In equation form, the net external force is 

F net = 4 T f . F net = 4 T f . 

Newton s second law tells us that F net = m a , so we get 

m a = 4 T f . m a = 4 T f . 

After a little algebra, we solve for the total thrust 4 T : 

4 T = m a + f , 4 T = m a + f , 

which means that the individual thrust is 

T = m a + f 4 . T = m a + f 4 . 

Inserting the known values yields 

T = ( 2100 kg)(49 m/s 2 ) + 650 N 4 = 2.6 10 4 N . T = ( 2100 kg)(49 m/s 2 ) + 650 N 4 = 2.6 10 4 N . Discussion 

The numbers are quite large, so the result might surprise you. Experiments such as this were performed in the early 1960s to test the limits of human endurance and to test the apparatus designed to protect fighter pilots in emergency ejections. Speeds of 1000 km/h were obtained, with accelerations of 45 g . (Recall that g, the acceleration due to gravity, is 9 .80 m/s 2 . 9 .80 m/s 2 . An acceleration 45 g is 45 9 .80 m/s 2 , 45 9 .80 m/s 2 , which is approximately 440 m/s 2 . 440 m/s 2 . ) Living subjects are no longer used, and land speeds of 10,000 km/h have now been obtained with rocket sleds. In this example, as in the preceding example, the system of interest is clear. We will see in later examples that choosing the system of interest is crucial and that the choice is not always obvious. Practice Problems 

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[link] Section Summary Acceleration is a change in velocity, meaning a change in speed, direction, or both. An external force acts on a system from outside the system, as opposed to internal forces, which act between components within the system. Newton s second law of motion states that the acceleration of a system is directly proportional to and in the same direction as the net external force acting on the system, and inversely proportional to the system s mass. In equation form, Newton s second law of motion is F net = m a F net = m a or F = m a F = m a This is sometimes written as a = F net m a = F net m or a = F m a = F m . The weight of an object of mass m is the force of gravity that acts on it. From Newton s second law, weight is given by W = m g W = m g If the only force acting on an object is its weight, then the object is in freefall. Key Equations Newton s second law of motion: F net = m a F net = m a or F = m a F = m a Newton s second law of motion to solve acceleration a = F net m or a = F m a = F net m or a = F m Newton s second law of motion to solve weight W = m g W = m g Check Your Understanding 

Use the questions in Check Your Understanding to assess whether students achieve the section learning objectives. If students are struggling with a specific objective, the assessment through Check Your Understanding will help identify which is causing the problem and direct students to the relevant content. 

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[link] Glossary freefall a situation in which the only force acting on an object is the force of gravity Newton s second law of motion the net external force F net F net on an object is proportional to and in the same direction as the acceleration of the object, a , and also proportional to the object s mass m ; defined mathematically as F net = m a F net = m a or F = m a . F = m a . weight the force of gravity, W , acting on an object of mass m ; defined mathematically as W = m g , where g is the magnitude and direction of the acceleration due to gravityNewton s Third Law of Motion Newton s Third Law of Motion Section Learning Objectives 

By the end of this section, you will be able to: Describe Newton s Third Law both verbally and mathematically Use Newton s Third Law to solve problems 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4D) : calculate the effect of forces on objects, including the law of inertia, the relationship between force and acceleration, and the nature of force pairs between objects Section Key Terms Newton s third law of motion normal force tension thrust Describing Newton s Third Law of Motion 

[BL] [OL] Review Newton s First and Second Laws. 

[AL] Start a discussion about action and reaction by giving examples. Introduce the concepts of systems and systems of interest. Explain how forces can be classified as internal or external to the system of interest. Give examples of systems. Ask students which forces are internal and which are external in each scenario. 

If you have ever stubbed your toe, you have noticed that although your toe initiates the impact, the surface that you stub it on exerts a force back on your toe. Although the first thought that crosses your mind is probably ouch, that hurt rather than this is a great example of Newton s third law, both statements are true. 

This is exactly what happens whenever one object exerts a force on another each object experiences a force that is the same strength as the force acting on the other object but that acts in the opposite direction. Everyday experiences, such as stubbing a toe or throwing a ball, are all perfect examples of Newton s third law in action. 

Newton s third law of motion states that, whenever a first object exerts a force on a second object, the first object experiences a force equal in magnitude but opposite in direction to the force that it exerts. 

Newton s third law of motion tells us that forces always occur in pairs, and one object cannot exert a force on another without experiencing the same strength force in return. We sometimes refer to these force pairs as action-reaction pairs, where the force exerted is the action, and the force experienced in return is the reaction (although which is which depends on your point of view). 

Newton s third law is useful for figuring out which forces are external to a system. Recall that identifying external forces is important when setting up a problem, because the external forces must be added together to find the net force . 

We can see Newton s third law at work by looking at how people move about. Consider a swimmer pushing off from the side of a pool, as illustrated in [link] . She pushes against the pool wall with her feet and accelerates in the direction opposite to her push. The wall has thus exerted on the swimmer a force of equal magnitude but in the direction opposite that of her push. You might think that two forces of equal magnitude but that act in opposite directions would cancel, but they do not because they act on different systems. 

In this case, there are two different systems that we could choose to investigate: the swimmer or the wall. If we choose the swimmer to be the system of interest, as in the figure, then F wall on feet F wall on feet is an external force on the swimmer and affects her motion. Since acceleration is in the same direction as the net external force , the swimmer moves in the direction of F wall on feet . F wall on feet . Since the swimmer is our system (or object of interest) and not the wall, we do not need to consider the force F feet on wall F feet on wall because it originates from the swimmer rather than acting on the swimmer. Therefore, F feet on wall F feet on wall does not directly affect the motion of the system and does not cancel F wall on feet . F wall on feet . Note that the swimmer pushes in the direction opposite to the direction in which she wants to move. When the swimmer exerts a force F feet on wall F feet on wall on the wall, she accelerates in the direction opposite to that of her push. This means that the net external force on her is in the direction opposite to F feet on wall . F feet on wall . This opposition is the result of Newton s third law of motion, which dictates that the wall exerts a force F wall on feet F wall on feet on the swimmer that is equal in magnitude but that acts in the direction opposite to the force that the swimmer exerts on the wall. 

Other examples of Newton s third law are easy to find. As a teacher paces in front of a blackboard, he exerts a force backward on the floor. The floor exerts a reaction force in the forward direction on the teacher that causes him to accelerate forward. Similarly, a car accelerates because the ground pushes forward on the drive wheels in reaction to the drive wheels pushing backward on the ground. You can see evidence of the wheels pushing backward when tires spin on a gravel road and throw rocks backward. 

Another example is the force of a baseball as it makes contact with the bat. Helicopters create lift by pushing air down, creating an upward reaction force. Birds fly by exerting force on air in the direction opposite that in which they wish to fly. For example, the wings of a bird force air downward and backward in order to get lift and move forward. An octopus propels itself forward in the water by ejecting water backward through a funnel in its body, which is similar to how a jet ski is propelled. In these examples, the octopus or jet ski push the water backward, and the water in turn pushes the octopus or jet ski forward. Applying Newton s Third Law 

[BL] Review the concept of weight as a force. 

[OL] Ask students what happens when an object is dropped from a height. Why does it stop when it hits the ground? Introduce the term normal force. 

[BL] [OL] [AL] Demonstrate the concept of tension by using physical objects. Suspend an object such as an eraser from a peg by using a rubber band. Hang another rubber band beside the first but with no object attached. Ask students what the difference is between the two. What are the forces on the first peg? Explain how the rubber band (i.e., the connector) transmits force. Now ask students the direction of the external forces acting on the connector. Also ask what internal forces are acting on the connector. If you remove the eraser, in which direction will the rubber band move? This is the direction of the force the rubber band applied to the eraser. 

Forces are classified and given names based on their source, how they are transmitted, or their effects. In previous sections, we discussed the forces called push, weight, and friction. In this section, applying Newton s third law of motion will allows us to explore three more forces: the normal force , tension , and thrust . However, because we haven t yet covered vectors in depth, we ll only consider one-dimensional situations in this chapter. Another chapter will consider forces acting in two dimensions. 

The gravitational force (or weight ) acts on objects at all times and everywhere on Earth. We know from Newton s second law that a net force produces an acceleration; so why is everything not in a constant state of freefall toward the center of Earth? The answer is the normal force. The normal force is the force that a surface applies to an object to support the weight of that object; it acts perpendicular to the surface upon which the object rests. If an object on a flat surface is not accelerating, the net external force is zero, and the normal force has the same magnitude as the weight of the system but acts in the opposite direction. In equation form, we write that N = m g . N = m g . 

Note that this equation is only true for a horizontal surface. 

The word tension comes from the Latin word meaning to stretch. Tension is the force along the length of a flexible connector, such as a string, rope, chain, or cable. Regardless of the type of connector attached to the object of interest, one must remember that the connector can only pull (or exert tension ) in the direction parallel to its length. Tension is a pull that acts parallel to the connector, and that acts in opposite directions at the two ends of the connector. This is possible because a flexible connector is simply a long series of action-reaction forces, except at the two ends where outside objects provide one member of the action-reaction forces. 

Consider a person holding a mass on a rope as shown in [link] . When a perfectly flexible connector (one requiring no force to bend it) such as an ideal rope transmits a force T , this force must be parallel to the length of the rope, as shown. The pull that such a flexible connector exerts is a tension. Note that the rope pulls with equal magnitude force but in opposite directions on the hand and on the mass (neglecting the weight of the rope). This is an example of Newton s third law. The rope is the medium that transmits between the two objects forces of equal magnitude but that act in opposite directions. 

Tension in the rope must equal the weight of the supported mass, as we can prove by using Newton s second law. If the 5.00 kg mass in the figure is stationary, then its acceleration is zero, so F net = 0. F net = 0. The only external forces acting on the mass are its weight W and the tension T supplied by the rope. Summing the external forces to find the net force, we obtain F net = T W = 0 , F net = T W = 0 , 

where T and W are the magnitudes of the tension and weight and their signs indicate direction, with up being positive. By substituting m g for F net and rearranging the equation, the tension equals the weight of the supported mass, just as you would expect: T = W = m g . T = W = m g . 

For a 5.00 kg mass (neglecting the mass of the rope), we see that T = m g = ( 5.00 kg)(9 .80 m/s 2 ) = 49.0 N . T = m g = ( 5.00 kg)(9 .80 m/s 2 ) = 49.0 N . 

Another example of Newton s third law in action is thrust. Rockets move forward by expelling gas backward at high velocity. This means that the rocket exerts a large force backward on the gas in the rocket combustion chamber, and the gas in turn exerts a large force forward on the rocket in response. This reaction force is called thrust. 

A common misconception is that rockets propel themselves by pushing on the ground or on the air behind them. They actually work better in a vacuum, where they can expel exhaust gases more easily. Math: Problem-Solving Strategy for Newton s Laws of Motion 

The basics of problem solving, presented earlier in this text, are followed here with specific strategies for applying Newton s laws of motion. These techniques also reinforce concepts that are useful in many other areas of physics. 

First, identify the physical principles involved. If the problem involves forces, then Newton s laws of motion are involved, and it is important to draw a careful sketch of the situation. Such a sketch is shown in [link] . Next, as in [link] , use vectors to represent all forces. Label the forces carefully and make sure that their lengths are proportional to the magnitude of the forces and that the arrows point in the direction in which the forces act. (a) A sketch of Tarzan hanging motionless from a vine. (b) Arrows are used to represent all forces. T is the tension exerted on Tarzan by the vine, F T F T is the force exerted on the vine by Tarzan, and W is Tarzan s weight (i.e., the force exerted on Tarzan by Earth s gravity ). All other forces, such as a nudge of a breeze, are assumed to be negligible. (c) Suppose we are given Tarzan s mass and asked to find the tension in the vine. We define the system of interest as shown and draw a free-body diagram as shown in (d). F T F T is no longer shown because it does not act on the system of interest; rather, F T F T acts on the outside world. (d) The free-body diagram shows only the external forces acting on Tarzan. For these to sum to zero, we must have T = W . T = W . 

Next, make a list of knowns and unknowns and assign variable names to the quantities given in the problem. Figure out which variables need to be calculated; these are the unknowns. Now carefully define the system, meaning which objects are of interest for the problem. This decision is important, because Newton s second law involves only external forces. Once the system is identified, it s possible to see which forces are external and which are internal (see [link] ). 

If the system acts on an object outside the system, you then know that the outside object exerts a force of equal magnitude but in the opposite direction on the system. 

A diagram showing the system of interest and all the external forces acting on it is called a free-body diagram. Only external forces are shown on free-body diagrams, not acceleration or velocity. [link] shows a free-body diagram for the system of interest. 

After drawing a free-body diagram, apply Newton s second law to solve the problem. This is done in [link] for the case of Tarzan hanging from a vine. When external forces are clearly identified in the free-body diagram, translate the forces into equation form and solve for the unknowns. Note that forces acting in opposite directions have opposite signs. By convention, forces acting downward or to the left are usually negative. 

[link] Newton s Third Law of Motion 

This video explains Newton s third law of motion through examples involving push, normal force, and thrust (the force that propels a rocket or a jet). 

[link] An Accelerating Subway Train 

A physics teacher pushes a cart of demonstration equipment to a classroom, as in [link] Her mass is 65.0 kg, the cart s mass is 12.0 kg, and the equipment s mass is 7.0 kg. To push the cart forward, the teacher s foot applies a force of 150 N in the opposite direction (backward) on the floor. Calculate the acceleration produced by the teacher. The force of friction, which opposes the motion, is 24.0 N. Strategy 

Since they accelerate together, we define the system to be the teacher, the cart, and the equipment. The teacher pushes backward with a force F foot F foot of 150 N. According to Newton s third law, the floor exerts a forward force F floor F floor of 150 N on the system. Because all motion is horizontal, we can assume that no net force acts in the vertical direction, and the problem becomes one dimensional. As noted in the figure, the friction f opposes the motion and therefore acts opposite the direction of F floor . F floor . 

We should not include the forces F teacher F teacher , F cart F cart , or F foot F foot because these are exerted by the system, not on the system. We find the net external force by adding together the external forces acting on the system (see free-body diagram in the figure) and then use Newton s second law to find the acceleration. Solution 

Newton s second law is a = F net m . a = F net m . 

The net external force on the system is the sum of the external forces: the force of the floor acting on the teacher, cart, and equipment (in the horizontal direction) and the force of friction. Because friction acts in the opposite direction, we assign it a negative value. Thus, for the net force, we obtain F net = F floor f = 150 N 24 .0 N = 126 N F net = F floor f = 150 N 24 .0 N = 126 N 

The mass of the system is the sum of the mass of the teacher, cart, and equipment: m = ( 6 5 . 0 + 1 2 . 0 + 7 . 0 ) k g = 8 4 k g . m = ( 6 5 . 0 + 1 2 . 0 + 7 . 0 ) k g = 8 4 k g . 

Insert these values of net F and m into Newton s second law to obtain the acceleration of the system: a = F net m a = 1 2 6 N 84 kg = 1 . 5 m/s 2 . a = F net m a = 1 2 6 N 84 kg = 1 . 5 m/s 2 . Discussion 

None of the forces between components of the system, such as between the teacher s hands and the cart, contribute to the net external force because they are internal to the system. Another way to look at this is to note that forces between components of a system cancel because they are equal in magnitude and opposite in direction. For example, the force exerted by the teacher on the cart is of equal magnitude but in the opposite direction of the force exerted by the cart on the teacher. In this case both forces act on the same system, so they cancel. Defining the system was crucial to solving this problem. Practice Problems 

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[link] Section Summary Newton s third law of motion states that, when one body exerts a force on a second body, the first body experiences a force that is equal in magnitude and opposite in direction to the force that it exerts. When objects rest on a surface, the surface applies a force on the object that opposes the weight of the object. This force acts perpendicular to the surface and is called the normal force. The pulling force that acts along a stretched flexible connector, such as a rope or cable, is called tension. When a rope supports the weight of an object at rest, the tension in the rope is equal to the weight of the object. Thrust is a force that pushes an object forward in response to the backward ejection of mass by the object. Rockets and airplanes are pushed forward by thrust. Key Equations Normal force for a non-accelerating horizontal surface N = m g N = m g Tension for an object at rest T = m g T = m g Check Your Understanding 

Use the questions in Check Your Understanding to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, the assessment through Check Your Understanding will help identify which objective is causing the problem and direct students to the relevant content. 

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This performance task gives your students the opportunity to practice content and skills that support the following NGSS performance expectations and/or science practices: NGSS HS-PS2-1 : Students who demonstrate understanding can: Analyze data to support the claim that Newton s second law of motion describes the mathematical relationship among the net force on a macroscopic object, its mass, and its acceleration. Test Prep Multiple Choice 

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[link] Glossary Newton s third law of motion when one body exerts a force on a second body, the first body experiences a force that is equal in magnitude and opposite in direction to the force that it exerts normal force the force that a surface applies to an object; acts perpendicular and away from the surface with which the object is in contact tension a pulling force that acts along a connecting medium, especially a stretched flexible connector, such as a rope or cable; when a rope supports the weight of an object, the force exerted on the object by the rope is called tension thrust a force that pushes an object forward in response to the backward ejection of mass by the object; rockets and airplanes are pushed forward by a thrust reaction force in response to ejecting gases backwards.Consequences of Special Relativity Consequences of Special Relativity Section Learning Objectives 

By the end of this section, you will be able to: Describe the relativistic effects seen in time dilation, length contraction, and conservation of relativistic momentum Explain and perform calculations involving mass-energy equivalence 

The learning objectives in this section will help your students master the following TEKS: (4F) : identify and describe motion relative to different frames of reference. (8C) : describe the significance of mass-energy equivalence and apply it in explanations of phenomena such as nuclear stability, fission, and fusion. Section Key Terms binding energy length contraction mass defect proper length relativistic relativistic momentum relativistic energy relativistic factor rest mass time dilation 

In this section, you will see how the postulates lead to the theory of special relativity and see how that theory predicts effects on time, distance, momentum, and energy at velocities approaching the speed of light. 

[BL] Begin a discussion by asking if students have ever seen a science fiction movie where space travelers age more slowly than the people left behind on Earth. Tell them there is some basis in fact to these stories. Discuss nuclear power. Ask if they know the basic difference between the nuclear power and combustion power. 

[OL] Explain that Newton s laws are valid for everyday mechanics, but break down at speeds approaching the speed of light. Discuss the relationship between relativity theory and Newton s laws. Briefly describe the changes predicted for measurements of time, length, momentum, and energy. See how much they know about energy derived from nuclear reactions. 

[AL] Ask what the students already know about relativity theory. See if they know that relative motion is an old idea and ask for examples of relative motion in everyday situations. Explain that special relativity is similar but describes unexpected results at speeds approaching the speed of light. Ask if anyone can explain why this statement is true: The original source of all the energy we use is the conversion of matter into energy. Relativistic Effects on Time, Distance, and Momentum 

Consideration of the measurement of elapsed time and simultaneity leads to an important relativistic effect. Time dilation is the phenomenon of time passing more slowly for an observer who is moving relative to another observer. 

For example, suppose an astronaut measures the time it takes for light to travel from the light source, cross her ship, bounce off a mirror, and return. (See [link] ). How does the elapsed time the astronaut measures compare with the elapsed time measured for the same event by a person on the Earth? Asking this question (another thought experiment) produces a profound result. We find that the elapsed time for a process depends on who is measuring it. In this case, the time measured by the astronaut is smaller than the time measured by the Earth-bound observer. The passage of time is different for the two observers because the distance the light travels in the astronaut s frame is smaller than in the Earth-bound frame. Light travels at the same speed in each frame, and so it will take longer to travel the greater distance in the Earth-bound frame. 

[OL] Discuss the expression for the relativistic factor. Explain that this is involved in all relativistic effects. Show how to tell when relativistic effects are significant and when they are negligible by plugging in values of v and c. (a) An astronaut measures the time t 0 t 0 for light to cross her ship using an electronic timer. Light travels a distance 2 D 2 D in the astronaut s frame. (b) A person on the Earth sees the light follow the longer path 2 s 2 s and take a longer time t t . 

[AL] [link] , like [link] , may be hard for some students to grasp. Refer back to the previous figure. The animation in the discussion of length contraction further on should also be some help. 

The relationship between t and t o is given by t = t 0 , t = t 0 , 

where is the relativistic factor given by = 1 1 v 2 c 2 , = 1 1 v 2 c 2 , 

and v and c are the speeds of the moving observer and light, respectively. 

Try putting some values for v into the expression for the relativistic factor ( ). Observe at which speeds this factor will make a difference and when is so close to 1 that it can be ignored. Try 225 m/s, the speed of an airliner; 2.98 10 4 m/s, the speed of Earth in its orbit; and 2.990 10 8 m/s, the speed of a particle in an accelerator. 

Try putting some values for v into the expression for the relativistic factor. Observe at which speeds this factor will make a difference and when it is so close to 1 that it can be ignored. 

Notice that when the velocity v is small compared to the speed of light c , then v/c becomes small, and becomes close to 1. When this happens, time measurements are the same in both frames of reference. Relativistic effects, meaning those that have to do with special relativity, usually become significant when speeds become comparable to the speed of light. This is seen to be the case for time dilation. 

You may have seen science fiction movies in which space travelers return to Earth after a long trip to find that the planet and everyone on it has aged much more than they have. This type of scenario is a based on a thought experiment, known as the twin paradox , which imagines a pair of twins, one of whom goes on a trip into space while the other stays home. When the space traveler returns, she finds her twin has aged much more than she. This happens because the traveling twin has been in two frames of reference , one leaving Earth and one returning. 

Time dilation has been confirmed by comparing the time recorded by an atomic clock sent into orbit to the time recorded by a clock that remained on Earth. GPS satellites must also be adjusted to compensate for time dilation in order to give accurate positioning. 

Have you ever driven on a road, like that shown in [link] , that seems like it goes on forever? If you look ahead, you might say you have about 10 km left to go. Another traveler might say the road ahead looks like it s about 15 km long. If you both measured the road, however, you would agree. Traveling at everyday speeds, the distance you both measure would be the same. You will read in this section, however, that this is not true at relativistic speeds. Close to the speed of light, distances measured are not the same when measured by different observers moving with respect to each other. People might describe distances differently, but at relativistic speeds, the distances really are different. (credit: Corey Leopold, Flickr) 

[OL] Discuss the relationship between time dilation and length contraction. If observers agree on speed, but not on time, they must also disagree on length because v = d/t . 

One thing all observers agree upon is their relative speed . When one observer is traveling away from another, they both see the other receding at the same speed, regardless of whose frame of reference is chosen. Remember that speed equals distance divided by time: v = d/t . If the observers experience a difference in elapsed time, they must also observe a difference in distance traversed. This is because the ratio d/t must be the same for both observers. 

The shortening of distance experienced by an observer moving with respect to the points whose distance apart is measured is called length contraction . Proper length , L 0 , is the distance between two points measured in the reference frame where the observer and the points are at rest. The observer in motion with respect to the points measures L . These two lengths are related by the equation L = L 0 L = L 0 

Because is the same expression used in the time dilation equation above, the equation becomes L = L 0 1 v 2 c 2 . L = L 0 1 v 2 c 2 . 

To see how length contraction is seen by a moving observer, go to this simulation . Here you can also see that simultaneity, time dilation, and length contraction are interrelated phenomena. 

This link is to a simulation that illustrates the relativity of simultaneous events. 

In classical physics, momentum is a simple product of mass and velocity. When special relativity is taken into account, objects that have mass have a speed limit. What effect do you think mass and velocity have on the momentum of objects moving at relativistic speeds, i.e., speeds close to the speed of light? 

Momentum is one of the most important concepts in physics. The broadest form of Newton s second law is stated in terms of momentum. Momentum is conserved in classical mechanics whenever the net external force on a system is zero. This makes momentum conservation a fundamental tool for analyzing collisions. We will see that momentum has the same importance in modern physics. Relativistic momentum is conserved, and much of what we know about subatomic structure comes from the analysis of collisions of accelerator-produced relativistic particles. 

One of the postulates of special relativity states that the laws of physics are the same in all inertial frames. Does the law of conservation of momentum survive this requirement at high velocities? The answer is yes, provided that the momentum is defined as follows. 

Relativistic momentum, p , is classical momentum multiplied by the relativistic factor . p = m u , p = m u , 

where m m is the rest mass of the object (that is the mass measured at rest, without any factor involved), u u is its velocity relative to an observer, and , as before, is the relativistic factor. We use the mass of the object as measured at rest because we cannot determine its mass while it is moving. 

Note that we use u u for velocity here to distinguish it from relative velocity v v between observers. Only one observer is being considered here. With p p defined in this way, p tot p tot is conserved whenever the net external force is zero, just as in classical physics. Again we see that the relativistic quantity becomes virtually the same as the classical at low velocities. That is, relativistic momentum m u m u becomes the classical m u m u at low velocities, because is very nearly equal to 1 at low velocities. 

Relativistic momentum has the same intuitive feel as classical momentum. It is greatest for large masses moving at high velocities. Because of the factor , , however, relativistic momentum behaves differently from classical momentum by approaching infinity as u u approaches c c . (See [link] .) This is another indication that an object with mass cannot reach the speed of light. If it did, its momentum would become infinite, which is an unreasonable value. Relativistic momentum approaches infinity as the velocity of an object approaches the speed of light. 

[OL] Discuss the graph. Explain how it shows that objects that have mass cannot reach the speed of light. Have them analyze the equation for relativistic momentum and see how this supports this conclusion. Explain that light can travel at the speed of light because it has no rest mass. 

Relativistic momentum is defined in such a way that the conservation of momentum will hold in all inertial frames. Whenever the net external force on a system is zero, relativistic momentum is conserved, just as is the case for classical momentum. This has been verified in numerous experiments. Mass-Energy Equivalence 

Let us summarize the calculation of relativistic effects on objects moving at speeds near the speed of light. In each case we will need to calculate the relativistic factor, given by: = 1 1 v 2 c 2 , = 1 1 v 2 c 2 , 

where v and c are as defined earlier. We use u as the velocity of a particle or an object in one frame of reference, and v for the velocity of one frame of reference with respect to another. Time Dilation 

Elapsed time on a moving object, t 0 t 0 , as seen by a stationary observer is given by t = t 0 , t = t 0 , where t 0 t 0 is the time observed on the moving object when it is taken to be the frame or reference. Length Contraction 

Length measured by a person at rest with respect to a moving object, L , is given by L = L 0 , L = L 0 , 

where L 0 is the length measured on the moving object. Relativistic Momentum 

Momentum, p , of an object of mass, m , traveling at relativistic speeds is given by p = m u p = m u , where u is velocity of a moving object as seen by a stationary observer. Relativistic Energy 

The original source of all the energy we use is the conversion of mass into energy. Most of this energy is generated by nuclear reactions in the sun and radiated to Earth in the form of electromagnetic radiation, where it is then transformed into all the forms with which we are familiar. The remaining energy from nuclear reactions is produced in nuclear power plants and in Earth s interior. In each of these cases, the source of the energy is the conversion of a small amount of mass into a large amount of energy. These sources are shown in [link] . The Sun (a) and the Susquehanna Steam Electric Station (b) both convert mass into energy. (credits: (a) NASA/Goddard Space Flight Center, Scientific Visualization Studio; (b) U.S. government) 

The first postulate of relativity states that the laws of physics are the same in all inertial frames. Einstein showed that the law of conservation of energy is valid relativistically, if we define energy to include a relativistic factor. The result of his analysis is that a particle or object of mass m moving at velocity u has relativistic energy given by E = m c 2 . E = m c 2 . 

This is the expression for the total energy of an object of mass m at any speed u and includes both kinetic and potential energy . Look back at the equation for and you will see that it is equal to 1 when u is 0, that is, when an object is at rest. Then the rest energy, E 0 , is simply E 0 = m c 2 . E 0 = m c 2 . 

This is the correct form of Einstein s famous equation. 

This equation is very useful to nuclear physicists because it can be used to calculate the energy released by a nuclear reaction. This is done simply by subtracting the mass of the products of such a reaction from the mass of the reactants. The difference is the m in E 0 = m c 2 E 0 = m c 2 . Here is a simple example: 

A positron is a type of antimatter that is just like an electron, except that it has a positive charge. When a positron and an electron collide, their masses are completely annihilated and converted to energy in the form of gamma rays. Because both particles have a rest mass of 9.11 10 31 kg, we multiply the mc 2 term by 2. So the energy of the gamma rays is E 0 = 2 ( 9.11 10 31 kg ) ( 3.00 10 8 m s ) 2 = 1.64 10 13 kg m 2 s 2 = 1.64 10 13 J E 0 = 2 ( 9.11 10 31 kg ) ( 3.00 10 8 m s ) 2 = 1.64 10 13 kg m 2 s 2 = 1.64 10 13 J 

where we have the expression for the joule (J) in terms of its SI base units of kg, m, and s. In general, the nuclei of stable isotopes have less mass then their constituent subatomic particles. The energy equivalent of this difference is called the binding energy of the nucleus. This energy is released during the formation of the isotope from its constituent particles because the product is more stable than the reactants. Expressed as mass, it is called the mass defect . For example, a helium nucleus is made of two neutrons and two protons and has a mass of 4.0003 atomic mass units (u). The sum of the masses of two protons and two neutrons is 4.0330 u. The mass defect then is 0.0327 u. Converted to kg, the mass defect is 5.0442 10 30 kg. Multiplying this mass times c 2 gives a binding energy of 4.540 10 12 J. This doesn t sound like much because it is only one atom. If you were to make one gram of helium out of neutrons and protons, it would release 683,000,000,000 J. By comparison, burning one gram of coal releases about 24 J. 

[BL] In regards to the change in the law of conservation of energy to the law of conservation of mass-energy, it may help to think of mass as simply a very concentrated form of energy. 

[OL] Impress upon the students the enormous amount of energy derived from the conversion of a small amount of mass. Have them note that c 2 is a very large number. Students try to understand new concepts by using previous knowledge, and that may result in a misconception here. They are comfortable with chemical reactions and may try to relate this to the burning of a piece of wood. Tell them that burning the wood chemically might provide energy for a single room in a house, but converting the mass of the wood completely to energy according to E = mc 2 would provide power for thousands of houses. 

[AL] Ask students if they know the difference between fission and fusion and where examples of each of these occur. The RHIC Collider 

[link] shows the Brookhaven National Laboratory in Upton, NY. The circular structure houses a particle accelerator called the RHIC, which stands for Relativistic Heavy Ion Collider. The heavy ions in the name are gold nuclei that have been stripped of their electrons. Streams of ions are accelerated in several stages before entering the big ring seen in the figure. Here they are accelerated to their final speed, which is about 99.7% the speed of light. Such high speeds are called relativistic. All the relativistic phenomena we have been discussing in this chapter are very pronounced in this case. At this speed = 12.9, so that relativistic time dilates by a factor of about 13, and relativistic length contracts by the same factor. Brookhaven National Laboratory. The circular structure houses the RHIC. (credit: energy.gov, Wikimedia Commons) 

Two ion beams circle the 2.4-mile long track around the big ring in opposite directions. The paths can then be made to cross thereby causing ions to collide. The collision event is very short-lived but amazingly intense. The temperatures and pressures produced are greater than those in the hottest suns. At 4 trillion degrees Celsius, this is the hottest material ever created in a laboratory 

But what is the point of creating such an extreme event? Under these conditions, the neutrons and protons that make up the gold nuclei are smashed apart into their components, which are called quarks and gluons. The goal is to recreate the conditions that theorists believe existed at the very beginning of the universe. It is thought that at that time matter was a sort of soup of quarks and gluons. When things cooled down after the initial bang, these particles condensed to form protons and neutrons. 

Some of the results have been surprising and unexpected. It was thought the quark-gluon soup would resemble a gas or plasma. Instead it behaves more like a liquid. It has been called a perfect liquid because it has virtually no viscosity (meaning that it has no resistance to flow.) 

Discuss particle colliders such as the relatively new Large Hadron Collider built by CERN. Students may want to know more about this project and the God particle. Explain why there are so many applications of special relativity theory in the field of particle physics. 

[link] The Speed of Light 

One night you are out looking up at the stars and an extraterrestrial spaceship flashes across the sky. The ship is 50 meters long and is travelling at 95% of the speed of light. What would the ship s length be when measured from your Earthbound frame of reference? Strategy 

List the knowns and unknowns: 

knowns: proper length of the ship, L 0 = 50 m; velocity, v , = 0.95 c 

unknowns: observed length of the ship accounting for relativistic length contraction, L . 

Choose the relevant equation: L = L 0 = L 0 1 u 2 c 2 . L = L 0 = L 0 1 u 2 c 2 . Solution L = 50 m 1 ( 0.95 ) 2 c 2 c 2 = 50 m 1 ( 0.95 ) 2 = 16 m L = 50 m 1 ( 0.95 ) 2 c 2 c 2 = 50 m 1 ( 0.95 ) 2 = 16 m Discussion 

Calculations of can usually be simplified in this way when v is expressed as a percentage of c because the c 2 terms cancel. Be sure to also square the decimal representing the percentage before subtracting from 1. Note that the aliens will still see the length as L 0 because they are moving with the frame of reference that is the ship. 

Identify the variables, the knowns and unknowns, and the relevant equation. Understand clearly which length applies to your frame of reference and which applies to the ship s frame of reference, that is, which is proper length. Practice Problems 

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Use the Check Your Understanding questions to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify which and direct students to the relevant content. Section Summary Time dilates, length contracts, and momentum increases as an object approaches the speed of light. Energy and mass are interchangeable, according to the relationship E = mc 2. The laws of conservation of mass and energy are combined into the law of conservation of mass-energy. Key Equations Elapsed time t = t 0 t = t 0 Relativistic factor = 1 1 u 2 c 2 = 1 1 u 2 c 2 Length contraction L = L 0 L = L 0 Relativistic momentum p = m u p = m u Relativistic energy E = m c 2 E = m c 2 Rest energy E 0 = m c 2 . E 0 = m c 2 . Concept Items 

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People are fascinated by the possibility of traveling across the universe to discover intelligent life on other planets. To do this, we would have to travel enormous distances. Suppose we could somehow travel at up to 90% of the speed of light. The closest star is Alpha Centauri, which is 4.37 light years away. (A light year is the distance light travels in one year.) How long, from the point of view of people on Earth, would it take a space ship to travel to Alpha Centauri and back at 0.9 c ? How much would the astronauts on the spaceship have aged by the time they got back to Earth? Discuss the problems related to travel to stars that are 20 or 30 light years away. Assume travel speeds near the speed of light. Glossary binding energy the energy equivalent of the difference between the mass of a nucleus and the masses of its nucleons length contraction the shortening of an object as seen by an observer who is moving relative to the frame of reference of the object mass defect of the difference between the mass of a nucleus and the masses of its nucleons. proper length the length of an object within its own frame of reference, as opposed to the length observed by an observer moving relative to that frame of reference relativistic having to do with modern relativity, such as the effects that become significant only when an object is moving close enough to the speed of light for to be significantly greater than 1 relativistic energy the total energy of a moving object or particle E = m c 2 E = m c 2 , which includes both its rest energy mc 2 and its kinetic energy relativistic factor = 1 1 u 2 c 2 = 1 1 u 2 c 2 , where u is the velocity of a moving object and c is the speed of light relativistic momentum p = m u , where is the relativistic factor, m is rest mass of an object, and u is the velocity relative to an observer rest mass the mass of an object that is motionless with respect to its frame of reference time dilation the contraction of time as seen by an observer in a frame of reference that is moving relative to the observerPostulates of Special Relativity Postulates of Special Relativity Section Learning Objectives 

By the end of this section, you will be able to: Describe the experiments and scientific problems that led Albert Einstein to develop the special theory of relativity Understand the postulates on which the special theory of relativity was based 

The learning objectives in this section will help your students master the following TEKS: (2C) : Know that scientific theories are based on natural and physical phenomena and are capable of being tested by multiple independent researchers. Unlike hypotheses, scientific theories are well-established and well-tested explanations, but may be subject to change as new areas of science and new technologies are developed. (3D) : Explain the impacts of the scientific contributions of a variety of historical and contemporary scientists on scientific thought and society. (4F) : Identify and describe motion relative to different frames of reference. Section Key Terms ether frame of reference inertial reference frame general relativity postulate relativity simultaneity special relativity 

[AL] Discuss the history of the concept of the ether. Explain that it more of a philosophical concept that was important prior to the development of modern science. It arose from the belief that matter was continuous and vacuums were impossible. Ether was sometimes considered to be one of the elements. 

[BL] [OL] Mention that electromagnetic waves are unique among wave-propagated energy forms, in that they can travel across empty space. This was difficult to believe and caused scientists to doggedly hang onto the idea that there must be an ether permeating space. Ask students what they know about Einstein and dispel any misconceptions. Explain what thought experiments and postulates are. Scientific Experiments and Problems 

Relativity is not new. Way back around the year 1600, Galileo explained that motion is relative. Wherever you happen to be, it seems like you are at a fixed point and that everything moves with respect to you. Everyone else feels the same way. Motion is always measured with respect to a fixed point. This is called establishing a frame of reference . But the choice of the point is arbitrary, and all frames of reference are equally valid. A passenger in a moving car is not moving with respect to the driver, but they are both moving from the point of view of a person on the sidewalk waiting for a bus. They are moving even faster as seen by a person in a car coming toward them. It s all relative. 

[OL] [AL] Focus students thinking on the speed of light. Can the students think of anything else that has a maximum allowable value and is also a universal constant? Most constants are just numbers, like the value of pi. Most properties, such as mass and volume have no fixed upper limit. Why does speed have a limit? 

A frame of reference is not a complicated concept. It is just something you decide is a fixed point or group of connected points. It is completely up to you. For example, when you look up at celestial objects in the sky, you choose the Earth as your frame of reference and the sun, moon, etc. seem to move across the sky. 

Light is involved in the discussion of relativity because theories related to electromagnetism are inconsistent with Galileo s and Newton s explanation of relativity. The true nature of light was a hot topic of discussion and controversy in the late nineteenth century. At the time, it was not generally believed that light could travel across empty space. It was known to travel as waves, and all other types of energy that propagated as waves needed to travel though a material medium. It was believed that space was filled with an invisible medium that light waves traveled through. This imaginary (as it turned out) material was called the ether (also spelled aether). It was thought that everything moved through this mysterious fluid. In other words, ether was the one fixed frame of reference. The Michelson Morley experiment proved it was not. 

In 1887 Albert Michelson and Edward Morley designed the interferometer shown in [link] to measure the speed of Earth through the ether. A light beam is split into two perpendicular paths and then recombined. Recombining the waves produces an inference pattern, with a bright fringe at the locations where the two waves arrive in phase, that is, with the crests of both waves arriving together and the troughs arriving together. A dark fringe appears where the crest of one wave coincides with a trough of the other, so that the two cancel. If Earth is traveling through the ether as it orbits the sun, the peaks in one arm would take longer than in the other to reach the same location. The places where the two waves arrive in phase would change, and the interference pattern would shift. But, using the interferometer, there was no shift seen! This result led to two conclusions: that there is no ether and that the speed of light is the same regardless of the relative motion of source and observer. The Michelson Morley investigation has been called the most famous failed experiment in history. This is a diagram of the instrument used in the Michelson-Morley experiment. 

[BL] [OL] Explain the geometry of the Michelson Morley experiment. Explain why failure in this case was actually a success. Discuss how accepting unexpected results is an important ability for scientists. Ask students to memorize the value of the speed of light in m/s to three significant figures. 

To see what Michelson and Morley expected to find when they measured the speed of light in two directions, watch this animation . In the video, two people swimming in a lake are represented as an analogy to light beams leaving Earth as it moves through the ether (if there were any ether). The swimmers swim away from and back to a platform that is moving through the water. The swimmers swim in different directions with respect to the motion of the platform. Even though they swim equal distances at the same speed, the motion of the platform causes them to arrive at different times. 

[AL] Be sure students understand that this animation does not explain how light behaves. It shows what Michelson and Morley expected to observe. It may work best to just introduce the Michelson-Morley experiment briefly and then watch the animation. Einstein s Postulates 

The results described above left physicists with some puzzling and unsettling questions, such as: why doesn t light emitted by a fast moving object travel faster than light from a street lamp? A radical new theory was needed, and Albert Einstein, shown in [link] , was about to become everyone s favorite genius. Einstein began with two simple postulates based on the two things we have discussed so far in this chapter. The laws of physics are the same in all inertial reference frames. The speed of light is the same in all inertial reference frames and is not affected by the speed of its source. Albert Einstein (1879 1955) developed modern relativity and also made fundamental contributions to the foundations of quantum mechanics. (credit: The Library of Congress) 

The speed of light is given the symbol c and is equal to exactly 299,792,458 m/s. This is the speed of light in vacuum, that is, in the absence of air. For most purposes, we round this number off to 3.00 10 8 m/s 3.00 10 8 m/s . The term inertial reference frame simply refers to a frame of reference where all objects follow Newton s first law of motion: Objects at rest remain at rest, and objects in motion remain in motion at a constant velocity in a straight line, unless acted upon by an external force. The inside of a car moving along a road at constant velocity and the inside of a stationary house are inertial reference frames. 

[BL] Ask students to round off the value given for c to 3 significant figures and express in scientific notation. Stress the units of measurements. 

[OL] Explain the postulates carefully. Note that, although they both seem true they lead to problems with the classical mechanics of Newton. Explain the concept of reference frame and ask students to think of examples of reference frames that are moving relative to each other. Use vehicles and celestial bodies. Explain that the understanding of relative motion goes back hundreds of years and did not begin with relativity theory. 

[AL] Explain that it is the combination of these two postulates that leads to unusual results that will follow in the next section and that it is the combination of these postulates that forces us to abandon some aspects of Newtonian physics in some scenarios. 

Note that the very precise value for the speed of light only applies to light traveling through a vacuum and that in all transparent material media it is slower. The Speed of Light 

This lecture on light summarizes the most important facts about the speed of light. If you are interested, you can watch the whole video, but the parts relevant to this chapter are found between 3:25 and 5:10, which you find by running your cursor along the bottom of the video. 

Only the section from 3:25 to 5:10 minutes is completely relevant to an understanding of the speed of light. If students watch it just after the text above, they will be adequately prepared. 

[link] Measure the Speed of Light 

In this experiment, you will measure the speed of light using a microwave oven and a slice of bread. The waves generated by a microwave oven are not part of the visible spectrum, but they are still electromagnetic radiation, so they travel at the speed of light. If we know the wavelength, , and frequency, f , of a wave we can calculate its speed, v , using the equation v = f . You can measure the wavelength. You will find the frequency on a label on the back of a microwave oven. The wave in a microwave is a standing wave with areas of high and low intensity. The high intensity sections are one-half wavelength apart. High temperature: Very hot temperatures are encountered in this lab. These can cause burns. a microwave oven one slice of plain white bread a centimeter ruler a calculator Work with a partner. Turn off the revolving feature of the microwave oven or remove the wheels under the microwave dish that make it turn. It is important that the dish doesn t turn. Place the slice of bread on the dish, set the microwave on high, close the door, run the microwave for about 15 seconds. A row of brown or black marks should appear on the bread. Stop the microwave as soon as they appear. Measure the distance between two adjacent burn marks and multiply the result by 2. This is the wavelength. The frequency of the waves is written on the back of the microwave. Look for something like 2,450 MHz. Hz is the unit hertz, which means per second. The M represents mega, which stands for million, so multiply the number by 10 6 . Express the wavelength in meters and multiply it times the frequency. If you did everything correctly, you will get a number very close to the speed of light. Do not eat the bread. It is a general laboratory safety rule never to eat anything in the lab. 

This experiment could be demonstrated to the class if a microwave is available in the classroom. It might be better to let the students do the experiment at home so they can get more of a hands-on experience. Before the lab you might have them watch this video . 

To continue the discussion, you could tell them about how light is refracted when it changes speed as it passes from one medium to another. Because light speed in air is slower than in a vacuum, light is refracted as it enters Earth s atmosphere. 

This link takes you to a video demonstrating how to measure the speed of light using a microwave, a ruler, and a bar of chocolate. There is also an accompanying article with background information on measuring the speed of light. 

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[AL] This will be difficult to grasp completely for some students. The fact that the observers see different things is the result of the two postulates being true. If light speed is a constant and the two frames of reference are both valid, then simultaneity is not the same for all observers. Ask them to try the thought experiment in their own head to grasp what is being shown here. Sometimes students have fun sketching a cartoon that explains or demonstrates difficult concepts. They can then show the cartoon to the class and explain their reasoning. 

[OL] If students are struggling with this explanation of simultaneity, let them know that there will be an animation in the next section that should make it clearer. 

[OL] [BL] Point out that the relationship between special relativity and Newton s mechanics is an excellent example of how science advances. Explain that new theories rarely reverse old theories. It is more common that new theories extend and expand on old theories. Ask students if they can think of other examples from the history of science. 

Einstein s postulates were carefully chosen, and they both seemed very likely to be true. Einstein proceeded despite realizing that these two ideas taken together and applied to extreme conditions led to results that contradict Newtonian mechanics. He just took the ball and ran with it. 

In the traditional view, velocities are additive. If you are running at 3 m/s and you throw a ball forward at a speed of 10 m/s, the ball should have a net speed of 13 m/s. However, according to relativity theory, the speed of a moving light source is not added to the speed of the emitted light. 

In addition, Einstein s theory shows that if you were moving forward relative to Earth at nearly c (the speed of light) and could throw a ball forward at c , an observer at rest on the Earth would not see the ball moving at nearly twice the speed of light. The observer would see it moving at a speed that is still less than c . This result conforms to both of Einstein s postulates: The speed of light has a fixed maximum and neither reference frame is privileged. 

Consider how we measure elapsed time. If we use a stopwatch, for example, how do we know when to start and stop the watch? One method is to use the arrival of light from the event, such as observing a light turn green to start a drag race. The timing will be more accurate if some sort of electronic detection is used, avoiding human reaction times and other complications. 

Now suppose we use this method to measure the time interval between two flashes of light produced by flash lamps on a moving train. (See [link] ) Light arriving to observer A as seen by two different observers. 

A woman (observer A) is seated in the center of a rail car, with two flash lamps at opposite sides equidistant from her. Multiple light rays that are emitted from the flash lamps move towards observer A (as shown with arrows). A velocity vector arrow for the rail car is shown towards the right. A man (observer B) standing on the platform is facing her and also observes the flashes of light. 

Observer A moves with the lamps on the rail car as the rail car moves towards the right of observer B. Observer B receives the light flashes simultaneously, and sees the bulbs as both having flashed at the same time. However, he sees observer A receive the flash from the right first. Because the pulse from the right reaches her first, in her frame of reference she sees the bulbs as not having flashed simultaneously. Here, a relative velocity between observers affects whether two events at well-separated locations are observed to be simultaneous. Simultaneity , or whether different events occur at the same instant, depends on the frame of reference of the observer. Remember that velocity equals distance divided by time, so t = d/ v . If velocity appears to be different, then duration of time appears to be different. 

This illustrates the power of clear thinking. We might have guessed incorrectly that if light is emitted simultaneously, then two observers halfway between the sources would see the flashes simultaneously. But careful analysis shows this not to be the case. Einstein was brilliant at this type of thought experiment (in German, Gedankenexperiment ). He very carefully considered how an observation is made and disregarded what might seem obvious. The validity of thought experiments, of course, is determined by actual observation. The genius of Einstein is evidenced by the fact that experiments have repeatedly confirmed his theory of relativity. No experiments after that of Michelson and Morley were able to detect any ether medium. We will describe later how experiments also confirmed other predictions of special relativity , such as the distance between two objects and the time interval two events being different for two observers moving with respect to each other. 

In summary: Two events are defined to be simultaneous if an observer measures them as occurring at the same time (such as by receiving light from the events). Two events are not necessarily simultaneous to all observers. 

The discrepancies between Newtonian mechanics and relativity theory illustrate an important point about how science advances. Einstein s theory did not replace Newton s, but rather extended it. It is not unusual that a new theory must be developed to account for new information. In most cases, the new theory is built on the foundation of older theory. It is rare that old theories are completely replaced. 

In this chapter, you will learn about the theory of special relativity, but, as mentioned in the introduction, Einstein developed two relativity theories: special and general. [link] summarizes the differences between the two theories Comparing Special Relativity and General Relativity Special Relativity General Relativity Published in 1905 Final form published in 1916 A theory of space-time A theory of gravity Applies to observers moving at constant speed Applies to observers that are accelerating Most useful in the field of nuclear physics Most useful in the field of astrophysics Accepted quickly and put to practical use by nuclear physicists and quantum chemists Largely ignored until 1960 when new mathematical techniques made the theory more accessible and astronomers found some important applications Also note that the theory of general relativity includes the theory of special relativity. Calculating the Time it Takes Light to Travel a Given Distance 

The sun is 1.50 10 8 km from Earth. How long does it take light to travel from the sun to Earth in minutes and seconds? Strategy 

Identify knowns: 

Distance = 1.50 10 8 km 

Speed = 3.00 10 8 m/s 

Identify unknowns: 

Time 

Find the equation that relates knowns and unknowns: 

v = d t ; t = d v v = d t ; t = d v 

Be sure to use consistent units. Solution t = d v = ( 1.50 10 8 k m ) 10 3 m km 3.00 10 8 m s = 5.00 10 2 s t = d v = ( 1.50 10 8 k m ) 10 3 m km 3.00 10 8 m s = 5.00 10 2 s 500 s = 8 min and 20 s 500 s = 8 min and 20 s Discussion 

The answer is written as 5.00 10 2 rather than 500, in order to show that there are three significant figures. When astronomers witness an event on the sun, such as a sunspot, it actually happened minutes earlier. Compare 8 light minutes to the distance to stars, which are light years away. Any events on other stars happened years ago. 

Identify the three variables and choose the relevant equation. In physics, calculations are usually done using units of meters and seconds. Use scientific notation to keep track of significant figures. Practice Problems 

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[link] Check Your Understanding 

Use the Check Your Understanding questions to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify which and direct students to the relevant content. 

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[link] Section Summary One postulate of special relativity theory is that the laws of physics are the same in all inertial frames of reference. The other postulate is that the speed of light in a vacuum is the same in all inertial frames. Einstein showed that simultaneity (or lack of it) depends on the frame of reference of the observer. Key Equations Speed of light v = f v = f Constant value for the speed of light c = 3.00 10 8 m/s c = 3.00 10 8 m/s Concept Items 

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[link] Glossary ether scientists once believed there was a medium that carried light waves; eventually, experiments proved that ether does not exist frame of reference the point or collection of points arbitrarily chosen which motion is measured in relation to inertial reference frame a frame of reference where all objects follow Newton s first law of motion general relativity the theory proposed to explain gravity and acceleration postulate a statement that is assumed to be true for the purposes of reasoning in a scientific or mathematic argument relativity the explanation of how object move relative to one another simultaneity the property of events that occur at the same time special relativity the theory proposed to explain the consequences of requiring the speed of light and the laws of physics to be the same in all inertial framesIntroduction Introduction In this chapter you will learn about: Postulates of Special Relativity Consequences of Special Relativity class="summary" title="Section Summary" class="key-equations" title="Key Equations" class="concept" title="Concept Items" class="critical-thinking" title="Critical Thinking Items" class="problem" title="Problems" class="performance" title="Performance Task" class="multiple-choice" title="Multiple Choice" class="short-answer" title="Short Answer" class="extended-response" title="Extended Response" Special relativity explains why travel to other star systems, such as these in the Orion Nebula, is unlikely using our current level of technology. (credit: s58y, Flickr) 

Start a discussion that taps into the longing of humans to explore worlds beyond our planet. Is this basic human nature? Perhaps it is; humans have now been almost everywhere there is to go on this planet. Ask students why we haven t traveled to other star systems yet. Is it just a matter waiting a few years for technological advances, or is there a more daunting problem? If no one knows, tell them it all has to do with achievable speeds, and use this as a lead-in to Einstein s postulate related to the speed of light. 

Have you ever dreamed of travelling to other planets in faraway star systems? The trip might seem possible by traveling fast enough, but you will read in this chapter why it is not. In 1905 Albert Einstein developed the theory of special relativity . Einstein developed the theory to help explain inconsistencies between the equations describing electromagnetism and Newtonian mechanics and to explain why the ether didn t exist. This theory explains the limit on an object s speed among other implications. 

Relativity is the study of how different observers moving with respect to each other measure the same events. Galileo and Newton developed the first correct version of classical relativity. Einstein developed the modern theory of relativity. Modern relativity is divided into two parts. Special relativity deals with observers moving at constant velocity. General relativity deals with observers who are moving at constant acceleration. Einstein s theories of relativity made revolutionary predictions. Most importantly, his predictions have been verified by experiments. 

In this chapter you learn how experiments and puzzling contradictions in existing theories led to the development of the theory of special relativity. You will also learn the simple postulates on which the theory was based; a postulate is a statement that is assumed to be true for the purposes of reasoning in a scientific or mathematic argument. 

Before students begin this chapter, it is useful to review these concepts: Using significant figures in calculations Demonstrate how use the proper number of significant figures when adding and multiplying. Using scientific notation in calculations Demonstrate how use the proper scientific notation and operations in scientific notation (e.g. addition/subtraction, multiplication/division). Converting units Demonstrate how to convert from km/h to m/s. Calculating average Demonstrate how to average two numbers by dividing their sum by 2. Review the difference between mass and weight. Commonly used terms Explain that constant means "unchanging." Constant speed refers to speed that is not changing. Explain that initial means "starting. Initial time is the time at which the action of a problem begins. Explain that an object that is not moving is often described in physics as being at rest. 

To reinforce this description, and to open the door for a discussion of frame of reference, take an object, place it in front of the class, and ask someone to describe its motion. Students will likely respond that the object is at rest. Explain that this correct, but it is not the only correct answer. Help students to understand that the object is sitting still, but also moving at a high rate of speed as the earth rotates, orbits the sun, etc. It all depends on how you define the frame of reference. 

Initiate a discussion aimed at making relativity theory less intimidating. Dispel the misconception that Only three people in the world understand Einstein s theories. Stories like this come about because Einstein s second relativity theory, called general relativity, was more difficult to understand. In this chapter we will only learn about special relativity.Introduction Introduction class="introduction" In this chapter you will learn about: Physics: Definitions and Applications The Scientific Methods The Language of Physics: Physical Quantities and Units class="summary" title="Section Summary" class="key-equations" title="Key Equations" class="concept" title="Concept Items" class="critical-thinking" title="Critical Thinking Items" class="problem" title="Problems" class="performance" title="Performance Task" class="multiple-choice" title="Multiple Choice" class="short-answer" title="Short Answer" class="extended-response" title="Extended Response" 

Before students begin this chapter, it is useful to review these concepts: The definition of the atom and subatomic particles (electron, proton, neutron) Metric units Using significant figures in calculations Galaxies, such as the Andromeda galaxy pictured here, are immense in size. The small blue spots in this photo are also galaxies. The same physical laws apply to objects as large as galaxies or objects as small as atoms. The laws of physics are, therefore, surprisingly few in number. (credit: NASA, JPL-Caltech, P. Barmby, Harvard-Smithsonian Center for Astrophysics). 

The photo of the Andromeda galaxy and its subsequent mention in this chapter is meant to show students that the same laws of physics apply to extremely large systems, such as a galaxy, as apply also to smaller systems in our universe. The same laws that govern the movement of the stars within the Andromeda galaxy also explain the gravitational forces on Earth that all humans experience and interact with every second of their lives. 

Take a look at the image above of the Andromeda Galaxy ( [link] ), which contains billions of stars. This galaxy is the nearest one to our own galaxy (the Milky Way) but is still a staggering 2.5 million light years from Earth. (A light year is a measurement of the distance light travels in a year.) Yet, the primary force that affects the movement of stars within Andromeda is the same force that we contend with here on Earth namely, gravity. 

You may soon realize that physics plays a much larger role in your life than you thought. This section introduces you to the realm of physics, and discusses applications of physics in other disciplines of study. It also describes the methods by which science is done, and how scientists communicate their results to each other.Physics: Definitions and Applications Physics: Definitions and Applications Section Learning Objectives 

By the end of this section, you will be able to: Describe the definition, aims, and branches of physics Describe and distinguish classical physics from modern physics and describe the importance of relativity, quantum mechanics, and relativistic quantum mechanics in modern physics Describe how aspects of physics are used in other sciences (e.g. biology, chemistry, geology, etc.) as well as in everyday technology 

The learning objectives in this section will help your students master the following TEKS: (2A) : Know the definition of science and understand that it has limitations, as specified in subsection (b)(2) of this section. (3A) : In all fields of science, analyze, evaluate, and critique scientific explanations by using empirical evidence, logical reasoning, and experimental and observational testing, including examining all sides of scientific evidence of those scientific explanations, so as to encourage critical thinking by the student. (3B) : Communicate and apply scientific information extracted from various sources such as current events, news reports, published journal articles, and marketing materials. (3C) : Draw inferences based on data related to promotional materials for products and services. (3D) : Explain the impacts of the scientific contributions of a variety of historical and contemporary scientists on scientific thought and society. Section Key Terms atom classical physics modern physics physics quantum mechanics theory of relativity 

To help meet the multimodal needs of classrooms today, OpenStax Tutor s Physics provides Teacher Support tips for on-level [OL], below-level [BL], and above-level [AL] students. 

[OL] Pre-assessment for this section could involve asking students the definition of matter, atoms, electrons, protons, neutrons, subatomic particles, and energy. Students could also be asked to name some prominent classical and modern physicists and to describe some of their work in general terms. 

[OL] The introduction and opening picture are meant to show students that the physical laws governing their own everyday surroundings also govern the movement of stars in a galaxy. Teachers could ask students how gravity affects life on Earth. Students will likely mention how gravity keeps us on Earth s surface. Prompt them, if necessary, to also think about Earth s orbital motion around the sun. This motion allows Earth bask in the warmth of the sun s light. Without the Sun s gravity, Earth would continue moving in a straight line and move away from the sun, while people would float off of Earth s surface. The orbit of the moon could also be brought into this discussion, because Earth s gravity keeps the moon moving around Earth rather than continuing in a straight path. What Physics Is 

Think about all of the technological devices that you use on a regular basis. Computers, wireless internet, smart phones, tablets, global positioning system (GPS), MP3 players, and satellite radio might come to mind. Next, think about the most exciting modern technologies that you have heard about in the news, such as trains that levitate above their tracks, invisibility cloaks that bend light around them, and microscopic robots that fight cancer cells in our bodies. All of these groundbreaking advancements rely on the principles of physics . 

Physics is the science aimed at describing the fundamental aspects of our universe, such as what things are in it, what properties of those things are noticeable, and what processes those things or their properties undergo. In simpler terms, physics attempts to describe the basic mechanisms that make our universe behave the way it does. For example, consider a smart phone ( [link] ). Physics describes how electric current interacts with the various circuits inside the device. This knowledge helps engineers select the appropriate materials and circuit layout when building the smart phone. Next, consider a GPS. Physics describes the relationship between the speed of an object, the distance over which it travels, and the time it takes to travel that distance. When you use a GPS device in a vehicle, it utilizes these physics relationships to determine the travel time from one location to another. Physics describes the way that electric charge flows through the circuits of this device. Engineers use their knowledge of physics to construct a smart phone with features that consumers will enjoy, such as a GPS function. GPS uses physics equations to determine the driving time between two locations on a map. (credit: @gletham GIS, Social, Mobile Tech Images) 

[AL] Ask what parts of a cell phone should contain conducting materials (wires, circuit boards, etc.) versus insulating materials (e.g., places where electrical insulation keeps humans from touching electrical circuits inside the phone). 

[AL] You can delve into GPS usage at this point by defining velocity = distance/time, discussing triangulation, and/or discussing line of sight. 

As our technology evolved over the centuries, physics expanded into many branches. Ancient peoples could only study things that they could see with the naked eye or otherwise experience without the aid of scientific equipment. This included the study of kinematics , which is the study of moving objects. For example, ancient people often studied the apparent motion of objects in the sky, such as the Sun, Moon, and stars. This is evident in the construction of prehistoric astronomical observatories, such as Stonehenge in England (shown in [link] ). 

Ancient people also studied statics and dynamics , which focus on how objects start moving, stop moving, and change speed and direction in response to forces that push or pull on the objects. This early interest in kinematics and dynamics allowed humans to invent simple machines, such as the lever, the pulley, the ramp, and the wheel. These simple machines were gradually combined and integrated to produce more complicated machines, such as wagons and cranes. Machines allowed humans to gradually do more work more effectively in less time, allowing them to create larger and more complicated buildings and structures, many of which still exist today from ancient times. Stonehenge is a monument located in England that was built between 3000 and 2000 BCE. It functions as an ancient astronomical observatory, with certain rocks in the monument aligning with the position of the Sun during the summer and winter solstices. Other rocks align with the rising and setting of the Moon during certain days of the year. (credit: Citypeek, Wikimedia Commons) 

As technology advanced, the branches of physics diversified even more. These include branches such as acoustics , the study of sound, and optics , the study of the light. The invention of the telescope by Hans Lippershey, a German spectacle maker, in 1608, led to huge breakthroughs in astronomy , the study of objects or phenomena in space. One year later, in 1609, Galileo Galilei began the first studies of the solar system and the universe using a telescope. During the Renaissance era, Isaac Newton used observations made by Galileo to construct his three laws of motion. These laws were the standard for studying kinematics and dynamics even today. 

Another major branch of physics is thermodynamics , which includes the study of thermal energy and the transfer of heat. James Prescott Joule, an English physicist, studied the nature of heat and its relationship to work. Joule s work helped lay the foundation for the first of three laws of thermodynamics that describe how energy in our universe is transferred from one object to another or transformed from one form to another. Studies in thermodynamics were motivated by the need to make engines more efficient, keep people safe from the elements, and preserve food. 

The eighteenth and nineteenth centuries also saw great strides in the study of electricity and magnetism. Electricity involves the study of electric charges and their movements. Magnetism had long ago been noticed as an attractive force between a magnetized object and a metal like iron, or between the opposite poles (North and South) of two magnetized objects. In 1820, Danish physicist Hans Christian Oersted showed that electric currents create magnetic fields. In 1831, English inventor Michael Faraday showed that moving a wire through a magnetic field could induce an electric current. These studies led to the inventions of the electric motor and electric generator, which revolutionized human life by bringing electricity and magnetism into our machines. 

The end of the 19 th century saw the discovery of radioactive substances by the French scientists Marie and Pierre Curie. Nuclear physics involves studying the nuclei of atoms , the source of nuclear radiation. In the 20 th century, the study of nuclear physics eventually led to the ability to split the nucleus of an atom, a process called nuclear fission. This process is the basis for nuclear power plants and nuclear weapons. Also, the field of quantum mechanics , which involves the mechanics of atoms and molecules, saw great strides during the 20 th century as our understanding of atoms and subatomic particles increased (see below). 

Early in the 20th century, Albert Einstein revolutionized several branches of physics, especially relativity . Relativity revolutionized our understanding of motion and the universe in general as described further in this chapter. Now, in the 21 st century, physicists continue to study these and many other branches of physics. 

By studying the most important topics in physics, you will gain analytical abilities that will enable you to apply physics far beyond the scope of what can be included in a single book. These analytical skills will help you to excel academically, and they will also help you to think critically in any career you choose to pursue. Physics: Past and Present 

The word physics is thought to come from the Greek word phusis, meaning nature. The study of nature later came to be called natural philosophy. From ancient times through the Renaissance, natural philosophy encompassed many fields, including astronomy, biology, chemistry, mathematics, and medicine. Over the last few centuries, the growth of scientific knowledge has resulted in ever-increasing specialization and branching of natural philosophy into separate fields, with physics retaining the most basic facets. Physics, as it developed from the Renaissance to the end of the 19th century, is called classical physics . Revolutionary discoveries starting at the beginning of the 20th century transformed physics from classical physics to modern physics . 

[BL] [EL]English learners may need philosophy and classical defined during this section. Relate the definition of classical physics to the use of the word classical in a context that is probably more familiar to students, such as classic films. 

Classical physics is not an exact description of the universe, but it is an excellent approximation under the following conditions: 1) matter must be moving at speeds less than about 1% of the speed of light, 2) the objects dealt with must be large enough to be seen with the naked eye, and 3) only weak gravity, such as that generated by Earth, can be involved. Very small objects, such as atoms and molecules, cannot be adequately explained by classical physics. These three conditions apply to almost all of everyday experience. As a result, most aspects of classical physics should make sense on an intuitive level. 

[OL] To better relate to student experience, express the speed of light in units used while driving a car, for example, 1.080 million km/h or 671 million miles per hour. Relate this to the approximately 8 minute trip that light takes to travel 150 billion kilometers (93 billion miles) from the Sun to the Earth. 

Many laws of classical physics have been modified during the twentieth century, resulting in revolutionary changes in technology, society, and our view of the universe. This new physics is called physics. As a result, many aspects of modern physics, which occur outside of the range of our everyday experience, may seem bizarre or unbelievable. So why is most of this textbook devoted to classical physics? There are two main reasons. The first is that knowledge of classical physics is necessary to understand modern physics. The second reason is that classical physics still gives an accurate description of the universe under a wide range of everyday circumstances. 

Modern physics includes two revolutionary theories: relativity and quantum mechanics. These theories deal with the very fast and the very small, respectively. The theory of relativity was developed by Albert Einstein in 1905. By examining how two observers moving relative to each other would see the same phenomena, Einstein devised radical new ideas about time and space. He came to the startling conclusion that the measured length of an object travelling at high speeds (greater than about 1% of the speed of light) is shorter than the same object measured at rest. Perhaps even more bizarre is the idea the time for the same process to occur is different depending on the motion of the observer. Time passes more slowly for an object travelling at high speeds. A trip to the nearest star system, Alpha Centauri, might take an astronaut 4.5 Earth years if the ship travels near the speed of light. However, because time is slowed at higher speeds, the astronaut would age only 0.5 years during the trip. Einstein s ideas of relativity were accepted after they were confirmed by numerous experiments. 

Gravity, the force that holds us to Earth, can also affect time and space. For example, time passes more slowly on Earth s surface than for objects farther from the surface, such as a satellite in orbit. The very accurate clocks on global positioning satellites have to correct for this. They slowly keep getting ahead of clocks at Earth s surface. This is called time dilation, and it occurs because gravity, in essence, slows down time. 

[AL] By saying that time passes more slowly at near-light speeds or high gravity, it is important to mention that people in both locations perceive the second as the same length of time. 

Large objects, like Earth, have strong enough gravity to distort space. To visualize this idea, think about a bowling ball placed on a trampoline. The bowling ball depresses or curves the surface of the trampoline. If you rolled a marble across the trampoline, it would follow the surface of the trampoline, roll into the depression caused by the bowling ball, and hit the ball. Similarly, the Earth curves space around it in the shape of a funnel. These curves in space due to the Earth cause objects to be attracted to Earth (i.e., gravity). 

Because of the way gravity affects space and time, Einstein stated that gravity affects the space-time continuum, as illustrated in [link] . This is why time proceeds more slowly at Earth s surface than in orbit. In black holes, whose gravity is hundreds of times that of Earth, time passes so slowly that it would appear to a far-away observer to have stopped! Einstein s theory of relativity describes space and time as an interweaved mesh. Large objects, such as a planet, distort space, causing objects to fall in toward the planet due to the action of gravity. Large objects also distort time, causing time to proceed at a slower rate near the surface of Earth compared with the area outside of the distorted region of space-time. 

[AL] Black holes are much more dense and massive than Earth. The greater an object s mass, the stronger the gravitational field it produces, and the more that gravity slows down time. 

In summary, relativity says that in describing the universe, it is important to realize that time, space, speed and gravity are not absolute. Instead, they can appear different to different observers. Einstein s ability to reason out relativity is even more amazing because we cannot see the effects of relativity in our everyday lives. 

Quantum mechanics is the second major theory of modern physics. Quantum mechanics deals with the very small, namely, the subatomic particles that make up atoms. Atoms ( [link] ) are the smallest units of elements. However, atoms themselves are constructed of even smaller subatomic particles, such as protons, neutrons and electrons. Quantum mechanics strives to describe the properties and behavior of these and other subatomic particles. Often, these particles do not behave in the ways expected by classical physics. One reason for this is that they are small enough to travel at great speeds, near the speed of light, for example. Using a scanning tunneling microscope (STM), scientists can see the individual atoms that compose this sheet of gold. (credit: Erwinrossen) 

[OL] [AL] Assess prior knowledge of subatomic particles by asking students if they have heard of protons, electrons, neutrons, as well as quarks, Higgs-Boson particles, and so on. 

[AL] Scanning electron microscopes generate highly-detailed surface views of objects such as that shown in [link] . They scan the object s surface with beams of electrons to detect the object s microscopic topography. 

At particle colliders ( [link] ), such as the Large Hadron Collider on the France-Swiss border, particle physicists can make subatomic particles travel at very high speeds within a 27 km (17 mi) long superconducting tunnel. They can then study the properties of the particles at high speeds, as well as collide them with each other to see how they exchange energy. This has led to many intriguing discoveries such as the Higgs-Boson particle, which gives matter the property of mass, and antimatter, which causes a huge energy release when it comes in contact with matter. Particle colliders such as the Large Hadron Collider in Switzerland or Fermilab in the United States (pictured here), have long tunnels that allows subatomic particles to be accelerated to near light speed (credit: Andrius.v ) 

Physicists are currently trying to unify the two theories of modern physics, relativity and quantum mechanics into a single, comprehensive theory called relativistic quantum mechanics. Relating the behavior of subatomic particles to gravity, time, and space will allow us to explain how the universe works in a much more comprehensive way. Application of Physics 

You need not be a scientist to use physics. On the contrary, knowledge of physics is useful in everyday situations as well as in nonscientific professions. For example, physics can help you understand why you shouldn t put metal in the microwave, why a black car radiator helps remove heat in a car engine, and why a white roof helps keep the inside of a house cool. (See [link] ) The operation of a car s ignition system, as well as the transmission of electrical signals through our nervous system, are much easier to understand when you think about them in terms of the basic physics of electricity. Microwave ovens use electromagnetic waves to heat food. (credit: MoneyBlogNewz) 

[AL] It is hazardous to put metal in the microwave because metal reflects microwaves, which, when free to bounce around the oven, can damage the oven. Also, the metal in the microwave oven gets very hot and begins generating an electrical field. This electrical field ionizes the air surrounding the metal, creating sparks. 

Physics is the foundation of many important scientific disciplines. For example, chemistry deals with the interactions of atoms and molecules. Not surprisingly, chemistry is rooted in atomic and molecular physics. Most branches of engineering are also applied physics. In architecture, physics is at the heart of determining structural stability, acoustics, heating, lighting, and cooling for buildings. Parts of geology, the study of the nonliving parts of Earth, rely heavily on physics, including radioactive dating, earthquake analysis, and heat transfer across Earth s surface. Indeed, some disciplines, such as biophysics and geophysics, are hybrids of physics and other disciplines. 

[BL] [EL]Students may need acoustics to be explained as the properties of a room or structure that determine how sound is transmitted within it. 

Physics also has many applications in biology, the study of life. For example, physics describes how cells can protect themselves using their cell walls and cell membranes. It also describes the chemical processes that power the human body. Physics is involved in medical diagnostics, such as x-rays, magnetic resonance imaging (MRI), and ultrasonic blood flow measurements ( [link] and [link] ). Medical therapy sometimes directly involves physics, such as in using radiation to treat cancer. Physics can also explain what we perceive with our senses, such as how the ears detect sound or the eye detects color. Magnetic resonance imaging (MRI) also uses electromagnetic waves to yield an image of the brain, from which the exact location of tumors can be determined. (credit: Rashmi Chawla, Daniel Smith, and Paul E. Marik) Physics, chemistry, and biology help describe the properties of cell walls in plant cells, such as the onion cells seen here. (credit: Umberto Salvagnin) 

[BL] Cell membranes (found in the cells of all organisms) control the transport of materials into and out of a cell. Cell walls (found in plant cells, fungus cells, bacteria, and plant-like microbes) mainly provide structure and support. 

[AL] X-rays easily penetrate skin and soft tissues but are absorbed to a far greater extent by bone. This produces an image where bones within the body are clearly visible while soft tissue is not. MRI scans for the magnetic properties of atoms within the body, allowing the solid versus empty areas within the body to be visualized. Ultrasonic blood flow measurements use sound waves and the Doppler effect to measure blood flow speed and volume. The Physics of Landing on a Comet 

On November 12, 2014, the European Space Agency s Rosetta spacecraft (shown in [link] ) became the first ever to reach and orbit a comet. Shortly after, Rosetta s rover, Philae, landed on the comet, representing the first time humans have ever landed a space probe on a comet. The Rosetta spacecraft, with its large and revolutionary solar panels, carried the Philae lander to a comet. The lander then detached and landed on the comet s surface. (Photo Credits: European Space Agency) 

The comet Rosetta landed on, named 67P/Churyumov-Gerasimenko, after traveling 6.4 billion kilometers starting from its launch on Earth. The comet, itself, is only 4 km wide. Physics was needed to successfully plot the course to reach such a small, distant, and rapidly moving target. Rosetta s path to the comet was not straight forward. The probe first had to travel to Mars so that Mars s gravity could accelerate it and divert it in the exact direction of the comet. 

This was not the first time humans used gravity to power our spaceships, however. Voyager 2, a space probe launched in 1977, used the gravity of Saturn to slingshot over to Uranus and Neptune (illustrated in [link] ), providing the first pictures ever taken of these planets. Now, almost 40 years after its launch, Voyager 2 is at the very edge of our solar system and is about to enter interstellar space. Its sister ship, Voyager 1 (illustrated in [link] ), which was also launched in 1977, is already there. 

To listen to the sounds of interstellar space or see images that have been transmitted back from the Voyager I or to learn more about the Voyager mission, visit the Voyager s Mission website . a) Voyager 2, launched in 1977, used the gravity of Saturn to slingshot over to Uranus and Neptune. Photo credit: NASA b) A rendering of Voyager 1, the first space probe to ever leave our solar system and enter interstellar space. Photo credit: NASA 

Both Voyagers have electrical power generators based on the decay of radioisotopes. These generators have served them for almost 40 years. Rosetta, on the other hand, is solar-powered. In fact, Rosetta became the first space probe to travel beyond the asteroid belt by relying only on solar cells for power generation. 

At 800 million kilometers from the Sun, Rosetta receives sunlight that is only 4% as strong as on Earth. In addition, it is very cold in space. Therefore, a lot of physics went into developing Rosetta s low-intensity low-temperature solar cells. 

In this sense, the Rosetta project nicely shows the huge range of topics encompassed by physics: from modeling the movement of gigantic planets over huge distances within our solar systems, to learning how to generate electric power from low-intensity light. Physics is, by far, the broadest field of science. 

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This passage describes the physics behind getting the Rosetta and Voyager probes across the solar system using gravitational sling shots. In addition, the physics behind the power systems of these probes is compared. This is meant to reinforce how physics applies over wide ranges, from the immense distances in our universe to the tiny sizes of subatomic particles. 

Answers to the Grasp Check may vary. A sample answer: You would have to how the target planet moves to know when to launch the probe so it actually reaches the planet. You would also need to know and account for the effects of gravity from other planets during the path followed during its journey. 

In summary, physics studies many of the most basic aspects of science. A knowledge of physics is, therefore, necessary to understand all other sciences. This is because physics explains the most basic ways in which our universe works. However, it is not necessary to formally study all applications of physics. A knowledge of the basic laws of physics will be most useful to you, so that you can use them to solve some everyday problems. In this way, the study of physics can improve your problem-solving skills. Check Your Understanding 

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Use the Check Your Understanding questions to assess students mastery of the sections learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify the source of the problem and direct students to the relevant content. Section Summary Physics is the most fundamental of the sciences, concerning itself with energy, matter, space and time, and their interactions. Modern physics involves the theory of relativity, which describes how time, space and gravity are not constant in our universe can be different for different observers, and quantum mechanics, which describes the behavior of subatomic particles. Physics is the basis for all other sciences, such as chemistry, biology and geology, because physics describes the fundamental way in which the universe functions. Concept Items 

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[link] Glossary atom smallest and most basic units of matter classical physics physics, as it developed from the Renaissance to the end of the nineteenth century modern physics physics as developed from the twentieth century to the present, involving the theories of relativity and quantum mechanics physics science aimed at describing the fundamental aspects of our universe, namely: energy, matter, space, motion, and time quantum mechanics major theory of modern physics which describes the properties and nature of atoms and their subatomic particles theory of relativity theory constructed by Albert Einstein which describes how space, time and energy are different for different observers in relative motionInclined Planes Inclined Planes Section Learning Objectives 

By the end of this section, you will be able to: Distinguish between static friction and kinetic friction Solve problems involving inclined planes 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in two dimensions for a variety of situations. The student is expected to: (D) : calculate the effect of forces on objects, including the law of inertia, the relationship between force and acceleration, and the nature of force pairs between objects Section Key Terms kinetic friction static friction Static Friction and Kinetic Friction 

Recall from the previous chapter that friction is a force that opposes motion, and is around us all the time. Friction allows us to move (which you have discovered if you have ever tried to walk on ice). 

There are different types of friction kinetic and static. Kinetic friction acts on an object in motion, while static friction acts on an object or system at rest. The maximum static friction is usually greater than the kinetic friction between the objects. 

[BL] [OL] Review the concept of friction. 

[AL] Start a discussion about the two kinds of friction: static and kinetic. Ask students which one they think would be greater for two given surfaces. Explain the concept of coefficient of friction and what the number would imply in practical terms. Look at the table of static and kinetic friction and ask students to guess which other systems would have higher or lower coefficients. 

Imagine, for example, trying to slide a heavy crate across a concrete floor. You may push harder and harder on the crate and not move it at all. This means that the static friction responds to what you do it increases to be equal to and in the opposite direction of your push. But if you finally push hard enough, the crate seems to slip suddenly and starts to move. Once in motion, it is easier to keep it in motion than it was to get it started because the kinetic friction force is less than the static friction force. If you were to add mass to the crate, (for example, by placing a box on top of it) you would need to push even harder to get it started and also to keep it moving. If, on the other hand, you oiled the concrete you would find it easier to get the crate started and keep it going. 

[link] shows how friction occurs at the interface between two objects. Magnifying these surfaces shows that they are rough on the microscopic level. So when you push to get an object moving (in this case, a crate), you must raise the object until it can skip along with just the tips of the surface hitting, break off the points, or do both. The harder the surfaces are pushed together (such as if another box is placed on the crate), the more force is needed to move them. Frictional forces, such as f , always oppose motion or attempted motion between objects in contact. Friction arises in part because of the roughness of the surfaces in contact, as seen in the expanded view. 

The magnitude of the frictional force has two forms: one for static friction, the other for kinetic friction. When there is no motion between the objects, the magnitude of static friction f s is f s s N s f s s N s 

where s s is the coefficient of static friction and N is the magnitude of the normal force. (Recall that the normal force opposes the force of gravity and acts perpendicular to the surface in this example, but not always). 

Since the symbol means less than or equal to, this equation says that static friction can have a maximum value of s N . s N . That is, f s (max) = s N f s (max) = s N 

Static friction is a responsive force that increases to be equal and opposite to whatever force is exerted, up to its maximum limit. Once the applied force exceeds f s(max), the object will move. Once an object is moving, the magnitude of kinetic friction f k is given by f k = k N f k = k N 

where k k is the coefficient of kinetic friction. 

Friction varies from surface to surface because different substances are rougher than others. [link] compares values of static and kinetic friction for different surfaces. The coefficient of the friction depends on the two surfaces that are in contact. Coefficients of Static and Kinetic Friction System Static Friction s s Kinetic Friction k k Rubber on dry concrete 1.0 0.7 Rubber on wet concrete 0.7 0.5 Wood on wood 0.5 0.3 Waxed wood on wet snow 0.14 0.1 Metal on wood 0.5 0.3 Steel on steel (dry) 0.6 0.3 Steel on steel (oiled) 0.05 0.03 Teflon on steel 0.04 0.04 Bone lubricated by synovial fluid 0.016 0.015 Shoes on wood 0.9 0.7 Shoes on ice 0.1 0.05 Ice on ice 0.1 0.03 Steel on ice 0.4 0.02 

Since the direction of friction is always opposite to the direction of motion, friction runs parallel to the surface between objects and perpendicular to the normal force. For example, if the crate you try to push (with a force parallel to the floor) has a mass of 100 kg, then the normal force would be equal to its weight W = m g = ( 100 kg ) ( 9.80 m/s 2 ) = 980 N , W = m g = ( 100 kg ) ( 9.80 m/s 2 ) = 980 N , 

perpendicular to the floor. If the coefficient of static friction is 0.45, you would have to exert a force parallel to the floor greater than f s (max) = s N = ( 0.45 ) ( 980 N) = 440 N f s (max) = s N = ( 0.45 ) ( 980 N) = 440 N 

to move the crate. Once there is motion, friction is less and the coefficient of kinetic friction might be 0.30, so that a force of only 290 N f k = k N = ( 0.30 ) ( 980 N) = 290 N f k = k N = ( 0.30 ) ( 980 N) = 290 N 

would keep it moving at a constant speed. If the floor were lubricated, both coefficients would be much smaller than they would be without lubrication. The coefficient of friction is unitless and is a number usually between 0 and 1.0. Working with Inclined Planes 

We discussed previously that when an object rests on a horizontal surface, there is a normal force supporting it equal in magnitude to its weight. Up until now, we dealt only with normal force in one dimension, with gravity and normal force acting perpendicular to the surface in opposing directions (gravity downward, and normal force upward). Now that you have the skills to work with forces in two dimensions, we can explore what happens to weight and the normal force on a tilted surface such as an inclined plane. For inclined plane problems, it is easier breaking down the forces into their components if we rotate the coordinate system, as illustrated in [link] . The first step when setting up the problem is to break down the force of weight into components. The diagram shows perpendicular and horizontal components of weight on an inclined plane. 

[BL] Review the concepts of mass, weight, gravitation and normal force. 

[OL] Review vectors and components of vectors. 

When an object rests on an incline that makes an angle with the horizontal, the force of gravity acting on the object is divided into two components: a force acting perpendicular to the plane, w w , and a force acting parallel to the plane, w | | w | | . The perpendicular force of weight, w w , is typically equal in magnitude and opposite in direction to the normal force, N . N . The force acting parallel to the plane, w | | w | | , causes the object to accelerate down the incline. The force of friction, f f , opposes the motion of the object, so it acts upward along the plane. 

It is important to be careful when resolving the weight of the object into components. If the angle of the incline is at an angle to the horizontal, then the magnitudes of the weight components are w | | = w s i n ( ) = m g s i n ( ) and w | | = w s i n ( ) = m g s i n ( ) and w = w c o s ( ) = m g c o s ( ) w = w c o s ( ) = m g c o s ( ) 

Instead of memorizing these equations, it is helpful to be able to determine them from reason. To do this, draw the right triangle formed by the three weight vectors. Notice that the angle of the incline is the same as the angle formed between w w and w w . Knowing this property, you can use trigonometry to determine the magnitude of the weight components: c o s ( ) = w w w = w c o s ( ) = m g c o s ( ) c o s ( ) = w w w = w c o s ( ) = m g c o s ( ) s i n ( ) = w | | w w | | = w s i n ( ) = m g s i n ( ) s i n ( ) = w | | w w | | = w s i n ( ) = m g s i n ( ) 

[BL] [OL] [AL] Experiment with sliding different objects on inclined planes to understand static and kinetic friction. Which objects need a larger angle to slide down? What does this say about the coefficients of friction of those systems? Is a greater force required to start the motion of an object than to keep it in motion? What does this say about static and kinetic friction? When does an object slide down at constant velocity? What does this say about friction and normal force? Inclined Plane Force Components 

This video shows how the weight of an object on an inclined plane is broken down into components perpendicular and parallel to the surface of the plane. It explains the geometry for finding the angle in more detail. 

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Normal force is represented by the variable N . N . This should not be confused with the symbol for the newton, which is also represented by the letter N. It is important to tell apart these symbols, especially since the units for normal force ( N N ) happen to be newtons (N). For example, the normal force, N N , that the floor exerts on a chair might be N = 100 N . N = 100 N . One important difference is that normal force is a vector, while the newton is simply a unit. Be careful not to confuse these letters in your calculations! 

To review, the process for solving inclined plane problems is as follows: Draw a sketch of the problem. Identify known and unknown quantities, and identify the system of interest. Draw a free-body diagram (which is a sketch showing all of the forces acting on an object) with the coordinate system rotated at the same angle as the inclined plane. Resolve the vectors into horizontal and vertical components and draw them on the free-body diagram. Write Newton s second law in the horizontal and vertical directions and add the forces acting on the object. If the object does not accelerate in a particular direction (for example, the x -direction) then F net x = 0. If the object does accelerate in that direction, F net x = m a . Check your answer. Is the answer reasonable? Are the units correct? Finding the Coefficient of Kinetic Friction on an Inclined Plane 

A skier, illustrated in [link] (a) , with a mass of 62 kg is sliding down a snowy slope at an angle of 25 degrees. Find the coefficient of kinetic friction for the skier if friction is known to be 45.0 N. Use the diagram to help find the coefficient of kinetic friction for the skier. Strategy 

The magnitude of kinetic friction was given as 45.0 N. Kinetic friction is related to the normal force N as f k = k N f k = k N . Therefore, we can find the coefficient of kinetic friction by first finding the normal force of the skier on a slope. The normal force is always perpendicular to the surface, and since there is no motion perpendicular to the surface, the normal force should equal the component of the skier s weight perpendicular to the slope. 

That is, N = w = w cos ( 25 ) = m g cos ( 25 ) N = w = w cos ( 25 ) = m g cos ( 25 ) 

Substituting this into our expression for kinetic friction, we get f k = k m g cos 25 , f k = k m g cos 25 , 

which can now be solved for the coefficient of kinetic friction k . Solution 

Solving for k k gives 

k = f k w cos 25 = f k m g cos 25 k = f k w cos 25 = f k m g cos 25 

Substituting known values on the right-hand side of the equation, 

k = 45.0 N ( 62 kg)(9 .80 m/s 2 ) ( 0.906 ) = 0.082 k = 45.0 N ( 62 kg)(9 .80 m/s 2 ) ( 0.906 ) = 0.082 Discussion 

This result is a little smaller than the coefficient listed in Table 5.1 for waxed wood on snow, but it is still reasonable since values of the coefficients of friction can vary greatly. In situations like this, where an object of mass m slides down a slope that makes an angle with the horizontal, friction is given by f k = k m g cos . f k = k m g cos . Weight on an Incline, a Two-Dimensional Problem 

The skier s mass, including equipment, is 60.0 kg. (See [link] (b) .) (a) What is her acceleration if friction is negligible? (b) What is her acceleration if the frictional force is 45.0 N? Now use the diagram to help find the skier's acceleration if friction is negligible and if the frictional force is 45.0 N. Strategy 

The most convenient coordinate system for motion on an incline is one that has one coordinate parallel to the slope and one perpendicular to the slope. (Remember that motions along perpendicular axes are independent.) We use the symbol to mean perpendicular, and | | | | to mean parallel. 

The only external forces acting on the system are the skier s weight, friction, and the normal force exerted by the ski slope, labeled w w , f f , and N N in the free-body diagram. N N is always perpendicular to the slope and f f is parallel to it. But w w is not in the direction of either axis, so we must break it down into components along the chosen axes. We define w | | w | | to be the component of weight parallel to the slope and w w the component of weight perpendicular to the slope. Once this is done, we can consider the two separate problems of forces parallel to the slope and forces perpendicular to the slope. Solution 

The magnitude of the component of the weight parallel to the slope is w | | = w sin ( 25 ) = m g sin ( 25 ) w | | = w sin ( 25 ) = m g sin ( 25 ) , and the magnitude of the component of the weight perpendicular to the slope is w = w cos ( 25 ) = m g cos ( 25 ) w = w cos ( 25 ) = m g cos ( 25 ) . 

(a) Neglecting friction: Since the acceleration is parallel to the slope, we only need to consider forces parallel to the slope. (Forces perpendicular to the slope add to zero, since there is no acceleration in that direction.) The forces parallel to the slope are the amount of the skier s weight parallel to the slope w | | w | | and friction f f . Assuming no friction, by Newton s second law the acceleration parallel to the slope is a | | = F net || m , a | | = F net || m , 

Where the net force parallel to the slope F net || = w | | = m g sin ( 25 ) F net || = w | | = m g sin ( 25 ) , so that a | | = F net || m = m g sin ( 25 ) m = g sin ( 25 ) = ( 9.80 m/s 2 ) ( 0.423 ) = 4.14 m/s 2 a | | = F net || m = m g sin ( 25 ) m = g sin ( 25 ) = ( 9.80 m/s 2 ) ( 0.423 ) = 4.14 m/s 2 

is the acceleration. 

(b) Including friction: Here we now have a given value for friction, and we know its direction is parallel to the slope and it opposes motion between surfaces in contact. So the net external force is now F net | | = w | | f , F net | | = w | | f , 

and substituting this into Newton s second law, a | | = F net || m a | | = F net || m gives a | | = F net || m = w | | f m = m g sin ( 25 ) f m . a | | = F net || m = w | | f m = m g sin ( 25 ) f m . 

We substitute known values to get a | | = (60 .0 kg)(9 .80 m/s 2 )(0 .423) 45 .0 N 60 .0 kg , a | | = (60 .0 kg)(9 .80 m/s 2 )(0 .423) 45 .0 N 60 .0 kg , 

or a | | = 3 .39 m/s 2 , a | | = 3 .39 m/s 2 , 

which is the acceleration parallel to the incline when there is 45 N opposing friction. Discussion 

Since friction always opposes motion between surfaces, the acceleration is smaller when there is friction than when there is not. Practice Problems 

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[link] Friction at an Angle: Sliding a Coin 

An object will slide down an inclined plane at a constant velocity if the net force on the object is zero. We can use this fact to measure the coefficient of kinetic friction between two objects. As shown in the first Worked Example , the kinetic friction on a slope f k = k m g cos f k = k m g cos , and the component of the weight down the slope is equal to m g sin m g sin . These forces act in opposite directions, so when they have equal magnitude, the acceleration is zero. Writing these out: f k = F g x k m g cos = m g sin . f k = F g x k m g cos = m g sin . 

Solving for k k , since tan = sin /cos tan = sin /cos we find that 

k = m g sin m g cos = tan k = m g sin m g cos = tan 1 coin 1 book 1 protractor Put a coin flat on a book and tilt it until the coin slides at a constant velocity down the book. You might need to tap the book lightly to get the coin to move. Measure the angle of tilt relative to the horizontal and find k k . 

[link] Section Summary Friction is a contact force between systems that opposes the motion or attempted motion between them. Simple friction is proportional to the normal force N pushing the systems together. (A normal force is always perpendicular to the contact surface between systems.) Friction depends on both of the materials involved. s is the coefficient of static friction, which depends on both of the materials. k is the coefficient of kinetic friction, which also depends on both materials. When objects rest on an inclined plane that makes an angle with the horizontal surface, the weight of the object can be broken into components that act perpendicular ( w w ) and parallel ( w | | w | | ) to the surface of the plane. Key Equations force of static friction f s s N f s s N force of kinetic friction f k = k N f k = k N perpendicular component of weight on an inclined plane w = w cos ( ) = m g cos ( ) w = w cos ( ) = m g cos ( ) parallel component of weight on an inclined plane w | | = w sin ( ) = m g sin ( ) w | | = w sin ( ) = m g sin ( ) Check Your Understanding 

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[link] Glossary kinetic friction a force that opposes the motion of two systems that are in contact and moving relative to one another static friction a force that opposes the motion of two systems that are in contact and are not moving relative to one anotherThe Scientific Method The Scientific Method 

By the end of this section, you will be able to: Explain how the methods of science are used to make scientific discoveries Define a scientific model and describe examples of physical and mathematical models used in physics Compare and contrast hypothesis, theory, and law 

The learning objectives in this section will help your students master the following TEKS: (2A) : Know the definition of science and understand that it has limitations, as specified in subsection (b)(2) of this section. (2B) : Know that scientific hypotheses are tentative and testable statements that must be capable of being supported or not supported by observational evidence. Hypotheses of durable explanatory power which have been tested over a wide variety of conditions are incorporated into theories. (2C) : Know that scientific theories are based on natural and physical phenomena and are capable of being tested by multiple independent researchers. Unlike hypotheses, scientific theories are well-established and highly-reliable explanations, but may be subject to change as new areas of science and new technologies are developed. (2D) : Distinguish between scientific hypotheses and scientific theories. Section Key Terms experiment hypothesis model observation principle scientific law scientific method theory universal 

[OL] Pre-assessment for this section could involve students sharing or writing down an anecdote about when they used the methods of science. Then, students could label their thought processes in their anecdote with the appropriate scientific methods. The class could also discuss their definitions of theory and law, both outside and within the context of science. 

[OL] It should be noted and possibly mentioned that "a scientist," as mentioned in this section, does not necessarily mean a trained scientist. It could be anyone using methods of science. Scientific Methods 

Scientists often plan and carry out investigations to answer questions about the universe around us. Such laws are intrinsic to the universe, meaning that humans did not create them and cannot change them. We can only discover and understand them. Their discovery is a very human endeavor, with all the elements of mystery, imagination, struggle, triumph, and disappointment inherent in any creative effort. The cornerstone of discovering natural laws is observation. Science must describe the universe as it is, not as we imagine or wish it to be. 

We all are curious to some extent. We look around, make generalizations, and try to understand what we see. For example, we look up and wonder whether one type of cloud signals an oncoming storm. As we become serious about exploring nature, we become more organized and formal in collecting and analyzing data. We attempt greater precision, perform controlled experiments (if we can), and write down ideas about how data may be organized. We then formulate models, theories, and laws based on the data we have collected, and communicate those results with others. This, in a nutshell, describes the scientific method , a term used for the techniques that scientists employ to decide scientific issues on the basis of evidence from observation and experiment. 

An investigation often begins with a scientist making an observation . The scientist observes a pattern or trend within the natural world. Observation may generate questions that the scientist wishes to answer. Next, the scientist may perform some research about the topic and devise a hypothesis . A hypothesis is a testable statement that describes how something in the natural world works. In essence, a hypothesis is an educated guess that explains something about an observation. 

[OL] Educated guess is used throughout this section in describing a hypothesis to combat the tendency to think of a theory as an educated guess. 

Scientists may test the hypothesis by performing an experiment . During an experiment, the scientist collects data that will help them learn about the phenomenon they are studying. Then the scientists analyze the results of the experiment (that is, the data), often using statistical, mathematical, and/or graphical methods. From the data analysis, they draw conclusions. They may conclude that their experiment either supports or rejects their hypothesis. If the hypothesis is supported, the scientist usually goes on to test another hypothesis related to the first. If their hypothesis is rejected, they will often then test a new and different hypothesis in their effort to learn more about whatever they are studying. 

Scientific processes can be applied to many situations. Let s say that you try to turn on your car, but it will not start. You have just made an observation! You ask yourself, "Why won t my car start?" You can now use scientific processes to answer this question. First, you generate a hypothesis such as, "The car won t start because it has no gasoline in the gas tank." To test this hypothesis, you put gasoline in the car and try to start it again. If the car starts, then your hypothesis is supported by the experiment. If the car does not start, then your hypothesis is rejected. You will then need to think up a new hypothesis to test such as, "My car won t start because the fuel pump is broken." Hopefully, your experiments lead you to discover why the car won t start, and enable you to fix it. Modeling 

A model is a representation of something that is often too difficult (or impossible) to study directly. Models can take the form of physical models, equations, computer programs, or simulations computer graphics/animations. Models are tools that are especially useful in modern physics because they let us visualize phenomena that we normally cannot observe with our senses, such as very small objects or objects that move at high speeds. For example, we can understand the structure of an atom using models, despite the fact that no one has ever seen an atom with their own eyes. Models are always approximate, so they are simpler to consider than the real situation; the more complete a model is, the more complicated it must be. Models put the intangible or the extremely complex into human terms that we can visualize, discuss, and hypothesize about. 

Scientific models are constructed based on the results of previous experiments. Even still, models often only describe a phenomenon partially or in a few limited situations. Some phenomena are so complex that it may be impossible to model it in its entirety, even using computers. An example is the electron cloud model of the atom in which electrons are moving around the atom s center in distinct clouds. (See [link] ) that represent the likelihood of finding an electron in different places. This model helps us to visualize the structure of an atom. However, it does not show us exactly where an electron will be within its cloud at any one particular time. The electron cloud model of the atom predicts the geometry and shape of areas where different electrons may be found in an atom. However, it cannot indicate exactly where an electron will be at any one time. 

As mentioned previously, physicists use a variety of models including equations, physical models, computer simulations, etc. For example, three-dimensional models are often commonly used in chemistry and physics to model molecules. Properties other than appearance or location are usually modelled using mathematics, where functions are used to show how these properties relate to one another. Processes such as the formation of a star or the planets, can also be modelled using computer simulations. Once a simulation is correctly programmed based on actual experimental data, the simulation can allow us to view processes that happened in the past or happen too quickly or slowly for us to observe directly. In addition, scientists can also run virtual experiments using computer based models . In a model of planet formation, for example, the scientist could alter the amount or type of rocks present in space and see how it affects planet formation. 

Scientists use models and experimental results to construct explanations of observations or design solutions to problems. For example, one way to make a car more fuel efficient is to reduce the friction or drag caused by air flowing around the moving car. This can be done by designing the body shape of the car to be more aerodynamic, such as by using rounded corners instead of sharp ones. Engineers can then construct physical models of the car body, place them in a wind tunnel, and examine the flow of air around the model (This can also be done mathematically in a computer simulation). The air flow pattern can be analyzed for regions smooth air flow and for eddies that indicate drag. The model of the car body may have to be altered slightly to produce the smoothest pattern of air flow (i.e., the least drag). The pattern with the least drag may be the solution to increasing fuel efficiency of the car. This solution might then be incorporated into the car design. Using Models and the Scientific Processes 

Be sure to secure loose items before opening the window or door. 

In this activity, you will learn about scientific models by making a model of how air flows through your classroom or a room in your house. One room with at least 1 window or door that can be opened Piece of single-ply tissue paper Work with a group of four, as directed by your teacher. Close all of the windows and doors in the room you are working in. Your teacher may assign you a specific window or door to study. Before opening any windows or doors, draw a to-scale diagram of your room. First, measure the length and width of your room using the tape measure. Then, transform the measurement using a scale that could fit on your paper, such as 1/2 inch = 1 foot or 5 centimeters = 1 meter. Your teacher will assign you a specific window or door to study air flow. On your diagram, add arrows showing your hypothesis (before opening any windows or doors) of how air will flow through the room when your assigned window or door is opened. Use pencil so that you can easily make changes to your diagram. On you diagram, mark 4 locations where you would like to test air flow in your room. To test for airflow, hold a strip of single ply tissue paper between the thumb and index finger. Note the direction that the paper moves by when exposed to the airflow. Then, for each location, predict which way the paper will move if your air flow diagram is correct. Now, each member of your group will stand in one of the four selected areas. Each member will test the airflow Agree upon an approximate height at which everyone will hold their papers. When you teacher tells you to, open your assigned window and/or door. Each person should note the direction that their paper points immediately after the window or door was opened. Record your results on your diagram. Did the airflow test data support or refute the hypothetical model of air flow shown in your diagram? Why or why not? Correct your model based on your experimental evidence. With your group, discuss how accurate your model is. What limitations did it have? Write down the limitations that your group agreed upon. 

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This Snap Lab! has students construct a model of how air flows in their classroom. Each group of 4 students will create a model of air flow in their classroom using a scale drawing of the room. Then, the groups will test the validity of their model by placing weathervanes that they have constructed around the room and opening a window or door. By observing the weather vanes, students will see how air actually flows through the room from a specific window or door. Students will then correct their model based on their experimental evidence. The material list is given per group: One room with at least 1 window or door that can be opened (An optimal configuration would be 1 window or door per group.) several pieces of construction paper (at least 4 per group) strips of single ply tissue paper One tape measure (long enough to measure the dimensions of the room) straws scissors tape Group size can vary depending on the number of windows/doors available and the number of students in the class. The room dimensions could be provided by the teacher. Also, students may need a brief introduction in how to make a drawing to scale. This is another opportunity to discuss controlled experiments in terms of why the students should hold the strips of tissue paper at the same height and in the same way. One student could also serve as a control and stand far away from the window/door or in another area that will not receive air flow from the window/door. You will probably need to coordinate this when multiple windows or doors are used. Only one window or door should be opened at a time for best results. Between openings, allow a short period (5 minutes) when all windows and doors are closed, if possible. 

Answers to the Grasp Check will vary, but the air flow in the new window or door should be based on what the students observed in their experiment. Scientific Laws and Theories 

A scientific law is a description of a pattern in nature that is true in all circumstances that have been studied. That is, physical laws are meant to be universal , meaning that they apply throughout the known universe. Laws are often also concise, whereas theories are more complicated. A law can be expressed in the form of a single sentence or mathematical equation. For example, Newton s second law of motion , which relates the motion of an object to the force applied ( F ), the mass of the object ( m ), and the object s acceleration ( a ), is simply stated using the equation: F = m a F = m a 

Scientific ideas and explanations that are true in many, but not all situations in the universe are usually called principles . An example is Pascal s principle , which explains properties of liquids, but not solids or gases. However, the distinction between laws and principles is sometimes not carefully made in science. 

A theory is an explanation for patterns in nature that is supported by much scientific evidence and verified multiple times by multiple researchers. While many people confuse theories with educated guesses o hypotheses, theories have withstood more rigorous testing and verification than hypotheses. 

[OL] Explain to students that in informal, everyday English the word "theory" can be used to describe an idea that is possibly true but that has not been proven to be true. This use of the word "theory" often leads people to think that scientific theories are nothing more than educated guesses. This is not just a misconception among students, but among the general public as well. 

As a closing idea about scientific processes, we want to point out that scientific laws and theories, even those that have been supported by experiments for centuries, can still be changed by new discoveries. This is especially true when new technologies emerge that allow us to observe things that were formerly unobservable. Imagine how viewing previously invisible objects with a microscope or viewing Earth for the first time from space may have instantly changed our scientific theories and laws! What discoveries still await us in the future? The constant retesting and perfecting of our scientific laws and theories allows our knowledge of nature to progress. For this reason, many scientists are reluctant to say that their studies "prove" anything. By saying "support" instead of "prove," it keeps the door open for future discoveries, even if they won t occur for centuries or even millennia. 

[OL] With regard to scientists avoiding using the word "prove," the general public knows that science has proven certain things such as that the heart pumps blood and the Earth is round. However, scientists should shy away from using "prove" because it is impossible to test every single instance and every set of conditions in a system to absolutely prove anything. Using "support" or similar terminology leaves the door open for further discovery. Check Your Understanding 

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Use the Check Your Understanding questions to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify which objective and direct students to the relevant content. Section Summary Science seeks to discover and describe the underlying order and simplicity in nature. The processes of science include observation, hypothesis, experiment, and conclusion. Theories are scientific explanations that are supported by a large body experimental results. Scientific laws are concise descriptions of the universe that are universally true. Concept Items 

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[link] Glossary experiment process involved with testing a hypothesis hypothesis testable statement that describes how something in the natural world works model system that is analogous to the real system of interest in essential ways but more easily analyzed observation step where a scientist observes a pattern or trend within the natural world. principle description of nature that is true in many, but not all situations scientific law pattern in nature that is true in all circumstances studied thus far scientific method the techniques and processes used in the constructing and testing of scientific hypotheses, laws, and theories, and in deciding issues on the basis of experiment and observation theory explanation of patterns in nature that is supported by much scientific evidence and verified multiple times by various groups of researchers universal applies throughout the known universeThe Language of Physics: Physical Quantities and Units The Language of Physics: Physical Quantities and Units 

By the end of this section, you will be able to: Associate physical quantities with their SI units and perform conversions among SI units using scientific notation Relate measurement uncertainty to significant figures and apply the rules for using significant figures in calculations Correctly create, label, and identify relationships in graphs using mathematical relationships (e.g.: slope, y -intercept, inverse, quadratic and logarithmic) 

The learning objectives in this section will help your students master the following TEKS: (2H) : Make measurements with accuracy and precision and record data using scientific notation and International System (SI) units. (2L) : Express and manipulate relationships among physical variables quantitatively, including the use of graphs, charts, and equations. Section Key Terms accuracy ampere constant conversion factor dependent variable derived units English units exponential relationship fundamental physical units independent variable inverse relationship inversely proportional kilogram linear relationship logarithmic (log) scale log-log plot meter method of adding percents order of magnitude precision quadratic relationship scientific notation second semi-log plot SI units significant figures slope uncertainty variable y -intercept 

[OL] Pre-assessment for this section could involve asking students what experience they have had with the four fundamental units in their daily lives. One could also poll the class for what they think accuracy, precision, and uncertainty refer to. For graphing, students could make a quick graph of some data and then edit their graph after reading to note ways they could improve the clarity of their graph. The Role of Units 

Physicists, like other scientists, make observations and ask basic questions. For example: how big is an object? How much mass does it have? How far did it travel? To answer these questions, they make measurements with various instruments (e.g., meter stick, balance, stopwatch, etc.). 

The measurements of physical quantities are expressed in terms of units, which are standardized values. For example, the length of a race, which is a physical quantity, can be expressed in meters (for sprinters) or kilometers (for distance runners.) Without standardized units, it would be extremely difficult for scientists to express and compare measured values in a meaningful way. (See [link] ). Distances given in unknown units are maddeningly useless. 

All physical quantities in the SI system of units are expressed in terms of combinations of seven fundamental physical units, which are units for: length, mass, time, electric current, temperature, amount of a substance, and luminous intensity. SI Units: Fundamental and Derived Units 

There are two major systems of units used in the world: SI units (acronym for the French Syst me International, also known as the metric system) and English units (also known as the imperial system). English units were historically used in nations once ruled by the British Empire. Today, the United States is the only country that still uses English units extensively. Virtually every other country in the world now uses the metric system, which is the standard system agreed upon by scientists and mathematicians. 

[OL] As a clarification, certain countries use the British system for a few of their measurements. For example, Britain still uses the pint to measure beer, miles to measure road distances, and pounds to measure body weight (although weight must be reported in kg in British medical records). The British people still use the British system extensively in their everyday lives, but the metric system is the official standard for the government. Likewise, many oil-producing countries measure oil in British gallons. 

Some physical quantities are more fundamental than others. In physics, there are seven fundamental physical quantities (which are measured in base units , or fundamental physical units): length, mass, time, electric current, temperature, amount of a substance, and luminous intensity. Units for other physical quantities (such as force, speed, and electric charge) described by mathematically combining these 7 base units. In this course, we will mainly use five of these: length, mass, time, electric current and temperature. The units in which they are measured are the meter, kilogram, second, ampere, kelvin, mole, and candela ( [link] ). All other units are made by mathematically combining the fundamental units. These are called derived units . SI Base Unit Quantity Name Symbol length meter m mass kilogram kg time second s electric current ampere a temperature kelvin k amount of substance mole mol luminous intensity candela cd The Meter 

The SI unit for length is the meter (abbreviated as m). The definition of the meter has changed over time to become more accurate and precise. The meter was first defined in 1791 as 1/10,000,000 of the distance from the equator to the North Pole. This measurement was improved in 1889 by redefining the meter to be the distance between two engraved lines on a platinum-iridium bar. (The bar is now housed at the International Bureau of Weights and Meaures, near Paris). By 1960, some distances could be measured more precisely by comparing them to wavelengths of light. The meter was redefined as 1,650,763.73 wavelengths of orange light emitted by krypton atoms. In 1983, the meter was given its present definition as the distance light travels in a vacuum in 1/ 299,792,458 of a second. (See [link] ). The meter is defined to be the distance light travels in 1/299,792,458 of a second through a vacuum. Distance traveled is speed multiplied by time. The Kilogram 

The SI unit for mass is the kilogram (abbreviated as kg). It is defined to be the mass of a platinum-iridium cylinder, housed at the International Bureau of Weights and Measures near Paris. Exact replicas of the standard kilogram cylinder are kept in numerous locations throughout the world, such as the National Institute of Standards and Technology in Gaithersburg, Maryland. The determination of all other masses can be done by comparing them with one of these standard kilograms. The Second 

The SI unit for time, the second (abbreviated as s) also has a long history. For many years it was defined as 1/86,400 of an average solar day. However, the average solar day is actually very gradually getting longer due to gradual slowing of Earth s rotation. Accuracy in the fundamental units is essential, since all other measurements are derived from them. Therefore, a new standard was adopted to define the second in terms of a non-varying, or constant, physical phenomenon. One constant phenomenon is the very steady vibration of Cesium atoms, which can be observed and counted. This vibration forms the basis of the cesium atomic clock . In 1967, the second was redefined as the time required for 9,192,631,770 Cesium atom vibrations. (See [link] .) An atomic clock such as this one uses the vibrations of cesium atoms to keep time to a precision of one microsecond per year. The fundamental unit of time, the second, is based on such clocks. This image is looking down from the top of an atomic clock. (credit: Steve Jurvetson/Flickr) 

[BL] An average solar day was used to originally define the second because the length of a solar day varies throughout the year due to Earth s tilt of its axis as well as its elliptical orbit. The accumulation of these variations could result in a day length difference of up to 16 minutes during different seasons. Using an average solar day resolves these variations in day length. The Ampere 

Electric current is measured in the ampere (named for Andre Ampere and abbreviated A). You have probably heard of amperes, or "amps," when people discuss electrical currents or electrical devices. Understanding an ampere requires a basic understanding of electricity and magnetism, something that will be explored in depth in later chapters of this book. Basically, two parallel wires with an electric current running through them will produce an attractive force on each other. One ampere is defined as the amount of electric current that will produce an attractive force of 2.7 10 7 newton per meter of separation between the two wires (the newton is the derived unit of force). 

[BL] Some students may not know that a vacuum is a region of space that contains no air. Kelvins 

The SI unit of temperature is the kelvin (or kelvins, but not degrees kelvin). This scale is named after physicist William Thomson, Lord Kelvin, who was the first to call for an absolute temperature scale. The Kelvin scale is based on absolute zero. This is the point at which all thermal energy has been removed from all atoms or molecules in a system. This temperature, 0 K, is equal to 273.15 C and 459.67 F. Conveniently, the Kelvin scale actually changes in the same way as the Celsius scale. For example, the freezing point (0 C) and boiling points of water (100 C) are 100 degrees apart on the Celsius scale. These two temperatures are also 100 kelvins apart (freezing point = 273.15 K; boiling point = 373.15 K). Metric Prefixes 

Physical objects or phenomena may vary widely. For example, the size of objects varies from something very small (like an atom) to something very large (like a star). Yet the standard metric unit of length is the meter. So, the metric system includes many prefixes that can be attached to a unit. Each prefix is based on factors of 10 (10, 100, 1000, etc. as well as 0.1, 0.01, 0.001, etc.). [link] gives the metric prefixes and symbols used to denote the different various factors of 10 in the metric system. 

The metric system is convenient because conversions between metric units can be done simply by moving the decimal place of a number. This is because the metric prefixes are sequential powers of 10. There are 100 centimeters in a meter, 1000 meters in a kilometer, and so on. In nonmetric systems, such as U.S. customary units , the relationships are less simple there are 12 inches in a foot, 5280 feet in a mile, 4 quarts in a gallon, and so on. Another advantage of the metric system is that the same unit can be used over extremely large ranges of values simply by switching to the most-appropriate metric prefix. For example, distances in meters are suitable for building construction, but kilometers are used to describe road construction. Therefore, with the metric system, there is no need to invent new units when measuring very small or very large objects you just have to move the decimal point (and use the appropriate prefix). Prefix Symbol Value[1] Example (some are approximate) exa E 10 18 exameter Em 10 18 m distance light travels in a century peta P 10 15 petasecond Ps 10 15 s 30 million years tera T 10 12 terawatt TW 10 12 W powerful laser output giga G 10 9 gigahertz GHz 10 9 Hz a microwave frequency mega M 10 6 megacurie MCi 10 6 Ci high radioactivity kilo k 10 3 kilometer km 10 3 m about 6/10 mile hector h 10 2 hectoliter hL 10 2 L 26 gallons deka da 10 1 dekagram dag 10 1 g teaspoon of butter ____ ____ 10 0 (=1) deci d 10 1 deciliter dL 10 1 L less than half a soda centi c 10 2 centimeter Cm 10 2 m fingertip thickness mili m 10 3 millimeter Mm 10 3 m flea at its shoulder micro 10 6 micrometer m 10 6 m detail in microscope nano n 10 9 nanogram Ng 10 9 g small speck of dust pico p 10 12 picofarad pF 10 12 F small capacitor in radio femto f 10 15 femtometer Fm 10 15 m size of a proton atto a 10 18 attosecond as 10 18 s time light takes to cross an atom Known Ranges of Length, Mass, and Time 

[link] lists known lengths, masses, and time measurements. You can see that scientists use a range of measurement units. This wide range demonstrates the vastness and complexity of the universe, as well as the breadth of phenomena physicists study. As you examine this table, note how the metric system allows us to discuss and compare an enormous range of phenomena, using one system of measurement. (See [link] and [link] .) Approximate Values of Length, Mass, and Time Lengths in meters Masses in kilogram (more precise values in parentheses) Times in seconds (more precise values in parentheses) 10 18 Present experimental limit to smallest observable detail 10 30 Mass of an electron (9.11 10 31 kg) 10 23 Time for light to cross an proton 10 15 Diameter of a proton 10 27 Mass of a hydrogen atom (1.67 10 27 kg) 10 22 Mean life of an extremely unstable nucleus 10 14 Diameter of a uranium nucleus 10 15 Mass of a bacterium 10 15 Time for one oscillation of a visible light 10 10 Diameter of a hydrogen atom 10 5 Mass of a mosquito 10 13 Time for one vibration of an atom in a solid 10 8 Thickness of membranes in cell of living organism 10 2 Mass of a hummingbird 10 8 Time for one oscillation of an FM radio wave 10 6 Wavelength of visible light 1 Mass of a liter of water (about a quart) 10 3 Duration of a nerve impulse 10 3 Size of a grain of sand 10 2 Mass of a person 1 Time for one heartbeat 1 Height of a 4 year-old child 10 3 Mass of a car 10 5 One day (8.64 10 4 s) 10 2 Length of a football field 10 8 Mass of a large ship 10 7 One year (y) (3.16 10 7 s) 10 4 Greatest ocean depth 10 12 Mass of a large iceberg 10 9 About half the life expectancy of a human 10 7 Diameter of the Earth 10 15 Mass of the nucleus of a comet 10 11 Recorded history 10 11 Distance from the Earth to the Sun 10 23 Mass of the Moon (7.35 10 22 kg) 10 17 Age of the Earth 10 16 Distance traveled by light in 1 year (a light year) 10 25 Mass of Earth (5.97 10 24 kg) 10 18 Age of the universe 10 21 Diameter of the Milky Way galaxy 10 30 Mass of the Sun (1.99 10 24 kg) 10 22 Distance from Earth to the nearest large galaxy (Andromeda) 10 42 Mass of the Milky Way galaxy (current upper limit) 10 26 Distance from the Earth to the edges of the known universe 10 53 Mass of the known universe (current upper limit) Tiny phytoplankton float among crystals of ice in the Antarctic Sea. They range from a few micrometers to as much as 2 millimeters in length. (credit: Prof. Gordon T. Taylor, Stony Brook University; NOAA Corps Collections) Galaxies collide 2.4 billion light years away from Earth. The tremendous range of observable phenomena in nature challenges the imagination. (credit: NASA/CXC/UVic./A. Mahdavi et al. Optical/lensing: CFHT/UVic./H. Hoekstra et al.) Using Scientific Notation with Physical Measurements 

Scientific notation is a way of writing numbers that are too large or small to be conveniently written as a decimal. For example, consider the number 840,000,000,000,000. It s a rather large number to write out. The scientific notation for this number is 8.40 10 14 . Scientific notation follows this general format: x 10 y x 10 y 

In this format x is the value of the measurement with all placeholder zeros removed. In the example above, x is 8.4. The x is multiplied by a factor, 10 y , which indicates the number of placeholder zeros in the measurement. Placeholder zeros are those at the end of a number that is 10 or greater, and at the beginning of a decimal number that is less than 1. In the example above, the factor is 10 14 . This tells you that you should move the decimal point 14 positions to the right, filling in placeholder zeros as you go. In this case, moving the decimal point 14 places creates only 13 placeholder zeros, indicating that the actual measurement value is 840,000,000,000,000. 

Numbers that are fractions can be indicated by scientific notation as well. Consider the number 0.0000045. Its scientific notation is 4.5 10 6 . Its scientific notation has the same format: x 10 y x 10 y 

Here, x is 4.5. However, the value of y in the 10 y factor is negative, which indicates that the measurement is a fraction of 1. Therefore, we move the decimal place to the left, for a negative y . In our example of 4.5 10 6 , the decimal point would be moved to the left six times to yield the original number, which would be 0.0000045. 

The term order of magnitude refers to the power of 10 when numbers are expressed in scientific notation. Quantities that have the same power of 10 when expressed in scientific notation, or come close to it, are said to be of the same order of magnitude. For example, the number 800 can be written as 8 10 2 , and the number 450 can be written as 4.5 10 2 . Both numbers have the same value for y . Therefore, 800 and 450 are of the same order of magnitude. Similarly, 101 and 99 would be regarded as the same order of magnitude, 10 2 . Order of magnitude can be thought of as a ballpark estimate for the scale of a value. The diameter of an atom is on the order of 10 9 m, while the diameter of the sun is on the order of 10 9 m. These two values are 18 orders of magnitude apart. 

Scientists make frequent use of scientific notation because of the vast range of physical measurements possible in the universe, such as the distance from Earth to the Moon, seen in [link] , or to the nearest star. The distance from Earth to the Moon may seem immense, but it is just a tiny fraction of the distance from Earth to our closest neighboring star. (credit: NASA) Unit Conversion and Dimensional Analysis 

It is often necessary to convert from one type of unit to another. For example, if you are reading a European cookbook in the United States, some quantities may be expressed in liters and you need to convert them to cups. A Canadian tourist driving through the United States might want to convert miles to kilometers, to have a sense of how far away his next destination is. A doctor in the United States might convert a patient s weight in pounds to kilograms. 

Let s consider a simple example of how to convert units within the metric system. How can we want to convert 1 hour to seconds? 

Next, we need to determine a conversion factor relating meters to kilometers. A conversion factor is a ratio expressing how many of one unit are equal to another unit. A conversion factor is simply a fraction which equals 1. You can multiply any number by 1 and get the same value. When you multiply a number by a conversion factor, you are simply multiplying it by one. For example, the following are conversion factors: (1 foot)/(12 inches) = 1 to convert inches to feet, (1 meter)/(100 centimeters) = 1 to convert centimeters to meters, (1 minute)/(60 seconds) = 1 to convert seconds to minutes. In this case, we know that there are 1,000 meters in 1 kilometer. 

Now we can set up our unit conversion. We will write the units that we have and then multiply them by the conversion factor (1 km/1000m) = 1, so we are simply multiplying 80 m by "1: 1 h 60 min 1 h 60 s 1 min = 3600 s = 3 .6 10 2 s 1 h 60 min 1 h 60 s 1 min = 3600 s = 3 .6 10 2 s 

When there is a unit in the original number, and a unit in the denominator (bottom) of the conversion factor, the units cancel. In this case, hours and minutes cancel and the value in seconds remains. 

You can use this method to convert between any types of unit, including between the U.S. customary system and metric system. Notice also that, although you can multiply and divide units algebraically, you cannot add or subtract different units. An expression like 10 km + 5 kg makes no sense. Even adding two lengths in different units, such as 10 km + 20 m does not make sense. You express both lengths in the same unit. See Appendix C for a more complete list of conversion factors. Unit Conversions: A Short Drive Home 

Suppose that you drive the 10.0 km from your university to home in 20.0 min. Calculate your average speed (a) in kilometers per hour (km/h) and (b) in meters per second (m/s). (Note: Average speed is distance traveled divided by time of travel.) Strategy 

First we calculate the average speed using the given units. Then we can get the average speed into the desired units by picking the correct conversion factor and multiplying by it. The correct conversion factor is the one that cancels the unwanted unit and leaves the desired unit in its place. Solution for (a) 

Calculate average speed. Average speed is distance traveled divided by time of travel. (Take this definition as a given for now average speed and other motion concepts will be covered in a later module.) In equation form, average speed = distance time average speed = distance time 

Substitute the given values for distance and time. average speed = 10.0 km 20.0 min = 0.500 km min average speed = 10.0 km 20.0 min = 0.500 km min 

Convert km/min to km/h: multiply by the conversion factor that will cancel minutes and leave hours. That conversion factor is 60 min/1 h 60 min/1 h . Thus, average speed = 0.500 km min 60 min 1 h = 30.0 km h . average speed = 0.500 km min 60 min 1 h = 30.0 km h . Discussion for (a) 

To check your answer, consider the following: 

Be sure that you have properly cancelled the units in the unit conversion. If you have written the unit conversion factor upside down, the units will not cancel properly in the equation. If you accidentally get the ratio upside down, then the units will not cancel; rather, they will give you the wrong units as follows: km min 1 hr 60 min = 1 60 km h min 2 km min 1 hr 60 min = 1 60 km h min 2 

which are obviously not the desired units of km/h. Check that the units of the final answer are the desired units. The problem asked us to solve for average speed in units of km/h and we have indeed obtained these units. Check the significant figures. Because each of the values given in the problem has three significant figures, the answer should also have three significant figures. The answer 30.0 km/h does indeed have three significant figures, so this is appropriate. Note that the significant figures in the conversion factor are not relevant because an hour is defined to be 60 minutes, so the precision of the conversion factor is perfect. Next, check whether the answer is reasonable. Let us consider some information from the problem if you travel 10 km in a third of an hour (20 min), you would travel three times that far in an hour. The answer does seem reasonable. Solution (b) 

There are several ways to convert the average speed into meters per second. Start with the answer to (a) and convert km/h to m/s. Two conversion factors are needed one to convert hours to seconds, and another to convert kilometers to meters. 

Multiplying by these yields Average speed = 30.0 km h 1 h 3,600 s 1 , 000 m 1 km Average speed = 30.0 km h 1 h 3,600 s 1 , 000 m 1 km Average speed = 8.33 m s Average speed = 8.33 m s Discussion for (b) 

If we had started with 0.500 km/min, we would have needed different conversion factors, but the answer would have been the same: 8.33 m/s. 

You may have noted that the answers in the worked example just covered were given to three digits. Why? When do you need to be concerned about the number of digits in something you calculate? Why not write down all the digits your calculator produces? Accuracy, Precision and Significant Figures 

Science is based on experimentation that requires good measurements. The validity of a measurement can be described in terms of its accuracy and its precision (see [link] and [link] ). Accuracy is how close a measurement is to the correct value for that measurement. For example, let us say that you are measuring the length of standard piece of printer paper. The packaging in which you purchased the paper states that it is 11 inches long, and suppose this stated value is correct. You measure the length of the paper three times and obtain the following measurements: 11.1 in., 11.2 in., and 10.9 in. These measurements are quite accurate because they are very close to the correct value of 11.0 inches. In contrast, if you had obtained a measurement of 12 inches, your measurement would not be very accurate. This is why measuring instruments are calibrated based on a known measurement. If the instrument consistently returns the correct value of the known measurement, it is safe for use in finding unknown values. A double-pan mechanical balance is used to compare different masses. Usually an object with unknown mass is placed in one pan and objects of known mass are placed in the other pan. When the bar that connects the two pans is horizontal, then the masses in both pans are equal. The known masses are typically metal cylinders of standard mass such as 1 gram, 10 grams, and 100 grams. (credit: Serge Melki) Whereas a mechanical balance may only read the mass of an object to the nearest tenth of a gram, some digital scales can measure the mass of an object up to the nearest thousandth of a gram. As in other measuring devices, the precision of a scale is limited to the last measured figures. This is the hundredths place in the scale pictured here. (credit: Splarka, Wikimedia Commons) 

Precision states how well repeated measurements of something generate the same or similar results. Therefore, the precision of measurements refers to how close together the measurements are when you measure the same thing several times. One way to analyze the precision of measurements would be to determine the range, or difference between the lowest and the highest measured values. In the case of the printer paper measurements, the lowest value was 10.9 in. and the highest value was 11.2 in. Thus, the measured values deviated from each other by, at most, 0.3 in. These measurements were reasonably precise because they varied by only a fraction of an inch. However, if the measured values had been 10.9 in., 11.1 in., and 11.9 in., then the measurements would not be very precise because there is a lot of variation from one measurement to another. 

The measurements in the paper example are both accurate and precise, but in some cases, measurements are accurate but not precise, or they are precise but not accurate. Let us consider a GPS system that is attempting to locate the position of a restaurant in a city. Think of the restaurant location as existing at the center of a bull s-eye target. Then think of each GPS attempt to locate the restaurant as a black dot on the bull s eye. 

In [link] , you can see that the GPS measurements are spread far apart from each other, but they are all relatively close to the actual location of the restaurant at the center of the target. This indicates a low precision, high accuracy measuring system. However, in [link] , the GPS measurements are concentrated quite closely to one another, but they are far away from the target location. This indicates a high precision, low accuracy measuring system. Finally, in [link] , the GPS is both precise and accurate, allowing the restaurant to be located. A GPS system attempts to locate a restaurant at the center of the bull s-eye. The black dots represent each attempt to pinpoint the location of the restaurant. The dots are spread out quite far apart from one another, indicating low precision, but they are each rather close to the actual location of the restaurant, indicating high accuracy. (credit: Dark Evil) In this figure, the dots are concentrated close to one another, indicating high precision, but they are rather far away from the actual location of the restaurant, indicating low accuracy. (credit: Dark Evil) In this figure, the dots are concentrated close to one another, indicating high precision, but they are rather far away from the actual location of the restaurant, indicating low accuracy. (credit: Dark Evil) Uncertainty 

The accuracy and precision of a measuring system determine the uncertainty of its measurements. Uncertainty is a way to describe how much your measured value deviates from the actual value that the object has. If your measurements are not very accurate or precise, then the uncertainty of your values will be very high. In more general terms, uncertainty can be thought of as a disclaimer for your measured values. For example, if someone asked you to provide the mileage on your car, you might say that it is 45,000 miles, plus or minus 500 miles. The plus or minus amount is the uncertainty in your value. That is, you are indicating that the actual mileage of your car might be as low as 44,500 miles or as high as 45,500 miles, or anywhere in between. All measurements contain some amount of uncertainty. In our example of measuring the length of the paper, we might say that the length of the paper is 11 in. plus or minus 0.2 in or 11 in. 0.2 in. The uncertainty in a measurement, A , is often denoted as A ("delta A "), 

The factors contributing to uncertainty in a measurement include: Limitations of the measuring device The skill of the person making the measurement Irregularities in the object being measured Any other factors that affect the outcome (highly dependent on the situation) 

In the printer paper example, uncertainty could be caused by 1) the fact that the smallest division on the ruler is 0.1 in., 2) the person using the ruler has bad eyesight, or 3) uncertainty caused by the paper cutting machine (e.g. one side of the paper is slightly longer than the other). It is good practice to carefully consider all possible sources of uncertainty in a measurement and reduce or eliminate them, if possible. Percent Uncertainty 

One method of expressing uncertainty is as a percent of the measured value. If a measurement, A , is expressed with uncertainty, A , the percent uncertainty is: % uncertainty = A A 100 % % uncertainty = A A 100 % Calculating Percent Uncertainty: A Bag of Apples 

A grocery store sells 5-lb bags of apples. You purchase four bags over the course of a month and weigh the apples each time. You obtain the following measurements: Week 1 weight: 4. 8 lb 4. 8 lb Week 2 weight: 5.3 lb 5.3 lb Week 3 weight: 4. 9 lb 4. 9 lb Week 4 weight: 5.4 lb 5.4 lb 

You determine that the weight of the 5 lb bag has an uncertainty of 0.4 lb. What is the percent uncertainty of the bag s weight? Strategy 

First, observe that the expected value of the bag s weight, A A , is 5 lb. The uncertainty in this value, A A , is 0.4 lb. We can use the following equation to determine the percent uncertainty of the weight: % uncertainty = A A 100 % % uncertainty = A A 100 % Solution 

Plug the known values into the equation: % uncertainty = 0.4 lb 5 lb 100 % = 8 % . % uncertainty = 0.4 lb 5 lb 100 % = 8 % . Discussion 

We can conclude that the weight of the apple bag is 5 lb 8%. Consider how this percent uncertainty would change if the bag of apples were half as heavy, but the uncertainty in the weight remained the same. Hint for future calculations: when calculating percent uncertainty, always remember that you must multiply the fraction by 100%. If you do not do this, you will have a decimal quantity, not a percent value. Uncertainty in Calculations 

There is an uncertainty in anything calculated from measured quantities. For example, the area of a floor calculated from measurements of its length and width has an uncertainty because the both the length and width have uncertainties. How big is the uncertainty in something you calculate by multiplication or division? If the measurements in the calculation have small uncertainties (a few percent or less), then the method of adding percents can be used. This method says that the percent uncertainty in a quantity calculated by multiplication or division is the sum of the percent uncertainties in the items used to make the calculation. For example, if a floor has a length of 4.00 m and a width of 3.00 m, with uncertainties of 2% and 1%, respectively, then the area of the floor is 12.0 m 2 and has an uncertainty of 3% (expressed as an area this is 0.36 m 2 , which we round to 0.4 m 2 since the area of the floor is given to a tenth of a square meter). 

For a quick demonstration of the accuracy, precision, and uncertainty of measurements based upon the units of measurement, try this simulation . You will have the opportunity to measure the length and weight of a desk, using milli- versus centi- units. Which do you think will provide greater accuracy, precision and uncertainty when measuring the desk and the notepad in the simulation? Consider how the nature of the hypothesis or research question might influence how precise of a measuring tool you need to collect data. Precision of Measuring Tools and Significant Figures 

An important factor in the accuracy and precision of measurements is the precision of the measuring tool. In general, a precise measuring tool is one that can measure values in very small increments. For example, consider measuring the thickness of a coin. A standard ruler can measure thickness to the nearest millimeter, while a micrometer can measure the thickness to the nearest 0.005 millimeter. The micrometer is a more precise measuring tool because it can measure extremely small differences in thickness. The more precise the measuring tool, the more precise and accurate the measurements can be. 

When we express measured values, we can only list as many digits as we initially measured with our measuring tool (such as the rulers shown in [link] ). For example, if you use a standard ruler to measure the length of a stick, you may measure it with a decimeter ruler as 3.6 cm. You could not express this value as 3.65 cm because your measuring tool was not precise enough to measure a hundredth of a centimeter. It should be noted that the last digit in a measured value has been estimated in some way by the person performing the measurement. For example, the person measuring the length of a stick with a ruler notices that the stick length seems to be somewhere in between 36 mm and 37 mm. He or she must estimate the value of the last digit. The rule is that the last digit written down in a measurement is the first digit with some uncertainty. For example, the last measured value 36.5 mm has three digits, or three significant figures. The number of significant figures in a measurement indicates the precision of the measuring tool. The more precise a measuring tool is, the greater the number of significant figures it can report. Three metric rulers are shown. The first ruler is in decimeters and can measure point three decimeters. The second ruler is in centimeters long and can measure three point six centimeters. The last ruler is in millimeters and can measure thirty-six point five millimeters. Zeros 

Special consideration is given to zeros when counting significant figures. For example, the zeros in 0.053 are not significant because they are only placeholders that locate the decimal point. There are two significant figures in 0.053 the 5 and the 3. However, if the zero occurs between other significant figures, the zeros are significant. For example, both zeros in 10.053 are significant, as these zeros were actually measured. Therefore, the 10.053 placeholder has five significant figures. The zeros in 1300 may or may not be significant, depending on the style of writing numbers. They could mean the number is known to the last zero, or the zeros could be placeholders. So 1300 could have two, three, or four significant figures. To avoid this ambiguity, write 1300 in scientific notation as 1.3 10 3 . Only significant figures are given in the x factor for a number in scientific notation (in the form x 10 y x 10 y ). Therefore, we know that 1 and 3 are the only significant digits in this number. In summary, zeros are significant except when they serve only as placeholders. [link] provides examples of the number of significant figures in various numbers. Number Significant figures Rationale 1.657 4 There are no zeros and all non-zero numbers are always significant. 0.4578 4 The first zero is only a placeholder for the decimal point. 0.000458 3 The first four zeros are placeholders needed to report the data to the ten-thoudsandths place. 2000.56 6 The three zeros are significant here because they occur between other significant figures. 45,600 3 With no underlines or scientific notation, we assume that the last two zeros are placeholders and are not significant. 15895 00 0 7 The two underlined zeros are significant, while the last zero is not, as it is not underlined. 5.457 10 13 4 In scientific notation, all numbers reported in front of the multiplication sign are significant 6.520 10 23 4 In scientific notation, all numbers reported in front of the multiplication sign are significant, including zeros. Significant Figures in Calculations 

When combining measurements with different degrees of accuracy and precision, the number of significant digits in the final answer can be no greater than the number of significant digits in the least precise measured value. There are two different rules, one for multiplication and division and another rule for addition and subtraction, as discussed below. 

For multiplication and division: The answer should have the same number of significant figures as the starting value with the fewest significant figures. For example, the area of a circle can be calculated from its radius using A = r 2 A = r 2 . Let us see how many significant figures the area will have if the radius has only two significant figures, for example, r = 2.0 m. Then, using a calculator that keeps eight significant figures, you would get A = r 2 = ( 3.1415927... ) ( 2.0 m ) 2 = 4.5238934 m 2 . A = r 2 = ( 3.1415927... ) ( 2.0 m ) 2 = 4.5238934 m 2 . 

But because the radius has only two significant figures, the area calculated is meaningful only to two significant figures or A = 4.5 m 2 A = 4.5 m 2 

even though the value of is meaningful to at least eight digits. 

For addition and subtraction : The answer should have the same number places (e.g. tens place, ones place, tenths place, etc.) as the least-precise starting value. Suppose that you buy 7.56 kg of potatoes in a grocery store as measured with a scale having a precision of 0.01 kg. Then you drop off 6.052 kg of potatoes at your laboratory as measured by a scale with a precision of 0.001 kg. Finally, you go home and add 13.7 kg of potatoes as measured by a bathroom scale with a precision of 0.1 kg. How many kilograms of potatoes do you now have, and how many significant figures are appropriate in the answer? The mass is found by simple addition and subtraction: 



7.56 kg 6.052 kg + 13.7 kg _ 15.208 kg 7.56 kg 6.052 kg + 13.7 kg _ 15.208 kg 

The least precise measurement is 13.7 kg. This measurement is expressed to the 0.1 decimal place, so our final answer must also be expressed to the 0.1 decimal place. Thus, the answer should be rounded to the tenths place, giving 15.2 kg. The same is true for non-decimal numbers. For example: 6527.23 + 2 = 6528.23 = 6528 6527.23 + 2 = 6528.23 = 6528 

We cannot report the decimal places in the answer because "2" has no decimal places that would be significant. Therefore, we can only report to the ones place. 

It is a good idea to keep extra significant figures while calculating, and to round off to the correct number of significant figures only in the final answers. The reason is that small errors from rounding while calculating can sometimes produce significant errors in the final answer. As an example, try calculating 5098 ( 5.000 ) ( 1010 ) 5098 ( 5.000 ) ( 1010 ) to obtain a final answer to only two significant figures. Keeping all significant during the calculation gives 48. Rounding to two significant figures in the middle of the calculation changes it to 5100 ( 5.000 ) ( 1000 ) = 100 5100 ( 5.000 ) ( 1000 ) = 100 , which is way off. You would similarly avoid rounding in the middle of the calculation in counting and in doing accounting, where many small numbers need to be added and subtracted accurately to give possibly much larger final numbers. 

Remind students that they will be expected to report the proper number of significant figures on assignment and test problems. Significant Figures in this Text 

In this textbook, most numbers are assumed to have three significant figures. Furthermore, consistent numbers of significant figures are used in all worked examples. You will note that an answer given to three digits is based on input good to at least three digits. If the input has fewer significant figures, the answer will also have fewer significant figures. Care is also taken that the number of significant figures is reasonable for the situation posed. In some topics, such as optics, more than three significant figures will be used. Finally, if a number is exact, such as the "2" in the formula, c = 2 r c = 2 r , it does not affect the number of significant figures in a calculation. Approximating Vast Numbers: a Trillion Dollars 

The U.S. federal deficit in the 2008 fiscal year was a little greater than $10 trillion. Most of us do not have any concept of how much even one trillion actually is. Suppose that you were given a trillion dollars in $100 bills. If you made 100-bill stacks, like that shown in [link] , and used them to evenly cover a football field (between the end zones), make an approximation of how high the money pile would become. (We will use feet/inches rather than meters here because football fields are measured in yards.) One of your friends says 3 in., while another says 10 ft. What do you think? A bank stack contains one hundred $100 bills, and is worth $10,000. How many bank stacks make up a trillion dollars? (Credit: Andrew Magill) Strategy 

When you imagine the situation, you probably envision thousands of small stacks of 100 wrapped $100 bills, such as you might see in movies or at a bank. Since this is an easy-to-approximate quantity, let us start there. We can find the volume of a stack of 100 bills, find out how many stacks make up one trillion dollars, and then set this volume equal to the area of the football field multiplied by the unknown height. Solution Calculate the volume of a stack of 100 bills. The dimensions of a single bill are approximately 3 in. by 6 in. A stack of 100 of these is about 0.5 in. thick. So the total volume of a stack of 100 bills is: volume of stack = length width height, volume of stack = 6 in . 3 in . 0 .5 in ., volume of stack = 9 in . 3 . volume of stack = length width height, volume of stack = 6 in . 3 in . 0 .5 in ., volume of stack = 9 in . 3 . 

Calculate the number of stacks. Note that a trillion dollars is equal to $ 1 10 12 $ 1 10 12 , and a stack of one-hundred $ 100 $ 100 bills is equal to $ 10 , 000 , $ 10 , 000 , or $ 1 10 4 $ 1 10 4 . The number of stacks you will have is: 

$ 1 10 12 $ 1 10 12 (a trillion dollars) / $ 1 10 4 $ 1 10 4 per stack = 1 10 8 1 10 8 stacks. 

Calculate the area of a football field in square inches. The area of a football field is 100 yd 50 yd 100 yd 50 yd , which gives 5 , 000 yd 2 5 , 000 yd 2 . Because we are working in inches, we need to convert square yards to square inches: 



Area = 5,000 yd 2 3 ft 1yd 3 ft 1yd 12 in . 1 foot 12 in . 1 foot = 6 , 480 , 000 in . 2 , Area 6 10 6 in . 2 . Area = 5,000 yd 2 3 ft 1yd 3 ft 1yd 12 in . 1 foot 12 in . 1 foot = 6 , 480 , 000 in . 2 , Area 6 10 6 in . 2 . 

This conversion gives us 6 10 6 in . 2 6 10 6 in . 2 for the area of the field. (Note that we are using only one significant figure in these calculations.) Calculate the total volume of the bills. The volume of all the $ 100 $ 100 -bill stacks is 9 in . 3 / stack 10 8 stacks = 9 10 8 in . 3 9 in . 3 / stack 10 8 stacks = 9 10 8 in . 3 . Calculate the height. To determine the height of the bills, use the equation: volume of bills = area of field height of money: Height of money = volume of bills area of field Height of money = 9 10 8 in . 3 6 10 6 in . 2 = 1.33 10 2 in . Height of money 1 10 2 in . = 100 in . volume of bills = area of field height of money: Height of money = volume of bills area of field Height of money = 9 10 8 in . 3 6 10 6 in . 2 = 1.33 10 2 in . Height of money 1 10 2 in . = 100 in . 

The height of the money will be about 100 in. high. Converting this value to feet gives 100 in . 1ft 12 in . = 8.33 ft 8 ft . 100 in . 1ft 12 in . = 8.33 ft 8 ft . Discussion 

The final approximate value is much higher than the early estimate of 3 in., but the other early estimate of 10 ft (120 in.) was roughly correct. How did the approximation measure up to your first guess? What can this exercise tell you in terms of rough "guesstimates" versus carefully calculated approximations? 

In the example above, the final approximate value is much higher than the first friend s early estimate of 3 in. However, the other friend s early estimate of 10 ft. (120 in.) was roughly correct. How did the approximation measure up to your first guess? What can this exercise suggest about the value of rough "guesstimates" versus carefully calculated approximations? 

In [link] , point out to students the importance of precision in their measurements. Greater precision allows measurements to be less uncertain, and therefore, a close approximation rather than a "guesstimate." Graphing in Physics 

Most results in science are presented in scientific journal articles using graphs. Graphs present data in a way that is easy to visualize for humans in general, especially someone unfamiliar with what is being studied. They are also useful for presenting large amounts of data or data with complicated trends in an easily-readable way. 

One commonly-used graph in physics and other sciences is the line graph , probably because it is the best graph for showing how one quantity changes in response to the other. Let s build a line graph based on the data in [link] , which shows the measured distance that a train travels from its station versus time. Our two variables , or things that change along the graph, are time in minutes, and distance from the station, in kilometers. Remember that measured data may not have perfect accuracy. Time (min) Distance from Station (km) 0 0 10 24 20 36 30 60 40 84 50 97 60 116 70 140 Draw the two axes. The horizontal axis, or x -axis, shows the independent variable , which is the variable that is controlled or manipulated. The vertical axis, or y -axis, shows the dependent variable , the non-manipulated variable that changes with (or is dependent on) the value of the independent variable. In the data above, time is the independent variable and should be plotted on the x -axis. Distance from the station is the dependent variable and should be plotted on the y -axis. Label each axes on the graph with the name of each variable, followed by the symbol for its units in parentheses. Be sure to leave room so that you can number each axis. In this example, use "Time (min)" as the label for the x -axis. 

Next, you must determine the best scale to use for numbering each axis. Because the time values on the x -axis are taken every 10 minutes, we could easily number the x -axis from 0 to 70 minutes with a tick mark every 10 minutes. Likewise, the y -axis scale should start low enough and continue high enough to include all of the "distance from station" values. A scale from 0 km to 160 km should suffice, perhaps with a tick mark every 10 km. 

In general, you want to pick a scale for both axes that 1) shows all of your data, and 2) makes it easy to identify trends in your data. If you make your scale too large, it will be harder to see how your data change. Likewise, the smaller and more fine you make your scale, the more space you will need to make the graph. The number of significant figures in the axis values should be coarser than the number of significant figures in the measurements. Now that your axes are ready, you can begin plotting your data. For the first data point, count along the x -axis until you find the 10 min tick mark. Then, count up from that point to the 10 km tick mark on the y -axis, and approximate where 22 km is along the y -axis. Place a dot at this location. Repeat for the other six data points ( [link] ). Add a title to the top of the graph to state what the graph is describing, such as the y -axis parameter vs. the x -axis parameter. In the graph shown here, the title is "train motion." It could also be titled distance of the train from the station vs. time. The graph of the train s distance from the station versus time from the exercise above. Finally, with data points now on the graph, you should draw a trend line ( [link] ). The trend line represents the dependence you think the graph represents, so that the person who looks at your graph can see how close it is to the real data. In the present case, since the data points look like they ought to fall on a straight line, you would draw a straight line as the trend line. Draw it to come closest to all the points. Real data may have some inaccuracies, and the plotted points may not all fall on the trend line. In some cases, none of the data points fall exactly on the trend line. The completed graph with the trend line included. 

[OL] The importance of bar graphs should also be mentioned as a useful way to show data relations when one variable is not continuous, such as in a frequency histogram, which compares how many data points fall into discrete categories. 

[OL] If students have difficulty understanding the difference between dependent and independent variables in the train example, explain that time is independent because it will continue to move forward at the same rate whether the train leaves the station or not. Analyzing a Graph Using Its Equation 

One way to get a quick snapshot of a dataset is to look at the equation of its trend line . If the graph produces a straight line, the equation of the trend line takes the form: y = m x + b y = m x + b 

The b in the equation is the y -intercept while the m in the equation is the slope . The y -intercept tells you at what y value the line intersects the y -axis. In the case of the graph above, the y -intercept occurs at 0, at the very beginning of the graph. The y -intercept, therefore, lets you know immediately where on the y -axis the plot line begins. 

The m in the equation is the slope. This value describes how much the line on the graph moves up or down on the y -axis along the line s length. The slope is found using the following equation: m = Y 2 Y 1 X 2 X 1 m = Y 2 Y 1 X 2 X 1 

In order to solve this equation, you need to pick two points on the line (preferably far apart on the line so the slope you calculate describes the line accurately). The quantities Y 2 and Y 1 represent the y -values from the two points on the line (not data points) that you picked, while X 2 and X 1 represent the two x -values of the those points. 

What can the slope value tell you about the graph? The slope of a perfectly horizontal line will equal 0, while the slope of a perfectly vertical line will be undefined because you cannot divide by 0. A positive slope indicates that the line moves up the y -axis as the x -value increases while a negative slope means that the line moves down the y -axis. The more negative or positive the slope is, the steeper the line moves up or down, respectively. The slope of our graph in [link] is calculated below based on the two endpoints of the line: 



m = Y 2 Y 1 X 2 X 1 m = ( 80 km ) ( 20 km ) ( 40 min ) ( 10 min ) m = 60 km 30 min m = 2.0 km/min m = Y 2 Y 1 X 2 X 1 m = ( 80 km ) ( 20 km ) ( 40 min ) ( 10 min ) m = 60 km 30 min m = 2.0 km/min 

Equation of line: y = ( 2.0 km/min ) x + 0 y = ( 2.0 km/min ) x + 0 

Because the x axis is time in minutes, we would actually be more likely to use the time t as the independent ( x- axis) variable and write the equation as y = ( 2.0 km/min ) t + 0. y = ( 2.0 km/min ) t + 0. 

The formula y = m x + b y = m x + b only applies to linear relationships , or ones that produce a straight line. Another common type of line in physics is the quadratic relationship , which occurs when one of the variables is squared. One quadratic relationship in physics is the relation between the speed of an object its centripetal acceleration, which is used to determine the force needed to keep an object moving in a circle. Another common relationship in physics is the inverse relationship , in which one variable decreases whenever the other variable increases. An example in physics is Coulomb s law. As the distance between two charged objects increases, the electrical force between the two charged objects decreases. Inverse proportionality , such the relation between x and y in the equation y = k / x y = k / x 

for some number k , is one particular kind of inverse relationship. A third commonly-seen relationship is the exponential relationship , in which a change in the independent variable produces a proportional change in the dependent variable. As the value of the dependent variable gets larger, its rate of growth also increases. For example, bacteria often reproduce at an exponential rate when grown under ideal conditions. As each generation passes, there are more and more bacteria to reproduce. As a result, the growth rate of the bacterial population increases every generation. ( [link] ). Examples of (a) linear, (b) quadratic, (c) inverse, and (d) exponential relationship graphs. Using Logarithmic Scales in Graphing 

Sometimes a variable can have a very large range of values. This presents a problem when you re trying to figure out the best scale to use for your graph s axes. One option is to use a logarithmic (log) scale . In a logarithmic scale, the value each mark labels is the previous mark s value multiplied by some constant. For a log base 10 scale, each mark labels a value that is 10 times the value of the mark before it. Therefore, a base 10 logarithmic scale would be numbered: 0, 10, 100, 1000, etc. You can see how the logarithmic scale covers a much larger range of values than the corresponding linear scale, in which the marks would label the values 0, 10, 20, 30, and so on. 

If you use a logarithmic scale on one axis of the graph and a linear scale on the other axis, you are using a semi-log plot . The Richter scale, which measures the strength of earthquakes, uses a semi-log plot. The degree of ground movement is plotted on a logarithmic scale against the assigned intensity level of the earthquake, which ranges linearly from 1-10 (see [link] (a) ). 

If a graph has both axes in a logarithmic scale, then it is referred to as a log-log plot . The relationship between the wavelength and frequency of electromagnetic radiation such as light is usually shown as a log-log plot (see [link] (b) ). Log-log plots are also commonly used to describe exponential functions, such as radioactive decay. (a) The Richter scale uses a log base 10 scale on its y-axis (microns of amplified maximum ground motion). (b) The relationship between the frequency and wavelength of electromagnetic radiation can be plotted as a straight line if a log-log plot is used. Graphing Lines 

In this simulation you will examine how changing the slope and y-intercept of an equation changes the appearance of a plotted line. Select slope-intercept form and drag the blue circles along the line to change the line s characteristics. Then, play the line game and see if you can determine the slope or y-intercept of a given line. Click here for the simulation 

[link] Check Your Understanding 

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Use the Check Your Understanding questions to assess students achievement of the sections learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify which and direct students to the relevant content. Section Summary Physical quantities are a characteristic or property of an object that can be measured or calculated from other measurements. The four fundamental units we will use in this textbook are the meter (for length), the kilogram (for mass), the second (for time), and the ampere (for electric current). These units are part of the metric system, which uses powers of 10 to relate quantities over the vast ranges encountered in nature. Unit conversions involve changing a value expressed in one type of unit to another type of unit. This is done by using conversion factors, which are ratios relating equal quantities of different units. Accuracy of a measured value refers to how close a measurement is to the correct value. The uncertainty in a measurement is an estimate of the amount by which the measurement result may differ from this value. Precision of measured values refers to how close the agreement is between repeated measurements. Significant figures express the precision of a measuring tool. When multiplying or dividing measured values, the final answer can contain only as many significant figures as the least precise value. When adding or subtracting measured values, the final answer cannot contain more decimal places than the least precise value. Key Equations Slope intercept form y = m x + b y = m x + b Quadratic formula y = a x 2 + b x + c y = a x 2 + b x + c Positive exponential formula y = a x y = a x Negative exponential formula y = a x y = a x Concept Items 

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[link] Performance Task Create a new system of units to describe something that interests you. Your unit should be described using at least two subunits. For example, you can decide to measure the quality of songs using a new unit called song awesomeness. Song awesomeness is measured by: 1) the number of song downloads and 2) the number of times the song was used in movies. Create an equation that shows how to calculate your unit. Then, using your equation, create a sample dataset that you could graph. Are your two subunits related linearly, quadratically or inversely? Test Prep Multiple Choice 

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[link] Glossary accuracy how close a measurement is to the correct value for that measurement ampere the SI unit for electrical current constant a quantity that does not change conversion factor a ratio expressing how many of one unit are equal to another unit dependent variable the vertical, or y -axis, variable, which changes with (or is dependent on) the value of the independent variable derived units units that are derived by combining the fundamental physical units English units (also known as the customary or imperial system) system of measurement used in the United States; includes units of measurement such as feet, gallons, degrees Fahrenheit, and pounds exponential relationship relation between variables in which a constant change in the independent variable is accompanied by change in the dependent variable that is proportional to the value it already had fundamental physical units the seven fundamental physical units in the SI system of units are length, mass, time, electric current, temperature, amount of a substance, and luminous intensity. independent variable the horizontal, or x -axis, variable, which is not influence by the second variable on the graph, the dependent variable inverse proportionality a relation between two variables expressible by an equation of the form y = k / x y = k / x where k stays constant when x and y change; the special form of inverse relationship that satisfies this equation inverse relationship any relation between variables where one variable decreases as the other variable increases kilogram the SI unit for mass (abbreviated kg) linear relationships relation between variables that produce a straight line when graphed logarithmic scale a graphing scale in which each tick on an axis is the previous tick multiplied by some value. log-log plot a plot that uses a logarithmic scale in both axes meter the SI unit for length, abbreviated (m) method of adding percents calculating the percent uncertainty of a quantity in multiplication or division by adding the percent uncertainties in the quantities being added or divided order of magnitude the size of a quantity in terms of its power of 10 when expressed in scientific notation precision how well repeated measurements generate the same or closely similar results quadratic relationship relation between variables that can be expressed in the form y = a x 2 + b x + c y = a x 2 + b x + c , which produces a curved line when graphed scientific notation way of writing numbers that are too large or small to be conveniently written in simple decimal form; the measurement is multiplied by a power of 10, which indicates the number of placeholder zeros in the measurement second the SI unit for time, abbreviated (s) semi-log plot A plot that uses a logarithmic scale on one axis of the graph and a linear scale on the other axis. standard international (SI) units (also known as the metric system) the international system of units that scientists in most countries have agreed to use; includes units such as meters, liters, and grams significant figures when writing a number, the digits, or number of digits, that express the precision of a measuring tool used to measure the number slope the ratio of the change of a graph on the y axis to the change along the x- axis, the value of m in the equation of a line, y = m x + b y = m x + b uncertainty a quantitative measure of how much measured values deviate from a standard or expected value y -intercept the point where a plot line intersects the y-axisIntroduction Introduction In this chapter you will learn about: Vector Addition and Subtraction: Graphical Methods Vector Addition and Subtraction: Analytical Methods Projectile Motion Inclined Planes Simple Harmonic Motion class="summary" title="Section Summary" class="key-equations" title="Key Equations" class="concept" title="Concept Items" class="critical-thinking" title="Critical Thinking Items" class="problem" title="Problems" class="performance" title="Performance Task" class="multiple-choice" title="Multiple Choice" class="short-answer" title="Short Answer" class="extended-response" title="Extended Response" 

Physics learning objectives come from 112.39 (c) Knowledge and Skills Billiard balls on a pool table are in motion after being hit with a cue stick. (credit: Popperipopp, Wikimedia Commons) 

Point out to the students that most motion is in two or three dimensions and can be described in a similar fashion to one-dimensional motion. This chapter is about motion in two dimensions. Motion in two dimensions can be analyzed using vectors. We will first learn the practical skills of adding and subtracting vectors graphically (in drawings) and analytically (with math). Once we re able to work with two-dimensional vectors, we can then apply these skills to problems of projectile motion, inclined planes, and harmonic motion. 

In Chapter 2, we learned to distinguish between vectors and scalars; the difference being that a vector has magnitude and direction, whereas a scalar has only magnitude. We learned how to deal with vectors in physics by working straightforward one-dimensional vector problems, which may be treated mathematically in the same as scalars. In this chapter, we ll use vectors to expand our understanding of forces and motion into two dimensions. Most real-world physics problems (such as with the game of pool pictured here) are, after all, either two- or three-dimensional problems and physics is most useful when applied to real physical scenarios. We start by learning the practical skills of graphically adding and subtracting vectors (by using drawings) and analytically (with math). Once we re able to work with two-dimensional vectors, we apply these skills to problems of projectile motion, inclined planes, and harmonic motion. 

Before students begin this chapter, review the concepts of displacement, velocity, acceleration, vectors, representing vectors, free-body diagrams.Simple Harmonic Motion Simple Harmonic Motion Section Learning Objectives 

By the end of this section, you will be able to: Describe Hooke s law and Simple Harmonic Motion Describe periodic motion, oscillations, amplitude, frequency, and period Solve problems in simple harmonic motion involving springs and pendulums 

The learning objectives in this section will help your students master the following TEKS: (7) Science concepts. The student knows the characteristics and behavior of waves. The student is expected to: (7A) : examine and describe oscillatory motion and wave propagation in various types of media Section Key Terms amplitude deformation equilibrium position frequency Hooke s law oscillate period periodic motion restoring force simple harmonic motion simple pendulum Hooke s Law and Simple Harmonic Motion 

Imagine a car parked against a wall. If a bulldozer pushes the car into the wall, the car will not move but it will noticeably change shape. A change in shape due to the application of a force is a deformation . Even very small forces are known to cause some deformation. For small deformations, two important things can happen. First, unlike the car and bulldozer example, the object returns to its original shape when the force is removed. Second, the size of the deformation is proportional to the force. This second property is known as Hooke s law . In equation form, Hooke s law is F = k x F = k x 

where x is the amount of deformation (the change in length, for example) produced by the restoring force F , and k is a constant that depends on the shape and composition of the object. The restoring force is the force that brings the object back to its equilibrium position; the minus sign is there because the restoring force acts in the direction opposite to the displacement. Note that the restoring force is proportional to the deformation x . The deformation can also be thought of as a displacement from equilibrium. It is a change in position due to a force. In the absence of force, the object would rest at its equilibrium position. The force constant k is related to the stiffness of a system. The larger the force constant, the stiffer the system. A stiffer system is more difficult to deform and requires a greater restoring force. The units of k are newtons per meter (N/m). One of the most common uses of Hooke s law is solving problems involving springs and pendulums, which we will cover at the end of this section. 

[BL] Review the concept of force. 

[BL] [OL] [AL] Introduce Hooke s law and force constant of a spring. Oscillations and Periodic Motion 

What do an ocean buoy, a child in a swing, a guitar, and the beating of hearts all have in common? They all oscillate . That is, they move back and forth between two points, like the ruler illustrated in [link] . All oscillations involve force. For example, you push a child in a swing to get the motion started. A ruler is displaced from its equilibrium position. 

[BL] [OL] [AL] Find springs or rubber bands with different amounts of stiffness. Ask students to attach weights to these to construct oscillators. Introduce the terms frequency and time period. Ask students to observe how the stiffness of the spring affects them. How does mass of the system affect them? How does the initial force applied affect them? 

Newton s first law implies that an object oscillating back and forth is experiencing forces. Without force, the object would move in a straight line at a constant speed rather than oscillate. Consider, for example, plucking a plastic ruler to the left as shown in [link] . The deformation of the ruler creates a force in the opposite direction, known as a restoring force . Once released, the restoring force causes the ruler to move back toward its stable equilibrium position, where the net force on it is zero. However, by the time the ruler gets there, it gains momentum and continues to move to the right, producing the opposite deformation. It is then forced to the left, back through equilibrium, and the process is repeated until it gradually loses all of its energy. The simplest oscillations occur when the restoring force is directly proportional to displacement. Recall that Hooke s law describes this situation with the equation F = kx . Therefore, Hooke s law describes and applies to the simplest case of oscillation, known as simple harmonic motion . (a) The plastic ruler has been released, and the restoring force is returning the ruler to its equilibrium position. (b) The net force is zero at the equilibrium position, but the ruler has momentum and continues to move to the right. (c) The restoring force is in the opposite direction. It stops the ruler and moves it back toward equilibrium again. (d) Now the ruler has momentum to the left. (e) In the absence of damping (caused by frictional forces), the ruler reaches its original position. From there, the motion will repeat itself. 

When you pluck a guitar string, the resulting sound has a steady tone and lasts a long time. Each vibration of the string takes the same time as the previous one. Periodic motion is a motion that repeats itself at regular time intervals, such as with an object bobbing up and down on a spring or a pendulum swinging back and forth. The time to complete one oscillation (a complete cycle of motion) remains constant and is called the period T . Its units are usually seconds. 

Frequency f is the number of oscillations per unit time. The SI unit for frequency is the hertz (Hz), defined as the number of oscillations per second. The relationship between frequency and period is f = 1 / T f = 1 / T 

As you can see from the equation, frequency and period are different ways of expressing the same concept. For example, if you get a paycheck twice a month, you could say that the frequency of payment is two per month, or that the period between checks is half a month. 

If there is no friction to slow it down, then an object in simple motion will oscillate forever with equal displacement on either side of the equilibrium position. The equilibrium position is where the object would naturally rest in the absence of force. The maximum displacement from equilibrium is called the amplitude X . The units for amplitude and displacement are the same, but depend on the type of oscillation. For the object on the spring, shown in [link] , the units of amplitude and displacement are meters. An object attached to a spring sliding on a frictionless surface is a simple harmonic oscillator. When displaced from equilibrium, the object performs simple harmonic motion that has an amplitude X and a period T . The object s maximum speed occurs as it passes through equilibrium. The stiffer the spring is, the smaller the period T . The greater the mass of the object is, the greater the period T . 

The mass m and the force constant k are the only factors that affect the period and frequency of simple harmonic motion. The period of a simple harmonic oscillator is given by T = 2 m k T = 2 m k 

and, because f = 1/ T , the frequency of a simple harmonic oscillator is f = 1 2 k m f = 1 2 k m Introduction to Harmonic Motion 

This video shows how to graph the displacement of a spring in the x-direction over time, based on the period. Watch the first ten minutes of the video (you can stop when the narrator begins to cover calculus). 

[link] Solving Spring and Pendulum Problems with Simple Harmonic Motion 

Before solving problems with springs and pendulums, it is important to first get an understanding of how a pendulum works. [link] provides a useful illustration of a simple pendulum. A simple pendulum has a small-diameter bob and a string that has a very small mass but is strong enough not to stretch. The linear displacement from equilibrium is s, the length of the arc. Also shown are the forces on the bob, which result in a net force of mg sin toward the equilibrium position that is, a restoring force. 

[BL] Review simple harmonic motion. 

Everyday examples of pendulums include old-fashioned clocks, a child s swing, or the sinker on a fishing line. For small displacements of less than 15 degrees, a pendulum experiences simple harmonic oscillation, meaning that its restoring force is directly proportional to its displacement. A pendulum in simple harmonic motion is called a simple pendulum . A pendulum has an object with a small mass, also known as the pendulum bob, which hangs from a light wire or string. The equilibrium position for a pendulum is where the angle is zero (that is, when the pendulum is hanging straight down). It makes sense that without any force applied, this is where the pendulum bob would rest. 

[BL] [OL] [AL] Construct simple pendulums of different lengths. Ask students to measure their time periods or frequencies. Are they constant for a given pendulum? How does the mass impact the frequency? How does the initial displacement affect it? What happens if a small push is given to the pendulum to get it started? Does that change the frequency? In what way does the length affect the frequency? 

The displacement of the pendulum bob is the arc length s . The weight m g has components m g cos along the string and m g sin tangent to the arc. Tension in the string exactly cancels the component m g cos parallel to the string. This leaves a net restoring force back toward the equilibrium position that runs tangent to the arc and equals m g sin . 

For a simple pendulum, The period is T = 2 L g . T = 2 L g . 

The only things that affect the period of a simple pendulum are its length and the acceleration due to gravity. The period is completely independent of other factors, such as mass or amplitude. However, note that T does depend on g . This means that if we know the length of a pendulum, we can actually use it to measure gravity! This will come in useful in [link] . 

Tension is represented by the variable T , and period is represented by the variable T . It is important not to confuse the two, since tension is a force and period is a length of time. Measuring Acceleration due to Gravity: The Period of a Pendulum 

What is the acceleration due to gravity in a region where a simple pendulum having a length 75.000 cm has a period of 1.7357 s? Strategy 

We are asked to find g given the period T and the length L of a pendulum. We can solve T = 2 L g T = 2 L g for g , assuming that the angle of deflection is less than 15 degrees. Recall that when the angle of deflection is less than 15 degrees, the pendulum is considered to be in simple harmonic motion, allowing us to use this equation. Solution Square T = 2 L g T = 2 L g and solve for g : g = 4 2 L T 2 g = 4 2 L T 2 Substitute known values into the new equation: g = 4 2 0.75000 m ( 1.7357 s ) 2 g = 4 2 0.75000 m ( 1.7357 s ) 2 Calculate to find g : g = 9.8281 m / s 2 . g = 9.8281 m / s 2 . Discussion 

This method for determining g can be very accurate. This is why length and period are given to five digits in this example. Hooke s Law: How Stiff Are Car Springs? 

What is the force constant for the suspension system of a car, like that shown in [link] , that settles 1.20 cm when an 80.0-kg person gets in? A car in a parking lot. (credit: exfordy, Flickr) Strategy 

Consider the car to be in its equilibrium position x = 0 before the person gets in. The car then settles down 1.20 cm, which means it is displaced to a position x = 1.20 10 2 m. 

At that point, the springs supply a restoring force F equal to the person s weight 

w = m g = (80.0 kg)(9.80 m/s 2 ) = 784 N. We take this force to be F in Hooke s law. 

Knowing F and x , we can then solve for the force constant k . Solution 

Solve Hooke s law, F = kx , for k : k = F x k = F x 

Substitute known values and solve for k : k = 784 N 1.20 10 2 m = 6.53 10 4 N/m k = 784 N 1.20 10 2 m = 6.53 10 4 N/m Discussion 

Note that F and x have opposite signs because they are in opposite directions the restoring force is up, and the displacement is down. Also, note that the car would oscillate up and down when the person got in, if it were not for the shock absorbers. Bouncing cars are a sure sign of bad shock absorbers. Practice Problems 

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Use a simple pendulum to find the acceleration due to gravity g in your home or classroom. 1 string 1 stopwatch 1 small dense object Cut a piece of a string or dental floss so that it is about 1 m long. Attach a small object of high density to the end of the string (for example, a metal nut or a car key). Starting at an angle of less than 10 degrees, allow the pendulum to swing and measure the pendulum s period for 10 oscillations using a stopwatch. Calculate g . 

[link] Section Summary An oscillation is a back and forth motion of an object between two points of deformation. An oscillation may create a wave, which is a disturbance that propagates from where it was created. The simplest type of oscillations are related to systems that can be described by Hooke s law Periodic motion is a repetitious oscillation. The time for one oscillation is the period T The number of oscillations per unit time is the frequency A mass m suspended by a wire of length L is a simple pendulum and undergoes simple harmonic motion for amplitudes less than about 15 degrees. Key Equations Hooke s law F = k x F = k x period in simple harmonic motion T = 2 m k T = 2 m k frequency in simple harmonic motion f = 1 2 k m f = 1 2 k m period of a simple pendulum T = 2 L g T = 2 L g Check Your Understanding 

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[AL] Ask two students to demonstrate pushing a table from two different directions. Ask students what they feel the direction of resultant motion will be. How would they represent this graphically? Recall that a vector s magnitude is represented by the length of the arrow. Demonstrate the head-to-tail method of adding vectors, using the example given in the chapter. Ask students to practice this method of addition using a scale and a protractor. 

[BL] [OL] [AL] Ask students if anything changes by moving the vector from one place to another on a graph. How about the order of addition? Would that make a difference? Introduce negative of a vector and vector subtraction. 

Construct a seconds pendulum (pendulum with time period 2 seconds). Test Prep Multiple Choice 

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[link] Glossary amplitude the maximum displacement from the equilibrium position of an object oscillating around the equilibrium position deformation displacement from equilibrium, or change in shape due to the application of force equilibrium position where an object would naturally rest in the absence of force frequency number of events per unit of time Hooke s law proportional relationship between the force F on a material and the deformation L L it causes, F = k L F = k L oscillate moving back and forth regularly between two points period time it takes to complete one oscillation periodic motion motion that repeats itself at regular time intervals restoring force force acting in opposition to the force caused by a deformation simple harmonic motion the oscillatory motion in a system where the net force can be described by Hooke s law simple pendulum an object with a small mass suspended from a light wire or stringProjectile Motion Projectile Motion Section Learning Objectives 

By the end of this section, you will be able to: Describe the properties of projectile motion Apply kinematic equations and vectors to solve problems involving projectile motion 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in two dimensions for a variety of situations. The student is expected to: (4C) : analyze and describe accelerated motion in two dimensions using equations Section Key Terms air resistance maximum height (of a projectile) projectile projectile motion range trajectory Properties of Projectile Motion 

Projectile motion is the motion of an object thrown (projected) into the air. After the initial force that launches the object, it only experiences the force of gravity. The object is called a projectile , and its path is called its trajectory . As an object travels through the air, it encounters a frictional force that slows its motion called air resistance . Air resistance does significantly alter trajectory motion, but due to the difficulty in calculation, it is ignored in introductory physics. 

[BL] [OL] Review addition of vectors graphically and analytically. 

[BL] [OL] [AL] Explain the term projectile motion . Ask students to guess what the motion of a projectile might depend on? Is the initial velocity important? Is the angle important? How will these things affect its height and the distance it covers? Introduce the concept of air resistance. Review kinematic equations. 

The most important concept in projectile motion is that horizontal and vertical motions are independent , meaning that they don t influence one another. [link] compares a cannonball in free fall (in blue) to a cannonball launched horizontally in projectile motion (in red). You can see that the cannonball in free fall falls at the same rate as the cannonball in projectile motion. Keep in mind that if the cannon launched the ball with any vertical component to the velocity, the vertical displacements would not line up perfectly. 

Since vertical and horizontal motions are independent, we can analyze them separately, along perpendicular axes. To do this, we separate projectile motion into the two components of its motion, one along the horizontal axis and the other along the vertical. The diagram shows the projectile motion of a cannonball shot at a horizontal angle versus one dropped with no horizontal velocity. Note that both cannonballs have the same vertical position over time. 

We ll call the horizontal axis the x -axis and the vertical axis the y -axis. For notation, d is the total displacement, and x and y are its components along the horizontal and vertical axes. The magnitudes of these vectors are x and y , as illustrated in [link] . A boy kicks a ball at angle , and it is displaced a distance of s along its trajectory. 

As usual, we use velocity, acceleration, and displacement to describe motion. We must also find the components of these variables along the x - and y -axes. The components of acceleration are then very simple: a y = g = 9.80 m/s 2 . (Note that this definition defines the upwards direction as positive). Because gravity is vertical, a x = 0. Both accelerations are constant, so we can use the kinematic equations. For review, the kinematic equations from a previous chapter are summarized in [link] . Summary of Kinematic Equations (constant a) x = x 0 + v a v g t x = x 0 + v a v g t (when a = 0 a = 0 ) v a v g = v 0 + v 2 v a v g = v 0 + v 2 (when a = 0 a = 0 ) v = v 0 + a t v = v 0 + a t x = x 0 + v 0 t + 1 2 a t 2 x = x 0 + v 0 t + 1 2 a t 2 v 2 = v 0 2 + 2 a ( x x 0 ) v 2 = v 0 2 + 2 a ( x x 0 ) 

Where x is position, x 0 is initial position, v is velocity, v avg is average velocity, t is time and a is acceleration. Solve Problems Involving Projectile Motion 

The following steps are used to analyze projectile motion: Separate the motion into horizontal and vertical components along the x- and y-axes. These axes are perpendicular, so A x = A cos A x = A cos and A y = A sin A y = A sin are used. The magnitudes of the displacement s s along x- and y-axes are called x x and y . y . The magnitudes of the components of the velocity v v are v x = v cos v x = v cos and v y = v sin v y = v sin , where v v is the magnitude of the velocity and is its direction. Initial values are denoted with a subscript 0. Treat the motion as two independent one-dimensional motions, one horizontal and the other vertical. The kinematic equations for horizontal and vertical motion take the following forms: Horizontal Motion ( a x = 0 ) x = x 0 + v x t v x = v 0 x = v x = velocity is a constant Horizontal Motion ( a x = 0 ) x = x 0 + v x t v x = v 0 x = v x = velocity is a constant Vertical motion (assuming positive is up a y = g = 9.80 m/s 2 a y = g = 9.80 m/s 2 ) y = y 0 + 1 2 ( v 0 y + v y ) t v y = v 0 y g t y = y 0 + v 0 y t 1 2 g t 2 v y 2 = v 0 y 2 2 g ( y y 0 ) y = y 0 + 1 2 ( v 0 y + v y ) t v y = v 0 y g t y = y 0 + v 0 y t 1 2 g t 2 v y 2 = v 0 y 2 2 g ( y y 0 ) Solve for the unknowns in the two separate motions (one horizontal and one vertical). Note that the only common variable between the motions is time t t . The problem solving procedures here are the same as for one-dimensional kinematics. Recombine the two motions to find the total displacement s s and velocity v v . We can use the analytical method of vector addition, which uses A = A x 2 + A y 2 A = A x 2 + A y 2 and = tan 1 ( A y / A x ) = tan 1 ( A y / A x ) to find the magnitude and direction of the total displacement and velocity. Displacement: d = x 2 + y 2 = tan 1 ( y / x ) Velocity: v = v x 2 + v y 2 v = tan 1 ( v y / v x ) Displacement: d = x 2 + y 2 = tan 1 ( y / x ) Velocity: v = v x 2 + v y 2 v = tan 1 ( v y / v x ) is the direction of the displacement d d , and v v is the direction of the velocity v v . (See [link] (a) We analyze two-dimensional projectile motion by breaking it into two independent one-dimensional motions along the vertical and horizontal axes. (b) The horizontal motion is simple, because a x = 0 a x = 0 and v x v x is thus constant. (c) The velocity in the vertical direction begins to decrease as the object rises; at its highest point, the vertical velocity is zero. As the object falls towards the Earth again, the vertical velocity increases again in magnitude but points in the opposite direction to the initial vertical velocity. (d) The x - and y -motions are recombined to give the total velocity at any given point on the trajectory. 

Demonstrate the path of a projectile by doing a simple demonstration. Toss a dark beanbag in front of a white board so that students can get a good look at the projectile path. Vary the toss angles, so different paths can be displayed. This demonstration could be extended by using digital photography. Draw a reference grid on the whiteboard , then toss the bag at different angles while taking a video. Replay this in slow motion to observe and compare the altitudes and trajectories. 

For problems of projectile motion, it is important to set up a coordinate system. The first step is to choose an initial position for x x and y y . Usually, it is simplest to set the initial position of the object so that x 0 = 0 x 0 = 0 and y 0 = 0 y 0 = 0 . Projectile at an Angle 

This video presents an example of finding the displacement (or range) of a projectile launched at an angle. It also reviews basic trigonometry for finding the sine, cosine and tangent of an angle. 

[link] A Fireworks Projectile Explodes High and Away 

During a fireworks display like the one illustrated in [link] , a shell is shot into the air with an initial speed of 70.0 m/s at an angle of 75 above the horizontal. The fuse is timed to ignite the shell just as it reaches its highest point above the ground. (a) Calculate the height at which the shell explodes. (b) How much time passed between the launch of the shell and the explosion? (c) What is the horizontal displacement of the shell when it explodes? The diagram shows the trajectory of a fireworks shell. Strategy 

The motion can be broken into horizontal and vertical motions in which a x = 0 a x = 0 and a y = g a y = g . We can then define x 0 x 0 and y 0 y 0 to be zero and solve for the maximum height . Solution for (a) 

By height we mean the altitude or vertical position y y above the starting point. The highest point in any trajectory, the maximum height, is reached when v y = 0 v y = 0 ; this is the moment when the vertical velocity switches from positive (upwards) to negative (downwards). Since we know the initial velocity, initial position, and the value of v y when the firework reaches its maximum height, we use the following equation to find y y : v y 2 = v 0 y 2 2 g ( y y 0 ) . v y 2 = v 0 y 2 2 g ( y y 0 ) . 

Because y 0 y 0 and v y v y are both zero, the equation simplifies to 0 = v 0 y 2 2 g y . 0 = v 0 y 2 2 g y . 

Solving for y y gives y = v 0 y 2 2 g . y = v 0 y 2 2 g . 

Now we must find v 0 y v 0 y , the component of the initial velocity in the y -direction. It is given by v 0 y = v 0 sin v 0 y = v 0 sin , where v 0 y v 0 y is the initial velocity of 70.0 m/s, and = 75 = 75 is the initial angle. Thus, v 0 y = v 0 sin 0 = ( 70.0 m/s ) ( sin 75 ) = 67.6 m/s v 0 y = v 0 sin 0 = ( 70.0 m/s ) ( sin 75 ) = 67.6 m/s 

and y y is y = ( 67.6 m/s ) 2 2 ( 9.80 m/s 2 ) , y = ( 67.6 m/s ) 2 2 ( 9.80 m/s 2 ) , 

so that y = 233 m . y = 233 m . Discussion for (a) 

Since up is positive, the initial velocity and maximum height are positive, but the acceleration due to gravity is negative. The maximum height depends only on the vertical component of the initial velocity. The numbers in this example are reasonable for large fireworks displays, the shells of which do reach such heights before exploding. Solution for (b) 

There is more than one way to solve for the time to the highest point. In this case, the easiest method is to use y = y 0 + 1 2 ( v 0 y + v y ) t y = y 0 + 1 2 ( v 0 y + v y ) t . Because y 0 y 0 is zero, this equation reduces to y = 1 2 ( v 0 y + v y ) t y = 1 2 ( v 0 y + v y ) t 

Note that the final vertical velocity, v y v y , at the highest point is zero. Therefore, t = 2 y ( v 0 y + v y ) = 2 ( 233 m) ( 67.6 m/s ) = 6.90 s t = 2 y ( v 0 y + v y ) = 2 ( 233 m) ( 67.6 m/s ) = 6.90 s Discussion for (b) 

This time is also reasonable for large fireworks. When you are able to see the launch of fireworks, you will notice several seconds pass before the shell explodes. (Another way of finding the time is by using y = y 0 + v 0 y t 1 2 g t 2 y = y 0 + v 0 y t 1 2 g t 2 , and solving the quadratic equation for t t .) Solution for (c) 

Because air resistance is negligible, a x = 0 a x = 0 and the horizontal velocity is constant. The horizontal displacement is horizontal velocity multiplied by time as given by x = x 0 + v x t x = x 0 + v x t , where x 0 x 0 is equal to zero: x = v x t , x = v x t , 

where v x v x is the x -component of the velocity, which is given by v x = v 0 cos 0 . v x = v 0 cos 0 . Now, v x = v 0 cos 0 = ( 70.0 m/s ) ( cos 75 ) = 18.1 m/s . v x = v 0 cos 0 = ( 70.0 m/s ) ( cos 75 ) = 18.1 m/s . 

The time t t for both motions is the same, and so x x is x = ( 18.1 m/s ) ( 6.90 s ) = 125 m x = ( 18.1 m/s ) ( 6.90 s ) = 125 m Discussion for (c) 

The horizontal motion is a constant velocity in the absence of air resistance. The horizontal displacement found here could be useful in keeping the fireworks fragments from falling on spectators. Once the shell explodes, air resistance has a major effect, and many fragments will land directly below, while some of the fragments may now have a velocity in the x direction due to the forces of the explosion. 

[BL] [OL] [AL] Talk about the sample problem. Discuss the variables or unknowns in each part of the problem Ask students which kinematic equations may be best suited to solve the different parts of the problem. 

The expression we found for y y while solving part (a) of the previous problem works for any projectile motion problem where air resistance is negligible. Call the maximum height y = h y = h ; then, h = v 0 y 2 2 g . h = v 0 y 2 2 g . 

This equation defines the maximum height of a projectile . The maximum height depends only on the vertical component of the initial velocity. Calculating Projectile Motion: Hot Rock Projectile 

Suppose a large rock is ejected from a volcano, as illustrated in [link] , with a speed of 25.0 m / s 25.0 m / s and at an angle 3 5 3 5 above the horizontal. The rock strikes the side of the volcano at an altitude 20.0 m lower than its starting point. (a) Calculate the time it takes the rock to follow this path. The diagram shows the projectile motion of a large rock from a volcano. Strategy 

Breaking this two-dimensional motion into two independent one-dimensional motions will allow us to solve for the time. The time a projectile is in the air depends only on its vertical motion. Solution 

While the rock is in the air, it rises and then falls to a final position 20.0 m lower than its starting altitude. We can find the time for this by using y = y 0 + v 0 y t 1 2 g t 2 y = y 0 + v 0 y t 1 2 g t 2 

If we take the initial position y 0 y 0 to be zero, then the final position is y = 20.0 m . y = 20.0 m . Now the initial vertical velocity is the vertical component of the initial velocity, found from 

v 0 y = v 0 sin 0 = ( 25.0 m/s ) ( sin 35 ) = 14.3 m/s . v 0 y = v 0 sin 0 = ( 25.0 m/s ) ( sin 35 ) = 14.3 m/s . 

Substituting known values yields 20.0 m = ( 14.3 m/s) t ( 4.90 m/s 2 ) t 2 20.0 m = ( 14.3 m/s) t ( 4.90 m/s 2 ) t 2 

Rearranging terms gives a quadratic equation in t t : ( 4.90 m/s 2 ) t 2 ( 14 .3 m/s ) t ( 20.0 m ) = 0 ( 4.90 m/s 2 ) t 2 ( 14 .3 m/s ) t ( 20.0 m ) = 0 

This expression is a quadratic equation of the form a t 2 + b t + c = 0 a t 2 + b t + c = 0 , where the constants are a = 4.90, b = 14.3, and c = 20.0. Its solutions are given by the quadratic formula: t = b b 2 4 a c 2 a t = b b 2 4 a c 2 a 

This equation yields two solutions: t = 3.96 and t = 1.03. (You may verify these solutions as an exercise). The time is t = 3.96 s or 1.03 s. The negative value of time implies an event before the start of motion, so we discard it. Therefore, t = 3.96 s t = 3.96 s Discussion 

The time for projectile motion is completely determined by the vertical motion. So any projectile that has an initial vertical velocity of 14.3 m / s 14.3 m / s and lands 20.0 m below its starting altitude will spend 3.96 s in the air. Practice Problems 

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The fact that vertical and horizontal motions are independent of each other lets us predict the range of a projectile. The range is the horizontal distance R traveled by a projectile on level ground, as illustrated in [link] . Throughout history, people have been interested in finding the range of projectiles for practical purposes, such as aiming cannons. Trajectories of projectiles on level ground. (a) The greater the initial speed v 0 v 0 , the greater the range for a given initial angle. (b) The effect of initial angle 0 0 on the range of a projectile with a given initial speed. Note that any combination of trajectories that add to 90 degrees will have the same range in the absence of air resistance, although the maximum heights of those paths are different. 

How does the initial velocity of a projectile affect its range? Obviously, the greater the initial speed v 0 v 0 , the greater the range, as shown in the figure above. The initial angle 0 0 also has a dramatic effect on the range. When air resistance is negligible, the range R R of a projectile on level ground is R = v 0 2 sin 2 0 g R = v 0 2 sin 2 0 g 

where v 0 v 0 is the initial speed and 0 0 is the initial angle relative to the horizontal. It is important to note that the range doesn t apply to problems where the initial and final y position are different, or to cases where the object is launched perfectly horizontally. Projectile Motion 

In this simulation you will learn about projectile motion by blasting objects out of a cannon. You can choose between objects such as a tank shell, a golf ball or even a Buick. Experiment with changing the angle, initial speed, and mass, and adding in air resistance. Make a game out of this simulation by trying to hit the target. Click here for the simulation 

[link] Section Summary Projectile motion is the motion of an object through the air that is subject only to the acceleration of gravity. Projectile motion in the horizontal and vertical directions are independent of one another. The maximum height of an projectile is the highest altitude, or maximum displacement in the vertical position reached in the path of a projectile. The range is the maximum horizontal distance traveled by a projectile. To solve projectile problems: choose a coordinate system; analyze the motion in the vertical and horizontal direction separately; then, recombine the horizontal and vertical components using vector addition equations. Key Equations angle of displacement = tan 1 ( y / x ) = tan 1 ( y / x ) velocity v = v x 2 + v y 2 v = v x 2 + v y 2 angle of velocity v = tan 1 ( v y / v x ) v = tan 1 ( v y / v x ) maximum height h = v 0 y 2 2 g h = v 0 y 2 2 g range R = v 0 2 sin 2 0 g R = v 0 2 sin 2 0 g Check Your Understanding 

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Use the Check Your Understanding questions to assess whether students achieve the learning objectives for this section. If students are struggling with a specific objective, the Check Your Understanding will help identify which objective is causing the problem and direct students to the relevant content. Concept Items 

[link] Problems 

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[link] Critical Thinking 

[link] Test Prep Multiple Choice 

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[link] Test Prep Short Answer 

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[link] Test Prep Extended Response 

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[link] Glossary air resistance a frictional force that slows the motion of objects as they travel through the air; when solving basic physics problems, air resistance is assumed to be zero maximum height (of a projectile) the highest altitude, or maximum displacement in the vertical position reached in the path of a projectile projectile an object that travels through the air and experiences only acceleration due to gravity projectile motion the motion of an object that is subject only to the acceleration of gravity range the maximum horizontal distance that a projectile travels trajectory the path of a projectile through the airVector Addition and Subtraction: Graphical Methods Vector Addition and Subtraction: Graphical Methods Section Learning Objectives 

By the end of this section, you will be able to: Describe the graphical method of vector addition and subtraction Use the graphical method of vector addition and subtraction to solve physics problems 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in two dimensions for a variety of situations. The student is expected to: (4E) : develop and interpret free-body force diagrams Section Key Terms graphical method head (of a vector) head-to-tail method resultant resultant vector tail vector addition vector subtraction The Graphical Method of Vector Addition and Subtraction 

Recall that a vector is a quantity that has magnitude and direction. For example, displacement, velocity, acceleration, and force are all vectors. In one-dimensional or straight-line motion, the direction of a vector can be given simply by a plus or minus sign. Motion that is forward, to the right, or upward is usually considered to be positive (+); and motion that is backward, to the left, or downward is usually considered to be negative ( ). 

In two dimensions, a vector describes motion in two perpendicular directions (such as vertical and horizontal). For vertical and horizontal motion, each vector is made up of vertical and horizontal components. In a one-dimensional problem, one of the components simply has a value of zero. For two-dimensional vectors, we work with vectors by using a frame of reference such as a coordinate system. Just as with one-dimensional vectors, we graphically represent vectors with an arrow having a length proportional to the vector s magnitude and pointing in the direction that the vector points. 

[BL] [OL] Review vectors and free body diagrams. Recall how velocity, displacement and acceleration vectors are represented. 

[link] shows a graphical representation of a vector; the total displacement for a person walking in a city. The person first walks nine blocks east and then five blocks north. Her total displacement does not match her path to her final destination. The displacement simply connects her starting point with her ending point using a straight line, which is the shortest distance. We use the notation that a boldface symbol, such as D , stands for a vector. Its magnitude is represented by the symbol in italics, D , and its direction is given by an angle represented by the symbol . . Note that her displacement would be the same if she had begun by first walking five blocks north and then walking nine blocks east. 

In this text, we represent a vector with a boldface variable. For example, we represent a force with the vector F , which has both magnitude and direction. The magnitude of the vector is represented by the variable in italics, F , and the direction of the variable is given by the angle . . A person walks nine blocks east and five blocks north. The displacement is 10.3 blocks at an angle 29.1 29.1 north of east. 

The head-to-tail method is a graphical way to add vectors. The tail of the vector is the starting point of the vector, and the head (or tip) of a vector is the pointed end of the arrow. The following steps describe how to use the head-to-tail method for graphical vector addition . Let the x-axis represent the east-west direction. Using a ruler and protractor, draw an arrow to represent the first vector (nine blocks to the east), as shown in [link] (a) . The diagram shows a vector with a magnitude of nine units and a direction of 0 . Let the y-axis represent the north-south direction. Draw an arrow to represent the second vector (five blocks to the north). Place the tail of the second vector at the head of the first vector, as shown in [link] (b) . A vertical vector is added. If there are more than two vectors, continue to add the vectors head-to-tail as described in step 2. In this example, we have only two vectors, so we have finished placing arrows tip to tail. Draw an arrow from the tail of the first vector to the head of the last vector, as shown in [link] (c) . This is the resultant , or the sum, of the vectors. The diagram shows the resultant vector, a ruler, and protractor. To find the magnitude of the resultant, measure its length with a ruler. (When we deal with vectors analytically in the next section, the magnitude will be calculated by using the Pythagorean theorem.) To find the direction of the resultant, use a protractor to measure the angle it makes with the reference direction (in this case, the x -axis). When we deal with vectors analytically in the next section, the direction will be calculated by using trigonometry to find the angle. 

[AL] Ask two students to demonstrate pushing a table from two different directions. Ask students what they feel the direction of resultant motion will be. How would they represent this graphically? Recall that a vector s magnitude is represented by the length of the arrow. Demonstrate the head-to-tail method of adding vectors, using the example given in the chapter. Ask students to practice this method of addition using a scale and a protractor. 

[BL] [OL] [AL] Ask students if anything changes by moving the vector from one place to another on a graph. How about the order of addition? Would that make a difference? Introduce negative of a vector and vector subtraction. Visualizing Vector Addition Examples 

This video shows four graphical representations of vector addition and matches them to the correct vector addition formula. 

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Vector subtraction is done in the same way as vector addition with one small change. We add the first vector to the negative of the vector that needs to be subtracted. A negative vector has the same magnitude as the original vector, but points in the opposite direction (as shown in [link] ). Subtracting the vector B from the vector A , which is written as A B , is the same as A + ( B ). Since it does not matter in what order vectors are added, A B is also equal to ( B ) + A . This is true for scalars as well as vectors. For example: 5 2 = 5 + ( 2) = ( 2) + 5. The diagram shows a vector, B, and the negative of this vector, B. 

Global angles are calculated in the counterclockwise direction. The clockwise direction is considered negative. For example, an angle of 30 30 south of west is the same as the global angle 210 , 210 , which can also be expressed as 150 150 from the positive x-axis. Using the Graphical Method of Vector Addition and Subtraction to Solve Physics Problems 

Now that we have the skills to work with vectors in two dimensions, we can apply vector addition to graphically determine the resultant vector , which represents the total force. Consider an example of force involving two ice skaters pushing a third as seen in [link] . Part (a) shows an overhead view of two ice skaters pushing on a third. Forces are vectors and add like vectors, so the total force on the third skater is in the direction shown. In part (b), we see a free-body diagram representing the forces acting on the third skater. 

In problems where variables such as force are already known, the forces can be represented by making the length of the vectors proportional to the magnitudes of the forces. For this, you need to create a scale. For example, each centimeter of vector length could represent 50 N worth of force. Once you have the initial vectors drawn to scale, you can then use the head-to-tail method to draw the resultant vector. The length of the resultant can then be measured and converted back to the original units using the scale you created. 

You can tell by looking at the vectors in the free-body diagram in [link] that the two skaters are pushing on the third skater with equal-magnitude forces, since the length of their force vectors are the same. (Note, however, that the forces are not equal because they act in different directions). If, for example, each force had a magnitude of 400 N, then we would find the magnitude of the total external force acting on the third skater by finding the magnitude of the resultant vector. Since the forces act at a right angle to one another, we can use the Pythagorean theorem. For a triangle with sides a, b, and c, the Pythagorean theorem tells us that a 2 + b 2 = c 2 c = a 2 + b 2 a 2 + b 2 = c 2 c = a 2 + b 2 

Applying this theorem to the triangle made by F 1 , F 2 , and F tot in [link] , we get F tot 2 = F 1 2 + F 1 2 , F tot 2 = F 1 2 + F 1 2 , 

or F tot = ( 400 N ) 2 + ( 400 N ) 2 = 566 N F tot = ( 400 N ) 2 + ( 400 N ) 2 = 566 N 

Note that, if the vectors were not at a right angle to each other ( 90 90 to one another), we would not be able to use the Pythagorean theorem to find the magnitude of the resultant vector. Another scenario where adding two-dimensional vectors is necessary is for velocity, where the direction may not be purely east-west or north-south, but some combination of these two directions. In the next section, we cover how to solve this type of problem analytically. For now let s consider the problem graphically. Adding Vectors Graphically by Using the Head-to-Tail Method: A Woman Takes a Walk 

Use the graphical technique for adding vectors to find the total displacement of a person who walks the following three paths (displacements) on a flat field. First, he walks 25 m in a direction 49 49 north of east. Then, he walks 23 m heading 15 15 north of east. Finally, he turns and walks 32 m in a direction 68 68 south of east. Strategy 

Graphically represent each displacement vector with an arrow, labeling the first A , the second B , and the third C . Make the lengths proportional to the distance of the given displacement and orient the arrows as specified relative to an east-west line. Use the head-to-tail method outlined above to determine the magnitude and direction of the resultant displacement, which we ll call R . Solution 

(1) Draw the three displacement vectors, creating a convenient scale (such as 1 cm of vector length on paper equals 1 m in the problem), as shown in [link] . The three displacement vectors are drawn first. 

(2) Place the vectors head to tail, making sure not to change their magnitude or direction, as shown in [link] . Next, the vectors are placed head to tail. 

(3) Draw the resultant vector R from the tail of the first vector to the head of the last vector, as shown in [link] . The resultant vector is drawn . 

(4) Use a ruler to measure the magnitude of R , remembering to convert back to the units of meters using the scale. Use a protractor to measure the direction of R . While the direction of the vector can be specified in many ways, the easiest way is to measure the angle between the vector and the nearest horizontal or vertical axis. Since R is south of the eastward pointing axis (the x-axis), we flip the protractor upside down and measure the angle between the eastward axis and the vector, as illustrated in [link] . A ruler is used to measure the magnitude of R , and a protractor is used to measure the direction of R . 

In this case, the total displacement R has a magnitude of 50 m and points 7 7 south of east. Using its magnitude and direction, this vector can be expressed as 

R = 50 m 

and 

= 7 = 7 south of east Discussion 

The head-to-tail graphical method of vector addition works for any number of vectors. It is also important to note that it does not matter in what order the vectors are added. Changing the order does not change the resultant. For example, we could add the vectors as shown in [link] , and we would still get the same solution. Vectors can be added in any order to get the same result. 

[BL] [OL] [AL] Ask three students to enact the situation shown in [link] . Recall how these forces can be represented in a free-body diagram. Giving values to these vectors, show how these can be added graphically. Subtracting Vectors Graphically: A Woman Sailing a Boat 

A woman sailing a boat at night is following directions to a dock. The instructions read to first sail 27.5 m in a direction 66.0 66.0 north of east from her current location, and then travel 30.0 m in a direction 112 112 north of east (or 22.0 22.0 west of north). If the woman makes a mistake and travels in the opposite direction for the second leg of the trip, where will she end up? (The two legs of the woman s trip are illustrated in [link] . In the diagram, the first leg of the trip is represented by vector A and the second leg is represented by vector B. Strategy 

We can represent the first leg of the trip with a vector A , and the second leg of the trip that she was supposed to take with a vector B . Since the woman mistakenly travels in the opposite direction for the second leg of the journey, the vector for second leg of the trip she actually takes is B . Therefore, she will end up at a location A + ( B ), or A B . Note that B has the same magnitude as B (30.0 m), but is in the opposite direction, 68 ( 180 112 ) 68 ( 180 112 ) south of east, as illustrated in [link] . Vector B represents traveling in the opposite direction of vector B. 

We use graphical vector addition to find where the woman arrives: A + ( B ). Solution 

(1) To determine the location at which the woman arrives by accident, draw vectors A and B . 

(2) Place the vectors head to tail. 

(3) Draw the resultant vector R . 

(4) Use a ruler and protractor to measure the magnitude and direction of R . 

These steps are demonstrated in [link] . The vectors are placed head to tail. 

In this case 

R = 23.0 m R = 23.0 m 

and 

= 7.5 south of east = 7.5 south of east Discussion 

Because subtraction of a vector is the same as addition of the same vector with the opposite direction, the graphical method for subtracting vectors works the same as for adding vectors. Adding Velocities: A Boat on a River 

A boat attempts to travel straight across a river at a speed of 3.8 m/s. The river current flows at a speed v river of 6.1 m/s to the right. What is the total velocity and direction of the boat? Note: you can represent each meter per second of velocity as one centimeter of vector length in your drawing. Strategy 

We start by choosing a coordinate system with its x-axis parallel to the velocity of the river. Because the boat is directed straight toward the other shore, its velocity is perpendicular to the velocity of the river. We draw the two vectors, v boat and v river , as shown in [link] . 

Using the head-to-tail method, we draw the resulting total velocity vector from the tail of v boat to the head of v river . A boat attempts to travel across a river. What is the total velocity and direction of the boat? Solution 

By using a ruler, we find that the length of the resultant vector is 7.2 cm, which means that the magnitude of the total velocity is 

v tot = 7.2 m/s. 

By using a protractor to measure the angle, we find = 32.0 = 32.0 Discussion 

If the velocity of the boat and river were equal, then the direction of the total velocity would have been 45 . However, since the velocity of the river is greater than that of the boat, the direction is less than 45 with respect to the shore (or x -axis). 

Plot the way from the classroom to the cafeteria (or any two places in the school on the same level). Ask students to come up with approximate distances. Ask them to do a vector analysis of the path. What is the total distance travelled? What is the displacement? Practice Problems 

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[link] Vector Addition 

In this simulation , you will experiment with adding vectors graphically. Click and drag the red vectors from the Grab One basket onto the graph in the middle of the screen. These red vectors can be rotated, stretched, or repositioned by clicking and dragging with your mouse. Check the Show Sum box to display the resultant vector (in green), which is the sum of all of the red vectors placed on the graph. To remove a red vector, drag it to the trash or click the Clear All button if you wish to start over. Notice that, if you click on any of the vectors, the | R | | R | is its magnitude, is its direction with respect to the positive x -axis, R x is its horizontal component, and R y is its vertical component. You can check the resultant by lining up the vectors so that the head of the first vector touches the tail of the second. Continue until all of the vectors are aligned together head-to-tail. You will see that the resultant magnitude and angle is the same as the arrow drawn from the tail of the first vector to the head of the last vector. Rearrange the vectors in any order head-to-tail and compare. The resultant will always be the same. Click here for the simulation 

[link] Section Summary The graphical method of adding vectors A A and B B involves drawing vectors on a graph and adding them by using the head-to-tail method. The resultant vector R R is defined such that A + B = R . The magnitude and direction of R R are then determined with a ruler and protractor. The graphical method of subtracting vectors A and B involves adding the opposite of vector B , which is defined as B . In this case, A B = A + ( B ) = R . A B = A + ( B ) = R . Next, use the head-to-tail method as for vector addition to obtain the resultant vector R R . Addition of vectors is independent of the order in which they are added; A + B = B + A . The head-to-tail method of adding vectors involves drawing the first vector on a graph and then placing the tail of each subsequent vector at the head of the previous vector. The resultant vector is then drawn from the tail of the first vector to the head of the final vector. Variables in physics problems, such as force or velocity, can be represented with vectors by making the length of the vector proportional to the magnitude of the force or velocity. Problems involving displacement, force, or velocity may be solved graphically by measuring the resultant vector s magnitude with a ruler and measuring the direction with a protractor. Check Your Understanding 

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Use the Check Your Understanding questions to assess whether students achieve the learning objectives for this section. If students are struggling with a specific objective, the Check Your Understanding will help identify which objective is causing the problem and direct students to the relevant content. Concept Items 

[link] Problems 

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[link] Critical Thinking 

[link] Test Prep Multiple Choice 

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[link] Test Prep Short Answer 

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[link] Test Prep Extended Response 

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[link] Glossary graphical method drawing vectors on a graph to add them using the head-to-tail method head (of a vector) the end point of a vector; the location of the vector s arrow; also referred to as the tip head-to-tail method a method of adding vectors in which the tail of each vector is placed at the head of the previous vector resultant the sum of the a collection of vectors resultant vector the vector sum of two or more vectors tail the starting point of a vector; the point opposite to the head or tip of the arrow vector addition adding together two or more vectorsVector Addition and Subtraction: Analytical Methods Vector Addition and Subtraction: Analytical Methods Section Learning Objectives 

By the end of this section, you will be able to: Define components of vectors Describe the analytical method of vector addition and subtraction Use the analytical method of vector addition and subtraction to solve problems 

The learning objectives in this section will help your students master the following TEKS: (3) Scientific processes. The student uses critical thinking, scientific reasoning, and problem solving to make informed decisions within and outside the classroom. The student is expected to: (3F) : express and interpret relationships symbolically in accordance with accepted theories to make predictions and solve problems mathematically, including problems requiring proportional reasoning and graphical vector addition (4) Science concepts. The student knows and applies the laws governing motion in two dimensions for a variety of situations. The student is expected to: (4E) : develop and interpret free-body force diagrams (4F) : identify and describe motion relative to different frames of reference Section Key Terms analytical method component (of a two-dimensional vector) Components of Vectors 

For the analytical method of vector addition and subtraction, we use some simple geometry and trigonometry, instead of using a ruler and protractor as we did for graphical methods. However, the graphical method will still come in handy to visualize the problem by drawing vectors using the head-to-tail method. The analytical method is more accurate than the graphical method, which is limited by the precision of the drawing. For a refresher on the definitions of the sine, cosine, and tangent of an angle, see [link] . For a right triangle, the sine, cosine, and tangent of are defined in terms of the adjacent side, the opposite side, or the hypotenuse. In this figure, x is the adjacent side, y is the opposite side, and h is the hypotenuse. 

[BL] [OL] Review trigonometric concepts of sine, cosine, tangent and the Pythagorean theorem. 

Since, by definition, cos = x / h cos = x / h , we can find the length x if we know h and by using x = h cos x = h cos . Similarly, we can find the length of y by using y = h sin y = h sin . These trigonometric relationships are useful for adding vectors. 

When a vector acts in more than one dimension, it is useful to break it down into its x and y components. For a two-dimensional vector, a component is a piece of a vector that points in either the x- or y-direction. Every 2-d vector can be expressed as a sum of its x and y components. 

For example, given a vector like A A in [link] , we may want to find what two perpendicular vectors, A x A x and A y A y , add to produce it. In this example, A x A x and A y A y form a right triangle, meaning that the angle between them is 90 degrees. This is a common situation in physics and happens to be the least complicated situation trigonometrically. The vector A A , with its tail at the origin of an x, y-coordinate system, is shown together with its x - and y -components, A x A x and A y . A y . These vectors form a right triangle. 

A x A x and A y A y are defined to be the components of A A along the x - and y -axes. The three vectors, A A , A x A x , and A y A y , form a right triangle: A x + A y = A . A x + A y = A . 

If the vector A A is known, then its magnitude A A (its length) and its angle (its direction) are known. To find A x A x and A y A y , its x - and y -components, we use the following relationships for a right triangle: A x = A cos A x = A cos 

and A y = A sin A y = A sin 

Where A x A x is the magnitude of A in the x-direction, A y A y is the magnitude of A in the y-direction, and is the angle of the resultant with respect to the x-axis, as shown in [link] . The magnitudes of the vector components A x A x and A y A y can be related to the resultant vector A A and the angle with trigonometric identities. Here we see that A x = A cos A x = A cos and A y = A sin . A y = A sin . 

[BL] [OL] [AL] Derive the formula for getting the magnitude and direction of a vector. 

Students might be confused between the relationship A x + A y = A A x + A y = A , which shows the addition of vectors and A = A x 2 + A y 2 A = A x 2 + A y 2 which shows the addition of magnitudes of vectors. 

Suppose, for example, that A A is the vector representing the total displacement of the person walking in a city, as illustrated in [link] . We can use the relationships A x = A cos A x = A cos and A y = A sin A y = A sin to determine the magnitude of the horizontal and vertical component vectors in this example. 

Then A = 10.3 blocks and = 29.1 = 29.1 , so that: 

A x = A cos = ( 10.3 blocks)(cos29 .1 ) = ( 10.3 blocks)(0 .874) = 9 .0 blocks A x = A cos = ( 10.3 blocks)(cos29 .1 ) = ( 10.3 blocks)(0 .874) = 9 .0 blocks 

This magnitude indicates that the walker has traveled 9 blocks to the east in other words, a 9-block eastward displacement. Similarly, 

A y = A sin = ( 10.3 blocks)(sin29 .1 ) = ( 10.3 blocks)(0 .846) = 5 .0 blocks A y = A sin = ( 10.3 blocks)(sin29 .1 ) = ( 10.3 blocks)(0 .846) = 5 .0 blocks 

indicating that the walker has traveled 5 blocks to the north a 5-block northward displacement. Analytical Method of Vector Addition and Subtraction 

Calculating a resultant vector (or vector addition) is the reverse of breaking the resultant down into its components. If the perpendicular components A x A x and A y A y of a vector A A are known, then we can find A A analytically. How do we do this? Since, by definition, tan = y / x (or in this case tan = A y / A x ), tan = y / x (or in this case tan = A y / A x ), 

we solve for to find the direction of the resultant = tan 1 ( A y / A x ) = tan 1 ( A y / A x ) 

Since this is a right triangle, the Pythagorean theorem (x 2 + y 2 = h 2 ) for finding the hypotenuse applies. In this case, it becomes 

A 2 = A x 2 + A y 2 A 2 = A x 2 + A y 2 

Solving for A gives A = A x 2 + A y 2 A = A x 2 + A y 2 

In summary, to find the magnitude A A and direction of a vector from its perpendicular components A x A x and A y A y , as illustrated in [link] , we use the following relationships: A = A x 2 + A y 2 = tan 1 ( A y / A x ) A = A x 2 + A y 2 = tan 1 ( A y / A x ) The magnitude and direction of the resultant vector A A can be determined once the horizontal components A x A x and A y A y have been determined. 

[BL] [OL] [AL] Demonstrate a problem involving displacement by physically walking along the specified direction. Show how this can be represented on a graph. Explain that even when solving problems analytically; representing it on a graph would make it easier to visualize the problem. 

Sometimes, the vectors added are not perfectly perpendicular to one another. An example of this is the case below, where the vectors A A and B B are added to produce the resultant R R , as illustrated in [link] . Vectors A A and B B are two legs of a walk, and R R is the resultant or total displacement. You can use analytical methods to determine the magnitude and direction of R R . 

If A A and B B represent two legs of a walk (two displacements), then R R is the total displacement. The person taking the walk ends up at the tip of R R . There are many ways to arrive at the same point. The person could have walked straight ahead first in the x -direction and then in the y -direction. Those paths are the x - and y -components of the resultant, R x R x and R y . R y . If we know R x R x and R y R y , we can find R R and using the equations R = R x 2 + R y 2 R = R x 2 + R y 2 and = t a n 1 ( R y / R x ) = t a n 1 ( R y / R x ) . Draw in the x and y components of each vector (including the resultant) with a dashed line. Use the equations A x = A cos A x = A cos and A y = A sin A y = A sin to find the components. In [link] , these components are A x A x , A y A y , B x B x , and B y . B y . Vector A A makes an angle of A A with the x-axis, and vector B B makes and angle of B B with its own x-axis (which is slightly above the x-axis used by vector A ). To add vectors A A and B , B , first determine the horizontal and vertical components of each vector. These are the dotted vectors A x , A x , A y A y B y B y shown in the image. Find the x component of the resultant by adding the x component of the vectors: R x = A x + B x R x = A x + B x 

and find the y component of the resultant (as illustrated in [link] ) by adding the y component of the vectors: R y = A y + B y R y = A y + B y The vectors A x A x and B x B x add to give the magnitude of the resultant vector in the horizontal direction, R x . R x . Similarly, the vectors A y A y and B y B y add to give the magnitude of the resultant vector in the vertical direction, R y . R y . 

Now that we know the components of R , R , we can find its magnitude and direction. To get the magnitude of the resultant R, use the Pythagorean theorem: R = R x 2 + R y 2 . R = R x 2 + R y 2 . To get the direction of the resultant: = tan 1 ( R y / R x ) . = tan 1 ( R y / R x ) . Classifying Vectors and Quantities Example 

This video contrasts and compares three vectors in terms of their magnitudes, positions, and directions. 

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In the video, the vectors were represented with an arrow above them rather than in bold. This is a common notation in math classes. Using the Analytical Method of Vector Addition and Subtraction to Solve Problems 

The [link] uses the analytical method to add vectors. An Accelerating Subway Train 

Add the vector A A to the vector B B shown in [link] , using the steps above. The x -axis is along the east west direction, and the y -axis is along the north south directions. A person first walks 53 .0 m 53 .0 m in a direction 20 .0 20 .0 north of east, represented by vector A . A . The person then walks 34 .0 m 34 .0 m in a direction 63 .0 63 .0 north of east, represented by vector B . B . You can use analytical models to add vectors. Strategy 

The components of A A and B B along the x - and y -axes represent walking due east and due north to get to the same ending point. We will solve for these components and then add them in the x-direction and y-direction to find the resultant. Solution 

First, we find the components of A A and B B along the x - and y -axes. From the problem, we know that A = 53.0 m A = 53.0 m , A = 20.0 A = 20.0 , B B = 34 .0 m 34 .0 m , and B = 63.0 B = 63.0 . We find the x -components by using A x = A cos A x = A cos , which gives A x = A cos A = ( 53.0 m ) ( cos 20.0 ) = ( 53.0 m ) ( 0.940 ) = 49.8 m A x = A cos A = ( 53.0 m ) ( cos 20.0 ) = ( 53.0 m ) ( 0.940 ) = 49.8 m 

and B x = B cos B = ( 34.0 m ) ( cos 63.0 ) = ( 34.0 m ) ( 0.454 ) = 15.4 m B x = B cos B = ( 34.0 m ) ( cos 63.0 ) = ( 34.0 m ) ( 0.454 ) = 15.4 m 

Similarly, the y -components are found using A y = A sin A A y = A sin A : A y = A sin A = ( 53.0 m ) ( sin 20.0 ) = ( 53.0 m ) ( 0.342 ) = 18.1 m A y = A sin A = ( 53.0 m ) ( sin 20.0 ) = ( 53.0 m ) ( 0.342 ) = 18.1 m 

and B y = B sin B = ( 34.0 m ) ( sin 63.0 ) = ( 34.0 m ) ( 0.891 ) = 30.3 m . B y = B sin B = ( 34.0 m ) ( sin 63.0 ) = ( 34.0 m ) ( 0.891 ) = 30.3 m . 

The x - and y -components of the resultant are R x = A x + B x = 49.8 m + 15.4 m = 65.2 m R x = A x + B x = 49.8 m + 15.4 m = 65.2 m 

and R y = A y + B y = 18.1 m + 30.3 m = 48.4 m . R y = A y + B y = 18.1 m + 30.3 m = 48.4 m . 

Now we can find the magnitude of the resultant by using the Pythagorean theorem: R = R x 2 + R y 2 = ( 65.2 ) 2 + ( 48.4 ) 2 m R = R x 2 + R y 2 = ( 65.2 ) 2 + ( 48.4 ) 2 m 

so that R = 6601 m = 81.2 m . R = 6601 m = 81.2 m . 

Finally, we find the direction of the resultant: = tan 1 ( R y / R x ) = + tan 1 ( 48.4 / 65.2 ) . = tan 1 ( R y / R x ) = + tan 1 ( 48.4 / 65.2 ) . 

This is = tan 1 ( 0.742 ) = 36.6 . = tan 1 ( 0.742 ) = 36.6 . Discussion 

This example shows vector addition using the analytical method. Vector subtraction using the analytical method is very similar. It is just the addition of a negative vector. That is, A B A + ( B ) A B A + ( B ) . The components of B B are the negatives of the components of B B . Therefore, the x - and y -components of the resultant A B = R A B = R are R x = A x + - B x R x = A x + - B x 

and R y = A y + - B y R y = A y + - B y 

and the rest of the method outlined above is identical to that for addition. Practice Problems 

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[link] Atmospheric Science This picture shows Bert Foord during a television Weather Forecast from the Meteorological Office in 1963. (credit: BBC TV) 

Atmospheric science is a physical science , meaning that it is a science based heavily on physics. Atmospheric science includes meteorology (the study of weather) and climatology (the study of climate). Climate is basically the average weather over a longer time scale. Weather changes quickly over time, whereas the climate changes more gradually. 

The movement of air, water and heat is vitally important to climatology and meteorology. Since motion is such a major factor in weather and climate, this field uses vectors for much of its math. 

Vectors are used to represent currents in the ocean, wind velocity and forces acting on a parcel of air. You have probably seen a weather map using vectors to show the strength (magnitude) and direction of the wind. 

Vectors used in atmospheric science are often three-dimensional. We won t cover three-dimensional motion in this text, but to go from two-dimensions to three-dimensions, you simply add a third vector component. Three-dimensional motion is represented as a combination of x-, y- and z components, where z is the altitude. 

Vector calculus combines vector math with calculus, and is often used to find the rates of change in temperature, pressure or wind speed over time or distance. This is useful information, since atmospheric motion is driven by changes in pressure or temperature. The greater the variation in pressure over a given distance, the stronger the wind to try to correct that imbalance. Cold air tends to be more dense and therefore has higher pressure than warm air. Higher pressure air rushes into a region of lower pressure and gets deflected by the spinning of the Earth, and friction slows the wind at Earth s surface. 

Finding how wind changes over distance and multiplying vectors lets meteorologists, like the one shown in [link] , figure out how much rotation (spin) there is in the atmosphere at any given time and location. This is an important tool for tornado prediction. Conditions with greater rotation are more likely to produce tornadoes. 

[link] Section Summary The analytical method of vector addition and subtraction uses the Pythagorean theorem and trigonometric identities to determine the magnitude and direction of a resultant vector. The steps to add vectors A A and B B using the analytical method are as follows: Determine the coordinate system for the vectors. Then, determine the horizontal and vertical components of each vector using the equations: A x = A cos B x = B cos A x = A cos B x = B cos 

And A y = A sin B y = B sin A y = A sin B y = B sin Add the horizontal and vertical components of each vector to determine the components R x R x and R y R y of the resultant vector, R R : R x = A x + B x R x = A x + B x 

and R y = A y + B y . R y = A y + B y . Use the Pythagorean theorem to determine the magnitude, R R , of the resultant vector R R : R = R x 2 + R y 2 . R = R x 2 + R y 2 . Use a trigonometric identity to determine the direction, , of R R : = tan 1 ( R y / R x ) . = tan 1 ( R y / R x ) . Key Equations resultant magnitude R = R x 2 + R y 2 R = R x 2 + R y 2 resultant direction = tan 1 ( R y / R x ) = tan 1 ( R y / R x ) x-component of a vector A (when an angle is given relative to the horizontal) A x = A cos A x = A cos y-component of a vector A (when an angle is given relative to the horizontal) A y = A sin A y = A sin addition of vectors A x + A y = A A x + A y = A Check Your Understanding 

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[link] Glossary analytical method the method of determining the magnitude and direction of a resultant vector using the Pythagorean theorem and trigonometric identities component (of a 2-dimensional vector) a piece of a vector that points in either the vertical or the horizontal direction; every 2-d vector can be expressed as a sum of two vertical and horizontal vector componentsKepler s Laws of Planetary Motion Kepler s Laws of Planetary Motion Section Learning Objectives 

By the end of this section, you will be able to: Explain Kepler s three laws of planetary motion Apply Kepler s laws to calculate characteristics of orbits 

The learning objectives in this section will help your students master the following TEKS: (4C) : Analyze and describe accelerated motion in two dimensions using equations, including projectile and circular examples. 

In this section students will apply Kepler s laws of planetary motion to objects in the solar system. 

[BL] [OL] Discuss the historical setting in which Kepler worked. Most people still thought the Earth was the center of the universe, and yet Kepler not only knew that the planets circled the sun, he found patterns in the paths they followed. What would it be like to be that far ahead of almost everyone? A fascinating description of this is given in the program "Cosmos" with Carl Sagan (Episode 3, Harmony of the Worlds). 

[AL] Explain that Kepler s laws were laws and not theories. Laws describe patterns in nature that always repeat themselves under the same set of conditions. Theories provide an explanation for the patterns. Kepler provided no explanation. Section Key Terms aphelion Copernican model eccentricity Kepler s laws of planetary motion perihelion Ptolemaic model Concepts Related to Kepler s Laws of Planetary Motion 

Examples of orbits abound. Hundreds of artificial satellites orbit Earth together with thousands of pieces of debris. The moon s orbit around Earth has intrigued humans from time immemorial. The orbits of planets, asteroids, meteors, and comets around the sun are no less interesting. If we look farther, we see almost unimaginable numbers of stars, galaxies, and other celestial objects orbiting one another and interacting through gravity. 

All these motions are governed by gravitational force. The orbital motions of objects in our own solar system are simple enough to describe with a few fairly simple laws. The orbits of planets and moons satisfy the following two conditions: The mass of the orbiting object, m , is small compared to the mass of the object it orbits, M . The system is isolated from other massive objects. 

[OL] Ask the students to explain the criteria to see if they understand relative mass and isolated systems. 

Based on the motion of the planets about the sun, Kepler devised a set of three classical laws, called Kepler s laws of planetary motion , that describe the orbits of all bodies satisfying these two conditions. The orbit of each planet around the sun is an ellipse with the sun at one focus. Each planet moves so that an imaginary line drawn from the sun to the planet sweeps out equal areas in equal times. The ratio of the squares of the periods of any two planets about the sun is equal to the ratio of the cubes of their average distances from the sun. 

These descriptive laws are named for the German astronomer Johannes Kepler (1571 1630). He devised them after careful study (over some 20 years) of a large amount of meticulously recorded observations of planetary motion done by Tycho Brahe (1546 1601). Such careful collection and detailed recording of methods and data are hallmarks of good science. Data constitute the evidence from which new interpretations and meanings can be constructed. Let s look closer at each of these laws. 

[BL] Relate orbit to year and rotation to day. Be sure that students know that an object rotates on its axis and revolves around a parent body as it follows its orbit. 

[OL] See how many levels of orbital motion the students know and fill in the ones they don t. For example: moons orbit around planets; planets around stars; stars around the center of the galaxy, etc. 

[AL] From the point of view of Earth, which objects appear (incorrectly) to be orbiting Earth (stars, the sun, galaxies) and which can be seen to be orbiting parent bodies (the moon, moons of other planets, stars in other galaxies)? Kepler s First Law 

The orbit of each planet about the sun is an ellipse with the sun at one focus, as shown in [link] . The planet s closest approach to the sun is called aphelion and its farthest distance from the sun is called perihelion . (a) An ellipse is a closed curve such that the sum of the distances from a point on the curve to the two foci ( f 1 and f 2 ) is constant. (b) For any closed orbit, m follows an elliptical path with M at one focus. (c) The aphelion ( r a) is the closest distance between the planet and the sun, while the perihelion ( r p) is the farthest distance from the sun. 

[AL] Ask for a definition of planet. Prepare to discuss Pluto s demotion if it comes up. Discuss the first criterion in terms of center of rotation of a moon-planet system. Explain that for all planet-moon systems in the solar system, the center of rotation is within the planet. This is not true for Pluto and its largest moon, Charon, because their masses are similar enough that they rotate around a point in space between them. 

If you know the aphelion ( r a ) and perihelion ( r p ) distances, then you can calculate the semi-major axis ( a ) and semi-minor axis ( b ): a = ( r a + r p ) 2 b = r a r p a = ( r a + r p ) 2 b = r a r p 

[AL] If any students are interested and proficient in algebra and geometry, ask them to derive a formula that relates the length of the string and the distance between pins to the major and minor axes of an ellipse. Explain that this is a real world problem for workers who design elliptical tabletops and mirrors. 

[BL] [OL] Impress upon the students that Kepler had to crunch an enormous amount of data and that all his calculations had to be done by hand. Ask students to think of similar projects where scientists found order in a daunting amount of data (the periodic table, DNA structure, climate models, etc.). 

Demonstrate the pins and string method of drawing an ellipse, as shown in [link] , or have the students try it at home or in class. 

Ask students: Why does the string and pin method create a shape that conforms to Kepler's second law? That is, why is the shape an ellipse? 

Explain that the pins are the foci and explain what each of the three sections of string represents. Note that the pencil represents a planet and one of the pins represents the sun. You can draw an ellipse as shown by putting a pin at each focus, and then placing a loop of string around a pen and the pins and tracing a line on the paper. Kepler s Second Law 

Each planet moves so that an imaginary line drawn from the sun to the planet sweeps out equal areas in equal times, as shown in [link] . The shaded regions have equal areas. The time for m to go from A to B is the same as the time to go from C to D and from E to F. The mass m moves fastest when it is closest to M . Kepler s second law was originally devised for planets orbiting the sun, but it has broader validity. 

Ask the students to imagine how complicated it would be to describe the motion of the planets mathematically, if it is assumed that Earth is stationary. And yet, people tried to do this for hundreds of years, while overlooking the simple explanation that all planets circle the sun. 

[OL] Ask students to use this figure to understand why planets and comets travel faster when they are closer to the sun. Explain that time intervals and areas are constant, but both velocity and distance from the sun vary. 

Note that while, for historical reasons, Kepler s laws are stated for planets orbiting the sun, they are actually valid for all bodies satisfying the two previously stated conditions. Kepler s Third Law 

The ratio of the periods squared of any two planets around the sun is equal to the ratio of their average distances from the sun cubed. In equation form, this is T 1 2 T 2 2 = r 1 3 r 2 3 , T 1 2 T 2 2 = r 1 3 r 2 3 , 

where T is the period (time for one orbit) and r is the average distance (also called orbital radius). This equation is valid only for comparing two small masses orbiting a single large mass. Most importantly, this is only a descriptive equation; it gives no information about the cause of the equality. 

[BL] See if students can rearrange this equation to solve for any one of the variables when the other three are known. 

[AL] Show a solution for one of the periods T or radii r and ask students to interpret the fractional powers on the right hand side of the equation. 

[OL] Emphasize that this approach only works for two satellites orbiting the same parent body. The parent body must be the same because r 2 / T 2 = G M / ( 4 2 ) r 2 / T 2 = G M / ( 4 2 ) and M is the mass of the parent body. If M changes, the ratio r 3 / T 2 also changes. History: Ptolemy vs. Copernicus 

Before the discoveries of Kepler, Copernicus, Galileo, Newton, and others, the solar system was thought to revolve around Earth as shown in [link] (a) . This is called the Ptolemaic model , named for the Greek philosopher Ptolemy who lived in the second century AD. (Note that the P is silent.) The Ptolemaic model is characterized by a list of facts for the motions of planets, with no explanation of cause and effect. There tended to be a different rule for each heavenly body and a general lack of simplicity. 

[link] (b) represents the modern or Copernican model . In this model, a small set of rules and a single underlying force explain not only all planetary motion in the solar system, but also all other situations involving gravity. The breadth and simplicity of the laws of physics are compelling. (a) The Ptolemaic model of the universe has Earth at the center with the moon, the planets, the sun, and the stars revolving about it in complex circular paths. This geocentric (Earth-centered) model, which can be made progressively more accurate by adding more circles, is purely descriptive, containing no hints about the causes of these motions. (b) The Copernican heliocentric (sun-centered) model is a simpler and more accurate model. 

Nicolaus Copernicus (1473 1543) first had the idea that the planets circle the sun, in about 1514. It took him almost 20 years to work out the mathematical details for his model. He waited another 10 years or so to publish his work. It is thought he hesitated because he was afraid people would make fun of his theory. Actually, the reaction of many people was more one of fear and anger. Many people felt the Copernican model threatened their basic belief system. About 100 years later, the astronomer Galileo was put under house arrest for providing evidence that planets, including Earth, orbited the sun. In all, it took almost 300 years for everyone to admit that Copernicus had been right all along. 

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Introduce the historical debate around the geocentric versus the heliocentric view of the universe. Stress how controversial this debate was at the time. Explain that this was important to people because their worldview and religious beliefs were at stake. Acceleration 

This simulation allows you to create your own solar system so that you can see how changing distances and masses determines the orbits of planets. Click "Help" for instructions. Click here for the simulation 

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Give the students ample time to manipulate this animation. It may take some time to get the parameters adjusted so that they can see how mass and eccentricity affect the orbit. Initially, the planet is likely to disappear off the screen or crash into the sun. Calculations Related to Kepler s Laws of Planetary Motion Kepler s First Law 

Refer back to this figure (a) . Notice which distances are constant. The foci are fixed, so distance f 1 f 2 f 1 f 2 is a constant. The definition of an ellipse states that the sum of the distances f 1 m + m f 2 f 1 m + m f 2 is also constant. These two facts taken together mean that the perimeter of triangle f 1 m f 2 f 1 m f 2 must also be constant. Knowledge of these constants will help you determine positions and distances of objects in a system that includes one object orbiting another. Kepler s Second Law 

Refer back to this figure . The second law says that the segments have equal area and that it takes equal time to sweep through each segment. That is, the time it takes to travel from A to B equals the time it takes to travel from C to D, and so forth. Velocity v equals distance d divided by time t : v = d / t v = d / t . Then, t = d / v t = d / v , so distance divided by velocity is also a constant. For example, if we know the average velocity of Earth on June 21 and December 21, we can compare the distance Earth travels on those days. 

The degree of elongation of an elliptical orbit is called its eccentricity ( e ). Eccentricity is calculated by dividing the distance f from the center of an ellipse to one of the foci by half the long axis a : e = f / a e = f / a . When e = 0 e = 0 , the ellipse is a circle. 

The area of an ellipse is given by A = a b A = a b , where b is half the short axis. If you know the axes of Earth s orbit and the area Earth sweeps out in a given period of time, you can calculate the fraction of the year that has elapsed. 

[OL] Review the definitions of major and minor axes, semi-major and semi-minor axes, and distance f . The major axis is the length of the ellipse and passes through both foci. The minor axis is the width of the ellipse and is perpendicular to the major axis. The semi-major and semi-minor axes are half of the major and minor axes, respectively. Kepler s First Law 

At its closest approach, a moon comes within 200,000 km of the planet it orbits. At that point, the moon is 300,000 km from the other focus of its orbit, f 2 . The planet is focus f 1 of the moon s elliptical orbit. How far is the moon from the planet when it is 260,000 km from f 2 ? Strategy 

Show and label the ellipse that is the orbit in your solution. Picture the triangle f 1 m f 2 collapsed along the major axis and add up the lengths of the three sides. Find the length of the unknown side of the triangle when the moon is 260,000 km from f 2 . Solution 

Perimeter of f 1 m f 2 = 200 , 000 km + 100,000 km + 300,000 km = 600,000 km f 1 m f 2 = 200 , 000 km + 100,000 km + 300,000 km = 600,000 km . 

m f 1 = 600,000 km ( 100,000 km + 200,000 km ) = 240,000 km m f 1 = 600,000 km ( 100,000 km + 200,000 km ) = 240,000 km . Discussion 

The perimeter of triangle f 1 mf 2 must be constant because the distance between the foci does not change and Kepler s first law says the orbit is an ellipse. For any ellipse, the sum of the two sides of the triangle, which are f 1 m and mf 2 , is constant. 

Walk the students through the process of mentally collapsing the f 1 mf 2 at the end of the major axis to reveal what the three sides of the triangle f 1 mf 2 are equal to. Picture the sections of the string as the pencil approaches the major axis. This distance f 1 f 2 remains constant, f 1 m is the distance from f 1 to the end of the major axis, and mf 2 is f 1 m + f 1 f 2 . 

[OL] Have students relate eccentricity, distance between foci, and shape of orbit. 

[AL] Ask for examples of orbits with high eccentricity (comets, Pluto) and low eccentricity (moon, Earth). Kepler s Second Law 

[link] shows the major and minor axes of an ellipse. The semi-major and semi-minor axes are half of these, respectively. The major axis is the length of the ellipse, and the minor axis is the width of the ellipse. The semi-major axis is half the major axis, and the semi-minor axis is half the minor axis. 

The Earth s orbit is slightly elliptical, with a semi-major axis of 152 million km and a semi-minor axis of 147 million km. If Earth s period is 365.26 days, what area does an Earth-to-sun line sweep past in one day? Strategy 

Each day, the Earth sweeps past an equal-sized area, so we divide the total area by the number of days in a year to find the area swept past in one day. For total area use A = a b A = a b . Calculate A , the area inside Earth s orbit and divide by the number of days in a year (i.e., its period). Solution 

area per day = total area total number of days = a b 365 d = ( 1.47 10 8 km ) ( 1.52 10 3 km ) 365 d = 1.92 10 14 km 2 / d area per day = total area total number of days = a b 365 d = ( 1.47 10 8 km ) ( 1.52 10 3 km ) 365 d = 1.92 10 14 km 2 / d 

The area swept out in one day is thus 1.92 10 14 km 2 1.92 10 14 km 2 . Discussion 

The answer is based on Kepler s law, which states that a line from a planet to the sun sweeps out equal areas in equal times. 

Explain that this formula is easy to remember because it is similar to A = r 2 A = r 2 . Discuss Earth s eccentricity. Compare it with that of other planets, asteroids, or comets to further emphasize what defines a planet. Note that Earth has one of the least eccentric orbits and Mercury has the most eccentric orbit of the planets. 

[BL] Have the students memorized the value of ? 

[OL] [AL] What is the formula when a = b ? Is the formula familiar? 

[OL] Can the student verify this statement by rearranging the equation? Kepler s Third Law 

Kepler s third law states that the ratio of the squares of the periods of any two planets ( T 1 , T 2 ) is equal to the ratio of the cubes of their average orbital distance from the sun ( r 1 , r 2 ). Mathematically, this is represented by T 1 2 T 2 2 = r 1 3 r 2 3 T 1 2 T 2 2 = r 1 3 r 2 3 

From this equation, it follows that the ratio r 3 /T 2 is the same for all planets in the solar system. Later we will see how the work of Newton leads to a value for this constant. Kepler s Third Law 

Given that the moon orbits Earth each 27.3 d and that it is an average distance of 3.84 10 8 m 3.84 10 8 m from the center of Earth, calculate the period of an artificial satellite orbiting at an average altitude of 1500 km above Earth s surface. Strategy 

The period, or time for one orbit, is related to the radius of the orbit by Kepler s third law, given in mathematical form by T 1 2 T 2 2 = r 1 3 r 2 3 T 1 2 T 2 2 = r 1 3 r 2 3 . Let us use the subscript 1 for the moon and the subscript 2 for the satellite. We are asked to find T 2 . The given information tells us that the orbital radius of the moon is r 1 = 3.84 10 8 m r 1 = 3.84 10 8 m , and that the period of the moon is T 1 = 27.3 d T 1 = 27.3 d . The height of the artificial satellite above Earth s surface is given, so to get the distance r 2 from the center of Earth we must add the height to the radius of Earth (6380 km). This gives r 2 = 1500 km + 6380 km = 7880 km r 2 = 1500 km + 6380 km = 7880 km . Now all quantities are known, so T 2 can be found. Solution 

To solve for T 2 , we cross-multiply and take the square root, yielding 

T 2 2 = T 1 2 ( r 2 r 1 ) 3 ; T 2 = T 1 ( r 2 r 1 ) 3 2 T 2 = ( 27.3 d ) ( 24.0 h d ) ( 7880 km 3.84 10 5 km ) 3 2 = 1.93 h . T 2 2 = T 1 2 ( r 2 r 1 ) 3 ; T 2 = T 1 ( r 2 r 1 ) 3 2 T 2 = ( 27.3 d ) ( 24.0 h d ) ( 7880 km 3.84 10 5 km ) 3 2 = 1.93 h . Discussion 

This is a reasonable period for a satellite in a fairly low orbit. It is interesting that any satellite at this altitude will complete one orbit in the same amount of time. 

Remind the students that this only works when the satellites are small compared to the parent object and when both satellites orbit the same parent object. Practice Problems 

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Use the Check Your Answers questions to assess whether students master the learning objectives for this section. If students are struggling with a specific objective, the Check Your Answers will help identify which objective is causing the problem and direct students to the relevant content. Section Summary all satellites follow elliptical orbits the line from the satellite to the parent body sweeps out equal areas in equal time the radius cubed divided by the period squared is a constant for all satellites orbiting the same parent body Key Equations Kepler s third law T 1 2 T 2 2 = r 1 3 r 2 3 T 1 2 T 2 2 = r 1 3 r 2 3 eccentricity e = f a e = f a area of an ellipse A = a b A = a b semi-major axis of an ellipse a = ( r a + r p ) / 2 a = ( r a + r p ) / 2 semi-minor axis of an ellipse b = r a r p b = r a r p Concept Items 

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[link] Glossary aphelion closest distance between a planet and the sun (called apoapsis for other celestial bodies) Copernican model the model of the solar system where the sun is at the center of the solar system and all the planets orbit around it; this is also called the heliocentric model eccentricity a measure of the separation of the foci of an ellipse Kepler s laws of planetary motion three laws derived by Johannes Kepler that describe the properties of all orbiting satellites perihelion farthest distance between a planet and the sun (called periapsis for other celestial bodies) Ptolemaic model the model of the solar system where Earth is at the center of the solar system and the sun and all the planets orbit around it; this is also called the geocentric modelIntroduction Introduction In this chapter you will learn about: Kepler s Laws of Planetary Motion Newton s Law of Universal Gravitation and Einstein s Theory of General Relativity class="summary" title="Section Summary" class="key-equations" title="Key Equations" class="concept" title="Concept Items" class="critical-thinking" title="Critical Thinking Items" class="problem" title="Problems" class="performance" title="Performance Task" class="multiple-choice" title="Multiple Choice" class="short-answer" title="Short Answer" class="extended-response" title="Extended Response" 

Physics learning objectives come from 112.39 (c) Knowledge and Skills Johannes Kepler (left) showed how the planets move, and Isaac Newton (right) discovered that gravitational force caused them to move that way. (credits: (left) unknown, Public Domain; (right) Sir Godfrey Kneller, Public Domain) 

Contrast the type of work that each scientist did. Both were important and tackled difficult problems. Kepler found patterns in a mountain of data. Newton found the underlying cause of those patterns. 

What do a falling apple and the orbit of the moon have in common? You will learn in this chapter that each is caused by gravitational force. The motion of all celestial objects, in fact, is determined by the gravitational force, which depends on their mass and separation. 

Johannes Kepler discovered three laws of planetary motion that all orbiting planets and moons follow. Years later, Isaac Newton found these laws useful in developing his law of universal gravitation. This law relates gravitational force to the masses of objects and the distance between them. Many years later still, Albert Einstein showed there was a little more to the gravitation story when he published his theory of general relativity. 

Before students begin this chapter, it is useful to review these concepts: Using significant figures in calculations. Demonstrate how to use the proper number of significant figures when adding and multiplying. Review scientific notation as related to significant figures. Converting units: demonstrate how to convert from km/h to m/s. Review dimensional analysis. For example, N is equivalent to kg m/s 2 . Explain that metric units clearly distinguish between mass and weight, but that the commonly used English units do not. Calculating average: demonstrate how to average two numbers. Review manipulation of formulas so that they may be expressed in terms of the unknown. Review Newton s laws of motion.Introduction Introduction In this chapter, you will learn about: Linear Momentum, Force, and Impulse Conservation of Momentum Elastic and Inelastic Collisions NFC defensive backs Ronde Barber and Roy Williams along with linebacker Jeremiah Trotter gang tackle AFC running back Ladainian Tomlinson during the 2006 Pro Bowl in Hawaii. (Credit: United States Marine Corps.) 

Point out to the students how players often collide with each other while playing American football. How do these collisions affect the players? Does colliding into someone change your velocity? Does it change your mass? What about the force of collision? What does it depend on? Would it hurt more if a heavier person collided into you or a faster person? Tell students that in this chapter they will learn about momentum, its relation to force and about collisions. 

We know from everyday use of the word "momentum" that it is a tendency to continue on course in the same direction. Newscasters speak of sports teams or politicians gaining, losing, or maintaining the momentum to win. As we learned when studying about inertia (Newton's first law of motion), every object or system has inertia that is, a tendency for an object in motion to remain in motion or an object at rest to remain at rest. Mass is a useful variable that lets us quantify inertia. Momentum is mass in motion. 

Momentum is important because it is conserved in isolated systems; this fact is convenient for solving problems where objects collide. The magnitude of momentum grows with greater mass and/or speed. For example, look at the football players in the photograph ( [link] ). They collide and fall to the ground. During their collisions, momentum will play a large part. In this chapter, we will learn about momentum, the different types of collisions, and how to use momentum equations to solve collision problems. 

Before students begin this chapter, it would be useful to review these concepts: mass, inertia, Newton s laws of motion, angular motion, moment of inertia.Linear Momentum, Force, and Impulse Linear Momentum, Force, and Impulse Section Learning Objectives 

By the end of this section, you will be able to: Describe momentum, what can change momentum, impulse, and the impulse-momentum theorem Describe Newton s second law in terms of momentum Solve problems using the impulse-momentum theorem 

The learning objectives in this section will help your students master the following TEKS: (6) Science concepts. The student knows that changes occur within a physical system and applies the laws of conservation of energy and momentum. The student is expected to: (6C) : calculate the mechanical energy of, power generated within, impulse applied to, and momentum of a physical system Section Key Terms change in momentum impulse impulse momentum theorem linear momentum 

[BL] [OL] Review inertia and Newton s laws of motion. 

[AL] Start a discussion about movement and collision. Using the example of football players, point out that both the mass and the velocity of an object are important considerations in determining the impact of collisions. The direction as well as the magnitude of velocity is very important. Momentum, Impulse, and the Impulse-Momentum Theorem 

Linear momentum is the product of a system s mass and its velocity . In equation form, linear momentum p is p = m v p = m v 

You can see from the equation that momentum is directly proportional to the object s mass ( m ) and velocity ( v ). Therefore, the greater an object s mass or the greater its velocity, the greater its momentum. A large, fast-moving object has greater momentum than a smaller, slower object. 

Momentum is a vector and has the same direction as velocity v . Since mass is a scalar , when velocity is in a negative direction (i.e. opposite the direction of motion), the momentum will also be in a negative direction; and when velocity is in a positive direction, momentum will likewise be in a positive direction. The SI unit for momentum is kg m/s. 

Momentum is so important for understanding motion that it was called the quantity of motion by physicists such as Newton. Force influences momentum, and we can rearrange Newton s second law of motion to show the relationship between force and momentum. 

Recall our study of Newton s second law of motion ( F net = m a). Newton actually stated his second law of motion in terms of momentum: The net external force equals the change in momentum of a system divided by the time over which it changes. The change in momentum is the difference between the final and initial values of momentum. 

In equation form, this law is F net = p t F net = p t 

where F net is the net external force, p p is the change in momentum, and t t is the change in time. 

We can solve for p p by rearranging the equation F net = p t F net = p t 

to be p = F net t p = F net t 

F net t F net t is known as impulse and this equation is known as the impulse-momentum theorem . From the equation, we see that the impulse equals the average net external force multiplied by the time this force acts. It is equal to the change in momentum. The effect of a force on an object depends on how long it acts, as well as the strength of the force. Impulse is a useful concept because it quantifies the effect of a force. A very large force acting for a short time can have a great effect on the momentum of an object, such as the force of a racket hitting a tennis ball. A small force could cause the same change in momentum, but it would have to act for a much longer time. 

[OL] [AL] Explain that a large, fast-moving object has greater momentum than a smaller, slower object. This quality is called momentum. 

[BL] [OL] Review the equation of Newton s second law of motion. Point out the two different equations for the law. Newton s Second Law in Terms of Momentum 

When Newton s second law is expressed in terms of momentum, it can be used for solving problems where mass varies, since p = ( m v ) p = ( m v ) . In the more traditional form of the law that you are used to working with, mass is assumed to be constant. In fact, the form of Newton s second law in the form we re most familiar with is a special case of the law, where mass is constant. F net = m a F net = m a is actually derived from this equation: F net = p t F net = p t 

For the sake of understanding the relationship between Newton s second law in its two forms, let s recreate the derivation of F net = m a F net = m a from F net = p t F net = p t 

by substituting the definitions of acceleration and momentum. 

The change in momentum p p is given by p = ( m v ) p = ( m v ) 

If the mass of the system is constant, then ( m v ) = m v ( m v ) = m v 

By substituting m v m v for p p , Newton s second law of motion becomes F net = p t = m v t F net = p t = m v t 

for a constant mass. 

Because v t = a v t = a 

we can substitute to get the familiar equation F net = m a F net = m a 

when the mass of the system is constant. 

[BL] [OL] [AL] Show the two different forms of Newton s second law and how one can be derived from the other. 

We just showed how F net = m a F net = m a applies only when the mass of the system is constant. An example of when this formula would not apply would be a moving rocket that burns enough fuel to significantly change the mass of the rocket. In this case, you would need to use Newton s second law expressed in terms of momentum to account for the changing mass. Hand Movement and Impulse 

In this activity you will experiment with different types of hand motions to gain an intuitive understanding of the relationship between force, time and impulse. 1 ball 1 tub filled with water Try catching a ball while giving with the ball, pulling your hands toward your body. Next, try catching a ball while keeping your hands still. Hit water in a tub with your full palm. (Your full palm represents a swimmer doing a belly flop.) After the water has settled, hit the water again by diving your hand with your fingers first into the water. (Your diving hand represents a swimmer doing a dive.) Explain what happens in each case and why. 

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[OL] [AL] Discuss the impact one feels when one falls or jumps. List the factors that affect this impact. Engineering: Saving Lives Using the Concept of Impulse 

Cars over the past several decades have gotten much safer. Seat belts play a major role in automobile safety by preventing people from flying into the windshield in the event of a crash. Other safety features, such as airbags, are less visible or obvious, but are also effective at making auto crashes less deadly (see [link] ). Many of these other safety features make use of the concept of impulse from physics. Recall that impulse is the net force multiplied by the duration of time of the impact. This was expressed mathematically as p = F net t p = F net t . Vehicles have safety features like airbags and seatbelts installed. 

Airbags allow the net force on the occupants in the car to act over a much longer time when there is a sudden stop. The momentum change is the same for an occupant whether an air bag is deployed or not, but the force (to bring the occupant to a stop) will be much less if it acts over a larger time. By rearranging the equation for impulse to solve for force F net = p t , F net = p t , you can see how increasing t t as p p stays the same will decrease F net . (This is another example of an inverse relationship.) Similarly, a padded dashboard increases the time over which the force of impact acts, thereby reducing the force of impact. 

Cars today have many plastic components. One advantage of plastics is their lighter weight, which results in better gas mileage. Another advantage is that a car will crumple in a collision , especially in the event of a head-on collision. A longer collision time means the force on the occupants of the car will be less. Deaths during car races decreased dramatically when the rigid frames of racing cars were replaced with parts that could crumple or collapse in the event of an accident. 

[link] Solving Problems Using the Impulse-Momentum Theorem 

Talk about the different strategies to be used while solving problems. Make sure that students know the assumptions made in each equation regarding certain quantities being constant or some quantities being negligible. Calculating Momentum: A Football Player and a Football 

(a) Calculate the momentum of a 110 kg football player running at 8.00 m/s. (b) Compare the player s momentum with the momentum of a 0.410 kg football thrown hard at a speed of 25.00 m/s. Strategy 

No information is given about the direction of the football player or the football, so we can calculate only the magnitude of the momentum, p . (As usual, a symbol in italics represents magnitude.) In both parts of this example, the magnitude of momentum can be calculated directly from the definition of momentum: p = m v p = m v Solution for (a) 

To find the player s momentum, substitute the known values for the player s mass and speed into the equation. p player = ( 110 kg ) ( 8.00 m/s ) = 880 k g m / s p player = ( 110 kg ) ( 8.00 m/s ) = 880 k g m / s Solution for (b) 

To find the ball s momentum, substitute the known values for the ball s mass and speed into the equation. p ball = ( 0.410 kg ) ( 25.00 m/s ) = 10.25 k g m/s p ball = ( 0.410 kg ) ( 25.00 m/s ) = 10.25 k g m/s 

The ratio of the player s momentum to the ball s momentum is p player p ball = 880 10.3 = 85.9 p player p ball = 880 10.3 = 85.9 Discussion 

Although the ball has greater velocity, the player has a much greater mass. Therefore, the momentum of the player is about 86 times greater than the momentum of the football. Calculating Force: Venus Williams Racquet 

During the 2007 French Open, Venus Williams ( [link] ) hit the fastest recorded serve in a premier women s match, reaching a speed of 58 m/s (209 km/h). What was the average force exerted on the 0.057 kg tennis ball by Venus Williams racquet? Assume that the ball s speed just after impact was 58 m/s, the horizontal velocity before impact is negligible, and that the ball remained in contact with the racquet for 5.0 ms (milliseconds). Venus Williams playing in the 2013 US Open. (credit: Edwin Martinez, Flickr) Strategy 

Recall that Newton s second law stated in terms of momentum is F net = p t F net = p t 

As noted above, when mass is constant, the change in momentum is given by p = m v = m ( v f v i ) p = m v = m ( v f v i ) 

where v f is the final velocity and v i is the initial velocity. In this example, the velocity just after impact and the change in time are given, so after we solve for p p , we can use F net = p t F net = p t to find the force. Solution 

To determine the change in momentum, substitute the values for mass and the initial and final velocities into the equation above. 

p = m ( v f v i ) = ( 0 .057 kg ) ( 58 m/s 0 m/s ) = 3 .306 kg m/s 3 .3 kg m/s p = m ( v f v i ) = ( 0 .057 kg ) ( 58 m/s 0 m/s ) = 3 .306 kg m/s 3 .3 kg m/s 

Now we can find the magnitude of the net external force using F net = p t F net = p t : 

F net = p t = 3.306 5 10 3 = 661 N 660 N F net = p t = 3.306 5 10 3 = 661 N 660 N Discussion 

This quantity was the average force exerted by Venus Williams racquet on the tennis ball during its brief impact. This problem could also be solved by first finding the acceleration and then using F net = m a , but we would have had to do one more step. In this case, using momentum was a shortcut. Practice Problems 

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Use the Check Your Understanding questions to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, the assessment will help identify which objective is causing the problem and direct students to the relevant content. Section Summary Linear momentum ( momentum for short) is defined as the product of a system s mass multiplied by its velocity, p = m v . The SI unit for momentum is kg m/s. Newton s second law of motion in terms of momentum states that the net external force equals the change in momentum of a system divided by the time over which it changes, F net = p t F net = p t . Impulse is the average net external force multiplied by the time this force acts and impulse equals the change in momentum, p = F net t p = F net t . Forces are usually not constant over a period of time, so we use the average of the force over the time it acts. Key Equations impulse F net t F net t impulse momentum theorem p = F net t p = F net t linear momentum p = m v p = m v Newton s Second Law in terms of momentum F net = p t F net = p t Concept Items 

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[link] Glossary change in momentum the difference between the final and initial values of momentum; the mass times the change in velocity impulse average net external force multiplied by the time the force acts; equal to the change in momentum impulse momentum theorem the impulse (or change in momentum) is the product of the net external force and the time over which the force acts linear momentum the product of a system's mass and velocityNewton s Law of Universal Gravitation and Einstein s Theory of General Relativity Newton s Law of Universal Gravitation and Einstein s Theory of General Relativity Section Learning Objectives 

By the end of this section, you will be able to: Explain Newton s law of universal gravitation and compare it to Einstein s theory of general relativity Perform calculations using Newton s law of universal gravitation 

The learning objectives in this section will help your students master the following TEKS: (4D) : Calculate the effect of forces on objects, including the law of inertia, the relationship between force and acceleration, and the nature of force pairs between objects (5A) : Research and describe the historical development of the concepts of gravitational, electromagnetic, weak nuclear, and strong nuclear forces. (5B) : Describe and calculate how the magnitude of the gravitational force between two objects depends on their masses and the distance between their centers. Section Key Terms Einstein s theory of general relativity gravitational constant Newton s universal law of gravitation 

In this section, students will apply Newton s law of universal gravitation to objects close at hand and far off in the depths of the solar system. 

[BL] [OL] Compare the contributions of Kepler, Newton, and Einstein. Place them historically with dates. 

[AL] Ask if anyone knows the difference between special relativity and general relativity. Special relativity is a theory of spacetime and applies to observers moving at constant velocity. General relativity is a theory of gravity and applies to observers that are accelerating. General relativity is broader and includes special relativity, which was published first. Concepts Related to Newton s Law of Universal Gravitation 

Sir Isaac Newton was the first scientist to precisely define the gravitational force, and to show that it could explain both falling bodies and astronomical motions. See [link] . But Newton was not the first to suspect that the same force caused both our weight and the motion of planets. His forerunner, Galileo Galilei, had contended that falling bodies and planetary motions had the same cause. Some of Newton s contemporaries, such as Robert Hooke, Christopher Wren, and Edmund Halley, had also made some progress toward understanding gravitation. But Newton was the first to propose an exact mathematical form and to use that form to show that the motion of heavenly bodies should be conic sections circles, ellipses, parabolas, and hyperbolas. This theoretical prediction was a major triumph. It had been known for some time that moons, planets, and comets follow such paths, but no one had been able to propose an explanation of the mechanism that caused them to follow these paths and not others. The popular legend that Newton suddenly discovered the law of universal gravitation when an apple fell from a tree and hit him on the head has an element of truth in it. A more probable account is that he was walking through an orchard and wondered why all the apples fell in the same direction with the same acceleration. Great importance is attached to it because Newton s universal law of gravitation and his laws of motion answered very old questions about nature and gave tremendous support to the notion of underlying simplicity and unity in nature. Scientists still expect underlying simplicity to emerge from their ongoing inquiries into nature. 

[BL] [OL] Ask students if it really is obvious why all things fall straight down. Ask them to back up their reasons. Ask if the name Halley rings a bell. 

[OL] [AL] Ask if anyone thinks it is strange or even mysterious that a force can act at a distance across empty space. Ask the students to compare and contrast gravitational force with magnetic and electrostatic forces. Note how much force at a distance is like magic or having superpowers. 

The gravitational force is relatively simple. It is always attractive, and it depends only on the masses involved and the distance between them. Expressed in modern language, Newton s universal law of gravitation states that every object in the universe attracts every other object with a force that is directed along a line joining them. The force is directly proportional to the product of their masses and inversely proportional to the square of the distance between them. This attraction is illustrated by [link] . Gravitational attraction is along a line joining the centers of mass (CM) of the two bodies. The magnitude of the force on each body is the same, consistent with Newton s third law (action-reaction). 

For two bodies having masses m and M with a distance r between their centers of mass, the equation for Newton s universal law of gravitation is F = G m M r 2 F = G m M r 2 

where F is the magnitude of the gravitational force and G is a proportionality factor called the gravitational constant . G is a universal constant, meaning that it is thought to be the same everywhere in the universe. It has been measured experimentally to be G = 6.673 10 11 N m 2 /kg 2 G = 6.673 10 11 N m 2 /kg 2 . 

If a person has a mass of 60.0 kg, what would be the force of gravitational attraction on him at Earth s surface? G is given above, Earth s mass M is 5.97 10 24 kg, and the radius r of Earth is 6.38 10 6 m. Putting these values into Newton s universal law of gravitation gives F = G m M r 2 = ( 6.673 10 11 N m 2 kg 2 ) ( ( 60.0 kg ) ( 5.97 10 24 kg ) ( 6.38 10 6 m ) 2 ) = 584 N F = G m M r 2 = ( 6.673 10 11 N m 2 kg 2 ) ( ( 60.0 kg ) ( 5.97 10 24 kg ) ( 6.38 10 6 m ) 2 ) = 584 N 

We can check this result with the relationship: F = m g = ( 60 kg ) ( 9.8 m/s 2 ) = 588 N F = m g = ( 60 kg ) ( 9.8 m/s 2 ) = 588 N 

You may remember that g , the acceleration due to gravity, is another important constant related to gravity. By substituting g for a in the equation for Newton s second law of motion we get F = m g F = m g . Combining this with the equation for universal gravitation gives m g = G m M r 2 m g = G m M r 2 

Cancelling the mass m on both sides of the equation and filling in the values for the gravitational constant and mass and radius of the Earth, gives the value of g, which may look familiar. g = G M r 2 = ( 6.67 10 11 N m 2 kg 2 ) ( 5.98 10 24 kg ( 6.38 10 6 m ) 2 ) = 9.80 m/s 2 g = G M r 2 = ( 6.67 10 11 N m 2 kg 2 ) ( 5.98 10 24 kg ( 6.38 10 6 m ) 2 ) = 9.80 m/s 2 

This is a good point to recall the difference between mass and weight. Mass is the amount of matter in an object; weight is the force of attraction between the mass within two objects. Weight can change because g is different on every moon and planet. An object s mass m does not change but its weight m g can. 

[BL] [OL] Be sure no one is confusing G with g . 

[AL] Ask if anyone can explain why G is a universal constant that applies anywhere in the universe. Have them discuss the idea that the laws of physics are the same everywhere and that, at one time, people were not so sure about this. Emphasize that g is not a universal constant. Gravity and Orbits 

Move the sun, Earth, moon and space station in this simulation to see how it affects their gravitational forces and orbital paths. Visualize the sizes and distances between different heavenly bodies. Turn off gravity to see what would happen without it! Click here for the Gravity and Orbits simulation. 

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This is a good animation of the Earth-Moon-Sun system. Have the students try all of the buttons. This will show the paths of the Earth and the moon separately and together. Explain the gravitational force and velocity vectors. Point out the interesting shape of the moon s path around the sun. Explain that the velocity vector of the moon changes because sometimes the moon is traveling in the direction of Earth s orbit and sometimes it is traveling in the opposite direction. Take-Home Experiment: Falling Objects 

In this activity you will study the effects of mass and air resistance on the acceleration of falling objects. Make predictions (hypotheses) about the outcome of this experiment. Write them down to compare later with results. Four sheets of 8 - 1 / 2 11 8 - 1 / 2 11 -inch paper Take four identical pieces of paper. Crumple one up into a small ball. Leave one uncrumpled. Take the other two and crumple them up together, so that they make a ball of exactly twice the mass of the other crumpled ball. Now compare which ball of paper lands first when dropped simultaneously from the same height. Compare crumpled one-paper ball with crumpled two-paper ball. Compare crumpled one-paper ball with uncrumpled paper. 

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Ask for predictions (hypotheses) about the outcome of this experiment. Have the students write them down to compare later with results. 

It is possible to derive Kepler s third law from Newton s law of universal gravitation. Applying Newton s second law of motion to angular motion gives an expression for centripetal force, which can be equated to the expression for force in the universal gravitation equation. This expression can be manipulated to produce the equation for Kepler s third law. We saw earlier that the expression r 3 /T 2 is a constant for satellites orbiting the same massive object. The derivation of Kepler s third law from Newton s law of universal gravitation and Newton s second law of motion yields that constant: r 3 T 2 = G M 4 2 r 3 T 2 = G M 4 2 

where M is the mass of the central body about which the satellites orbit (for example, the sun in our solar system). The usefulness of this equation will be seen later. 

[OL] This equation illustrates the difference between Kepler s and Newton s work. Ask the students to explain why this is so. 

[AL] Ask the students what the attraction would be between two 10 kg balls separated by a distance of 1.0 m. Could they feel it? Later, ask them to calculate it after they have done some similar calculations. Solution: F = G m M r 2 = ( 6.67 10 11 N m 2 kg 2 ) ( 10 kg 10 kg ( 1 m ) 2 ) = 6.67 10 9 N F = G m M r 2 = ( 6.67 10 11 N m 2 kg 2 ) ( 10 kg 10 kg ( 1 m ) 2 ) = 6.67 10 9 N 

The universal gravitational constant G is determined experimentally. This definition was first done accurately in 1798 by English scientist Henry Cavendish (1731 1810), more than 100 years after Newton published his universal law of gravitation. The measurement of G is very basic and important because it determines the strength of one of the four forces in nature. Cavendish s experiment was very difficult because he measured the tiny gravitational attraction between two ordinary-sized masses (tens of kilograms at most) by using an apparatus like that in [link] . Remarkably, his value for G differs by less than 1% from the modern value. Cavendish used an apparatus like this to measure the gravitational attraction between two suspended spheres ( m ) and two spheres on a stand ( M ) by observing the amount of torsion (twisting) created in the fiber. The distance between the masses can be varied to check the dependence of the force on distance. Modern experiments of this type continue to explore gravity. Einstein s Theory of General Relativity 

Einstein s theory of general relativity explained some interesting properties of gravity not covered by Newton s theory. Einstein based his theory on the postulate that acceleration and gravity have the same effect and cannot be distinguished from each other. He concluded that light must fall in both a gravitational field and in an accelerating reference frame. [link] shows this effect (greatly exaggerated) in an accelerating elevator. In [link] (a) , the elevator accelerates upward in zero gravity. In [link] (b) , the room is not accelerating but is subject to gravity. The effect on light is the same: it falls downward in both situations. The person in the elevator cannot tell whether the elevator is accelerating in zero gravity or is stationary and subject to gravity. Thus, gravity affects the path of light, even though we think of gravity as acting between masses, while photons are massless. 

[BL] [OL] Ask the students to discuss the postulate. Can they relate the identity of gravity and acceleration to experience? (a) A beam of light emerges from a flashlight in an upward-accelerating elevator. Since the elevator moves up during the time the light takes to reach the wall, the beam strikes lower than it would if the elevator were not accelerated. (b) Gravity must have the same effect on light, since it is not possible to tell whether the elevator is accelerating upward or is stationary and acted upon by gravity. 

Einstein s theory of general relativity got its first verification in 1919 when starlight passing near the sun was observed during a solar eclipse. (See [link] .) During an eclipse, the sky is darkened and we can briefly see stars. Those on a line of sight nearest the sun should have a shift in their apparent positions. Not only was this shift observed, but it agreed with Einstein s predictions well within experimental uncertainties. This discovery created a scientific and public sensation. Einstein was now a folk hero as well as a very great scientist. The bending of light by matter is equivalent to a bending of space itself, with light following the curve. This is another radical change in our concept of space and time. It is also another connection that any particle with mass or energy (e.g., massless photons) is affected by gravity. This schematic shows how light passing near a massive body like the sun is curved toward it. The light that reaches the Earth then seems to be coming from different locations than the known positions of the originating stars. Not only was this effect observed, but the amount of bending was precisely what Einstein predicted in his general theory of relativity. 

To summarize the two views of gravity, Newton envisioned gravity as a tug of war along the line connecting any two objects in the universe. In contrast, Einstein envisioned gravity as a bending of space-time by mass. NASA gravity probe B 

NASA s Gravity Probe B (GP-B) mission has confirmed two key predictions derived from Albert Einstein s general theory of relativity. The probe, shown in [link] was launched in 2004. It carried four ultra-precise gyroscopes designed to measure two effects hypothesized by Einstein s theory: The geodetic effect , which is the warping of space and time by the gravitational field of a massive body (in this case, Earth) The frame-dragging effect , which is the amount by which a spinning object pulls space and time with it as it rotates Artist concept of Gravity Probe B spacecraft in orbit around the Earth. (credit: NASA/MSFC) 

Both effects were measured with unprecedented precision. This was done by pointing the gyroscopes at a single star while orbiting Earth in a polar orbit. As predicted by relativity theory, the gyroscopes experienced very small, but measureable, changes in the direction of their spin caused by the pull of Earth s gravity. 

The principle investigator suggested imagining Earth spinning in honey. As Earth rotates it drags space and time with it as it would a surrounding sea of honey. 

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Explain that it is very exciting when a prediction of relativity theory is tested successfully. Some of the predictions were in doubt because they sounded so bizarre. Calculations Based on Newton s Law of Universal Gravitation 

When performing calculations using the equations in this chapter, use units of kilograms for mass, meters for distances, newtons for force, and seconds for time. 

The mass of an object is constant, but its weight varies with the strength of the gravitational field. This means the value of g varies from place to place in the universe. The relationship between force, mass, and acceleration from the second law of motion can be written in terms of g . F = m a = m g F = m a = m g 

In this case, the force is the weight of the object, which is caused by the gravitational attraction of the planet or moon on which the object is located. We can use this expression to compare weights of an object on different moons and planets. 

[BL] Check to make sure students are clear about the distinction between mass and weight. 

[OL] Recall the antics of astronauts of on the moon performed to illustrate the effect of a different value for g . Mass and Weight Clarification 

This video shows the mathematical basis of the relationship between mass and weight. The distinction between mass and weight are clearly explained. The mathematical relationship between mass and weight are shown mathematically in terms of the equation for Newton s law of universal gravitation and in terms of his second law of motion. 

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This may be a rather long-winded explanation of the mass-weight distinction, but it should drive home the point. 

Two equations involving the gravitational constant, G , are often useful. The first is Newton s equation: F = G m M r 2 F = G m M r 2 . Several of the values in this equation are either constants or easily obtainable. F is often the weight of an object on the surface of a large object with mass M , which is usually known. The mass of the smaller object, m , is often known, and G is a universal constant with the same value anywhere in the universe. This equation can be used to solve problems involving an object on or orbiting the Earth or other massive celestial object. Sometimes it is helpful to equate the right-hand side of the equation to m g and cancel the m on both sides. 

The equation r 3 T 2 = G M 4 2 r 3 T 2 = G M 4 2 is also useful for problems involving objects in orbit. Note that there is no need to know the mass of the object. Often, we know the radius r or the period T and want to find the other. If these are both known, we can use the equation to calculate the mass of a planet or star. Mass and Weight Clarification 

This video demonstrates calculations involving Newton s universal law of gravitation. 

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This video is a thorough demonstration of many of the calculations to be learned in this subsection. Change in g 

The value of g on the planet Mars is 3.71 m/s 2 . If you have a mass of 60.0 kg on Earth, what would be your mass on Mars? What would be your weight on Mars? Strategy 

Weight equals acceleration due to gravity times mass: W = m g W = m g . An object s mass is constant. Call acceleration due to gravity on Mars g M and weight on Mars W M . Solution 

Mass on Mars would be the same, 60 kg. 

W M = m g M = ( 60.0 kg ) ( 3.71 m/s 2 ) = 223 N W M = m g M = ( 60.0 kg ) ( 3.71 m/s 2 ) = 223 N Discussion 

The value of g on any planet depends on the mass of the planet and the distance from its center. If the material below the surface varies from point to point, the value of g will also vary slightly. 

This is a typical mass-weight calculation. Earth s g at the Moon 

Find the acceleration due to Earth s gravity at the distance of the moon. 

G = 6.67 10 11 N m 2 /kg 2 G = 6.67 10 11 N m 2 /kg 2 

Earth-moon distance = 3.84 10 8 m 3.84 10 8 m 

Earth s mass = 5.98 10 24 kg 5.98 10 24 kg Strategy 

Express the force of gravity in terms of g . F = W = m a = m g F = W = m a = m g 

Combine with the equation for universal gravitation: 

m g = m G M r 2 m g = m G M r 2 Solution 

Cancel m and substitute. 

g = G M r 2 = ( 6.67 10 11 N m 2 kg 2 ) ( 5.98 10 24 kg ( 3.84 10 8 m ) 2 ) = 2.70 10 3 m/s 2 g = G M r 2 = ( 6.67 10 11 N m 2 kg 2 ) ( 5.98 10 24 kg ( 3.84 10 8 m ) 2 ) = 2.70 10 3 m/s 2 Discussion 

The value of g for the moon is 1.62 m/s 2 . Comparing this value to the answer, we see that Earth s gravitational influence on an object on the moon s surface would be insignificant. 

[BL] [OL] Review the meanings of all the symbols in these equations: F , G , m , M , r , T , and . 

[OL] [AL] Have the students memorize the values of G , g , and to three significant figures. Practice Problems 

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[link] Check Your Understanding 

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Use the Check Your Answers questions to assess whether students master the learning objectives for this section. If students are struggling with a specific objective, the Check Your Answers will help identify which objective is causing the problem and direct students to the relevant content. Section Summary Newton s law of universal gravitation provides a mathematical basis for gravitational force and Kepler s laws of planetary motion. Einstein s theory of general relativity shows that gravitational fields change the path of light and warp space and time. An object s mass is constant, but its weight changes when acceleration due to gravity, g , changes. Key Equations Newton s second law of motion F = m a = m g F = m a = m g Newton s universal law of gravitation F = G m M r 2 F = G m M r 2 acceleration due to gravity g = G M r 2 g = G M r 2 constant for satellites orbiting the same massive object r 3 T 2 = G M 4 2 r 3 T 2 = G M 4 2 Concept Items 

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Design an experiment to test whether magnetic force is inversely proportional to the square of distance. Gravitational, magnetic, and electrical fields all act at a distance, but do they all follow the inverse square law? One difference in the forces related to these fields is that gravity is only attractive, but the other two can repel as well. In general, the inverse square law says that force F equals a constant C divided by the distance between objects, d , squared: F = C / d 2 F = C / d 2 . 

Incorporate these materials into your design: Two strong, permanent bar magnets A spring scale that can measure small forces A short ruler calibrated in millimeters 

Use the magnets to study the relationship between attractive force and distance. What will be the independent variable? What will be the dependent variable? How will you measure each of these variables? If you plot the independent variable versus the dependent variable and the inverse square law is upheld, will the plot be a straight line? Explain. Which plot would be a straight line if the inverse square law were upheld? 

Magnets must be strong, such as neodymium magnets or cow magnets (ask a veterinarian). Suggest that they could either measure distance versus attractive force or repulsive force. Attractive force at various distances can be measured with the spring scale. Repulsive force could be measured by dropping the magnets into a transparent tube oriented so that they repel each other. The distance will be the distance between the magnets. Ask what the force will be. Ask how they could change the force and thereby change the distance. Test Prep Multiple Choice 

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[link] Glossary Einstein s theory of general relativity the theory that gravitational force results from the bending of spacetime by an object s mass gravitational constant the proportionality constant in Newton s law of universal gravitation Newton s universal law of gravitation states that gravitational force between two objects is directly proportional to the product of their masses and inversely proportional to the square of the distance between them.Conservation of Momentum Conservation of Momentum Section Learning Objectives Describe the law of conservation of momentum verbally and mathematically 

The learning objectives in this section will help your students master the following TEKS: (6) Science concepts. The student knows that changes occur within a physical system and applies the laws of conservation of energy and momentum. The student is expected to: (6C) : Calculate the mechanical energy of, power generated within, impulse applied to, and momentum of a physical system (6D) : Demonstrate and apply the laws of conservation of energy and conservation of momentum in one dimension; Section Key Terms angular momentum isolated system law of conservation of momentum 

In this section, students will apply what they have learned about momentum, impulse and force. 

[BL] [OL] Before students read the section, ask them what they understand by the word conservation . Have they come across it in any other law of physics? Conservation of Momentum 

It is important we realize that momentum is conserved during collisions, explosions, and other events involving objects in motion. To say that a quantity is conserved means that it is constant throughout the event. In the case of conservation of momentum, the total momentum in the system remains the same before and after the collision. 

You may have noticed that momentum was not conserved in this example , where forces acting on the objects produced large changes in momentum. Why is this? The systems of interest considered in those problems were not inclusive enough. If the systems were expanded to include more objects, then momentum would in fact be conserved in those sample problems. It is always possible to find a larger system where momentum is conserved, even though momentum changes for individual objects within the system. 

[OL] [AL] Caution students that momentum is only conserved when the entire system affected is taken into account. Explain isolated system. Ask students to give examples of isolated systems. Ask them is these are perfectly isolated. Would it be possible to have perfectly isolated systems on earth? 

For example, if a football player runs into the goalpost in the end zone, there will be a force on him that causes him to bounce backward. His momentum is obviously greatly changed, and considering only the football player, we would find that momentum is not conserved. However, the system can be expanded to contain the entire Earth! Surprisingly, the Earth also recoils conserving momentum because of the force applied to it through the goalpost. Of course, the effect on the Earth is not noticeable because Earth is so much more massive than the player, but the effect is real nevertheless. 

Next, consider what happens if the masses of two colliding objects are more similar than the masses of a football player and Earth for example, one car bumping into another, as shown in [link] . Both cars are coasting in the same direction when the lead car (labeled m 2 ) is bumped by the trailing car (labeled m 1 ). The only unbalanced force on each car is the force of the collision. (Assume that the effects due to friction are negligible.) Car 1 slows down as a result of the collision, losing some momentum, while car 2 speeds up and gains some momentum. If we choose the system to include both cars and assume that friction is negligible, then the momentum of the two-car system should remain constant. Now we will prove that the total momentum of the two-car system does in fact remain constant, and is therefore conserved. Car of mass m 1 moving with a velocity of v 1 bumps into another car of mass m 2 and velocity v 2 that it is following. As a result, the first car slows down to a velocity of v 1 and the second speeds up to a velocity of v 2 . The momentum of each car is changed, but the total momentum p tot of the two cars is the same before and after the collision (if you assume friction is negligible). 

Using the impulse-momentum theorem, the change in momentum of car 1 is given by p 1 = F 1 t p 1 = F 1 t 

where F 1 is the force on car 1 due to car 2, and t t is the time the force acts (the duration of the collision). 

Similarly, the change in momentum of car 2 is p 2 = F 2 t p 2 = F 2 t where F 2 is the force on car 2 due to car 1, and we assume the duration of the collision t t is the same for both cars. We know from Newton s third law that F 2 = F 1 , and so p 2 = F 1 t = p 1 p 2 = F 1 t = p 1 . 

Therefore, the changes in momentum are equal and opposite, and p 1 + p 2 = 0 p 1 + p 2 = 0 . 

Because the changes in momentum add to zero, the total momentum of the two-car system is constant. That is, p 1 + p 2 = constant p 1 + p 2 = constant p 1 + p 2 = p 1 + p 2 p 1 + p 2 = p 1 + p 2 

where p 1 and p 2 are the momenta of cars 1 and 2 after the collision. 

This result that momentum is conserved is true not only for this example involving the two cars, but momentum is conserved for any system where the net external force is zero (known as an isolated system ). The law of conservation of momentum states that for an isolated system with any number of objects in it, the total momentum is conserved. In equation form, the law of conservation of momentum for an isolated system is written as p tot = constant p tot = constant 

or p tot = p tot p tot = p tot 

where p tot is the total momentum (the sum of the momenta of the individual objects in the system) at a given time and p tot is the total momentum some time later. 

The conservation of momentum principle can be applied to systems as diverse as a comet striking Earth or a gas containing huge numbers of atoms and molecules. Conservation of momentum appears to be violated only when the net external force is not zero. But another larger system can always be considered in which momentum is conserved by simply including the source of the external force. For example, in the collision of two cars considered above, the two-car system conserves momentum while each one-car system does not. 

Momenta is the plural form of the word momentum. One object is said to have momentum, but two or more objects are said to have momenta. Angular Momentum in Figure Skating 

So far we ve covered linear momentum, which describes the inertia of objects traveling in a straight line. But we know that many objects in nature have a curved or circular path. Just as linear motion has linear momentum to describe its tendency to move forward, circular motion has the equivalent, angular momentum , to describe how rotational motion is carried forward. 

This is similar to how torque is analogous to force, angular acceleration is analogous to translational acceleration , and mr 2 is analogous to mass (or inertia). You may recall learning that the quantity mr 2 is called the rotational inertia or moment of inertia of a point mass m at a distance r from the center of rotation. 

We already know the equation for linear momentum, p = m v . Since angular momentum is analogous to linear momentum, the moment of inertia ( I ) is analogous to mass, and angular velocity ( ) is analogous to linear velocity, it makes sense that angular momentum ( L ) is defined as L = I L = I 

Angular momentum is conserved when the net external torque ( ) is zero, just as linear momentum is conserved when the net external force is zero. 

Figure skaters take advantage of the conservation of angular momentum, likely without even realizing it. In [link] , a figure skater is executing a spin. The net torque on her is very close to zero, because there is relatively little friction between her skates and the ice, and because the friction is exerted very close to the pivot point. (Both F and r are small, and so is negligibly small.) (a) An ice skater is spinning on the tip of her skate with her arms extended. In the next image, (b), her rate of spin increases greatly when she pulls in her arms. 

Consequently, she can spin for quite some time. She can do something else, too. She can increase her rate of spin by pulling her arms and legs in. Why does pulling her arms and legs in increase her rate of spin? The answer is that her angular momentum is constant, so that L = L . 

Expressing this equation in terms of the moment of inertia, I = I I = I 

where the primed quantities refer to conditions after she has pulled in her arms and reduced her moment of inertia. Because I is smaller, the angular velocity must increase to keep the angular momentum constant. This allows her to spin much faster without exerting any extra torque! 

A video is also available that shows a real figure skater executing a spin. It discusses the physics of spins in figure skating. 

You can demonstrate a similar exercise in class using a revolving stool or chair. Ask a student to sit on the stool with outstretched arms, holding some weight in each hand. Rotate the stool and once a good speed is achieved, ask him to bring his hands in close to his body. He will start spinning faster. 

[link] Check Your Understanding 

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Use the Check Your Understanding questions to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, the assessment will help identify which objective is causing the problem and direct students to the relevant content. Section Summary The law of conservation of momentum is written p tot = constant or p tot = p tot (isolated system), where p tot is the initial total momentum and p tot is the total momentum some time later. In an isolated system the net external force is zero. Conservation of momentum applies only when the net external force is zero within the defined system. Key Equations law of conservation of momentum p tot = constant, or p tot = p tot conservation of momentum for two objects p 1 + p 2 = constant, or p 1 + p 2 = p 1 + p 2 angular momentum L = I Concept Items 

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[link] Glossary angular momentum the product of the moment of inertia and angular velocity isolated system system in which the net external force is zero law of conservation of momentum when the net external force is zero, the total momentum of the system is conserved or constantElastic and Inelastic Collisions Elastic and Inelastic Collisions Section Learning Objectives 

By the end of this section, you will be able to: Distinguish between elastic and inelastic collisions Solve collision problems by applying the law of conservation of momentum 

The learning objectives in this section will help your students master the following TEKS: (6) Science concepts. The student knows that changes occur within a physical system and applies the laws of conservation of energy and momentum. The student is expected to: (6C) : Calculate the mechanical energy of, power generated within, impulse applied to, and momentum of a physical system (6D) : Demonstrate and apply the laws of conservation of energy and conservation of momentum in one dimension Section Key Terms elastic collision inelastic collision point masses recoil Elastic and Inelastic Collisions 

When objects collide, they can either stick together or bounce off one another, remaining separate. In this section, we ll cover these two different types of collisions , first in one dimension and then in two dimensions. 

In an elastic collision , the objects separate after impact and don t lose any of their kinetic energy . Kinetic energy is the energy of motion and is covered in detail elsewhere. The law of conservation of momentum is very useful here, and it can be used whenever the net external force on a system is zero. [link] shows an elastic collision where momentum is conserved. The diagram shows a one-dimensional elastic collision between two objects. 

An animation of an elastic collision between balls can be seen by watching this video . It replicates the elastic collisions between balls of identical masses as well as balls of different masses. 

Perfectly elastic collisions can happen only with subatomic particles. Everyday observable examples of perfectly elastic collisions don t exist some kinetic energy is always lost, as it is converted into heat transfer due to friction. However, collisions between everyday objects are almost perfectly elastic when they occur with objects and surfaces that are nearly frictionless, such as with two steel blocks on ice. 

Now, to solve problems involving one-dimensional elastic collisions between two objects, we can use the equation for conservation of momentum. First, the equation for conservation of momentum for two objects in a one-dimensional collision is p 1 + p 2 = p 1 + p 2 ( F net = 0 ) p 1 + p 2 = p 1 + p 2 ( F net = 0 ) 

Substituting the definition of momentum p = m v for each initial and final momentum, we get m 1 v 1 + m 2 v 2 = m 1 v 1 + m 2 v 2 m 1 v 1 + m 2 v 2 = m 1 v 1 + m 2 v 2 

where the primes (') indicate values after the collision; in some texts, you may see i for initial (before collision) and f for final (after collision). The equation assumes that the mass of each object does not change during the collision. Momentum: Ice Skater Throws a Ball 

This video covers an elastic collision problem in which we find the recoil velocity of an ice skater who throws a ball straight forward. (To clarify, Sal is using the equation 

m ball V ball + m skater V skater = m ball v ball + m skater v skater m ball V ball + m skater V skater = m ball v ball + m skater v skater .) 

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Now, let s turn to the second type of collision. An inelastic collision is one in which objects stick together after impact, and kinetic energy is not conserved. This lack of conservation means that the forces between colliding objects may convert kinetic energy to other forms of energy, such as potential energy or thermal energy. (The concepts of energy are discussed more thoroughly elsewhere). For inelastic collisions, kinetic energy may be lost in the form of heat. [link] shows an example of an inelastic collision. Two objects that have equal masses head toward each other at equal speeds and then stick together. The two objects come to rest after sticking together, conserving momentum but not kinetic energy after they collide. Some of the energy of motion gets converted to thermal energy, or heat. A one-dimensional inelastic collision between two objects. Momentum is conserved, but kinetic energy is not conserved. (a) Two objects of equal mass initially head directly toward each other at the same speed. (b) The objects stick together (a perfectly inelastic collision). In the case shown in this figure, the combined objects stop; this is not true for all inelastic collisions. 

Since the two objects stick together after collision, they move together at the same speed. This lets us simplify the conservation of momentum equation from m 1 v 1 + m 2 v 2 = m 1 v 1 + m 2 v 2 m 1 v 1 + m 2 v 2 = m 1 v 1 + m 2 v 2 

to m 1 v 1 + m 2 v 2 = ( m 1 + m 2 ) v m 1 v 1 + m 2 v 2 = ( m 1 + m 2 ) v 

for inelastic collisions, where v is the final velocity for both objects as they are stuck together (either in motion or at rest). 

[BL] [OL] Review the concept of internal energy. Ask students what they understand by the words elastic and inelastic. 

[AL] Start a discussion about collisions. Ask students to give examples of elastic and inelastic collisions. Introduction to Momentum 

This video reviews the definitions of momentum and impulse. It also covers an example of using conservation of momentum to solve a problem involving an inelastic collision between a car with constant velocity and a stationary truck. Note that Sal accidentally gives the unit for impulse as Joules; it is actually N s or k gm/s. 

[link] Ice Cubes and Elastic Collisions 

In this activity, you will observe an elastic collision by sliding an ice cube into another ice cube on a smooth surface, so that a negligible amount of energy is converted to heat. Several ice cubes (The ice must be in the form of cubes) A smooth surface Find a few ice cubes that are about the same size and a smooth kitchen tabletop or a table with a glass top. Place the ice cubes on the surface several centimeters away from each other. Flick one ice cube toward a stationary ice cube and observe the path and velocities of the ice cubes after the collision. (Try to avoid edge-on collisions and collisions with rotating ice cubes.) Explain the speeds and directions of the ice cubes using momentum. 

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Here s a trick for remembering which collisions are elastic and which are inelastic: Elastic is a bouncy material, so when objects bounce off one another in the collision and separate, it is an elastic collision. When they don t, the collision is inelastic. Solving Collision Problems 

The Khan Academy videos referenced in this section show examples of elastic and inelastic collisions in one dimension. In one-dimensional collisions, the incoming and outgoing velocities are all along the same line. But what about collisions, such as those between billiard balls, in which objects scatter to the side? These are two-dimensional collisions, and just as we did with two-dimensional forces, we will solve these problems by first choosing a coordinate system and separating the motion into its x and y components. 

One complication with two-dimensional collisions is that the objects might rotate before or after their collision. For example, if two ice skaters hook arms as they pass each other, they will spin in circles. We will not consider such rotation until later, and so for now, we arrange things so that no rotation is possible. To avoid rotation, we consider only the scattering of point masses that is, structureless particles that cannot rotate or spin. 

We start by assuming that F net = 0, so that momentum p is conserved. The simplest collision is one in which one of the particles is initially at rest. The best choice for a coordinate system is one with an axis parallel to the velocity of the incoming particle, as shown in [link] . Because momentum is conserved, the components of momentum along the x - and y -axes ( p x and p y ) will also be conserved. With the chosen coordinate system, p y is initially zero and p x is the momentum of the incoming particle. A two-dimensional collision with the coordinate system chosen so that m 2 is initially at rest and v 1 is parallel to the x -axis. 

Now, we will take the conservation of momentum equation, p 1 + p 2 = p 1 + p 2 and break it into its x and y components. 

Along the x -axis, the equation for conservation of momentum is p 1x + p 2x = p 1x + p 2x p 1x + p 2x = p 1x + p 2x 

In terms of masses and velocities, this equation is m 1 v 1 x + m 2 v 2 x = m 1 v 1 x + m 2 v 2 x m 1 v 1 x + m 2 v 2 x = m 1 v 1 x + m 2 v 2 x 

But because particle 2 is initially at rest, this equation becomes m 1 v 1 x = m 1 v 1 x + m 2 v 2 x m 1 v 1 x = m 1 v 1 x + m 2 v 2 x 

The components of the velocities along the x -axis have the form v cos . Because particle 1 initially moves along the x -axis, we find v 1 x = v 1 . Conservation of momentum along the x -axis gives the following equation: m 1 v 1 = m 1 v 1 cos 1 + m 2 v 2 cos 2 m 1 v 1 = m 1 v 1 cos 1 + m 2 v 2 cos 2 

where 1 1 and 2 2 are as shown in [link] . 

Along the y -axis, the equation for conservation of momentum is p 1 y + p 2 y = p 1 y + p 2 y p 1 y + p 2 y = p 1 y + p 2 y 

or m 1 v 1 y + m 2 v 2 y = m 1 v 1 y + m 2 v 2 y m 1 v 1 y + m 2 v 2 y = m 1 v 1 y + m 2 v 2 y 

But v 1 y is zero, because particle 1 initially moves along the x -axis. Because particle 2 is initially at rest, v 2 y is also zero. The equation for conservation of momentum along the y -axis becomes 0 = m 1 v 1 y + m 2 v 2 y 0 = m 1 v 1 y + m 2 v 2 y 

The components of the velocities along the y -axis have the form v sin . Therefore, conservation of momentum along the y -axis gives the following equation: 0 = m 1 v 1 sin 1 + m 2 v 2 sin 2 0 = m 1 v 1 sin 1 + m 2 v 2 sin 2 

Review conservation of momentum and the equations derived in the previous sections of this chapter. Say that in the problems of this section, all objects are assumed to be point masses. Explain point masses. Collision Lab 

In this simulation, you will investigate collisions on an air hockey table. Place checkmarks next to the momentum vectors and momenta diagram options. Experiment with changing the masses of the balls and the initial speed of ball 1. How does this affect the momentum of each ball? What about the total momentum? Next, experiment with changing the elasticity of the collision. You will notice that collisions have varying degrees of elasticity, ranging from perfectly elastic to perfectly inelastic. Click here for the simulation 

[link] Calculating Velocity: Inelastic Collision of a Puck and a Goalie 

Find the recoil velocity of a 70.0 kg ice hockey goalie who catches a 0.150-kg hockey puck slapped at him at a velocity of 35.0 m/s. Assume that the goalie is at rest before catching the puck, and friction between the ice and the puck-goalie system is negligible (see [link] ). An ice hockey goalie catches a hockey puck and recoils backward in an inelastic collision. Strategy 

Momentum is conserved because the net external force on the puck-goalie system is zero. Therefore, we can use conservation of momentum to find the final velocity of the puck and goalie system. Note that the initial velocity of the goalie is zero and that the final velocity of the puck and goalie are the same. Solution 

For an inelastic collision, conservation of momentum is m 1 v 1 + m 2 v 2 = ( m 1 + m 2 ) v m 1 v 1 + m 2 v 2 = ( m 1 + m 2 ) v 

where v is the velocity of both the goalie and the puck after impact. Because the goalie is initially at rest, we know v 2 = 0. This simplifies the equation to m 1 v 1 = ( m 1 + m 2 ) v m 1 v 1 = ( m 1 + m 2 ) v 

Solving for v yields v = ( m 1 m 1 + m 2 ) v 1 v = ( m 1 m 1 + m 2 ) v 1 

Entering known values in this equation, we get v = ( 0.150 kg 70.0 kg + 0.150 kg ) ( 35 m/s ) = 7.48 10 2 m/s v = ( 0.150 kg 70.0 kg + 0.150 kg ) ( 35 m/s ) = 7.48 10 2 m/s Discussion 

This recoil velocity is small and in the same direction as the puck s original velocity, as we might expect. Calculating Final Velocity: Elastic Collision of Two Carts 

Two hard steel carts collide head-on and then ricochet off each other in opposite directions on a frictionless surface (see [link] ). Cart 1 has a mass of 0.350 kg and an initial velocity of 2.00 m/s. Cart 2 has a mass of 0.500 kg and an initial velocity of 0.500 m/s. After the collision, cart 1 recoils with a velocity of 4.00 m/s. What is the final velocity of cart 2? Two carts collide with each other in an elastic collision. Strategy 

Since the track is frictionless, F net = 0 and we can use conservation of momentum to find the final velocity of cart 2. Solution 

As before, the equation for conservation of momentum for a one-dimensional elastic collision in a two-object system is m 1 v 1 + m 2 v 2 = m 1 v 1 + m 2 v 2 m 1 v 1 + m 2 v 2 = m 1 v 1 + m 2 v 2 

The only unknown in this equation is v 2 . Solving for v 2 and substituting known values into the previous equation yields v 2 = m 1 v 1 + m 2 v 2 m 1 v 1 m 2 = ( 0 .350 kg ) ( 2 .00 m/s ) + ( 0 .500 kg ) ( 0 .500 m/s ) ( 0 .350 kg ) ( 4 .00 m/s ) 0 .500 kg = 3 .70 m/s v 2 = m 1 v 1 + m 2 v 2 m 1 v 1 m 2 = ( 0 .350 kg ) ( 2 .00 m/s ) + ( 0 .500 kg ) ( 0 .500 m/s ) ( 0 .350 kg ) ( 4 .00 m/s ) 0 .500 kg = 3 .70 m/s Discussion 

The final velocity of cart 2 is large and positive, meaning that it is moving to the right after the collision. Calculating Final Velocity in a Two-Dimensional Collision 

Suppose the following experiment is performed ( [link] ). An object of mass 0.250 kg ( m 1 ) is slid on a frictionless surface into a dark room, where it strikes an initially stationary object of mass 0.400 kg ( m 2 ). The 0.250 kg object emerges from the room at an angle of 45.0 with its incoming direction. The speed of the 0.250 kg object is originally 2.00 m/s and is 1.50 m/s after the collision. Calculate the magnitude and direction of the velocity ( v 2 and 2 2 ) of the 0.400 kg object after the collision. The incoming object of mass m 1 is scattered by an initially stationary object. Only the stationary object s mass m 2 is known. By measuring the angle and speed at which the object of mass m 1 emerges from the room, it is possible to calculate the magnitude and direction of the initially stationary object s velocity after the collision. Strategy 

Momentum is conserved because the surface is frictionless. We chose the coordinate system so that the initial velocity is parallel to the x -axis, and conservation of momentum along the x - and y -axes applies. 

Everything is known in these equations except v 2 and , which we need to find. We can find two unknowns because we have two independent equations: the equations describing the conservation of momentum in the x and y directions. Solution 

First, we ll solve both conservation of momentum equations ( m 1 v 1 = m 1 v 1 cos 1 + m 2 v 2 cos 2 m 1 v 1 = m 1 v 1 cos 1 + m 2 v 2 cos 2 and 0 = m 1 v 1 sin 1 + m 2 v 2 sin 2 0 = m 1 v 1 sin 1 + m 2 v 2 sin 2 ) for v 2 sin 2 2 . 

For conservation of momentum along x-axis, let s substitute sin 2 2 /tan 2 2 for cos 2 2 so that terms may cancel out later on. (This comes from rearranging the definition of the trigonometric identity tan = sin /cos ). This gives us m 1 v 1 = m 1 v 1 cos 1 + m 2 v 2 sin 2 tan 2 m 1 v 1 = m 1 v 1 cos 1 + m 2 v 2 sin 2 tan 2 

Solving for v 2 sin 2 2 yields: v 2 sin 2 = ( m 1 v 1 m 1 v 1 cos 1 ) ( tan 2 ) m 2 v 2 sin 2 = ( m 1 v 1 m 1 v 1 cos 1 ) ( tan 2 ) m 2 

For conservation of momentum along y -axis, solving for v 2 sin 2 2 yields: v 2 sin 2 = ( m 1 v 1 sin 1 ) m 2 v 2 sin 2 = ( m 1 v 1 sin 1 ) m 2 

Since both equations equal v 2 sin 2 2 , we can set them equal to one another, yielding ( m 1 v 1 m 1 v 1 cos 1 ) ( tan 2 ) m 2 = ( m 1 v 1 sin 1 ) m 2 ( m 1 v 1 m 1 v 1 cos 1 ) ( tan 2 ) m 2 = ( m 1 v 1 sin 1 ) m 2 

Solving this equation for tan 2 2 , we get tan 2 = v 1 sin 1 v 1 cos 1 v 1 tan 2 = v 1 sin 1 v 1 cos 1 v 1 

Entering known values into the previous equation gives tan 2 = ( 1.50 ) ( 0.707 ) ( 1.50 ) ( 0.707 ) 2.00 = 1.129 tan 2 = ( 1.50 ) ( 0.707 ) ( 1.50 ) ( 0.707 ) 2.00 = 1.129 

Therefore, 2 = tan 1 ( 1.129 ) = 312 0 2 = tan 1 ( 1.129 ) = 312 0 

Since angles are defined as positive in the counterclockwise direction, m 2 is scattered to the right. 

We ll use the conservation of momentum along the y-axis equation to solve for v 2 . v 2 = m 1 m 2 v 1 sin 1 sin 2 v 2 = m 1 m 2 v 1 sin 1 sin 2 

Entering known values into this equation gives v 2 = ( 0.250 ) ( 0.400 ) ( 1.50 ) ( 0.7071 0.7485 ) v 2 = ( 0.250 ) ( 0.400 ) ( 1.50 ) ( 0.7071 0.7485 ) 

Therefore, v 2 = 0.886 m/s . v 2 = 0.886 m/s . Discussion 

Either equation for the x - or y -axis could have been used to solve for v 2 , but the equation for the y -axis is easier because it has fewer terms. Practice Problems 

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[link] Check Your Understanding 

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Use the Check Your Understanding questions to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, the assessment will help identify which objective is causing the problem and direct students to the relevant content. Section Summary If objects separate after impact, the collision is elastic, and if they stick together, the collision is inelastic. Kinetic energy is conserved in an elastic collision, but not in an inelastic collision. The approach to two-dimensional collisions is to choose a convenient coordinate system and break the motion into components along perpendicular axes. Choose a coordinate system with the x -axis parallel to the velocity of the incoming particle. Two-dimensional collisions of point masses where mass 2 is initially at rest conserve momentum along the initial direction of mass 1 (the x -axis) and along the direction perpendicular to the initial direction (the y -axis). Point masses are structureless particles that cannot spin. Key Equations conservation of momentum in an elastic collision m 1 v 1 + m 2 v 2 = m 1 v 1 + m 2 v 2 , m 1 v 1 + m 2 v 2 = m 1 v 1 + m 2 v 2 , conservation of momentum in an inelastic collision m 1 v 1 + m 2 v 2 = ( m 1 + m 2 ) v m 1 v 1 + m 2 v 2 = ( m 1 + m 2 ) v conservation of momentum along x-axis for 2D collisions m 1 v 1 = m 1 v 1 cos 1 + m 2 v 2 cos 2 m 1 v 1 = m 1 v 1 cos 1 + m 2 v 2 cos 2 conservation of momentum along y-axis for 2D collisions 0 = m 1 v 1 sin 1 + m 2 v 2 sin 2 0 = m 1 v 1 sin 1 + m 2 v 2 sin 2 Concept Items 

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[link] Performance Task You will need: balls of different weights a ruler or wooden strip some books a paper cup 

Make an inclined plane by resting one end of a ruler on a stack of books. Place a paper cup on the other end. Roll a ball from the top of the ruler so that it hits the paper cup. Measure the displacement of the paper cup due to the collision. Now use increasingly heavier balls for this activity and see how that affects the displacement of the cup. Plot a graph of mass vs displacement. Now repeat the same activity, but this time, instead of using different balls, change the incline of the ruler by varying the height of the stack of books. This will give you different velocities of the ball. See how this affects the displacement of the paper cup. Test Prep Multiple Choice 

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[link] Glossary elastic collision collision in which objects separate after impact and kinetic energy is conserved inelastic collision collision in which objects stick together after impact and kinetic energy is not conserved point masses structureless particles that cannot rotate or spin recoil backward movement of an object caused by the transfer of momentum from another object in a collisionWork, Power, and the Work Energy Theorem Work, Power, and the Work Energy Theorem Section Learning Objectives 

By the end of this section, you will be able to: Describe and apply the work energy theorem Describe and calculate work and power 

The learning objectives in this section will help your students master the following TEKS: (6A) : Describe and apply the work energy theorem. (6C) : Describe and calculate work and power. Section Key Terms energy gravitational potential energy joule kinetic energy mechanical energy potential energy power watt work work energy theorem 

In this section, students learn how work determines changes in kinetic energy and that power is the rate at which work is done. 

[BL] [OL] Review understanding of mass, velocity, and acceleration due to gravity. Define the general definitions of the words potential and kinetic . 

[AL] [AL] Remind students of the equation W = P E e = f m g W = P E e = f m g . Point out that acceleration due to gravity is a constant, therefore PE e that results from work done by gravity will also be constant. Compare this to acceleration due to other forces, such as applying muscles to lift a rock, which may not be constant. The Work Energy Theorem 

In physics, the term work has a very specific definition. Work is application of force, f f , to move an object over a distance, d , in the direction that the force is applied. Work, W , is described by the equation: W = f d W = f d 

Some things that we typically consider to be work are not work in the scientific sense of the term. Let s consider a few examples. Think about why each of the following statements is true. Homework is not work. Lifting a rock upwards off the ground is work. Carrying a rock in a straight path across the lawn at a constant speed is not work. 

The first two examples are fairly simple. Homework is not work because objects are not being moved over a distance. Lifting a rock up off the ground is work because the rock is moving in the direction that force is applied. The last example is less obvious. Recall from the laws of motion that force is not required to move an object at constant velocity. Therefore, while some force may be applied to keep the rock up off the ground, no net force is applied to keep the rock moving forward at constant velocity. 

[BL] [OL] Explain that, when this theorem is applied to an object that is initially at rest and then accelerates, the 1 2 m v 1 2 1 2 m v 1 2 term equals zero. 

[OL] [AL] Work is measured in joules and W = f d W = f d . Force is measured in newtons and distance in meters, so joules are equivalent to newton-meters ( N m ) ( N m ) 

Work and energy are closely related. When you do work to move an object, you change the object s energy. You (or an object) also expend energy to do work. In fact, energy can be defined as the ability to do work. Energy can take a variety of different forms, and one form of energy can transform to another. In this chapter we will be concerned with mechanical energy , which comes in two forms: kinetic energy and potential energy . Kinetic energy is also called energy of motion. A moving object has kinetic energy. Potential energy, sometimes called stored energy, comes in several forms. Gravitational potential energy is the stored energy an object has as a result of its position above Earth s surface (or another object in space). A roller coaster car at the top of a hill has gravitational potential energy. 

Let s examine how doing work on an object changes the object s energy. If we apply force to lift a rock off the ground, we increase the rock s potential energy, PE . If we drop the rock, the force of gravity increases the rock s kinetic energy as the rock moves downward until it hits the ground. 

The force we exert to lift the rock is equal to its weight, w , which is equal to its mass, m , multiplied by acceleration due to gravity, g : f = w = m g f = w = m g 

The work we do on the rock equals the force we exert multiplied by the distance, d , that we lift the rock. The work we do on the rock also equals the rock s gain in gravitational potential energy, PE e : W = P E e = f m g W = P E e = f m g 

Kinetic energy depends on the mass of an object and its velocity, v : K E = 1 2 m v 2 K E = 1 2 m v 2 

When we drop the rock the force of gravity causes the rock to fall, giving the rock kinetic energy. When work done on an object increases only its kinetic energy, then the net work equals the change in the value of the quantity 1 2 m v 2 1 2 m v 2 . This is a statement of the work energy theorem , which is expressed mathematically as: W = K E = 1 2 m v 2 2 1 2 m v 1 2 W = K E = 1 2 m v 2 2 1 2 m v 1 2 

The subscripts 2 and 1 indicate the final and initial velocity, respectively. This theorem was proposed and successfully tested by James Joule, shown in [link] . 

Does the name Joule sound familiar? The joule (J) is the metric unit of measurement for both work and energy. The measurement of work and energy with the same unit reinforces the idea that work and energy are related and can be converted into one another. 1.0 J = 1.0 N m, the units of force multiplied by distance. 1.0 N = 1.0 k m/s 2 , so 1.0 J = 1.0 k m 2 /s 2 . Analyzing the units of the term (1/2) m v 2 will produce the same units for joules. The joule is named after physicist James Joule (1818 1889). (credit: C. H. Jeens, Wikimedia Commons) Work and Energy 

This video explains the work energy theorem and discusses how work done on an object increases the object s KE. 

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Repeat the information on kinetic and potential energy discussed earlier in the section. Have the students distinguish between and understand the two ways of increasing the energy of an object (1) applying a horizontal force to increase KE and (2) applying a vertical force to increase PE. Calculations Involving Work and Power 

In applications that involve work, we are often interested in how fast the work is done. For example, in roller coaster design, the amount of time it takes to lift a roller coaster car to the top of the first hill is an important consideration. Taking a half hour on the ascent will surely irritate riders and decrease ticket sales. Let s take a look at how to calculate the time it takes to do work. 

Recall that a rate can be used to describe a quantity, such as work, over a period of time. Power is the rate at which work is done. In this case, rate means "per unit of time." Power is calculated by dividing the work done by the time it took to do the work: P = W t P = W t 

Let s consider an example that can help illustrate the differences among work, force, and power. Suppose the woman in [link] lifting the TV with a pulley gets the TV to the fourth floor in two minutes, and the man carrying the TV up the stairs takes five minutes to arrive at the same place. They have done the same amount of work ( f d ) ( f d ) on the TV, because they have moved the same mass over the same vertical distance, which requires the same amount of upward force. However, the woman using the pulley has generated more power. This is because she did the work in a shorter amount of time, so the denominator of the power formula, t , is smaller. (For simplicity s sake, we will leave aside for now the fact that the man climbing the stairs has also done work on himself.) No matter how you move a TV to the fourth floor, the amount of work performed and the potential energy gain are the same. 

Power can be expressed in units of watts (W). This unit can be used to measure power related to any form of energy or work. You have most likely heard the term used in relation to electrical devices, especially light bulbs. Multiplying power by time gives the amount of energy. Electricity is sold in kilowatt-hours because that equals the amount of electrical energy consumed. 

The watt unit was named after James Watt (1736 1819) (see [link] ). He was a Scottish engineer and inventor who discovered how to coax a lot more power out of steam engines. Is James Watt thinking about watts? (credit: Carl Frederik von Breda, Wikimedia Commons) 

[BL] [OL] Review the concept that work changes the energy of an object or system. Review the units of work, energy, force, and distance. Use the equations for mechanical energy and work to show what is work and what is not. Make it clear why holding something off the ground or carrying something over a level surface is not work in the scientific sense. 

[OL] Ask the students to use the mechanical energy equations to explain why each of these is or is not work. Ask them to provide more examples until they understand the difference between the scientific term work and a task that is simply difficult but not literally work (in the scientific sense). 

[BL] [OL] Stress that power is a rate and that rate means "per unit of time." In the metric system this unit is usually seconds. End the section by clearing up any misconceptions about the distinctions between force, work, and power. 

[AL] Explain relationships between the units for force, work, and power. If W = f d W = f d and work can be expressed in J, then P = W t = f d t P = W t = f d t so power can be expressed in units of N m s N m s 

Also explain that we buy electricity in kilowatt-hours because, when power is multiplied by time, the time units cancel, which leaves work or energy. Watt s Steam Engine 

James Watt did not invent the steam engine, but by the time he was done tinkering with it, it was a lot more useful. The first steam engines were not only inefficient, they only produced a back and forth, or reciprocal , motion. This was natural because pistons move in and out as the pressure in the chamber changes. This limitation was okay for simple tasks like pumping water or mashing potatoes, but did not work so well for moving a train. Watt was able build a steam engine that converted reciprocal motion to circular motion. With that one innovation, the industrial revolution was off and running. The world would never be the same. One of Watt's steam engines is shown in [link] . The video that follows the figure explains the importance of the steam engine in the industrial revolution. A late version of the Watt steam engine. (credit: Nehemiah Hawkins, Wikimedia Commons) 

Initiate a discussion on the historical significance of suddenly increasing the amount of power available to industry and transportation. Have students consider the fact that the speed of transportation increased roughly tenfold. Changes in how goods were manufactured were just as great. Ask students how they think the resulting changes in lifestyle compare to more recent changes brought about by innovations such as air travel and the Internet. Watt's Role in the Industrial Revolution 

This video demonstrates how all those watts that resulted from Watt's inventions helped make the industrial revolution possible and got England in on the ground floor of this new historical era. 

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Before proceeding, be sure you understand the distinctions among force, work, energy, and power. Force exerted on an object over a distance does work. Work can increase energy, and energy can do work. Power is the rate at which work is done. Applying the Work Energy Theorem 

An ice skater with a mass of 50 kg is gliding across the ice at a speed of 8 m/s when her friend comes up from behind and gives her a push, causing her speed to increase to 12 m/s. How much work did the friend do on the skater? Strategy 

The work energy theorem can be applied to the problem. Write the equation for the theorem and simplify it if possible. W = KE = 1 2 m v 2 2 1 2 m v 1 2 W = KE = 1 2 m v 2 2 1 2 m v 1 2 Simplify to W = 1 2 m ( v 2 2 v 1 2 ) Simplify to W = 1 2 m ( v 2 2 v 1 2 ) Solution 

Identify the variables: m = 50 kg, v 2 = 12 m s v 2 = 12 m s , and v 1 = 8 m s v 1 = 8 m s . 

Substitute: W = 1 2 50 ( 12 2 8 2 ) = 2 , 000 J W = 1 2 50 ( 12 2 8 2 ) = 2 , 000 J Discussion 

Work done on an object or system increases its energy. In this case, the increase is to the skater s kinetic energy. It follows that the increase in energy must be the difference in KE before and after the push. 

This problem illustrates a general technique for approaching problems that require you to apply formulas: identify the unknown and the known variables, express the unknown variables in terms of the known variables, and then enter all the known values. 

Identify the three variables and choose the relevant equation. Distinguish between initial and final velocity and pay attention to the minus sign 

Identify the variables: m = 50 kg, v 2 = 12 m s v 2 = 12 m s , and v 1 = 8 m s v 1 = 8 m s 

Substitute: W = 1 2 50 ( 12 2 8 2 ) = 2 , 000 J W = 1 2 50 ( 12 2 8 2 ) = 2 , 000 J Practice Problems 

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Use Check Your Understanding questions to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify which one and direct students to the relevant content. Section Summary Doing work on a system or object changes its energy. The work energy theorem states that an amount of work that changes the velocity of an object is equal to the change in kinetic energy of that object.The work energy theorem states that an amount of work that changes the velocity of an object is equal to the change in kinetic energy of that object. Power is the rate at which work is done. Key Equations equation for work W = f d W = f d force f = w = m g f = w = m g work equivalencies W = P E e = f m g W = P E e = f m g kinetic energy K E = 1 2 m v 2 K E = 1 2 m v 2 work energy theorem W = KE = 1 2 m v 2 2 1 2 m v 1 2 W = KE = 1 2 m v 2 2 1 2 m v 1 2 power P = W t P = W t Concept Items 

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[link] Glossary energy the ability to do work gravitational potential energy energy acquired by doing work against gravity joule the metric unit for work and energy; equal to 1 newton meter (N m) kinetic energy energy of motion mechanical energy kinetic or potential energy power the rate at which work is done potential energy stored energy watt the metric unit of power; equivalent to joules per second work force multiplied by distance work energy theorem states that the net work done on a system equals the change in kinetic energyIntroduction Introduction In this chapter, you will learn about: Work, Power, and the Work Energy Theorem Mechanical Energy and the Conservation of Energy Simple Machines class="summary" title="Section Summary" class="key-equations" title="Key Equations" class="concept" title="Concept Items" class="critical-thinking" title="Critical Thinking Items" class="problem" title="Problems" class="performance" title="Performance Task" class="multiple-choice" title="Multiple Choice" class="short-answer" title="Short Answer" class="extended-response" title="Extended Response" 

Physics learning objectives come from 112.39 (c) Knowledge and Skills People on a roller coaster experience thrills caused by changes in types of energy. (credit: Jonrev, Wikimedia Commons) 

Before students begin this chapter, it is useful to review these concepts: Using significant figures in calculations. Demonstrate how to use the proper number of significant figures when adding and multiplying. Converting units. Demonstrate how to convert from km/h to m/s. Calculating average. Demonstrate how to average two numbers by dividing their sum by two. Commonly used terms. Explain that constant means "unchanging," so constant speed refers to speed that is not changing. Explain that initial means "starting," so initial time is the time at which the action of a problem begins. Explain that an object that is not moving is often described in physics as being at rest. Review the difference between mass and weight. Review the force of gravity and acceleration due to gravity. 

Initiate a discussion about how speed changes at different points in a roller coaster ride. Also discuss acceleration and deceleration. Ask students to try to describe the physical experience of these changes. 

Roller coasters have provided thrills for daring riders around the world since the nineteenth century. Inventors of roller coasters used simple physics to build the earliest examples using railroad tracks on mountainsides and old mines. Modern roller coaster designers use the same basic laws of physics to create the latest amusement park favorites. Physics principles are used to engineer the machines that do the work to lift a roller coaster car up its first big incline before it is set loose to roll. Engineers also have to understand the changes in the car s energy that keep it speeding over hills, through twists, turns, and even loops. 

What exactly is energy? How changes in force and energy move objects like roller coaster cars? How can machines help us do work? In this chapter, you will discover the answers to these questions as you learn about work, energy, and simple machines.Mechanical Energy and the Conservation of Energy Mechanical Energy and the Conservation of Energy Section Learning Objectives 

By the end of this section, you will be able to: Explain the law of conservation of energy in terms of kinetic and potential energy Perform calculations related to kinetic and potential energy. Apply the law of conservation of energy 

The learning objectives in this section will help your students master the following TEKS: (6B) : investigate examples of kinetic and potential energy and their transformations. (6D) : demonstrate and apply the laws of conservation of energy and conservation of momentum in one dimension. Section Key Term law of conservation of energy 

[BL] [OL] Begin by distinguishing mechanical energy from other forms of energy. Explain how the general definition of energy as the ability to do work makes perfect sense in terms of either form of mechanical energy. Discuss the law of conservation of energy and dispel any misconceptions related to this law, such is the idea that moving objects just slow down naturally. Identify heat generated by friction as the usual explanation for apparent violations of the law. 

[AL] Start a discussion about how other useful forms of energy also end up as wasted heat, such as light, sound, and electricity. Try to get students to understand heat and temperature at a molecular level. Explain that energy lost to friction is really transforming kinetic energy at the macroscopic level to kinetic energy at the atomic level. Mechanical Energy and Conservation of Energy 

We saw earlier that mechanical energy can be either potential or kinetic. In this section we will see how energy is transformed from one of these forms to the other. We will also see that, in a closed system, the sum of these forms of energy remains constant. 

Quite a bit of potential energy is gained by a roller coaster car and its passengers when they are raised to the top of the first hill. Remember that the potential part of the term means that energy has been stored and can be used at another time. You will see that this stored energy can either be used to do work or can be transformed into kinetic energy. For example, when an object that has gravitational potential energy falls, its energy is converted to kinetic energy. Remember that both work and energy are expressed in joules. 

Refer back to this figure . The amount of work required to raise the TV from point A to point B is equal to the amount of gravitational potential energy the TV gains from its height above the ground. This is generally true for any object raised above the ground. If all the work done on an object is used to raise the object above the ground, the amount work equals the object s gain in gravitational potential energy. However, note that because of the work done by friction, these energy work transformations are never perfect. Friction causes the loss of some useful energy. In the discussions to follow, we will use the approximation that transformations are frictionless. 

Now, let s look at the roller coaster in [link] . Work was done on the roller coaster to get it to the top of the first rise; at this point, the roller coaster has gravitational potential energy. It is moving slowly, so it also has a small amount of kinetic energy. As the car descends the first slope, its PE is converted to KE . At the low point much of the original PE has been transformed to KE , and speed is at a maximum. As the car moves up the next slope, some of the KE is transformed back into PE and the car slows down. During this roller coaster ride, there are conversions between potential and kinetic energy. 

[OL] [AL] Ask if definitions of energy make sense to the class, and try to bring out any expressions of confusions or misconceptions. Help them make the logical leap that, if energy is the ability to do work, it makes sense that it is expressed by the same unit of measurement. Ask students to name all the forms of energy they can. Ask if this helps them get a feel for the nature of energy. Ask if they have a problem seeing how some forms of energy, such as sunlight, can do work. 

[BL] [OL] You may want to introduce the concept of a reference point as the starting point of motion. Relate this to the origin of a coordinate grid. 

[BL] Make it clear that energy is a different property with different units than either force or power. 

[OL] Help students understand that the speed with which the TV is delivered is not part of the calculation of PE . It is assumed that the speed is constant. Any KE due to increases in delivery speed will be lost when motion stops. 

[BL] Be sure there is a clear understanding of the distinction between kinetic and potential energy and between velocity and acceleration. Explain that the word potential means that the energy is available but it does not mean that it has to be used or will be used. Energy Skate Park Basics 

This simulation shows how kinetic and potential energy are related, in a scenario similar to the roller coaster. Observe the changes in KE and PE by clicking on the bar graph boxes. Also try the three differently shaped skate parks. Drag the skater to the track to start the animation. Click here for the simulation 

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This animation shows the transformations between KE and PE and how speed varies in the process. Later we can refer back to the animation to see how friction converts some of the mechanical energy into heat and how total energy is conserved. 

On an actual roller coaster, there are many ups and downs, and each of these is accompanied by transitions between kinetic and potential energy. Assume that no energy is lost to friction. At any point in the ride, the total mechanical energy is the same, and it is equal to the energy the car had at the top of the first rise. This is a result of the law of conservation of energy , which says that, in a closed system, total energy is conserved (that is, it is constant). Using subscripts 1 and 2 to represent initial and final energy, this law is expressed as: K E 1 + P E 1 = K E 2 + P E 2 K E 1 + P E 1 = K E 2 + P E 2 

Either side equals the total mechanical energy. The phrase in a closed system means we are assuming no energy is lost to the surroundings due to friction and air resistance. If we are making calculations on dense falling objects, this is a good assumption. For the roller coaster, this assumption introduces some inaccuracy to the calculation. Calculations involving Mechanical Energy and Conservation of Energy 

When calculating work or energy, use units of meters for distance, newtons for force, kilograms for mass, and seconds for time. This will assure that the result is expressed in joules. 

[BL] [OL] Impress upon the students the significant amount of work required to get a roller coaster car to the top of the first, highest point. Compare it to the amount of work it would take to walk to the top of the roller coaster. Ask students why they may feel tired if they had to walk or climb to the top of the roller coaster (they have to use energy to exert the force required to move their bodies upwards against the force of gravity). Check if students can correctly predict that the ratio of the mass of the car to a person s mass would be the ratio of work done and energy gained (for example, if the car s mass was 10 times a person s mass, the amount of work needed to move the car to the top of the hill would be 10 times the work needed to walk up the hill). Conservation of Energy 

This video discusses conversion of PE to KE and conservation of energy. The scenario is very similar to the roller coaster and the skate park. It is also a good explanation of the energy changes studied in the snap lab. 

Before showing the video, review all the equations involving kinetic and potential energy and conservation of energy. Also be sure the students have a qualitative understanding of the energy transformation taking place. Refer back to the snap lab and the simulation lab. 

[link] Applying the Law of Conservation of Energy 

A 10 kg rock falls from a 20 m cliff. What are the kinetic and potential energy when the rock has fallen 10 m? Strategy 

Choose the equation: 

K E 1 + P E 1 = K E 2 + P E 2 K E 1 + P E 1 = K E 2 + P E 2 

K E = 1 2 m v 2 ; P E = m g h K E = 1 2 m v 2 ; P E = m g h 

1 2 m v 1 2 + m g h 1 = 1 2 m v 2 2 + m g h 2 1 2 m v 1 2 + m g h 1 = 1 2 m v 2 2 + m g h 2 

List the knowns: 

m = 10 kg, v 1 = 0, g = 9.80 m s 2 m s 2 , h 1 = 20 m, h 2 = 10 m 

Identify the unknowns 

KE 2 and PE 2 

Plug in the knowns. Solution 

P E 2 = m g h 2 = 10 ( 9.80 ) 10 = 980 J P E 2 = m g h 2 = 10 ( 9.80 ) 10 = 980 J 

K E 2 = P E 2 ( K E 1 + P E 1 ) = 980 { [ 0 [ 10 ( 9.80 ) 20 ] ] } = 980 J K E 2 = P E 2 ( K E 1 + P E 1 ) = 980 { [ 0 [ 10 ( 9.80 ) 20 ] ] } = 980 J Discussion 

Alternatively, conservation of energy equation could be solved for v 2 and KE 2 could be calculated. Note that m could also be eliminated. 

Note that we can solve many problems involving conversion between KE and PE without knowing the mass of the object in question. This is because kinetic and potential energy are both proportional to the mass of the object. In a situation where KE = PE , we know that m g h = (1/2) m v 2 . Dividing both sides by m and rearranging, we get the relationship: 

2 g h = v 2 . 

Kinetic and potential energy are both proportional to the mass of the object. In a situation where KE = PE , we know that m g h = (1/2) m v 2 . Dividing both sides by m and rearranging, we get the relationship: 2 g h = v 2 . Practice Problems 

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In this activity, you will calculate the potential energy of an object and predict the object s speed when all that potential energy has been converted to kinetic energy. You will then check your prediction. You will be dropping objects from a height. Be sure to stay a safe distance from the edge. Don t lean over the railing too far. Make sure that you do not drop objects into an area where people or vehicles pass by. Make sure that dropping objects will not cause damage. Four marbles (or similar small, dense objects) Stopwatch Metric measuring tape long enough to measure the chosen height A scale Work with a partner. Find and record the mass of four small, dense objects per group. Choose a location where the objects can be safely dropped from a height of at least 15 meters. A bridge over water with a safe pedestrian walkway will work well. Measure the distance the object will fall. Calculate the potential energy of the object before you drop it using PE = m g h = (9.80) mh. Predict the kinetic energy and velocity of the object when it lands using PE = KE and so, m g h = m v 2 2 ; v = 2 ( 9.80 ) h = 4.43 h m g h = m v 2 2 ; v = 2 ( 9.80 ) h = 4.43 h One partner drops the object while the other measures the time it takes to fall. Take turns being the dropper and the timer until you have made four measurements. Average your drop multiplied by and calculate the velocity of the object when it landed using v = a t = g t = (9.80) t . Compare your results to your prediction. 

Before students begin the lab, find the nearest location where objects can be dropped safely from a height of at least 15 m. 

As students work through the lab, encourage lab partners to discuss their observations. Encourage them to discuss differences in results between partners. Ask if there is any confusion about the equations they are using and whether they seem valid based on what they have already learned about mechanical energy. Ask them to discuss the effect of air resistance and how density is related to that effect. 

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Use the Check Your Understanding questions to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify which one and direct students to the relevant content. Section Summary Mechanical energy may be either kinetic (energy of motion) or potential (stored energy). Doing work on an object or system changes its energy. Total energy in a closed, isolated system is constant. Key Equations conservation of energy K E 1 + P E 1 = K E 2 + P E 2 K E 1 + P E 1 = K E 2 + P E 2 Concept Items 

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[link] Glossary law of conservation of energy states that energy is neither created nor destroyedSimple Machines Simple Machines Section Learning Objectives 

By the end of this section, you will be able to: Describe simple and complex machines Calculate mechanical advantage and efficiency of simple and complex machines 

The learning objectives in this section will help your students master the following TEKS: (6C) : Describe simple and complex machines and solve problems involving simple machines. (6D) : Define input work, output work, mechanical advantage, and efficiency of machines. Section Key Terms complex machine efficiency output ideal mechanical advantage inclined plane input work lever mechanical advantage output work pulley screw simple machine wedge wheel and axle 

In this section you will apply what you have learned about work to find the mechanical advantage and efficiency of simple machines. 

[BL] [OL] Ask the students what they know about machines and work. Dispel any misconceptions that machines reduce the amount of work. Be sure students do not equate machines and motors by asking for (and, if necessary, providing) examples of machines that are not motorized. Explain that simple machines are often hand-held, and that they reduce force, not work. 

[AL] Ask for recall of the formula W = f d . Explain that the product of force and distance is critical to understanding simple machines. Because the amount of work is not changed, the term f d does not change, but force can decrease if distance increases. This is the underlying principle of all simple machines. Simple Machines 

Simple machines make work easier, but they do not decrease the amount of work you have to do. Why can t simple machines change the amount of work that you do? Recall that in closed systems the total amount of energy is conserved. A machine cannot increase the amount of energy you put into it. So, why is a simple machine useful? Although it cannot change the amount of work you do, a simple machine can change the amount of force you must apply to an object, and the distance over which you apply the force. In most cases, a simple machine is used to reduce the amount of force you must exert to do work. The down side is that you must exert the force over a greater distance, because the product of force and distance, f d , (which equals work) does not change. 

Let s examine how this works in practice. In Figure_09_03_lever(a) , the worker uses a type of lever to exert a small force over a large distance, while the pry bar pulls up on the nail with a large force over a small distance. Figure_09_03_lever(b) shows the how a lever works mathematically. The effort force, applied at F e , lifts the load (the resistance force) which is pushing down at F r . The triangular pivot is called the fulcrum ; the part of the lever between the fulcrum and F e is the effort arm, L e ; and the part to the left is the resistance arm, L r . The mechanical advantage is a number that tells us how many times a simple machine multiplies the effort force. The ideal mechanical advantage , IMA , is the mechanical advantage of a perfect machine with no loss of useful work caused by friction between moving parts. The equation for IMA is shown in Figure_09_03_lever(b) . (a) A pry bar is a type of lever. (b) The ideal mechanical advantage equals the length of the effort arm divided by the length of the resistance arm of a lever. 

In general, the IMA = the resistance force, F r , divided by the effort force, F e . IMA also equals the distance over which the effort is applied, d e , divided by the distance the load travels, d r . I M A = F r F e = d e d r I M A = F r F e = d e d r 

Getting back to conservation of energy, for any simple machine, the work put into the machine, W i , equals the work the machine puts out, W o . Combining this with the information in the paragraphs above, we can write: W i = W o F e d e = F r d r If F e F r , then d e d r W i = W o F e d e = F r d r If F e F r , then d e d r 

The equations show how a simple machine can output the same amount of work while reducing the amount of effort force by increasing the distance over which the effort force is applied. Introduction to Mechanical Advantage 

This video shows how to calculate the IMA of a lever by three different methods: (1) from effort force and resistance force; (2) from the lengths of the lever arms, and; (3) from the distance over which the force is applied and the distance the load moves. 

The beginning of this video may cause more confusion than illumination. It shows a derivation using trig functions that is beyond the scope of this chapter. Interested students may want to work their way through it. Most students should skip to the final two or three minutes which explain the basics of calculating IMA of a lever from different ratios. Review W = f d . 

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Some levers exert a large force to a short effort arm. This results in a smaller force acting over a greater distance at the end of the resistance arm. Examples of this type of lever are baseball bats, hammers, and golf clubs. In another type of lever, the fulcrum is at the end of the lever and the load is in the middle, as in the design of a wheelbarrow. 

[AL] Tell students there are two other classes of levers with different arrangements of load, fulcrum, and effort. Ask them first to try to sketch these. After they have discovered the three kinds, with or without your help, ask if they can think of examples of the types not shown in [link] . 

The simple machine shown in [link] is called a wheel and axle . It is actually a form of lever. The difference is that the effort arm can rotate in a complete circle around the fulcrum, which is the center of the axle. Force applied to the outside of the wheel causes a greater force to be applied to the rope that is wrapped around the axle. As shown in the figure, the ideal mechanical advantage is calculated by dividing the radius of the wheel by the radius of the axle. Any crank-operated device is an example of a wheel and axle Force applied to a wheel exerts a force on its axle. 

[BL] [OL] See if the students grasp the idea that a wheel and axle is really a type of lever. Show them that it looks more like a lever if the wheel is replaced by a crank. Give some examples: hand-powered windlass, steering wheel, door knob, and so on. Ask them why steering wheels had a greater diameter before power steering was invented. 

[AL] Explain that wheels on vehicles are not really simple machines in the same sense as the one in [link] . The axle on a vehicle does not do work on a load. Energy loss to friction is reduced, but nothing is lifted. 

An inclined plane and a wedge are two forms of the same simple machine. A wedge is simply two inclined planes back to back. [link] shows the simple formulas for calculating the IMA s of these machines. All sloping, paved surfaces for walking or driving are inclined planes. Knives and axe heads are examples of wedges. An inclined plane is shown on the left, and a wedge is shown on the right. 

[BL] [OL] Talk about how inclined planes and wedges are similar and different. Note that, when using an inclined plane the load moves, but when using a wedge the load is stationary and the machine moves. Explain why more energy is usually lost to friction with these machines than with other simple machines. 

The screw shown in [link] is actually a lever attached to a circular inclined plane. Wood screws (of course) are also examples of screws. The lever part of these screws is a screw driver. In the formula for IMA , the distance between screw threads is called pitch and has the symbol P . The screw shown here is used to lift very heavy objects, like the corner of a car or a house a short distance. 

[BL] [OL] Suggest that a screw is classified as a separate type of simple machine perhaps because it looks so different from what it really is: an inclined plane which sometimes is turned by a lever. Explain that the combined mechanical advantage can be very great. Devices like the one shown in [link] are used to lift cars and even houses. Have the students compare this screw to a wood screw and a circular stairway. 

[AL] Ask students how the forces exerted by a wood screw are different from those exerted by the screw in [link] . Ask for an explanation of the 2 in the equation for IMA . 

[link] shows three different pulley systems. Of all simple machines, mechanical advantage is easiest to calculate for pulleys. Simply count the number of ropes supporting the load. That is the IMA . Once again we have to exert force over a longer distance to multiply force. To raise a load 1 meter with a pulley system you have to pull N meters of rope. Pulley systems are often used to raise flags and window blinds and are part of the mechanism of construction cranes. Three pulley systems are shown here. 

[BL] [OL] The calculation for IMA of a pulley seems too easy to be true, but it is. Ask students to try to understand why IMA is simply N . Tell them that watching the video should make this point clear. Pulleys were once seen on sailing ships and farms, where they were used lift heavy loads. The overhang you may have seen on the end of old barn roofs is where a pulley was once attached. This way bales of hay could be lifted into the hay loft without getting wet. Pulleys can still be seen in use, most commonly on large building cranes. Mechanical Advantage of Inclined Planes and Pulleys 

The first part of this video shows how to calculate the IMA of pulley systems. The last part shows how to calculate the IMA of an inclined plane. 

Review what was learned about the IMA of inclined planes and pulley systems before watching the video. Remind the students that, for an ideal machine, work in = work out and that W = f d . The video shows how to find the f s and the d s. 

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A complex machine is a combination of two or more simple machines. The wire cutters in [link] combine two levers and two wedges. Bicycles include wheel and axles, levers, screws, and pulleys. Cars and other vehicles are combinations of many machines. Wire cutters are a common complex machine. 

[BL] [OL] Be sure students understand that a complex machine is just a combination of simple machines and is still fairly simple. Don t let them confuse the term with complicated machines such as computers. Note that the IMAs of the individual simple machines in a complex machine usually multiply because the output force of one machine becomes the input force of the other machine. For fun, you could ask the students to search Google images for Rube Goldberg machine. Calculating Mechanical Advantage and Efficiency of Simple Machines 

In general, the IMA = the resistance force, F r , divided by the effort force, F e . IMA also equals the distance over which the effort is applied, d e , divided by the distance the load travels, d r . I M A = F r F e = d e d r I M A = F r F e = d e d r 

Refer back to the discussions of each simple machine for the specific equations for the IMA for each type of machine. 

No simple or complex machines have the actual mechanical advantages calculated by the IMA equations. In real life, some of the applied work always ends up as wasted heat due to friction between moving parts. Both the input work ( W i ) and output work ( W o ) are the result of a force, F , acting over a distance, d . W i = F i d i and W o = F o d o W i = F i d i and W o = F o d o 

The efficiency output of a machine is simply the output work divided by the input work, and is usually multiplied by 100 so that it is expressed as a percent. % efficiency = W o W i 100 % efficiency = W o W i 100 

Look back at the pictures of the simple machines and think about which would have the highest efficiency. Efficiency is related to friction, and friction depends on the smoothness of surfaces and on the area of the surfaces in contact. How would lubrication affect the efficiency of a simple machine? 

[BL] [OL] Review the material on loss of mechanical energy to heat and the law of conservation of energy. Explain how heat lost because of friction assures that W o will always be less than W i preventing efficiency from ever reaching 100%. Efficiency of a Lever 

The input force of 11 N acting on the effort arm of a lever moves 0.4 m, which lifts a 40 N weight resting on the resistance arm a distance of 0.1 m. What is the efficiency of the machine? Strategy 

State the equation for efficiency of a simple machine: % efficiency = W o W i 100 % efficiency = W o W i 100 and calculate W o and W i . Both work values are the product Fd . Solution 

W i = F i d i W i = F i d i = (11)(0.4) = 4.4 J and W o = F o d o W o = F o d o = (40)(0.1) = 4.0 J, then % efficiency = W o W i 100 = 4.0 4.4 100 = 91 % % efficiency = W o W i 100 = 4.0 4.4 100 = 91 % Discussion 

Efficiency in real machines will always be less than 100% because of work that is converted to unavailable heat by friction and air resistance. W o and W i can always be calculated as a force multiplied by a distance, although these quantities are not always as obvious as they are in the case of a lever. 

Teaching tip: When calculating efficiency, it is easy enough to understand what force in and force out are: the force you apply is force in and the weight of the object that is being lifted is force out. The input and output distances are easy to see for the lever, inclined plane and wedge. The other three are not as obvious. For a pulley system, the input distance is how far you pull the rope, and the output distance is the distance the load rises. For a wheel and axle, the input distance is the circumference of the wheel, and the output distance is the circumference of the axle. For a screw, the input distance is the circumference of the circle over which the force is applied, and the output distance is the distance between the screw threads. Practice Problems 

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[link] Check Your Understanding 

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Use the Check Your Understanding questions to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify which one and direct students to the relevant content. Section Summary The six types of simple machines make work easier by changing the f d term so that force is reduced at the expense of increased distance. The ratio of output force to input force is a machine s mechanical advantage. Combinations of two or more simple machines are called complex machines. The ratio of output work to input work is a machine s efficiency. Key Equations ideal mechanical advantage (general) I M A = F r F e = d e d r I M A = F r F e = d e d r (lever) I M A = L e L r (wheel and axle) I M A = R r (inclined plane) I M A = L h (wedge) I M A = L t (pulley) I M A = N (screw) I M A = 2 L P (lever) I M A = L e L r (wheel and axle) I M A = R r (inclined plane) I M A = L h (wedge) I M A = L t (pulley) I M A = N (screw) I M A = 2 L P input work W i = F i d i W i = F i d i output work W o = F o d o W o = F o d o efficiency output % efficiency = W o W i 100 % efficiency = W o W i 100 Concept Items 

[link] Critical Thinking 

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Conservation of Energy and Energy Transfer; Cause and Effect; and S EP, Planning and Carrying Out Investigations 

Plan an investigation to measure the mechanical advantage of simple machines and compare to the IMA of the machine. Also measure the efficiency of each machine studied. Design an investigation to make these measurements for these simple machines: lever, inclined plane, wheel and axle and a pulley system. In addition to these machines, include a spring scale, a tape measure, and a weight with a loop on top that can be attached to the hook on the spring scale. A spring scale is shown in [link] . A spring scale measures weight, not mass. 

LEVER: Beginning with the lever, explain how you would measure input force, output force, effort arm, and resistance arm. Also explain how you would find the distance the load travels and the distance over which the effort force is applied. Explain how you would use this data to determine IMA and efficiency. 

INCLINED PLANE: Make measurements to determine IMA and efficiency of an inclined plane. Explain how you would use the data to calculate these values. Which property do you already know? Note that there are no effort and resistance arm measurements, but there are height and length measurements. 

WHEEL AND AXLE: Again, you will need two force measurements and four distance measurements. Explain how you would use these to calculate IMA and efficiency. 

SCREW: You will need two force measurements, two distance traveled measurements, and two length measurements. You may describe a screw like the one shown in [link] or you could use a screw and screw driver. (Measurements would be easier for the former). Explain how you would use these to calculate IMA and efficiency. 

PULLEY SYSTEM: Explain how you would determine the IMA and efficiency of the four-pulley system shown in [link] . Why do you only need two distance measurements for this machine? 

Design a table that compares the efficiency of the five simple machines. Make predictions as to the most and least efficient machines. Test Prep Multiple Choice 

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[link] Test Prep Short Answer 

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[link] Glossary complex machine a machine that combines two or more simple machines efficiency output work divided by input work ideal mechanical advantage the mechanical advantage of an idealized machine that loses no energy to friction inclined plane a simple machine consisting of a slope input work effort force multiplied by the distance over which it is applied lever a simple machine consisting of a rigid arm that pivots on a fulcrum mechanical advantage the number of times the input force is multiplied output work output force multiplied by the distance over which it acts pulley a simple machine consisting of a rope that passes over one or more grooved wheels screw a simple machine consisting of a spiral inclined plane simple machine a machine that makes work easier by changing the amount or direction of force required to move an object wedge a simple machine consisting of two back-to-back inclined planes wheel and axle a simple machine consisting of a rod fixed to the center of a wheelIntroduction Introduction In this chapter you will learn about: Relative Motion, Distance, and Displacementm Speed and Velocity Position vs. Time Graphs Velocity vs. Time Graphs The world s fastest train reached a speed of over 350 miles per hour. At this rate, a train traveling from Boston to Washington, DC, a distance of 439 miles, could make the trip in under an hour and a half. Presently, the fastest train on this route takes over six hours to cover this distance. (credit: Alex Needham, Public Domain) 

Have the students describe the photo of the train and discuss its motion. Tell them they will learn about motion. Start the discussion with how a train moves, and guide them toward discussing concepts of displacement, velocity, and acceleration. Ask questions: How do we know something is moving? What defines motion? What direction does the train move? What adjectives describe its motion? If it was a moving ball instead of a train, how would its motion be different? How would the train s motion change if its wheels were square instead of round or if it had studded tires? Try to uncover what ideas they already have about motion. 

Unless you have flown in an airplane, you have probably never traveled faster than 150 mph. Can you imagine traveling in a train like the one shown in [link] that goes over 300 mph? Despite the high speed, the people riding in this train may not notice that they are moving at all unless they look out the window! This is because motion, even motion at 300 mph, is relative to the observer. 

In this chapter, you will learn why it is important to identify a reference frame in order to clearly describe motion. For now, the motion you describe will be one-dimensional. Within this context, you will learn the difference between distance and displacement as well as the difference between speed and velocity. Then you will look at some graphing and problem-solving techniques. 

Before students begin this chapter, it would be useful to review these concepts: Using significant figures in calculations Demonstrate how to use the proper number of significant figures when adding, subtracting, multiplying, and dividing. Converting units Demonstrate how to convert from km/h to m/s. Calculating average Demonstrate how to average two numbers by dividing their sum by 2. Commonly used terms Explain that "constant" means "unchanging," so "constant speed" refers to speed that is not changing. Explain that "initial" means "starting," so "initial time" is the time at which the action mentioned in a problem begins. Explain that an object that is not moving is often described in physics as being "at rest."Relative Motion, Distance and Displacement Relative Motion, Distance and Displacement Section Learning Objectives 

By the end of this section, you will be able to: Describe motion in different reference frames Define distance and displacement, and distinguish between the two Solve problems involving distance and displacement 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4B) : describe and analyze motion in one dimension using equations with the concepts of distance, displacement, speed, average velocity, instantaneous velocity, and acceleration; (4F) : identify and describe motion relative to different frames of reference. Section Key Terms displacement distance kinematics magnitude position reference frame scalar vector 

[BL] [OL] Start by asking what "position" is and how it is defined. You can use a toy car or other object. Then ask how they know the object has moved. Lead them to the idea of a defined starting point. Then bring in the concept of a numbered line as a way of quantifying motion. 

[AL] Ask students to describe the path of movement and emphasize that direction is a necessary component of a definition of motion. Ask the students to form pairs, and ask each pair to come up with their own definition of motion. Then compare and discuss definitions as a class. What components are necessary for a definition of motion? Defining Motion 

Our study of physics opens with kinematics the study of motion without considering its causes. Objects are in motion everywhere you look. Everything from a tennis game to a space-probe flyby of the planet Neptune involves motion. When you are resting, your heart moves blood through your veins. Even in inanimate objects, atoms are always moving. 

How do you know something is moving? The location of an object at any particular time is its position . More precisely, you need to specify its position relative to a convenient reference frame . Earth is often used as a reference frame, and we often describe the position of an object as it relates to stationary objects in that reference frame. For example, a rocket launch would be described in terms of the position of the rocket with respect to the Earth as a whole, while a professor s position could be described in terms of where she is in relation to the nearby white board. In other cases, we use reference frames that are not stationary but are in motion relative to the Earth. To describe the position of a person in an airplane, for example, we use the airplane, not the Earth, as the reference frame. (See [link] .) Thus, you can only know how fast and in what direction an object's position is changing against a background of something else that is either not moving or moving with a known speed and direction. The reference frame is the coordinate system from which the positions of objects are described. Are clouds a useful reference frame for airplane passengers? Why or why not? (credit: Paul Brennan, Public Domain) 

[OL] [AL] Explain that the word "kinematics" comes from a Greek term meaning motion. It is related to other English words, such as "cinema" (movies, or moving pictures) and "kinesiology" (the study of human motion). 

Your classroom can be used as a reference frame. In the classroom, the walls are not moving. Your motion as you walk to the door, can be measured against the stationary background of the classroom walls. You can also tell if other things in the classroom are moving, such as your classmates entering the classroom or a book falling off a desk. You can also tell in what direction something is moving in the classroom. You might say, The teacher is moving toward the door. Your reference frame allows you to determine not only that something is moving but also the direction of motion. 

You could also serve as a reference frame for others movement. If you remained seated as your classmates left the room, you would measure their movement away from your stationary location. If you and your classmates left the room together, then your perspective of their motion would be change. You, as the reference frame, would be moving in the same direction as your other moving classmates. As you will learn in the Snap Lab, your description of motion can be quite different when viewed from difference reference frames. 

[BL] [OL] You may want to introduce the concept of a reference point as the starting point of motion. Relate this to the origin of a coordinate grid. 

[AL] Explain that the reference frames considered in this chapter are inertial reference frames, which means they are not accelerating. Engage students in a discussion of how it is the difference in motion between the reference frame of the observer and the reference frame of the object that is important in describing motion. The reference frames used in this chapter might be moving at a constant speed relative to each other, but they are not accelerating relative to each other. 

[BL] [OL] [Visual]Misconception: Students may assume that a reference frame is a background of motion instead of the frame from which motion is viewed. Demonstrate the difference by having one student stand at the front of the class. Explain that this student represents the background. Walk once across the room between the student and the rest of the class. Ask the student and others in the class to describe the direction of your motion. The class might describe your motion as "to the right," but the student who is standing as a background to your motion would describe the motion as "to the left." Conclude by reminding students that the reference frame is the viewpoint of the observer, not the background. 

[BL] Have students practice describing simple examples of motion in the class from different reference frames. For example, slide a book across a desk. Ask students to describe its motion from their reference point, from the book's reference point, and from another student's reference point. Looking at Motion from Two Reference Frames 

In this activity you will look at motion from two reference frames. Which reference frame is correct? Choose an open location with lots of space to spread out so there is less chance of tripping or falling due to collision and/or loose basketballs. 1 basketball Work with a partner. Stand about a couple of meters away from your partner. Have your partner turn to the side so that you are looking at your partner s profile. Have your partner begin bouncing the basketball while standing in place. Describe the motion of the ball. Next, have your partner again bounce the ball, but this time your partner should walk forward with the bouncing ball. You will remain stationary. Describe the ball's motion. Again have your partner walk forward with the bouncing ball. This time, you should move alongside your partner while continuing to view your partner s profile. Describe the ball's motion. Switch places with your partner, and repeat Steps 1 3. 

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Before students begin the lab, arrange a location where pairs of students can have ample room to walk forward at least several meters. 

As students work through the lab, encourage lab partners to discuss their observations. In Steps 1 and 3, students should observe the ball move straight up and straight down. In Step 2, students should observe the ball in a zigzag path away from the stationary observer. 

After the lab, lead students in discussing their observations. Ask them which reference frame is the correct one. Then emphasize that there is not a single correct reference frame. All reference frames are equally valid. History: Galileo's Ship Galileo Galilei (1564 1642) studied motion and developed the concept of a reference frame. (credit: Domenico Tintoretto) 

The idea that a description of motion depends on the reference frame of the observer has been known for hundreds of years. The 17th-century astronomer Galileo Galilei ( [link] ) was one of the first scientists to explore this idea. Galileo suggested the following thought experiment. Imagine a windowless ship moving at a constant speed and direction along a perfectly calm sea. Is there a way that a person inside the ship can determine whether the ship is moving? You can extend this thought experiment by also imagining a person standing on the shore. How can a person on the shore determine whether the ship is moving? 

Galileo came to an amazing conclusion. Only by looking at each other can a person in the ship or a person on shore describe the motion of one relative to the other. In addition, their descriptions of motion would be identical. A person inside the ship would describe the person on the land as moving past the ship. The person on shore would describe the ship and the person inside it as moving past. Galileo realized that observers moving at a constant speed and direction relative to each other describe motion in the same way. Galileo had discovered that a description of motion is only meaningful if you specify a reference frame. 

[link] Distance vs. Displacement 

As we study the motion of objects, we must first be able to describe the object s position. Before your parent drives you to school, the car is sitting in your driveway. Your driveway is the starting position for the car. When you reach your high school, the car has changed position. Its new position is your school. Your total change in position is measured from your house to your school. 

Physicists use variables to represent terms. We will use d to represent car s position. We will use a subscript to differentiate between the initial position, d 0 , and the final position, d f . In addition, vectors, which we will discuss later, will be in bold or will have an arrow above the variable. Scalars will be italicized. 

In some books, x or s is used instead of d to describe position. In d 0 , said d naught , the subscript 0 stands for initial . When we begin to talk about two-dimensional motion, sometimes other subscripts will be used to describe horizontal position, d x , or vertical position, d y . So, you might see references to d 0x and d fy . 

Now imagine driving from your house to a friend's house located several kilometers away. How far would you drive? The distance an object moves is the length of the path between its initial position and its final position. The distance you drive to your friend's house depends on your path. As shown in [link] , distance is different from the length of a straight line between two points. The distance you drive to your friend's house is probably longer than the straight line between the two houses. A short line separates the starting and ending points of this motion, but the distance along the path of motion is considerably longer. 

We often want to be more precise when we talk about position. The description of an object s motion often includes more than just the distance it moves. For instance, if it is a five kilometer drive to school, the distance traveled is 5 kilometers. After dropping you off at school and driving back home, your parent will have traveled a total distance of 10 kilometers. The car and your parent will end up in the same starting position in space. The net change in position of an object is its displacement , or d d . The Greek letter delta, , means change in . The total distance that your car travels is 10 miles, but the total displacement is 0. 

Help students learn the difference between distance and displacement by showing examples of motion. As students watch, walk straight across the room and have students estimate the length of your path. Then, at same starting point, walk along a winding path to the same ending point. Again, have students estimate the length of your path. 

Ask: Which motion showed displacement? Which showed distance? Point out that the first motion shows displacement, and the second shows distance along a path. In both cases, the starting and ending points were the same. 

[OL] Be careful that students do not assume that initial position is always zero. Emphasize that although initial position is often zero, motion can start from any position relative to a starting point. 

[Visual]Demonstrate positive and negative displacement by placing two meter sticks on the ground with their zero marks end-to-end. As students watch, place a small car at the zero mark. Slowly move the car to students' right a short distance and ask students what its displacement is. Then move the car to the left of the zero mark. Point out that the car now has a negative displacement. 

Students will learn more about vectors and scalars later when they study two-dimensional motion. For now, it is sufficient to introduce the terms and let students know that a vector includes information about direction. 

[BL] Ask students whether each of the following is a vector quantity or a scalar quantity: temperature (scalar), force (vector), mass (scalar). 

[OL] Ask students to provide examples of vector quantities and scalar quantities. 

[Kinesthetic] Provide students with large arrows cut from construction paper. Have them use the arrows to identify the magnitude (number or length of arrows) and direction of displacement. Emphasize that distance cannot be represented by arrows because distance does not include direction. Distance vs. Displacement 

In this activity you will compare distance and displacement. Which term is more useful when making measurements? 1 recorded song available on a portable device 1 tape measure 3 pieces of masking tape A room (like a gym) with a clear wall that is large and clear enough for all pairs of students to walk back and forth without running into each other. One student from each pair should stand with their back to the longest wall in the classroom. Students should stand at least 0.5 meters away from each other. Mark this starting point with a piece of masking tape. The second student from each pair should stand facing their partner, about two to three meters away. Mark this point with a second piece of masking tape. Student pairs line up at the starting point along the wall. The teacher turns on the music. Each pair walks back and forth from the wall to the second marked point until the music stops playing. Keep count of the number of times you walk across the floor. When the music stops, mark your ending position with the third piece of masking tape. Measure from your starting, initial position to your ending, final position. Measure the length of your path from the starting position to the second marked position. Multiply this measurement by the total number of times you walked across the floor. Then add this number to your measurement from step 6. Compare the two measurements from steps 6 and 7. 

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Choose a room that is large enough for all students to walk unobstructed. Make sure the total path traveled is short enough that students can walk back and forth across it multiple times during the course of a song. Have them measure the distance between the two points and come to a consensus. When students measure their displacement, make sure that they measure forward from the direction they marked as the starting position. After they have completed the lab, have them discuss their results. 

If you are describing only your drive to school, then the distance traveled and the displacement are the same 5 km. When you are describing the entire round trip, distance and displacement are different. When you describe distance, you only include the magnitude , the size or amount, of the distance traveled. However, when you describe the displacement, you take into account both the magnitude of the change in position and the direction of movement. 

In our previous example, the car travels a total of 10 km, but it drives 5 of those kilometers forward towards school and 5 of those kilometers back in the opposite direction. If we ascribe the forward direction a positive (+) and the opposite direction a negative ( ), then the two quantities will cancel each other out when added together. 

A quantity, such as distance, that has magnitude (i.e. how big or how much) but does not take into account direction is called a scalar . A quantity, such as displacement, that has both magnitude and direction is called a vector . Vectors Scalars 

This video introduces and differentiates between vectors and scalars. It also introduces quantities that we will be working with during the study of kinematics. 

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Define the concepts of vectors and scalars before watching the video. 

[OL] [BL] Come up with some examples of vectors and scalars and have the students classify each. 

[AL] Discuss how the concept of direction might be important for the study of motion. Displacement Problems 

Hopefully you now understand the conceptual difference between distance and displacement. Understanding concepts is half the battle in physics. The other half is math. A stumbling block to new physics students is trying to wade through the math of physics while also trying to understand the associated concepts. This struggle may lead to misconceptions and answers that make no sense. Once the concept is mastered, the math is far less confusing. 

So let s review and see if we can make sense of displacement in terms of numbers and equations. You can calculate an object's displacement by subtracting its original position, d 0 , from its final position d f . In math terms that means: d = d f d 0 d = d f d 0 

If the final position is the same as the initial position, then d = 0 d = 0 . 

To assign numbers and/or direction to these quantities, we need to define an axis with a positive and a negative direction. We also need to define an origin, or 0 . In this figure , the axis is in a straight line with home at zero and school in the positive direction. If we left home and drove the opposite way from school, motion would have been in the negative direction. We would have assigned it a negative value. In the round-trip drive, d f and d 0 were both at 0 km. In the one way trip to school, d f was at 5 km and d 0 was at 0 km. So, d d was 5 km. 

You may place your origin wherever you would like. You have to make sure that you calculate all distances consistently from your zero and you define one direction as positive and the other as negative. Therefore, it makes sense to choose the easiest axis, direction, and zero. In the example above, we took home to be zero because it allowed us to avoid having to interpret a solution with a negative sign. Calculating Distance and Displacement 

A cyclist rides 3 km west and then turns around and rides 2 km east. (a) What is her displacement? (b) What distance does she ride? (c) What is the magnitude of her displacement? Strategy 

To solve this problem, we need to find the difference between the final position and the initial position while taking care to note the direction on the axis. The final position is the sum of the two displacements, d 1 d 1 and d 2 d 2 . Solution Displacement: The rider s displacement is d = d f d 0 = 1 km d = d f d 0 = 1 km . Distance: The distance traveled is 3 km + 2 km = 5 km. The magnitude of the displacement is 1 km. Discussion 

The displacement is negative because we chose east to be positive and west to be negative. We could also have described the displacement as 1 km west. When calculating displacement, the direction mattered, but when calculating distance, the direction did not matter. The problem would work the same way if the problem were in the North South or y -direction. 

Physicists like to use standard units so it is easier to compare notes. The standard units for calculations are called SI units (System International). SI units are based on the metric system. The SI unit for displacement is the meter (m), but sometimes you will see a problem with kilometers, miles, feet, or other units of length. If one unit in a problem is an SI unit and another is not, you will need to convert all of your quantities to the same system before you can carry out the calculation. 

Point out to students that the distance for each segment is the absolute value of the displacement along a straight path. Practice Problems 

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[link] Mars Probe Explosion The Mars Climate Orbiter disaster illustrates the importance of using the correct calculations in physics. (credit: NASA) 

Physicists make calculations all the time, but they do not always get the right answers. In 1998, NASA, the National Aeronautics and Space Administration, launched the Mars Climate Orbiter, shown in [link] , a $125-million-dollar satellite designed to monitor the Martian atmosphere. It was supposed to orbit the planet and take readings from a safe distance. The American scientists made calculations in English units (feet, inches, pounds . . .) and forgot to convert their answers to the standard metric SI units. This was a very costly mistake. Instead of orbiting the planet as planned, the Mars Climate Orbiter ended up flying into the Martian atmosphere. The probe disintegrated. It was one of the biggest embarrassments in NASA s history. 

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The text feature describes a real-life miscalculation made by astronomers at NASA. In this case, the Mars Climate Orbiter s orbit needed to be calculated precisely because its machinery was designed to withstand only a certain amount of atmospheric pressure. The orbiter had to be close enough to the planet to take measurements and far enough away that it could remain structurally sound. One way to teach this concept would be to pick an orbital distance from Mars and have the students calculate the distance of the path and the height from the surface both in SI units and in English units. Ask why failure to convert might be a problem. Check Your Understanding 

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Use the questions under Check Your Understanding to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the formative assessment will help direct students to the relevant content. Section Summary A description of motion depends on the reference frame from which it is described. The distance an object moves is the length of the path along which it moves. Displacement is the difference in the initial and final positions of an object. Key Equations Displacement d = d f d 0 d = d f d 0 Concept Items 

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[link] Glossary displacement the change in position of an object against a fixed axis distance the length of the path actually traveled between an initial and a final position kinematics the study of motion without considering its causes magnitude size or amount position the location of an object at any particular time reference frame a coordinate system from which the positions of objects are described scalar a quantity that has magnitude but no direction vector a quantity that has both magnitude and directionSpeed and Velocity Speed and Velocity Section Learning Objectives 

By the end of this section, you will be able to: Calculate the average speed of an object. Relate displacement and average velocity. 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4B) : describe and analyze motion in one dimension using equations with the concepts of distance, displacement, speed, average velocity, instantaneous velocity, and acceleration; Section Key Terms average speed average velocity instantaneous speed instantaneous velocity speed velocity 

In this section, students will apply what they have learned about distance and displacement to the concepts of speed and velocity. 

[BL] [OL] Before students read the section, ask them to give examples of ways they have heard the word speed used. Then ask them if they have heard the word velocity used. Explain that these words are often used interchangeably in everyday life, but their scientific definitions are different. Tell students that they will learn about these differences as they read the section. 

[AL] Explain to students that velocity, like displacement, is a vector quantity. Ask them to speculate about ways that speed is different from velocity. After they share their ideas, follow up with questions that deepen their thought process, such as: Why do you think that? What is an example? How might apply these terms to motion that you see every day? Speed 

There is more to motion than distance and displacement. Questions such as, How long does a foot race take? and What was the runner s speed? cannot be answered without an understanding of other concepts. In this section we will look at time , speed, and velocity to expand our understanding of motion. 

A description of how fast or slow an object moves is its speed. Speed is the rate at which an object changes its location. Like distance, speed is a scalar because it has a magnitude but not a direction. Since speed is a rate, it depends on the time interval of motion. You can calculate the elapsed time or the change in time, t t , of motion as the difference between the ending time and the beginning time: t = t f t 0 t = t f t 0 

The SI unit of time is the second (s), and the SI unit of speed is meters per second (m/s), but sometimes kilometers per hour (km/h), miles per hour (mph) or other units of speed are used. 

When you describe an object's speed, you often describe the average over a time period. Average speed , v avg , is the distance traveled divided by the time during which the motion occurs: v avg = distance time v avg = distance time 

You can, of course, rearrange the equation to solve for either distance or time: time = distance v avg time = distance v avg distance = v avg time distance = v avg time 

Suppose, for example, a car travels 150 kilometers in 3.2 hours. Its average speed for the trip is: v avg = distance time = 150 km 3.2 h = 47 km/h v avg = distance time = 150 km 3.2 h = 47 km/h 

A car's speed would likely increase and decrease many times over a 3.2 hour trip. Its speed at a specific instant in time, however, is its instantaneous speed . A car's speedometer describes its instantaneous speed. 

[OL] [AL] Caution students that average speed is not always the average of an object's initial and final speeds. For example, suppose a car travels a distance of 100 km. The first 50 km it travels 30 km/h and the second 50 km it travels at 60 km/h. Its average speed would be distance /(time interval) = (100 km)/[(50 km)/(30 km/h) + (50 km)/(60 km/h)] = 40 km/h. If the car had spent equal times at 30 km and 60 km rather than equal distances at these speeds, its average speed would have been 45 km/h. 

[BL] [OL] Caution students that the terms speed, average speed, and instantaneous speed are all often referred to simply as speed in everyday language. Emphasize the importance in science to use correct terminology to avoid confusion and to properly communicate ideas. During a 30-minute round trip to the store, the total distance traveled is 6 km. The average speed is 12 km/h. The displacement for the round trip is zero, since there was no net change in position. Calculating Average Speed 

A marble rolls 5.2 m in 1.8 s. What was the marble's average speed? Strategy 

We know the distance the marble travels, 5.2 m, and the time interval, 1.8 s. We can use these values in the average speed equation. Solution v avg = distance time = 5.2 m 1.8 s = 2.9 m/s v avg = distance time = 5.2 m 1.8 s = 2.9 m/s Discussion 

Average speed is a scalar, so we do not include direction in the answer. We can check the reasonableness of the answer by estimating: 5 meters divided by 2 seconds is 2.5 m/s. Since 2.5 m/s is close to 2.9 m/s, the answer is reasonable. This is about the speed of a brisk walk, so it also makes sense. Practice Problems 

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[link] Velocity 

The vector version of speed is velocity. Velocity describes the speed and direction of an object. As with speed, it is useful to describe either the average velocity over a time period or the velocity at a specific moment. Average velocity is displacement divided by the time over which the displacement occurs: v avg = distance time = d t = d f d 0 t f t 0 v avg = distance time = d t = d f d 0 t f t 0 

Velocity, like speed, has SI units of meters per second (m/s), but since it is a vector, you must also include a direction. Furthermore, the variable v for velocity is bold because it is a vector, which is in contrast to the variable v for speed which is italicized because it is a scalar quantity. 

It is important to keep in mind that the average speed is not the same thing as the average velocity without its direction. Like we saw with displacement and distance in the last section, changes in direction over a time interval have a bigger effect on speed and velocity. 

Suppose a passenger moved toward the back of a plane with an average velocity of 4 m/s. We cannot tell from the average velocity whether the passenger stopped momentarily or backed up before he got to the back of the plane. To get more details, we must consider smaller segments of the trip over smaller time intervals such as those shown in [link] . If you consider infinitesimally small intervals, you can define instantaneous velocity , which is the velocity at a specific instant in time. Instantaneous velocity and average velocity are the same if the velocity is constant. The diagram shows a more detailed record of an airplane passenger heading toward the back of the plane, showing smaller segments of his trip. 

Earlier, you have read that distance traveled can be different than the magnitude of displacement. In the same way, speed can be different than the magnitude of velocity. For example, you drive to a store and return home in half an hour. If your car s odometer shows the total distance traveled was 6 km, then your average speed was 12 km/h. Your average velocity, however, was zero, because your displacement for the round trip is zero. Calculating Average Velocity or Speed 

This video reviews vectors and scalars and describes how to calculate average velocity and average speed when you know displacement and change in time. The video also reviews how to convert km/h to m/s. 

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This video does a good job of reinforcing the difference between vectors and scalars. The student is introduced to the idea of using s to denote displacement, which you may or may not wish to encourage. Before students watch the video, point out that the instructor uses s s for displacement instead of d, as used in this text. Explain the use of small arrows over variables is a common way to denote vectors in higher-level physics courses. Caution students that the customary abbreviations for hour and seconds are not used in this video. Remind students that in their own work they should use the abbreviations h for hour and s for seconds. Calculating Average Velocity 

A student has a displacement of 304 m north in 180 s. What was the student's average velocity? Strategy 

We know that the displacement is 304 m north and the time is 180 s. We can use the formula for average velocity to solve the problem. Solution 

v avg = d t = 304 m 180 s = 1.7 m/s north v avg = d t = 304 m 180 s = 1.7 m/s north Discussion 

Since average velocity is a vector quantity, you must include direction as well as magnitude in the answer. Notice, however, that the direction can be omitted until the end to avoid cluttering the problem. Pay attention to the significant figures in the problem. The distance 304 m has three significant figures, but the time interval 180 s has only two, so the quotient should have only two significant figures. 

Note the way scalars and vectors are represented. In this book, d represents distance, and d represents displacement. Similarly, v represents speed, and v represents velocity. A variable that is not bold indicates a scalar quantity, and a bold variable indicates a vector quantity. Vectors are sometimes represented by small arrows above the variable. 

Use this problem to emphasize the importance of using the correct number of significant figures in calculations. Some students have a tendency to include many digits in their final calculations. They incorrectly believe they are improving the accuracy of their answer by writing many of the digits shown on the calculator. Point out that doing this introduces errors into the calculations. In more complicated calculations, these errors can propagate and cause the final answer to be wrong. Instead, remind students to always carry one or two extra digits in intermediate calculations and to round the final answer to the correct number of significant figures. Solving for Displacement when Average Velocity and Time are Known 

Layla jogs with an average velocity of 2.4 m/s east. What is her displacement after 46 seconds? Strategy 

We know that Layla's average velocity is 2.4 m/s east, and the time interval is 46 seconds. We can rearrange the average velocity formula to solve for the displacement. Solution 

v avg = d t d = v a v g t = ( 2.4 m/s)(46 s) = 1.1 10 2 m east v avg = d t d = v a v g t = ( 2.4 m/s)(46 s) = 1.1 10 2 m east Discussion 

The answer is about 110 m east, which is a reasonable displacement for slightly less than a minute of jogging. A calculator shows the answer as 110.4 m. We chose to write the answer using scientific notation because we wanted to make it clear that we only used two significant figures. 

Dimensional analysis is a good way to determine whether you solved a problem correctly. Write the calculation using only units to be sure they match on opposite sides of the equal mark. In the worked example, you have: m = (m/s)(s). Since seconds is in the denominator for the average velocity and in the numerator for the time, the unit cancels out leaving only m and, of course, m = m. Solving for Time when Displacement and Average Velocity are Known 

Phillip walks along a straight path from his house to his school. How long will it take him to get to school if he walks 428 m west with an average velocity of 1.7 m/s west? Strategy 

We know that Phillip's displacement is 428 m west, and his average velocity is 1.7 m/s west. We can calculate the time required for the trip by rearranging the average velocity equation. Solution 

v avg = d t t = d v avg = 428 m 1.7 m/s = 2.5 10 2 s v avg = d t t = d v avg = 428 m 1.7 m/s = 2.5 10 2 s Discussion 

Here again we had to use scientific notation because the answer could only have two significant figures. Since time is a scalar, the answer includes only a magnitude and not a direction. Practice Problems 

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[link] The Walking Man 

In this simulation you will put your cursor on the man and move him first in one direction and then in the opposite direction. Keep the Introduction tab active. You can use the Charts tab after you learn about graphing motion later in this chapter. Carefully watch the sign of the numbers in the position and velocity boxes. Ignore the acceleration box for now. See if you can make the man s position positive while the velocity is negative. Then see if you can do the opposite. Click here for the simulation 

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This is a powerful interactive animation, and it can be used for many lessons. At this point it can be used to show that displacement can be either positive or negative. It can also show that when displacement is negative, velocity can be either positive or negative. Later it can be used to show that velocity and acceleration can have different signs. It is strongly suggested that you keep students on the Introduction tab. The Charts tab can be used after students learn about graphing motion later in this chapter. Check Your Understanding 

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Use the Check Your Understanding questions to assess students achievement of the sections learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify which and direct students to the relevant content. Assessment items in TUTOR will allow you to reassess. Section Summary Average speed is a scalar quantity that describes distance traveled divided by the time during which the motion occurs. Velocity is a vector quantity that describes the speed and direction of an object. Average velocity is displacement over the time period during which the displacement occurs. If the velocity is constant, then average velocity and instantaneous velocity are the same. Key Equations Average speed v avg = distance time v avg = distance time Average velocity v avg = d t = d f d 0 t f t 0 v avg = d t = d f d 0 t f t 0 Concept Items 

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[link] Glossary average speed distance traveled divided by time during which motion occurs average velocity displacement divided by time over which displacement occurs instantaneous speed speed at a specific instant in time instantaneous velocity velocity at a specific instant in time speed rate at which an object changes its location velocity the speed and direction of an objectPosition vs. Time Graphs Position vs. Time Graphs Section Learning Objectives 

By the end of this section, you will be able to: Explain the meaning of slope in position vs. time graphs Solve problems using position vs. time graphs 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4A) : generate and interpret graphs and charts describing different types of motion, including the use of real-time technology such as motion detectors or photogates. Section Key Terms dependent variable independent variable tangent 

[BL] [OL] Describe a scenario, for example, in which you launch a water rocket into the air. It goes up 150 ft, stops, and then falls back to the earth. Have the students assess the situation. Where would they put their zero? What is the positive direction, and what is the negative direction? Have a student draw a picture of the scenario on the board. Then draw a position vs. time graph describing the motion. Have students help you complete the graph. Is the line straight? Is it curved? Does it change direction? What can they tell by looking at the graph? 

[AL] Once the students have looked at and analyzed the graph, see if they can describe different scenarios in which the lines would be straight instead of curved? Where the lines would be discontinuous? Graphing Position as a Function of Time 

A graph , like a picture, is worth a thousand words. Graphs not only contain numerical information, they also reveal relationships between physical quantities. In this section, we will investigate kinematics by analyzing graphs of position over time . 

Graphs in this text have perpendicular axes, one horizontal and the other vertical. When two physical quantities are plotted against each other, the horizontal axis is usually considered the independent variable , and the vertical axis is the dependent variable . In algebra, you would have referred to the horizontal axis as the x -axis and the vertical axis as the y -axis. As in [link] , a straight-line graph has the general form y = m x + b y = m x + b . 

Here m is the slope, defined as the rise divided by the run (as seen in the figure) of the straight line. The letter b is the y -intercept which is the point at which the line crosses the vertical, y -axis. In terms of a physical situation in the real world, these quantities will take on a specific significance, as we will see below. The diagram shows a straight-line graph. The equation for the straight line is y equals mx + b . 

In physics, time is usually the independent variable. Other quantities, such as displacement, are said to depend upon it. A graph of position versus time, therefore, would have position on the vertical axis (dependent variable) and time on the horizontal axis (independent variable). In this case, to what would the slope and y -intercept refer? Let s look back at our original example when studying distance and displacement. 

The drive to school was five kilometers from home. Let s assume it took ten minutes to make the drive and that your parent was driving at a constant velocity the whole time. The position versus time graph for this section of the trip would look like that shown in [link] . A graph of position versus time for the drive to school is shown. What would the graph look like if we added the return trip? 

As we said before, d 0 = 0 because we call home our 0 and start calculating from there. In [link] , the line starts at d = 0, as well. This is the b in our equation for a straight line. Our initial position in a position versus time graph is always the place where the graph crosses the x -axis at t = 0. What is the slope? The rise is the change in position, (i.e., displacement) and the run is the change in time. This relationship can also be written: d t d t 

This relationship was how we defined average velocity. Therefore, the slope in a d versus t graph, is the average velocity. 

Sometimes, as is the case where we graph both the trip to school and the return trip, the behavior of the graph looks different during different time intervals. If the graph looks like a series of straight lines, then you can calculate the average velocity for each time interval by looking at the slope. If you then want to calculate the average velocity for the entire trip, you can do a weighted average. 

Let s look at another example. [link] shows a graph of position versus time for a jet-powered car on a very flat dry lake bed in Nevada. The diagram shows a graph of position versus time for a jet-powered car on the Bonneville Salt Flats. 

Using the relationship between dependent and independent variables, we see that the slope in the graph in [link] is average velocity, v avg and the intercept is displacement at time zero that is, d 0 . Substituting these symbols into y = mx + b gives d = v t + d 0 d = v t + d 0 

or d = d 0 + v t . d = d 0 + v t . 

Thus a graph of position versus time gives a general relationship among displacement, velocity, and time, as well as giving detailed numerical information about a specific situation. From the figure we can see that the car has a position of 400 m at t = 0 s, 650 m at t = 1.0 s, and so on. And we can learn about the object s velocity, as well. 

Help students learn what different graphs of displacement vs. time look like. 

[Visual] Set up a meter stick. If you can find a remote control car, have one student record times as you send the car forward along the stick, then backwards, then forward again with a constant velocity. Take the recorded times and the change in position and put them together. Get the students to coach you to draw a position vs. time graph. 

Each leg of the journey should be a straight line with a different slope. The parts where the car was going forward should have a positive slope. The part where it is going backwards would have a negative slope. 

[OL] Ask if the place that they take as zero affects the graph. 

[AL] Is it realistic to draw any position graph that starts at rest without some curve in it? Why might we be able to neglect the curve in some scenarios? 

[All]Discuss what can be uncovered from this graph. Students should be able to read the net displacement, but they can also use the graph to determine the total distance traveled. Then ask how the speed or velocity is reflected in this graph. Direct students in seeing that the steepness of the line (slope) is a measure of the speed and that the direction of the slope is the direction of the motion. 

[AL] Some students might recognize that a curve in the line represents a sort of slope of the slope, a preview of acceleration which they will learn about in the next chapter. Graphing Motion 

In this activity, you will release a ball down a ramp and graph the ball s displacement vs. time. Choose an open location with lots of space to spread out so there is less chance for tripping or falling due to rolling balls. 1 ball 1 board 2 or 3 books 1 stopwatch 1 tape measure 6 pieces of masking tape 1 piece of graph paper 1 pencil Build a ramp by placing one end of the board on top of the stack of books. Adjust location, as necessary, until there is no obstacle along the straight line path from the bottom of the ramp until at least the next 3 meters. Mark distances of 0.5 m, 1.0 m, 1.5 m, 2.0 m, 2.5 m, 3.0 m from the bottom of the ramp. Write the distances on the tape. Have one person take the role of the experimenter. This person will release the ball from the top of the ramp. If the ball does not reach the 3.0 m mark, then increase the incline of the ramp by adding another book. Repeat this Step as necessary. Have the experimenter release the ball. Have a second person, the timer, begin timing the trial once the ball reaches the bottom of the ramp and stop the timing once the ball reaches 0.5 m. Have a third person, the recorder, record the time in a data table. Repeat Step 4, stopping the times at the distances of 1.0 m, 1.5 m, 2.0 m, 2.5 m, 3.0 m from the bottom of the ramp. Use your measurements of time and the displacement to make a position vs. time graph of the ball s motion. 

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[BL] [OL] Emphasize that the motion in this lab is the motion of the ball as it rolls along the floor. Ask students where there zero should be. 

[AL] Ask students what the graph would look like if they began timing at the top versus the bottom of the ramp. Why would the graph look different? What might account for the difference? Solving Problems Using Position vs. Time Graphs 

So how do we use graphs to solve for things we want to know like velocity? Using Position Time Graph to Calculate Average Velocity: Jet Car 

Find the average velocity of the car whose position is graphed in this figure . Strategy 

The slope of a graph of d vs. t is average velocity, since slope equals rise over run. slope = d t = v slope = d t = v 

Since the slope is constant here, any two points on the graph can be used to find the slope. Solution Choose two points on the line. In this case, we choose the points labeled on the graph: (6.4 s, 2000 m) and (0.50 s, 525 m). (Note, however, that you could choose any two points.) Substitute the d and t values of the chosen points into the equation. Remember in calculating change ( ) we always use final value minus initial value. 

v = d t = 2000 m 525 m 6.4 s 0.50 s = 250 m/s , v = d t = 2000 m 525 m 6.4 s 0.50 s = 250 m/s , Discussion 

This is an impressively high land speed (900 km/h, or about 560 mi/h): much greater than the typical highway speed limit of 60 mi/h (27 m/s or 96 km/h), but considerably shy of the record of 343 m/s (1234 km/h or 766 mi/h), set in 1997. 

If the graph of position is a straight line, then the only thing students need to know to calculate the average velocity is the slope of the line, rise/run. They can use whichever points on the line are most convenient. 

But what if the graph of the position is more complicated than a straight line? What if the object speeds up or turns around and goes backward? Can we figure out anything about its velocity from a graph of that kind of motion? Let s take another look at the jet-powered car. The graph in [link] shows its motion as it is getting up to speed after starting at rest. Time starts at zero for this motion (as if measured with a stopwatch), and the displacement and velocity are initially 200 m and 15 m/s, respectively. The diagram shows a graph of the position of a jet-powered car during the time span when it is speeding up. The slope of a distance versus time graph is velocity. This is shown at two points. Instantaneous velocity at any point is the slope of the tangent at that point. A U.S. Air Force jet car speeds down a track. (credit: Matt Trostle, Flickr) 

The graph of position versus time in [link] is a curve rather than a straight line. The slope of the curve becomes steeper as time progresses, showing that the velocity is increasing over time. The slope at any point on a position-versus-time graph is the instantaneous velocity at that point. It is found by drawing a straight line tangent to the curve at the point of interest and taking the slope of this straight line. Tangent lines are shown for two points in [link] . The average velocity is the net displacement divided by the time traveled. Using Position Time Graph to Calculate Average Velocity: Jet Car, Take Two 

Calculate the instantaneous velocity of the jet car at a time of 25 s by finding the slope of the tangent line at point Q in this figure . Strategy 

The slope of a curve at a point is equal to the slope of a straight line tangent to the curve at that point. Solution Find the tangent line to the curve at t = 25 s t = 25 s . Determine the endpoints of the tangent. These correspond to a position of 1300 m at time 19 s and a position of 3120 m at time 32 s. Plug these endpoints into the equation to solve for the slope, v . 

slope = v Q = d Q t Q = ( 3120 1300 ) m ( 32 19 ) s = 1820 m 13 s = 140 m/s slope = v Q = d Q t Q = ( 3120 1300 ) m ( 32 19 ) s = 1820 m 13 s = 140 m/s Discussion 

The entire graph of v versus t can be obtained in this fashion. 

A curved line is a more complicated example. Define tangent as a line that touches a curve at only one point. Show that as a straight line changes its angle next to a curve, it actually hits the curve multiple times at the base, but only one line will never touch at all. This line forms a right angle to the radius of curvature, but at this level, they can just kind of eyeball it. The slope of this line gives the instantaneous velocity. The most useful part of this line is that students can tell when the velocity is increasing, decreasing, positive, negative, and zero. 

[AL] You could find the instantaneous velocity at each point along the graph and if you graphed each of those points, you would have a graph of the velocity. Practice Problems 

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Use the Check Your Understanding questions to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help identify direct students to the relevant content. Section Summary Graphs can be used to analyze motion. The slope of a position vs. time graph is the velocity. For a straight line graph of position, the slope is the average velocity. To obtain the instantaneous velocity at a given moment for a curved graph, find the tangent line at that point and take its slope. Key Equations Displacement d = d 0 + v t d = d 0 + v t . Concept Items 

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[link] Glossary dependent variable the variable that changes as the independent variable changes independent variable the variable, usually along the horizontal axis of a graph, that does not change based on human or experimental action; in physics this is usually time tangent a line that touches another at exactly one pointVelocity vs. Time Graphs Velocity vs. Time Graphs 

By the end of this section, you will be able to: Explain the meaning of slope and area in velocity vs. time graphs Solve problems using velocity vs. time graphs 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4A) : generate and interpret graphs and charts describing different types of motion, including the use of real-time technology such as motion detectors or photogates. Section Key Terms acceleration 

Ask students to use their knowledge of position graphs to construct velocity vs. time graphs. Alternatively, provide an example of a velocity time graph and ask students what information can be derived from the graph. Ask: Is it the same information as in a position time graph? How is the information portrayed differently? Is there any new information in a velocity time graph? Graphing Velocity as a Function of Time 

Earlier, we examined graph s of position vs. time . Now, we are going to build on that information as we look at graphs of velocity vs. time. Velocity is the rate of change of displacement . Acceleration is the rate of change of velocity; we will discuss acceleration more in another chapter. These concepts are all very interrelated. Maze Game 

In this simulation you will use a vector diagram to manipulate a ball into a certain location without hitting a wall. You can manipulate the ball directly with position or by changing its velocity. Explore how these factors change the motion. If you would like, you can put it on the a setting, as well. This is acceleration, which measures the rate of change of velocity. We will explore acceleration in more detail later, but it might be interesting to take a look at it here. Click here for the simulation 

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What can we learn about motion by looking at velocity time graphs? Let s return to our drive to school, and look at a graph of position versus time as shown in [link] . A graph of position versus time for the drive to and from school is shown. 

We assumed for our original calculation that your parent drove with a constant velocity to and from school. We now know that the car could not have gone from rest to a constant velocity without speeding up. So the actual graph would be curved on either end, but let s make the same approximation as we did then, anyway. 

It is common in physics, especially at the early learning stages, for certain things to be neglected, as we see here. This is because it makes the concept clearer or the calculation easier. Practicing physicists use these kinds of short-cuts, as well. It works out because usually the thing being neglected is small enough that it does not significantly affect the answer. In the earlier example, the amount of time it takes the car to speed up and reach its cruising velocity is very small compared to the total time traveled. 

Looking at this graph, and given what we learned, we can see that there are two distinct periods to the car s motion the way to school and the way back. The average velocity for the drive to school is 0.5 km/minute. We can see that the average velocity for the drive back is 0.5 km/minute. If we plot the data showing velocity versus time, we get another graph ( [link] ): Graph of velocity versus time for the drive to and from school. 

We can learn a few things. First, we can derive a v versus t graph from a d versus t graph. Second, if we have a straight-line position time graph that is positively or negatively sloped, it will yield a horizontal velocity graph. There are a few other interesting things to note. Just as we could use a position time graph to determine velocity, we can use a velocity time graph to determine position. We know that v = d / t . If we use a little algebra to re-arrange the equation, we see that d = v t . In [link] , we have velocity on the y -axis and time along the x -axis. Let s take just the first half of the motion. We get 0.5 km/minute 10 minutes. The units for "minutes" cancel each other, and we get 5 km, which is the displacement for the trip to school. If we calculate the same for the return trip, we get 5 km. If we add them together, we see that the net displacement for the whole trip is 0 km, which it should be because we started and ended at the same place. 

You can treat units just like you treat numbers, so a km/km=1 (or, we say, it cancels out). This is good because it can tell us whether or not we have calculated everything with the correct units. For instance, if we end up with m s for velocity instead of m/s, we know that something has gone wrong, and we need to check our math. This process is called dimensional analysis, and it is one of the best ways to check if your math makes sense in physics. 

The area under a velocity curve represents the displacement. The velocity curve also tells us whether the car is speeding up. In our earlier example, we stated that the velocity was constant. So, the car is not speeding up. Graphically, you can see that the slope of these two lines is 0. This slope tells us that the car is not speeding up, or accelerating. We will do more with this information in a later chapter. For now, just remember that the area under the graph and the slope are the two important parts of the graph. Just like we could define a linear equation for the motion in a position time graph, we can also define one for a velocity time graph. As we said, the slope equals the acceleration, a . And in this graph, the y -intercept is v 0 . Thus, v = v 0 + a t v = v 0 + a t . 

But what if the velocity is not constant? Let s look back at our Jet-Car example. At the beginning of the motion, as the car is speeding up, we saw that its position is a curve, as shown in [link] . A graph is shown of the position of a jet-powered car during the time span when it is speeding up. The slope of a d vs. t graph is velocity. This is shown at two points. Instantaneous velocity at any point is the slope of the tangent at that point. 

You do not have to do this, but you could, theoretically, take the instantaneous velocity at each point on this graph. If you did, you would get [link] , which is just a straight line with a positive slope. The graph shows the velocity of a jet-powered car during the time span when it is speeding up. 

Again, if we take the slope of the velocity time graph, we get the acceleration, the rate of change of the velocity. And, if we take the area under the slope, we get back to the displacement. 

Return to the scenario of the drive to and from school. Re-draw the V-shaped position graph. Ask the students what the velocity is at different times on that graph. Students should then be able to see that the corresponding velocity graph is a horizontal line at 0.5km/minute and then a horizontal line at 0.5 km/minute. Then draw a few velocity graphs and see if they can get the corresponding position graph. 

[OL] [AL] Have students describe the relationship between the velocity and the position on these graphs. Ask: Can a velocity graph be used to find the position? Can a velocity graph be used to find anything else? 

[AL] What is wrong with this graph? Ask students whether the velocity could actually be constant from rest or shift to negative so quickly. What would more realistic graphs look like? How inaccurate is it to ignore the non-constant portion of the motion? 

[OL] Students should be able to see that if a position graph is a straight line, then the velocity graph will be a horizontal line. Also, the instantaneous velocity can be read off the velocity graph at any moment, but more steps are needed to calculate the average velocity. 

[AL] Guide students in seeing that the area under the velocity curve is actually the position and the slope represents the rate of change of the velocity, just as the slope of the position line represents the rate of change of the position. Solving Problems using Velocity Time Graphs 

Most velocity time graphs will be straight lines. When this is the case, our calculations are fairly simple. Using Velocity Graph to Calculate Some Stuff: Jet Car 

Use this figure to (a) find the displacement of the jet car over the time shown (b) calculate the rate of change (acceleration) of the velocity. (c) give the instantaneous velocity at 5 s, and (d) calculate the average velocity over the interval shown. Strategy The displacement is given by finding the area under the line in the velocity time graph. The acceleration is given by finding the slope of the velocity graph. The instantaneous velocity can just be read off of the graph. To find the average velocity, recall that v avg = d t = d f d 0 t f t 0 v avg = d t = d f d 0 t f t 0 Solution Analyze the shape of the area to be calculated. In this case, the area is made up of a rectangle between 0 and 20 m/s stretching to 30 s. The area of a rectangle is length width. Therefore, the area of this piece is 600 m. Above that is a triangle whose base is 30 s and height is 140 m/s. The area of a triangle is 0.5 length width. The area of this piece, therefore, is 2100 m. Add them together to get a net displacement of 2700 m. Take two points on the velocity line. Say, t = 5 s and t = 25 s. At t = 5 s, the value of v = 40 m/s. At t = 25 s, v = 140 m/s. Find the slope. a = v t = 100 m/s 20 s = 5 m/s 2 a = v t = 100 m/s 20 s = 5 m/s 2 The instantaneous velocity at t = 5 s , as we found in part (b) is just 40 m/s. Find the net displacement, which we found in part (a) was 2700 m. Find the total time which for this case is 30 s. Divide 2700 m/30 s = 90 m/s. Discussion 

The average velocity we calculated here makes sense if we look at the graph. 100m/s falls about halfway across the graph and since it is a straight line, we would expect about half the velocity to be above and half below. 

The quantities solved for are slightly different in the different kinds of graphs, but students should begin to see that the process of analyzing or breaking down any of these graphs is similar. Ask: Where are the turning points in the motion? When is the object moving forward? What does a curve in the graph mean? Also, students should start to have an intuitive understanding of the relationship between position and velocity graphs. 

You can have negative position, velocity, and acceleration on a graph that describes the way the object is moving. You should never see a graph with negative time on an axis. Why? 

Most of the velocity time graphs we will look at will be simple to interpret. Occasionally, we will look at curved graphs of velocity time. More often, these curved graphs occur when something is speeding up, often from rest. Let s look back at a more realistic velocity time graph of the jet car s motion that takes this speeding up stage into account. The graph shows a more accurate graph of the velocity of a jet-powered car during the time span when it is speeding up. Using Curvy Velocity Graph to Calculate Some Stuff: Jet Car, Take Two 

Use [link] to (a) find the approximate displacement of the Jet Car over the time shown, (b) calculate the instantaneous acceleration at t = 30 s, (c) find the instantaneous velocity at 30 s, and (d) calculate the approximate average velocity over the interval shown. Strategy Because this graph is an undefined curve, we have to estimate shapes over smaller intervals in order to find the areas. Like when we were working with a curved displacement graph, we will need to take a tangent line at the instant we are interested and use that to calculate the instantaneous acceleration. The instantaneous velocity can still be read off of the graph. We will find the average velocity the same way we did in the previous example. Solution This problem is more complicated than the last example. To get a good estimate, we should probably break the curve into four sections. 0 10 0 10 s, 10 20 10 20 s, 20 40 20 40 s, and 40 70 40 70 s. Calculate the bottom rectangle (common to all pieces). 165 m/s 70 s=11,550 m. Estimate a triangle at the top, and calculate the area for each section. Section 1=225 m; section 2=100 m + 450 m= 550 m; section 3=150 m + 1300 m=1450 m; section 4=2550 m. Add them together to get a net displacement of 16325 m. Using the tangent line given, we find that the slope is 1 m/s 2 . The instantaneous velocity at t = 30 s, is 240 m/s. Find the net displacement, which we found in part (a), was 16325 m. Find the total time, which for this case is 70 s. Divide 16325 m 70 s 233 m/s 16325 m 70 s 233 m/s Discussion 

This is a much more complicated process than the first problem. If we were to use these estimates to come up with the average velocity over just the first 30 s we would get about 191 m/s. By approximating that curve with a line, we get an average velocity of 202.5 m/s. Depending on our purposes and how precise an answer we need, sometimes calling a curve a straight line is a worthwhile approximation. 

Finding the tangent line can be a challenging concept for high school students, and they need to understand it theoretically. If you drew a regular curve inside of the curve at the point you are interested in, you could draw a radius of that curve. The tangent line would be the line perpendicular to that radius. 

[OL] Have the students compare this problem and the last one. Ask: What is the difference? When would you care about the more accurate picture of the motion? And when would it really not matter? Why would you ever want to look at a less accurate depiction of motion? Practice Problems 

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In this activity, you will graph a moving ball s velocity vs. time. Your graph from the earlier Graphing Motion Snap Lab! 1 Piece of graph paper 1 Pencil Take your graph from the earlier Graphing Motion Snap Lab! and use it to create a graph of velocity vs. time. Use your graph to calculate the displacement. 

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In this lab, students will use the displacement graph they drew in the last snap lab to create a velocity graph. If the rolling ball slowed down in the last snap lab, perhaps due to the ramp being too low, then the graph may not show constant velocity. Check Your Understanding 

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Use the Check Your Understanding questions to assess students achievement of the section s learning objectives. If students are struggling with a specific objective, the Check Your Understanding will help direct students to the relevant content. Section Summary The slope of a velocity time graph is the acceleration. The area under a velocity time curve is the displacement. Average velocity can be found in a velocity time graph by taking the weighted average of all the velocities. Key Equations Velocity v = v 0 + a t v = v 0 + a t Acceleration a = v t a = v t Concept Items 

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The National Mall in Washington, DC, is a national park containing most of the highly treasured memorials and museums of the United States. However, the National Mall also hosts many events and concerts. The map in [link] shows the area for a benefit concert during which the president will speak. The concert stage is near the Lincoln Memorial. The seats and standing room for the crowd will stretch from the stage east to near the Washington Monument, as shown on the map. You are planning the logistics for the concert. Use the map scale to measure any distances needed to make the calculations below. 

The park has three new long-distance speakers. They would like to use these speakers to broadcast the concert audio to other parts of the National Mall. The speakers can project sound up to 0.35 miles away but they must be connected to one of the power supplies within the concert area (see map ). What is the minimum amount of wire needed for each speaker, in feet to the nearest foot, in order to project the audio to the following areas? Assume that wire cannot be placed over water, buildings or any memorials. The center of the Jefferson Memorial using power supply 1 The center of the Ellipse using power supply 2 The center of the lawn area between 14th Street and the Smithsonian metro station. How long will it take a concert-goer, in minutes, to travel from the Smithsonian metro to the eastern border of the concert area? Assume visitors are walking at an average speed of 3.0 mi/hour. The president s motorcade will be traveling to the concert from the White House. To avoid concert traffic, the motorcade travels from the White House west down E Street and then turns south on 23rd Street to reach the Lincoln memorial. What minimum speed, in miles per hour to the nearest tenth, would the motorcade have to travel to make the trip in 5 minutes? The president could also simply fly from the White House to the Lincoln Memorial using the presidential helicopter, Marine 1. How long would it take Marine 1, traveling slowly at 30 mph, to travel from directly above the White House landing zone (LZ) to directly above the Lincoln Memorial LZ? Disregard liftoff and landing times and report the travel time in minutes to the nearest minute. 

The content in this chapter will help your students master the following NGSS: 

HS-PS2-1: Analyze data to support the claim that Newton's second law of motion describes the mathematical relationship among the net force on a macroscopic object, its mass, and its acceleration. Test Prep Multiple Choice 

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[link] Glossary acceleration the rate at which velocity changesAngle of Rotation and Angular Velocity Angle of Rotation and Angular Velocity Section Learning Objectives 

By the end of this section, you will be able to: Describe the angle of rotation and relate it to its linear counterpart Describe angular velocity and relate it to its linear counterpart Solve problems involving angle of rotation and angular velocity 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4C) : Analyze and describe accelerated motion in two dimensions using equations, including projectile and circular examples Section Key Terms angle of rotation angular velocity arc length circular motion radius of curvature rotational motion spin tangential velocity Angle of Rotation 

What exactly do we mean by circular motion or rotation ? Rotational motion is the circular motion of an object about an axis of rotation. We will discuss specifically circular motion and spin. Circular motion is when an object moves in a circular path. Examples of circular motion include a race car speeding around a circular curve, a toy attached to a string swinging in a circle around your head, or the circular loop-the-loop on a roller coaster. Spin is rotation about an axis that goes through the center of mass of the object, such as Earth rotating on its axis, a wheel turning on its axle, the spin of a tornado on its path of destruction, or a figure skater spinning during a performance at the Olympics. Sometimes, objects will be spinning while in circular motion, like the Earth spinning on its axis while revolving around the Sun, but we will focus on these two motions separately. 

[BL] [OL] Explain the difference between circular and rotational motions by using the Earth s rotation about its axis and its revolution about the Sun. Explain that Earth s rotation is slightly elliptical, although it is very nearly circular. 

[OL] [AL] Ask students to come up with examples of circular motion. 

When solving problems involving rotational motion, we use variables that are similar to linear variables (distance, velocity, acceleration, and force) but take into account the curvature or rotation of the motion. Here, we define the angle of rotation , which is the angular equivalence of distance; and angular velocity , which is the angular equivalence of linear velocity. 

When objects rotate about some axis for example, when the CD in [link] rotates about its center each point in the object follows a circular path. All points on a CD travel in circular paths. The pits (dots) along a line from the center to the edge all move through the same angle in time t t . 

The arc length , , is the distance traveled along a circular path. The radius of curvature , r , is the radius of the circular path. Both are shown in [link] . The radius ( r ) of a circle is rotated through an angle . The arc length, s s , is the distance covered along the circumference. 

Consider a line from the center of the CD to its edge. In a given time, each pit (used to record information) on this line moves through the same angle. The angle of rotation is the amount of rotation and is the angular analog of distance. The angle of rotation is the arc length divided by the radius of curvature: = s r = s r 

The angle of rotation is often measured by using a unit called the radian . (Radians are actually dimensionless, because a radian is defined as the ratio of two distances, radius and arc length.) A revolution is one complete rotation, where every point on the circle returns to its original position. One revolution covers 2 2 radians (or 360 degrees), and therefore has an angle of rotation of 2 2 radians, and an arc length that is the same as the circumference of the circle. We can convert between radians, revolutions, and degrees using the relationship 

1 revolution = 2 2 rad = 360 . See [link] for the conversion of degrees to radians for some common angles. 

2 rad = 360 1 rad = 360 2 57.3 2 rad = 360 1 rad = 360 2 57.3 Commonly Used Angles in Terms of Degrees and Radians Degree Measures Radian Measures 30 30 6 6 60 60 3 3 90 90 2 2 120 120 2 3 2 3 135 135 3 4 3 4 180 180 Angular Velocity 

[BL] Review displacement, speed, velocity, acceleration. 

[AL] Ask students whether or not velocity changes in uniform circular motion. What about speed? What about acceleration? 

How fast is an object rotating? We can answer this question by using the concept of angular velocity. Consider first the angular speed, , is the rate at which the angle of rotation changes. In equation form, the angular speed is 

= t = t , 

which means that an angular rotation, , occurs in a time, t t . If an object rotates through a greater angle of rotation in a given time, it has a greater angular speed. The units for angular speed are radians per second (rad/s). 

Now let s consider the direction of the angular speed, which means we now must call it the angular velocity. The direction of the angular velocity is along the axis of rotation. For an object rotating clockwise, the angular velocity points away from you along the axis of rotation. For an object rotating counterclockwise, the angular velocity points toward you along the axis of rotation. 

Angular velocity, , is the angular version of linear velocity, v . Tangential velocity is the instantaneous linear velocity of an object in rotational motion . To get the precise relationship between angular velocity and tangential velocity, consider again a pit on the rotating CD. This pit moves through an arc length, s s , in a short time, t t , so its tangential speed is v = s t v = s t 

From the definition of the angle of rotation, = s r = s r , we see that s = r s = r . Substituting this into the expression for v gives v = r t = r v = r t = r 

The equation v = r v = r says that the tangential speed, v, is proportional to the distance r from the center of rotation. Consequently, tangential speed is greater for a point on the outer edge of the CD (with larger r ) than for a point closer to the center of the CD (with smaller r ). This makes sense because a point farther out from the center has to cover a longer arc length in the same amount of time as a point closer to the center. Note that both points will still have the same angular speed, regardless of their distance from the center of rotation. See [link] . Points 1 and 2 rotate through the same angle ( ), but point 2 moves through a greater arc length ( s 2 s 2 ) because it is farther from the center of rotation. 

[AL] Explain that the time period t t in the equation that defines tangential velocity ( v = s t v = s t ) must be short so that the arc described by the moving object can be approximated as a straight line. This allows us to define the direction of the tangential velocity as being tangent to the circle. This approximation becomes increasingly accurate as t t becomes increasingly small. 

Now, consider another example: the tire of a moving car (see [link] ). The faster the tire spins, the faster the car moves large means large v because v = r v = r . Similarly, a larger-radius tire rotating at the same angular velocity, , will produce a greater linear (tangential) velocity, v, for the car. This is because a larger radius means a longer arc length must contact the road, so the car must move farther in the same amount of time. A car moving at a velocity, v, to the right has a tire rotating with angular velocity . The speed of the tread of the tire relative to the axle is v , the same as if the car were jacked up and the wheels spinning without touching the road. Directly below the axle, where the tire touches the road, the tire tread moves backward with respect to the axle with tangential velocity v = r v = r , where r is the tire radius. Because the road is stationary with respect to this point of the tire, the car must move forward at the linear velocity v . A larger angular velocity for the tire means a greater linear velocity for the car. 

However, there are cases where linear velocity and tangential velocity are not equivalent, such as a car spinning its tires on ice. In this case, the linear velocity will be less than the tangential velocity. Due to the lack of friction under the tires of a car on ice, the arc length through which the tire treads move is greater than the linear distance through which the car moves. It s similar to running on a treadmill or pedaling a stationary bike; you are literally going nowhere fast. 

Angular velocity and tangential velocity v are vectors, so we must include magnitude and direction. The direction of the angular velocity is along the axis of rotation, and points away from you for an object rotating clockwise, and toward you for an object rotating counterclockwise. In mathematics this is described by the right-hand rule. Tangential velocity is usually described as up, down, left, right, north, south, east, or west, as shown in [link] . As the fly on the edge of an old-fashioned vinyl record moves in a circle, its instantaneous velocity is always at a tangent to the circle. The direction of the angular velocity is into the page this case. Relationship between Angular Velocity and Speed 

This video reviews the definition and units of angular velocity and relates it to linear speed. It also shows how to convert between revolutions and radians. 

[link] Solving Problems Involving Angle of Rotation and Angular Velocity Measuring Angular Speed 

In this activity, you will create and measure uniform circular motion and then contrast it with circular motions with different radii. 1 string (1 m long) 1 object (2-hole rubber stopper) to tie to the end 1 timer Tie an object to the end of a string. Swing the object around in a horizontal circle above your head (swing from your wrist). It is important that the circle be horizontal! Maintain the object at uniform speed as it swings. Measure the angular speed of the object in this manner. Measure the time it takes for the object to travel 10 revolutions. Divide that time by 10 to get the angular speed in revolutions per second, which you can convert to radians per second. What is the approximate linear speed of the object? Move your hand up the string so that the length of the string is 90 cm. Repeat steps 2 5. Move your hand up the string so that its length is 80 cm. Repeat steps 2 5. Move your hand up the string so that its length is 70 cm. Repeat steps 2 5. Move your hand up the string so that its length is 60 cm. Repeat steps 2 5 Move your hand up the string so that its length is 50 cm. Repeat steps 2 5 Make graphs of angular speed vs. radius (i.e. string length) and linear speed vs. radius. Describe what each graph looks like. 

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Now that we have an understanding of the concepts of angle of rotation and angular velocity, we ll apply them to the real-world situations of a clock tower and a spinning tire. Angle of rotation at a Clock Tower 

The clock on a clock tower has a radius of 1.0 m. (a) What s the angle of rotation between the hour hand of the clock when it moves from 12 pm to 3 pm? (b) What s the arc length along the outermost edge of the clock between the hour hand at these two times? Strategy 

We can figure out the angle of rotation by multiplying a full revolution ( 2 2 radians) by the fraction of the 12 hours covered by the hour hand in going from 12 to 3. Once we have the angle of rotation, we can solve for the arc length by rearranging the equation = s r = s r since the radius is given. Solution to (a) 

In going from 12 to 3, the hour hand covers 1/4 of the 12 hours needed to make a complete revolution. Therefore, the angle between the hour hand at 12 and at 3 is 1 4 2 rad = 2 1 4 2 rad = 2 (i.e., 90 degrees). Solution to (b) 

Rearranging the equation 

= s r = s r , 

we get 

s = r s = r . 

Inserting the known values gives an arc length of 

s = ( 1.0 m ) ( 2 rad ) = 1.6 m s = ( 1.0 m ) ( 2 rad ) = 1.6 m Discussion 

We were able to drop the radians from the final solution to part (b) because radians are actually dimensionless. This is because the radian is defined as the ratio of two distances (radius and arc length). Thus, the formula gives an answer in units of meters, as expected for an arc length. How Fast Does a Car Tire Spin? 

Calculate the angular speed of a 0.300 m radius car tire when the car travels at 15.0 m/s (about 54 km/h). See this figure . Strategy 

In this case, the speed of the tire tread with respect to the tire axle is the same as the speed of the car with respect to the road, so we have v = 15.0 m/s. The radius of the tire is r = 0.300 m. Since we know v and r , we can rearrange the equation v = r v = r , to get = v r = v r and find the angular speed. Solution 

To find the angular speed, we use the relationship: = v r = v r . 

Inserting the known quantities gives: 

= 15.0 m/s 0.300 m = 50.0 rad/s = 15.0 m/s 0.300 m = 50.0 rad/s Discussion 

When we cancel units in the above calculation, we get 50.0/s (i.e., 50.0 per second, which is usually written as 50.0 s 1). But the angular speed must have units of rad/s. Because radians are dimensionless, we can insert them into the answer for the angular speed because we know that the motion is circular. Also note that, if an earth mover with much larger tires, say 1.20 m in radius, were moving at the same speed of 15.0 m/s, its tires would rotate more slowly. They would have an angular speed of 

= 15.0 m/s 1.20 m = 12.5 rad/s = 15.0 m/s 1.20 m = 12.5 rad/s Practice Problems 

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Use the Check Your Understanding questions to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, the formative assessment will help identify which objective is causing the problem and direct students to the relevant content. Section Summary Circular motion is motion in a circular path. The angle of rotation is defined as the ratio of the arc length to the radius of curvature. The arc length s s is the distance traveled along a circular path and r is the radius of curvature of the circular path. The angle of rotation is measured in units of radians (rad), where 2 rad = 360 = 1 2 rad = 360 = 1 revolution. Angular velocity is the rate of change of an angle, where a rotation occurs in a time t t . The units of angular velocity are radians per second (rad/s). Tangential speed v and angular speed are related by v = r v = r , and tangential velocity has units of m/s. The direction of angular velocity is along the axis of rotation, toward (away) from you for clockwise (counterclockwise) motion. Key Equations Angle of rotation = s r = s r Angular speed: = t = t Tangential speed: v = r v = r Concept Items 

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[link] Glossary angle of rotation the ratio of the arc length to the radius of curvature of a circular path angular velocity ( ) the rate of change in the angular position of an object following a circular path arc length ( s s ) the distance traveled by an object along a circular path circular motion the motion of an object along a circular path radius of curvature the distance between the center of a circular path and the path rotational motion the circular motion of an object about an axis of rotation spin rotation about an axis that goes through the center of mass of the object tangential velocity the instantaneous linear velocity of an object in circular or rotational motionIntroduction Introduction In this chapter you will learn about: Angle of rotation and angular velocity Uniform circular motion Rotational motion class="summary" title="Section Summary" class="key-equations" title="Key Equations" class="concept" title="Concept Items" class="critical-thinking" title="Critical Thinking Items" class="problem" title="Problems" class="performance" title="Performance Task" class="multiple-choice" title="Multiple Choice" class="short-answer" title="Short Answer" class="extended-response" title="Extended Response" This Australian Grand Prix Formula 1 race car moves in a circular path as it makes the turn. Its wheels also spin rapidly. The same physical principles are involved in both of these motions. (credit: Richard Munckton). 

Before students begin this chapter, they may wish to review the concepts of distance, displacement, speed, velocity, acceleration, force and Newton s laws of motion. Address misconception about centrifugal force. 

Point out that we come across circular motion in our everyday lives; for instance, a car tire spinning, a fan rotating, and so forth. This chapter is about the quantities that describe rotational motion and the relationships between them. 

You may recall learning about various aspects of motion along a straight line: kinematics (where we learned about displacement, velocity, and acceleration), projectile motion (a special case of two-dimensional kinematics), force, and Newton s laws of motion. In some ways, this chapter is a continuation of Newton s laws of motion. Recall that Newton s first law tells us that objects move along a straight line at constant speed unless a net external force acts on them. Therefore, if an object moves along a circular path, such as the car in the photo, it must be experiencing an external force. In this chapter, we explore both circular motion and rotational motion.Uniform Circular Motion Uniform Circular Motion Section Learning Objectives 

By the end of this section, you will be able to: Describe centripetal acceleration and relate it to linear acceleration Describe centripetal force and relate it to linear force Solve problems involving centripetal acceleration and centripetal force 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4C) : Analyze and describe accelerated motion in two dimensions using equations, including projectile and circular examples (4D) : Calculate the effect of forces on objects, including the law of inertia, the relationship between force and acceleration, and the nature of force pairs between objects Section Key Terms centrifugal force centripetal acceleration centripetal force uniform circular motion Centripetal Acceleration 

[BL] [OL] Review uniform circular motion. Ask students to give examples of circular motion. Review linear acceleration. 

In the previous section, we defined circular motion . The simplest case of circular motion is uniform circular motion , where an object travels a circular path at a constant speed . Note that, unlike speed, the linear velocity of an object in circular motion is constantly changing because it is always changing direction. We know from kinematics that acceleration is a change in velocity , either in magnitude or in direction or both. Therefore, an object undergoing uniform circular motion is always accelerating, even though the magnitude of its velocity is constant. 

You experience this acceleration yourself every time you ride in a car while it turns a corner. If you hold the steering wheel steady during the turn and move at a constant speed, you are executing uniform circular motion. What you notice is a feeling of sliding (or being flung, depending on the speed) away from the center of the turn. This isn t an actual force that is acting on you it only happens because your body wants to continue moving in a straight line (as per Newton s first law) whereas the car is turning off this straight-line path. Inside the car it appears as if you are forced away from the center of the turn. This fictitious force is known as the centrifugal force . The sharper the curve and the greater your speed, the more noticeable this effect becomes. 

[BL] [OL] [AL] Demonstrate circular motion by tying a weight to a string and twirling it around. Ask students what would happen if you suddenly cut the string? In which direction would the object travel? Why? What does this say about the direction of acceleration? Ask students to give examples of when they have come across centripetal acceleration. 

[link] shows an object moving in a circular path at constant speed. The direction of the instantaneous tangential velocity is shown at two points along the path. Acceleration is in the direction of the change in velocity; in this case it points roughly toward the center of rotation. (The center of rotation is at the center of the circular path). If we imagine s s becoming smaller and smaller, then the acceleration would point exactly toward the center of rotation, but this case is hard to draw. We call the acceleration of an object moving in uniform circular motion the centripetal acceleration a c because centripetal means center seeking. The directions of the velocity of an object at two different points are shown, and the change in velocity v v is seen to point approximately toward the center of curvature (see small inset). For an extremely small value of s s , v v points exactly toward the center of the circle (but this is hard to draw). Because a c = v / t a c = v / t , the acceleration is also toward the center, so a c is called centripetal acceleration. 

Consider [link] . The figure shows an object moving in a circular path at constant speed and the direction of the instantaneous velocity of two points along the path. Acceleration is in the direction of the change in velocity and points toward the center of rotation. This is strictly true only as s s tends to zero. 

Now that we know that the direction of centripetal acceleration is toward the center of rotation, let s discuss the magnitude of centripetal acceleration. For an object traveling at speed v in a circular path with radius r , the magnitude of centripetal acceleration is a c = v 2 r a c = v 2 r 

Centripetal acceleration is greater at high speeds and in sharp curves (smaller radius), as you may have noticed when driving a car, because the car actually pushes you toward the center of the turn. But it is a bit surprising that a c is proportional to the speed squared. This means, for example, that the acceleration is four times greater when you take a curve at 100 km/h than at 50 km/h. 

We can also express a c in terms of the magnitude of angular velocity . Substituting v = r v = r into the equation above, we get a c = ( r ) 2 / r = r 2 a c = ( r ) 2 / r = r 2 . Therefore, the magnitude of centripetal acceleration in terms of the magnitude of angular velocity is a c = r 2 a c = r 2 . 

The equation expressed in the form a c = r 2 is useful for solving problems where you know the angular velocity rather than the tangential velocity. Ladybug Motion in 2D 

In this simulation, you experiment with the position, velocity, and acceleration of a ladybug in circular and elliptical motion. Switch the type of motion from linear to circular and observe the velocity and acceleration vectors. Next, try elliptical motion and notice how the velocity and acceleration vectors differ from those in circular motion. Click here for the simulation 

[link] Centripetal Force 

[BL] [OL] [AL] Using the same demonstration as before, ask students to predict the relationships between the quantities of angular velocity, centripetal acceleration, mass, centripetal force. Invite students to experiment by using various lengths of string and different weights. 

Because an object in uniform circular motion undergoes constant acceleration (by changing direction), we know from Newton s second law of motion that there must be a constant net external force acting on the object. 

Any force or combination of forces can cause a centripetal acceleration. Just a few examples are the tension in the rope on a tether ball, the force of Earth s gravity on the Moon, the friction between a road and the tires of a car as it goes around a curve, or the normal force of a roller coaster track on the cart during a loop the loop. 

Any net force causing uniform circular motion is called a centripetal force . The direction of a centripetal force is toward the center of rotation, the same as for centripetal acceleration. According to Newton s second law of motion, a net force causes the acceleration of mass according to F net = m a . For uniform circular motion, the acceleration is centripetal acceleration: a = a c . Therefore, the magnitude of centripetal force, F c , is F c = m a c F c = m a c . 

By using the two different forms of the equation for the magnitude of centripetal acceleration, a c = v 2 / r a c = v 2 / r and a c = r 2 a c = r 2 , we get two expressions involving the magnitude of the centripetal force F c . The first expression is in terms of tangential speed, the second is in terms of angular speed: F c = m v 2 r F c = m v 2 r and F c = m r 2 F c = m r 2 . 

Both forms of the equation depend on mass, velocity, and the radius of the circular path. You may use whichever expression for centripetal force is more convenient. Newton s second law also states that the object will accelerate in the same direction as the net force. By definition, the centripetal force is directed towards the center of rotation, so the object will also accelerate towards the center. A straight line drawn from the circular path to the center of the circle will always be perpendicular to the tangential velocity. Note that, if you solve the first expression for r , you get: r = m v 2 F c r = m v 2 F c 

From this expression, we see that, for a given mass and velocity, a large centripetal force causes a small radius of curvature that is, a tight curve. In this figure, the frictional force ( f ) serves as the centripetal force ( F c ). Centripetal force is perpendicular to tangential velocity and causes uniform circular motion. The larger the centripetal force F c , the smaller is the radius of curvature r and the sharper is the curve. The lower curve has the same velocity v , but a larger centripetal force F c produces a smaller radius r r . Centripetal Force and Acceleration Intuition 

This video explains why a centripetal force creates centripetal acceleration and uniform circular motion. It also covers the difference between speed and velocity and shows examples of uniform circular motion. 

Some students might be confused between centripetal force and centrifugal force. Centrifugal force is not a real force but the result of an accelerating reference frame, such as a turning car or the spinning Earth. Centrifugal force refers to a fictional center fleeing force. 

[link] Solving Centripetal Acceleration and Centripetal Force Problems 

To get a feel for the typical magnitudes of centripetal acceleration, we ll do a lab estimating the centripetal acceleration of a tennis racket and then, in our first Worked Example, compare the centripetal acceleration of a car rounding a curve to gravitational acceleration. For the second Worked Example, we ll calculate the force required to make a car round a curve. Estimating Centripetal Acceleration 

In this activity, you will measure the swing of a golf club or tennis racket to estimate the centripetal acceleration of the end of the club or racket. You may choose to do this in slow motion. Recall that the equation for centripetal acceleration is a c = v 2 r a c = v 2 r or a c = r 2 a c = r 2 . 1 tennis racket or golf club 1 timer 1 ruler or tape measure Work with a partner. Stand a safe distance away from your partner as he or she swings the golf club or tennis racket. Describe the motion of the swing is this uniform circular motion? Why or why not? Try to get the swing as close to uniform circular motion as possible. What adjustments did your partner need to make? Measure the radius of curvature. What did you physically measure? By using the timer, find either the linear or angular velocity, depending on which equation you decide to use. What is the approximate centripetal acceleration based on these measurements? How accurate do you think they are? Why? How might you and your partner make these measurements more accurate? 

The swing of the golf club or racket can be made very close to uniform circular motion. For this, the person would have to move it at a constant speed, without bending their arm. The length of the arm plus the length of the club or racket is the radius of curvature. Accuracy of measurements of angular velocity and angular acceleration will depend on resolution of the timer used and human observational error.The swing of the golf club or racket can be made very close to uniform circular motion. For this, the person would have to move it at a constant speed, without bending their arm. The length of the arm plus the length of the club or racket is the radius of curvature. Accuracy of measurements of angular velocity and angular acceleration will depend on resolution of the timer used and human observational error. 

[link] Comparing Centripetal Acceleration of a Car Rounding a Curve with Acceleration Due to Gravity 

A car follows a curve of radius 500 m at a speed of 25.0 m/s (about 90 km/h). What is the magnitude of the car s centripetal acceleration? Compare the centripetal acceleration for this fairly gentle curve taken at highway speed with acceleration due to gravity ( g ). Strategy 

Because linear rather than angular speed is given, it is most convenient to use the expression a c = v 2 r a c = v 2 r to find the magnitude of the centripetal acceleration. Solution 

Entering the given values of v = 25.0 m/s and r = 500 m into the expression for a c gives a c = v 2 r = ( 25.0 m/s ) 2 500 m = 1.25 m/s 2 a c = v 2 r = ( 25.0 m/s ) 2 500 m = 1.25 m/s 2 Discussion 

To compare this with the acceleration due to gravity ( g = 9.80 m/s 2 ), we take the ratio a c / g = ( 1.25 m/s 2 ) / ( 9.80 m/s 2 ) = 0.128 a c / g = ( 1.25 m/s 2 ) / ( 9.80 m/s 2 ) = 0.128 . Therefore, a c = 0.128 g a c = 0.128 g , which means that the centripetal acceleration is about one tenth the acceleration due to gravity. This acceleration is still noticeable, especially if you are not wearing a seat belt. Frictional Force on Car Tires Rounding a Curve Calculate the centripetal force exerted on a 900 kg car that rounds a 600-m-radius curve on horizontal ground at 25.0 m/s. Static friction prevents the car from slipping. Find the magnitude of the frictional force between the tires and the road that allows the car to round the curve without sliding off in a straight line. Strategy and Solution for (a) 

We know that F c = m v 2 r F c = m v 2 r . Therefore, F c = m v 2 r = ( 900 kg ) ( 25.0 m/s ) 2 600 m = 938 N F c = m v 2 r = ( 900 kg ) ( 25.0 m/s ) 2 600 m = 938 N Strategy and Solution for (b) 

The image above shows the forces acting on the car while rounding the curve. In this diagram, the car is traveling into the page as shown and is turning to the left. Friction acts toward the left, accelerating the car toward the center of the curve. Because friction is the only horizontal force acting on the car, it provides all of the centripetal force in this case. Therefore, the force of friction is the centripetal force in this situation and points toward the center of the curve. f = F c = 938 N f = F c = 938 N Discussion 

Since we found the force of friction in part (b), we could also solve for the coefficient of friction, since f = s N = s m g f = s N = s m g . Practice Problems 

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Use the Check Your Understanding questions to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, the formative assessment will help identify which objective is causing the problem and direct students to the relevant content. Section Summary Centripetal acceleration a c is the acceleration experienced while in uniform circular motion. Centripetal acceleration force is a center-seeking force that always points toward the center of rotation, perpendicular to the linear velocity, in the same direction as the net force, and in the direction opposite that of the radius vector. The standard unit for centripetal acceleration is m/s 2 . Centripetal force F c is any net force causing uniform circular motion. Key Equations Centripetal acceleration a c = v 2 r a c = v 2 r or a c = r 2 a c = r 2 Centripetal force F c = m a c F c = m a c , F c = m v 2 r F c = m v 2 r , F c = m r 2 F c = m r 2 Concept Items 

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[link] Glossary centrifugal force a fictitious force that acts in the direction opposite the centripetal acceleration centripetal acceleration the acceleration of an object moving in a circle, directed toward the center of the circle centripetal force any force causing uniform circular motion uniform circular motion the motion of an object in a circular path at constant speedRotational Motion Rotational Motion Section Learning Objectives 

By the end of this section, you will be able to: Describe rotational kinematic variables and equations and relate them to their linear counterparts Describe torque and lever arm Solve problems involving torque and rotational kinematics 

The learning objectives in this section will help your students master the following TEKS: (4) Science concepts. The student knows and applies the laws governing motion in a variety of situations. The student is expected to: (4C) : Analyze and describe accelerated motion in two dimensions using equations, including projectile and circular examples (4D) : Calculate the effect of forces on objects, including the law of inertia, the relationship between force and acceleration, and the nature of force pairs between objects Section Key Terms angular acceleration kinematics of rotational motion lever arm tangential acceleration torque Rotational Kinematics 

[BL] [OL] Review linear kinematic equations. 

Students may get confused between deceleration and increasing acceleration in the negative direction. 

In the section on uniform circular motion, we discussed motion in a circle at constant speed and, therefore, constant angular velocity. However, there are times when angular velocity is not constant rotational motion can speed up, slow down, or reverse directions. Angular velocity is not constant when a spinning skater pulls in her arms, when a child pushes a merry-go-round to make it rotate, or when a CD slows to a halt when switched off. In all these cases, angular acceleration occurs because the angular velocity changes. The faster the change occurs, the greater is the angular acceleration. Angular acceleration is the rate of change of angular velocity. In equation form, angular acceleration is = t = t 

where is the change in angular velocity and t t is the change in time. The units of angular acceleration are (rad/s)/s, or rad/s 2 . If increases, then is positive. If decreases, then is negative. Keep in mind that, by convention, counterclockwise is the positive direction and clockwise is the negative direction. For example, the skater in [link] is rotating counterclockwise as seen from above, so her angular velocity is positive. Acceleration would be negative, for example, when an object that is rotating counterclockwise slows down. It would be positive when an object that is rotating counterclockwise speeds up. A figure skater spins in the counterclockwise direction, so her angular velocity is normally considered to be positive. (credit: Luu, Wikimedia Commons) 

The relationship between the magnitudes of tangential acceleration , a , and angular acceleration, , is a = r or = a r , is a = r or = a r 

These equations mean that the magnitudes of tangential acceleration and angular acceleration are directly proportional to each other. The greater the angular acceleration, the larger the change in tangential acceleration, and vice versa. For example, consider riders in their pods on a Ferris wheel at rest. A Ferris wheel with greater angular acceleration will give the riders greater tangential acceleration because, as the Ferris wheel increases its rate of spinning, it also increases its tangential velocity . Note that the radius of the spinning object also matters. For example, for a given angular acceleration , a smaller Ferris wheel leads to a smaller tangential acceleration for the riders. 

Tangential acceleration is sometimes denoted a t . It is a linear acceleration in a direction tangent to the circle at the point of interest in circular or rotational motion. Remember that tangential acceleration is parallel to the tangential velocity (either in the same direction or in the opposite direction.) Centripetal acceleration is always perpendicular to the tangential velocity. 

So far, we have defined three rotational variables: , , and . These are the angular versions of the linear variables x , v , and a . [link] shows how they are related. Rotational and Linear Variables Rotational Linear Relationship x = x r = x r v = v r = v r a = a r = a r 

We can now begin to see how rotational quantities like , , and are related to each other. For example, if a motorcycle wheel that starts at rest has a large angular acceleration for a fairly long time, it ends up spinning rapidly and rotates through many revolutions. Putting this in terms of the variables, if the wheel s angular acceleration is large for a long period of time t , then the final angular velocity and angle of rotation are large. In the case of linear motion, if an object starts at rest and undergoes a large linear acceleration, then it has a large final velocity and will have traveled a large distance. 

The kinematics of rotational motion describes the relationships between the angle of rotation, angular velocity, angular acceleration, and time. It only describes motion it does not include any forces or masses that may affect rotation (these are part of dynamics). Recall the kinematics equation for linear motion: v = v 0 + a t v = v 0 + a t (constant a ) 

As in linear kinematics, we assume a is constant, which means that angular acceleration is also a constant, because a = r a = r . The equation for the kinematics relationship between , , and t is 

= 0 + t ( constant ) , = 0 + t ( constant ) , 

where 0 0 is the initial angular velocity. Notice that the equation is identical to the linear version, except with angular analogs of the linear variables. In fact, all of the linear kinematics equations have rotational analogs, which are given in [link] . These equations can be used to solve rotational or linear kinematics problem in which a and are constant. Equations for Rotational Kinematics Rotational Linear = t = t x = v t x = v t = 0 + t = 0 + t v = v 0 + t v = v 0 + t constant , a = 0 t + 1 2 t 2 = 0 t + 1 2 t 2 x = v 0 t + 1 2 t 2 x = v 0 t + 1 2 t 2 constant , a 2 = 0 2 + 2 2 = 0 2 + 2 v 2 = v 0 2 + 2 x v 2 = v 0 2 + 2 x constant , a 

In these equations, 0 0 and v 0 v 0 are initial values, t 0 t 0 is zero, and the average angular velocity, and average velocity v v are 

= 0 + 2 and v = v 0 + v 2 = 0 + 2 and v = v 0 + v 2 Storm Chasing Tornadoes descend from clouds in funnel-like shapes that spin violently. (credit: Daphne Zaras, U.S. National Oceanic and Atmospheric Administration) 

Storm chasers tend to fall into one of three groups: Amateurs chasing tornadoes as a hobby, atmospheric scientists gathering data for research, weather watchers for news media, or scientists having fun under the guise of work. Storm chasing is a dangerous pastime because tornadoes can change course rapidly with little warning. Since storm chasers follow in the wake of the destruction left by tornadoes, changing flat tires due to debris left on the highway is common. The most active part of the world for tornadoes, called tornado alley, is in the central United States, between the Rocky Mountains and Appalachian Mountains. 

Tornadoes are perfect examples of rotational motion in action in nature. They come out of severe thunderstorms called supercells, which have a column of air rotating around a horizontal axis, usually about four miles across. The difference in wind speeds between the strong cold winds higher up in the atmosphere in the jet stream and weaker winds traveling north from the Gulf of Mexico causes the column of rotating air to shift so that it spins around a vertical axis, creating a tornado. 

Tornadoes produce wind speeds as high as 500 km/h (approximately 300 miles/h), particularly at the bottom where the funnel is narrowest because the rate of rotation increases as the radius decreases. They blow houses away as if they were made of paper and have been known to pierce tree trunks with pieces of straw. 

[link] Torque 

If you have ever spun a bike wheel or pushed a merry-go-round, you know that force is needed to change angular velocity. The farther the force is applied from the pivot point (or fulcrum ), the greater the angular acceleration. For example, a door opens slowly if you push too close to its hinge, but opens easily if you push far from the hinges. Furthermore, we know that the more massive the door is, the more slowly it opens; this is because angular acceleration is inversely proportional to mass. These relationships are very similar to the relationships between force, mass, and acceleration from Newton s second law of motion. Since we have already covered the angular versions of distance, velocity and time, you may wonder what the angular version of force is, and how it relates to linear force. 

The angular version of force is torque , which is the turning effectiveness of a force. See [link] . The equation for the magnitude of torque is = r F sin , = r F sin , 

where r is the magnitude of the lever arm , F is the magnitude of the linear force, and is the angle between the lever arm and the force. The lever arm is the vector from the point of rotation (pivot point or fulcrum) to the location where force is applied. Since the magnitude of the lever arm is a distance, its units are in meters, and torque has units of N m. Torque is a vector quantity and has the same direction as the angular acceleration that it produces. A man pushes a merry-go-round at its edge and perpendicular to the lever arm to achieve maximum torque. 

Applying a stronger torque will produce a greater angular acceleration. For example, the harder the man pushes the merry-go-round in [link] , the faster it accelerates. Furthermore, the more massive the merry-go-round is, the slower it accelerates for the same torque. If the man wants to maximize the effect of his force on the merry-go-round, he should push as far from the center as possible to get the largest lever arm and, therefore, the greatest torque and angular acceleration. Torque is also maximized when the force is applied perpendicular to the lever arm. 

[BL] [OL] [AL] Demonstrate the physical relationships between torque, force, angle of application of force, and length of lever arm by using levers of different lengths. Help students make the connections between the physical observations and mathematical relationships. For instance, torque is maximum when the force is applied exactly perpendicular to the lever arm because sin = 1 sin = 1 for = 90 = 90 degrees. Solving Rotational Kinematics and Torque Problems 

Just as linear forces can balance to produce zero net force and no linear acceleration, the same is true of rotational motion. When two torques of equal magnitude act in opposing directions, there is no net torque and no angular acceleration, as you can see in the following video. If zero net torque acts on a system spinning at a constant angular velocity, the system will continue to spin at the same angular velocity. Introduction to Torque 

This video defines torque in terms of moment arm (which is the same as lever arm). It also covers a problem with forces acting in opposing directions about a pivot point. (At this stage, you can ignore Sal s references to work and mechanical advantage.) 

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Now let s look at Examples applying rotational kinematics to a fishing reel and the concept of torque to a merry-go-round. Calculating the Time for a Fishing Reel to Stop Spinning 

A deep-sea fisherman uses a fishing rod with a reel of radius 4.50 cm. A big fish takes the bait and swims away from the boat, pulling the fishing line from his fishing reel. As the fishing line unwinds from the reel, the reel spins at an angular velocity of 220 rad/s. The fisherman applies a brake to the spinning reel, creating an angular acceleration of 300 rad/s 2 . How long does it take the reel to come to a stop? Strategy 

We are asked to find the time t for the reel to come to a stop. The magnitude of the initial angular velocity is 0 = 220 0 = 220 rad/s, and the magnitude of the final angular velocity = 0 = 0 . The signed magnitude of the angular acceleration is = 3 0 0 = 3 0 0 rad/s 2 , where the minus sign indicates that it acts in the direction opposite to the angular velocity. Looking at the rotational kinematic equations, we see all quantities but t are known in the equation = 0 + t = 0 + t , making it the easiest equation to use for this problem. Solution 

The equation to use is = 0 + t = 0 + t . 

We solve the equation algebraically for t , and then insert the known values: t = 0 = 0 220 rad/s 300 rad/s 2 = 0.733 s t = 0 = 0 220 rad/s 300 rad/s 2 = 0.733 s Discussion 

The time to stop the reel is fairly small because the acceleration is fairly large. Fishing lines sometimes snap because of the forces involved, and fishermen often let the fish swim for a while before applying brakes on the reel. A tired fish will be slower, requiring a smaller acceleration and therefore a smaller force. Calculating the Torque on a Merry-Go-Round 

Consider the man pushing the playground merry-go-round in this figure . He exerts a force of 250 N at the edge of the merry-go-round and perpendicular to the radius, which is 1.50 m. How much torque does he produce? Assume that friction acting on the merry-go-round is negligible. Strategy 

To find the torque, note that the applied force is perpendicular to the radius and that friction is negligible. Solution = r F sin = ( 1.50 m ) ( 250 N ) sin ( 2 ) . = 375 N m = r F sin = ( 1.50 m ) ( 250 N ) sin ( 2 ) . = 375 N m Discussion 

The man maximizes the torque by applying force perpendicular to the lever arm, so that = 2 = 2 and sin = 1 sin = 1 . The man also maximizes his torque by pushing at the outer edge of the merry-go-round, so that he gets the largest-possible lever arm. Practice Problems 

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Use the Check Your Understanding questions to assess whether students master the learning objectives of this section. If students are struggling with a specific objective, these questions will help identify which objective is causing the problem and direct students to the relevant content. Section Summary Kinematics is the description of motion. The kinematics of rotational motion describes the relationships between rotation angle, angular velocity, angular acceleration, and time. Torque is the effectiveness of a force to change the rotational speed of an object. Torque is the rotational analog of force. The lever arm is the distance between the point of rotation (pivot point) and the location where force is applied. Torque is maximized by applying force perpendicular to the lever arm and at a point as far as possible from the pivot point or fulcrum. If torque is zero, angular acceleration is zero. Key Equations Angular acceleration = t = t Rotational kinematic equations = t = t , = 0 + t = 0 + t , = 0 t + 1 2 t 2 = 0 t + 1 2 t 2 , 2 = 0 2 + 2 2 = 0 2 + 2 Tangential (linear) acceleration a = r a = r Torque = r F sin = r F sin Concept Items 

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Design a lever arm capable of lifting a 0.5 kg object such as a stone. The force for lifting should be provided by placing coins on the other end of the lever. How many coins would you need? What happens if you shorten or lengthen the lever arm? What does this say about torque? Test Prep Multiple Choice 

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[link] Glossary angular acceleration the rate of change of angular velocity with time kinematics of rotational motion the relationships between rotation angle, angular velocity, angular acceleration, and time lever arm the distance between the point of rotation (pivot point) and the location where force is applied tangential acceleration the acceleration in a direction tangent to the circular path of motion and in the same direction or opposite direction as the tangential velocity torque the effectiveness of a force to change the rotational speed of an object