Acknowledgments

The Princeton Review would like to thank Katie Chamberlain, Ph.D, Craig Patches, Jim Melloan, and Dallin Law for their hard work on revisions to this edition.

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Part I

Using This Book to Improve Your AP Score

• Preview: Your Knowledge, Your Expectations

• Your Guide to Using This Book

• How to Begin

PREVIEW: YOUR KNOWLEDGE, YOUR EXPECTATIONS

Your route to a high score on the AP Biology Exam depends a lot on how you plan to use this book. Respond to the following questions.

YOUR GUIDE TO USING THIS BOOK

This book is organized to provide as much—or as little—support as you need, so you can use this book in whatever way will be most helpful to improving your score on the AP Biology Exam.

You may choose to prioritize some parts of this book over others, or you may work through the entire book. This will depend on your needs and how much time you have. Let’s now look how to make this determination.

HOW TO BEGIN

Part II

Practice Test 1

• Practice Test 1

• Practice Test 1: Answers and Explanations

Practice Test 1

Click here to download a PDF of Practice Test 1

The Exam

AP^® Biology Exam

SECTION I: Multiple-Choice Questions

DO NOT OPEN THIS BOOKLET UNTIL YOU ARE TOLD TO DO SO.

Instructions

Section I of this examination contains 69 multiple-choice questions. These are broken down into Part A (63 multiple-choice questions) and Part B (6 grid-in questions).

Indicate all of your answers to the multiple-choice questions on the answer sheet. No credit will be given for anything written in this exam booklet, but you may use the booklet for notes or scratch work. After you have decided which of the suggested answers is best, completely fill in the corresponding oval on the answer sheet. Give only one answer to each question. If you change an answer, be sure that the previous mark is erased completely. Here is a sample question and answer.

Sample Question

Chicago is a

(A) state

(B) city

(C) country

(D) continent

Sample Answer

Use your time effectively, working as quickly as you can without losing accuracy. Do not spend too much time on any one question. Go on to other questions and come back to the ones you have not answered if you have time. It is not expected that everyone will know the answers to all the multiple-choice questions.

About Guessing

Many candidates wonder whether or not to guess the answers to questions about which they are not certain. Multiple choice scores are based on the number of questions answered correctly. Points are not deducted for incorrect answers, and no points are awarded for unanswered questions. Because points are not deducted for incorrect answers, you are encouraged to answer all multiple-choice questions. On any questions you do not know the answer to, you should eliminate as many choices as you can, and then select the best answer among the remaining choices.

BIOLOGY

SECTION I

69 Questions

Time—90 minutes

Directions: Each of the questions or incomplete statements below is followed by four suggested answers or completions. Select the one that is best in each case and then fill in the corresponding oval on the answer sheet.

Questions 13–14 refer to the following passage.

The digestive system in humans can be divided into two parts: the alimentary canal and the accessory organs. The canal is where the food actually passes during its transition into waste. The accessory organs are any organs that aid in the digestion by supplying the organs in the alimentary canal with digestive hormones and enzymes.

Questions 22–23 refer to the following passage.

Pumping blood through the human heart must be carefully organized for maximal efficiency and to prevent backflow. In the figure below, the blood enters the heart through the vena cava, passes through the right atrium and right ventricle and then goes through the pulmonary artery towards the lungs. After the lungs, the blood returns through the pulmonary vein and then passes into the left atrium and the left ventricle before leaving the heart via the aorta.

Questions 29–32 refer to the following passage.

An experiment was performed to assess the growth of two species of plants when they were grown in different pHs, given different volumes of water, and watered at different times of day over 6 weeks. Two plants were grown of each species and the average heights are shown in the table.

Questions 38–40 refer to the following passage.

The rainfall and biomass of several trophic levels in an ecosystem were measured over several years. The results are shown in the graph below.

Questions 53–55 refer to the following information and table.

A marine ecosystem was sampled in order to determine its food chain. The results of the study are shown below.

                                               

Type of Organism	Number of Organisms
Shark	2
Small crustaceans	400
Mackerel	20
Phytoplankton	1,000
Herring	100

Questions 56–58 refer to the following information and diagram.

To understand the workings of neurons, an experiment was conducted to study the neural pathway of a reflex arc in frogs. A diagram of a reflex arc is given below.

Questions 59–61 refer to the figure and chart below.

Formation of a Protein

Questions 62 and 63 refer to the following information.

A scientist studies the storage and distribution of oxygen in humans and Weddell seals to examine the physiological adaptations that permit seals to descend to great depths and stay submerged for extended periods. The figure below depicts the oxygen storage in both organisms.

Directions: Part B consists of questions requiring numeric answers. Calculate the correct answer for each question.

Question 68 refers to the diagram below.

STOP

END OF SECTION I

IF YOU FINISH BEFORE TIME IS CALLED, YOU MAY CHECK YOUR WORK ON THIS SECTION. DO NOT GO ON TO SECTION II UNTIL YOU ARE TOLD TO DO SO.

BIOLOGY
 SECTION II

8 Questions

Planning Time—10 minutes

Writing Time—80 minutes

Directions: Questions 1 and 2 are long free-response questions that should require about 22 minutes each to answer and are worth 10 points each. Questions 3 through 8 are short free-response questions that should require about 6 minutes each to answer. Questions 3 through 5 are worth 4 points each, and questions 6 through 8 are worth 3 points each.

Read each question carefully and completely. Write your response in the space provided following each question. Only material written in the space provided will be scored. Answers must be written out in paragraph form. Outlines, bulleted lists, or diagrams alone are not acceptable.

STOP

END OF EXAM

Practice Test 1: Answers and Explanations

PRACTICE TEST 1 ANSWER KEY

PRACTICE TEST 1 EXPLANATIONS

Section I: Multiple Choice

Section II: Free Response

On the following pages you’ll find two types of aids for grading your essays: checklists and sample responses. Checklists like these are used to grade your essays on the actual test. They’re actually quite simple to use.

For each item you mentioned, give yourself the appropriate number of points (1 point, 2 points, and so on). Remember that you can only get a maximum of 10 points for each essay. As you evaluate your work, don’t be kind to yourself just because you like your own essay. If the checklist mentions an explanation of structure and function and you failed to give both, then do not give yourself a point. The testing board is very particular about this. You need to mention precisely the things they’ve listed, in the way they’ve listed them, in order to gain points.

What if something you’ve mentioned doesn’t appear on the list? Provided you know it’s valid, give yourself a point. If it was something you pulled out of your hat at the last minute, odds are it’s not directly applicable to the question. However, because you might come up with details even more specific than those contained in the checklist, it’s not unlikely that the example or structure you’ve cited is perfectly valid. If so, go ahead and give yourself the point. Remember that the testing board hires college professors and high school teachers to read your essays, so they’ll undoubtedly recognize any legitimate information you slip into the essay.

The second part of the answer key involves short paragraphs. These are not templates; the testing board does not expect you to write this way. They are simply additional tools to help illustrate the things you need to squeeze into your essay in order to rack up the points. They explain in some detail how the various parts of the checklist relate to one another and may give you an idea about how best to integrate them into your own essays come test time.

If you find that you didn’t do too well on the essay portion, be sure to carefully read Chapter 14 on the free-response questions. You can use the chapters themselves as checklists. If you find it too difficult to grade your own essays, see if your teacher or a classmate will help you out. Good luck!

Long-Form Free-Response Checklist 1

Sample Long-Form Free Response 1

The sodium potassium pump is responsible for maintaining the resting membrane potential. It actively pumps three Na⁺ ions out of the cell for every two K⁺ ions brought into the cell. Since this is active transport, these ions are pumped against the concentration gradient. The outside of the cell has more sodium, and the inside has more potassium. The inside is more negative, since more positives leave the cell than enter the cell. The potassium can also leak out a bit by potassium leak channels.

When a nerve cell is undisturbed, the membrane is said to be in a resting stage. The membrane is polarized, and the voltage charge is –70 millivolts. During a nerve impulse, there is a change in the membrane permeability, and the voltage charge becomes slightly positive. At a certain voltage, voltage-gated sodium channels are opened. Na⁺ ions rush into the cell, and the inside becomes more positively charged. The membrane is now said to be depolarized. Na⁺ move into the cell down its concentration gradient. Next, the Na⁺ channels close, voltage-gated K⁺ channels open, and K⁺ ions move out of the cell. The cell is now said to be repolarized as it gets more negative. Then, the original ion concentration is reestablished by the sodium-potassium pump.

If there were not any voltage-gated sodium channels, the action potential couldn’t “fire” when threshold is reached, and the cell would not have a rapid depolarization event.

Myelin is like an insulator that covers the outside of some axons. It allows action potentials to move more quickly because the wave of positive charge can jump along the axon.

Long-Form Free-Response Checklist 2

Sample Long-Form Free Response 2

Sickle-cell anemia is a disease in which the red blood cells have an abnormal shape because of a base substitution. Base substitution involves an error in DNA replication in which one nucleotide is replaced by another nucleotide. This causes the codon of an mRNA to contain an incorrect base. The codon, therefore, matches up with the anticodon of a different tRNA. This tRNA carries a different amino acid. The change in the amino acid alters the polypeptide. The polypeptide, in turn, alters the hemoglobin protein. In this case, the distorted red blood cell cannot efficiently carry oxygen.

Biologists must have determined the nature of the hemoglobin mutation by comparing the normal hemoglobin gene to the abnormal hemoglobin gene, using the technique gel electrophoresis. Gel electrophoresis identifies the difference between two molecules by examining the different rates each molecule moves across the gel. Substances move across a gel according to their molecular weight. For example, smaller fragments move faster than larger fragments. The biologists must have placed fragments of the two genes on an agarose gel and used the normal hemoglobin gene as the marker—the source of comparison to the abnormal hemoglobin gene. (A restriction enzyme was used to cut the two DNA sequences into several fragments prior to loading the gel.) The two DNA sequences should have been identical except for the fragment that contained the abnormal gene.

If a normal noncarrier female mates with a male who is homozygous for the disease, these are the results using a Punnett square.

All of the offspring would be heterozygotes. For sickle-cell anemia, these offspring would be carriers.

Short-Form Free-Response Checklist 3

Sample Short-Form Free Response 3

Cells need a certain surface area-to-volume ratio to exchange materials with the environment in order to maintain homeostasis. A high surface area-to-volume ratio allows cells to regulate ion concentrations as well as take in nutrients and eliminate wastes. As a cell becomes larger, the ratio of surface area to volume decreases, and if a cell grows too large, it cannot carry out these functions and therefore will not survive. Organisms have adapted a variety of ways to increase surface area. One example is alveoli, small air sacs in the lungs that maximize surface area in order to allow for maximum respiration. Another example of increasing surface area is villi in the small intestine, whose expansion results in a large surface area for the absorption of nutrients.

Depending on polarity, molecules cross the cell membrane in different ways. Small nonpolar molecules, like carbon dioxide, can freely diffuse through the cell membrane. However, due to the hydrophobic nature of the interior of the cell membrane, small polar molecules need protein channels to allow selective diffusion into or out of the cell. One example of a polar molecule is water, which crosses the membrane through channels called aquaporins.

Short-Form Free-Response Checklist 4

Sample Short-Form Free Response 4

Short-Form Free-Response Checklist 5

(1 point each)

Produces somatic cells versus produces gametes

One round of division versus two rounds of division

Meiosis only: recombination between homologous chromosomes

Sample Short-Form Free Response 5

The difference between meiosis and mitosis arises because of the different goals of these cellular processes. First, mitosis is designed to reproduce copies of somatic cells, while meiosis is designed to create gametes with greater variability. Second, in order to create the appropriate level of genetic information, meiosis requires two rounds of division, whereas recreating somatic cells only requires one round. Third, in order to increase genetic variability, recombination can occur as part of meiosis between homologous chromosomes. Such mixing is not part of mitosis since the goal is to simply recreate the original cell.

Short-Form Free-Response Checklist 6

(1 point each)

Definition of homologous structures

Relevant example (many possible)

Compare to analogous structures

Sample Short-Form Free Response 6

Homologous structures are those with similar structures because they arose from the same ancestral source. An example of homologous structures would be the arm of a human and the front leg of a cat. Their functions are different in their current form, but the ancestral origin is shared. They are different from analogous structures because they occur in species that have have a common ancestor. Analogous structures evolved separately in two lineages and don’t come from a common ancestor.

Short-Form Free-Response Checklist 7

(1 point each)

Transduction

Transformation

(2 points each)

Conjugation

Sample Short-Form Free Response 7

There are three ways in which bacteria transmit genetic information laterally to introduce new phenotypes. These are transduction, transformation, and conjugation. Transduction is the transmission of genetic material from one bacteria to another via a lysogenic virus. Transformation is the uptake of naked DNA from the environment. Conjugation is the cell-to-cell transfer of genetic material in the form of plasmids across a pilus formed between two cells.

Short-Form Free-Response Checklist 8

(1 point each)

No respiration

Not able to create own energy

Not able to reproduce independently

Not able to live outside host cells

Sample Short-Form Free Response 8

Viruses are typically not considered to be alive because they are not able to engage in many of the functions associated with life. Though viruses must engage in processes like translation that require energy, they do not engage in any process to create that energy. Along that same line, there is no respiration of any kind being done by viruses. Further, viruses have no active existence outside of their host cells; no viral functions happen outside of the context of a cell. Due to that restriction, viruses are also not able to reproduce themselves. Being entirely reliant on a host cellular environment for reproduction is another reason to consider them as not alive.

Part III

About the AP Biology Exam

• The Structure of the AP Biology Exam

• How the AP Biology Exam Is Scored

• Overview of Content Topics

• How AP Exams Are Used

• Other Resources

• Designing Your Study Plan

THE STRUCTURE OF THE AP BIOLOGY EXAM

The AP Biology Exam is three hours long and is divided into two sections: Section I (multiple-choice questions and grid-in quantitative question) and Section II (free-response questions).

Section I consists of 69 questions. These are broken down into Part A (63 multiple-choice questions) and Part B (6 grid-in questions). You will have 90 minutes to complete this section.

Section II involves free-response questions. You’ll be presented with two long-form free-response questions and six short-form free-response questions touching upon key issues in biology. You’ll be given a 10-minute reading period followed by 80 minutes to answer all eight questions.

If you’re thinking that this sounds like a heap of work to try to finish in three hours, you’re absolutely right. How can you possibly tackle so much science in so little time? Fortunately, there’s absolutely no need to. As you’ll soon see, we’re going to ask you to leave a small chunk of the test blank. Which part? The parts you don’t like. This selective approach to the test, which we call “pacing,” is probably the most important part of our overall strategy. But before we talk strategy, let’s look at the topics that are covered by the AP Biology Exam.

HOW THE AP BIOLOGY EXAM IS SCORED

AP scores are calculated from your scores on the multiple-choice and free-response sections. The final score is reported on a scale from 1 to 5. The following table explains what that final score means:

*The data above is from the College Board website and based on the May 2016 test administration.

Remember that colleges’ rules may vary when it comes to granting credit for AP courses. You should contact the individual admissions departments to find out what score you need on the exam to ensure you’ll be given credit.

For the AP Biology Exam, your scores on the multiple-choice section and free-response section are each worth 50 percent of your final score. On the multiple-choice section, your total score is based on the number of questions answered correctly, and you do not lose any points for incorrect answers. Unanswered questions do not receive points. The free-response section is graded on separate point system: long-form responses (Questions 1 and 2) are graded on a 10-point scale, while half of your short-form responses are graded on a 3-point scale and half are scored on a 4-point scale. Your scores are tallied to determine your total free-response score. The free-response score is then combined with your multiple-choice score and weighted to figure out where your score falls within the standard AP scoring scale (1 to 5).

OVERVIEW OF CONTENT TOPICS

The AP Biology Exam covers these four Big Ideas.

To fully understand the four big ideas, a solid grasp of the following topics is required. These topics include the following:

This might seem like an awful lot of information, but for each topic, there are just a few key facts you’ll need to know. Your biology textbooks may go into far greater detail about some of these topics than we do. That’s because they’re trying to teach you “correct science,” whereas we’re aiming to improve your scores. Our science is perfectly sound; it’s just cut down to size. We’ve focused on crucial details and given you only what’s important. Moreover, as you’ll soon see, our treatment of these topics is far easier to handle.

The AP Biology exam not only tests your content knowledge, but it also tests how you apply that knowledge during scientific inquiry. Simply put, the test’s authors are testing if you can design and/or think critically about experiments and the hypotheses, evidence, math, data, conclusions, and theories therein. There are seven broad science practices that are tested.

HOW AP EXAMS ARE USED

Different colleges use AP Exams in different ways, so it is important that you go to a particular college’s website to determine how it uses AP Exams. The three items below represent the main ways in which AP Exam scores can be used:

OTHER RESOURCES

There are many resources available to help you improve your score on the AP Biology Exam, not the least of which are your teachers. If you are taking an AP class, you may be able to get extra attention from your teacher, such as obtaining feedback on your essays. If you are not in an AP course, reach out to a teacher who teaches AP Biology and ask if the teacher will review your essays or otherwise help you with content.

Another wonderful resource is AP Central, the official site of the AP Exams. The scope of the information at this site is quite broad and includes:

The AP Students home page address is: http://apstudent.collegeboard.org/​home

For up-to-date information about the ongoing changes to the AP Biology Exam Course, please visit: https://apstudent.collegeboard.org/​apcourse/​ap-biology.

Finally, The Princeton Review offers tutoring and small group instruction. Our expert instructors can help you refine your strategic approach and add to your content knowledge. For more information, call 1-800-2REVIEW.

DESIGNING YOUR STUDY PLAN

As part of the Introduction, you identified some areas of potential improvement. Let’s now delve further into your performance on Practice Test 1 with the goal of developing a study plan appropriate to your needs and time commitment.

Read the answers and explanations associated with the multiple-choice questions (starting at this page). After you have done so, respond to the following questions:

Use those answers to create a study plan. Start with the topics that need the most work and map out when you will study and what you will study.

Remember, your schedule may evolve along the way. If a certain time/location is not working for you, then try mixing it up. If you are struggling with a topic, perhaps try tackling it with a teacher, tutor, or a classmate.

Part IV

Test-Taking Strategies for the AP Biology Exam

PREVIEW

Review your responses to the three questions on this page and then respond to the following questions:

HOW TO USE THE CHAPTERS IN THIS PART

For the following Strategy chapters, think about what you are doing now before you read the chapters. As you read and engage in the directed practice, be sure to appreciate the ways you can change your approach. At the end of Part IV, you will have the opportunity to reflect on how you will change your approach.

Chapter 1

How to Approach Multiple-Choice Questions

SECTION I

As we mentioned earlier, the multiple-choice section consists of the following two parts:

Part A

Part A of Section I consists of 63 run-of-the-mill multiple-choice questions. These questions test your grasp of the fundamentals of biology and your ability to apply biological concepts to help solve problems. Here’s an example:

Don’t worry about the answer to this question for now. By the end of this book, it will be a piece of cake. The majority of the questions in this section are presented in this format. A few questions may include a figure, a diagram, or a chart.

The second part of the first portion also consists of multiple-choice questions, but here you’re asked to think logically about different biological experiments or data. Here’s a typical example:

You’ll notice that these particular questions refer to an experiment. Many of the questions in this portion test your ability to integrate information, interpret data, and draw conclusions from the results.

Part B

Part B of Section I consists of six grid-in questions which require using information presented in the question to calculate an answer. That numeric response is then filled in on a grid and bubbled accordingly. Answers can be in the form of integers, decimals, or fractions. A four-function calculator can be used on these questions. Here’s a typical example:

We mentioned earlier that our approach is strategy-based. As you’re about to see, many of these strategies are based on common sense—for example, using mnemonics like “ROY G. BIV.” (Remember that one? It’s the mnemonic for red, orange, yellow, green, blue, indigo, violet—the colors of the spectrum of visible light.) Others do not make as much sense. In fact, we’re going to ask you to throw out much of what you’ve been taught when it comes to taking standardized tests.

PACE YOURSELF

When you take a test in school, how many questions do you answer? Naturally, you try to answer all of them. You do this for two reasons: (1) Your teacher told you to, and (2) if you left a question blank, your teacher would mark it wrong. However, that’s not the case when it comes to the AP Biology Exam. In fact, finishing the test is the worst thing you can do. Before we explain why, let’s talk about timing.

One of the main reasons that taking the AP Biology Exam can be so stressful is the time constraint we discussed above—75 seconds per multiple-choice question, 20 minutes per long essay, and 6 minutes per short essay. If you had all day, you would probably ace the test. We can’t give you all day, but we can do the next best thing: we can give you more time for each question. How? By having you slow down and answer fewer questions.

Slowing down and doing well on the questions you do answer is the best way to improve your score on the AP Biology Exam. Rushing through questions in order to finish, on the other hand, will always hurt your score. When you rush, you’re far more likely to make careless errors, misread, and fall into traps. Keep in mind that blank answers are not counted against you.

THE THREE-PASS SYSTEM

The AP Biology Exam covers a broad range of topics. There’s no way, even with our extensive review, that you will know everything about every topic in biology. So what should you do?

Do the Easiest Questions First

The best way to rack up points is to focus on the questions you find the easiest. If you know the answer, nail it and move on. Other questions, however, will be a little more complicated. As you read each question, decide if you think it’s easy, medium, or hard. During a first pass, do all the easy questions. If you come across a problem that seems time-consuming or completely incomprehensible, skip it. Remember:

Save the medium questions for the second pass. These questions are either time-consuming or require that you analyze all the answer choices (i.e., the correct answer doesn’t pop off the page). If you come across a question that makes no sense from the outset, save it for the last pass. You’re far less likely to fall into a trap or settle on a silly answer.

Watch Out for Those Bubbles!

Since you’re skipping problems, you need to keep careful track of the bubbles on your answer sheet. One way to accomplish this is by answering all the questions on a page and then transferring your choices to the answer sheet. If you prefer to enter them one by one, make sure you double-check the number beside the ovals before filling them in. We’d hate to see you lose points because you forgot to skip a bubble!

So then, what about the questions you don’t skip?

PROCESS OF ELIMINATION (POE)

On most tests, you need to know your material backward and forward to get the right answer. In other words, if you don’t know the answer beforehand, you probably won’t answer the question correctly. This is particularly true of fill-in-the-blank and essay questions. We’re taught to think that the only way to get a question right is by knowing the answer. However, that’s not the case on Section I of the AP Biology Exam. You can get a perfect score on this portion of the test without knowing a single right answer, provided you know all the wrong answers!

What are we talking about? This is perhaps the single most important technique in terms of the multiple-choice section of the exam. Let’s take a look at the example below.

Now if this were a fill-in-the-blank-style question, you might be in a heap of trouble. But let’s take a look at what we’ve got. You see “woody stem” in the question, which leads you to conclude that we’re talking about plants. Right away, you know the answer is not (A) or (C) because plants don’t have lungs or ganglia. Now we’ve narrowed it down to (B) and (D). Notice that (B) and (D) look very similar. Obviously, one of them is a trap. At this point, if you don’t know what “lentil beans” are, you have to guess. However, even if we don’t know precisely what they are, it’s safe to say that most of us know that lentil beans have nothing to do with plant respiration. Therefore, the correct answer is (B), lenticels.

Although our example is a little goofy and doesn’t look exactly like the questions you’ll be seeing on the test, it illustrates an important point:

Even if you don’t know the answer right off the bat, you’ll surely know that two or three of the answer choices are not correct. What then?

Aggressive Guessing

The testing board, the service that develops and administers the exam, tells you that random guessing will not affect your score. This is true. There is no guessing penalty on the AP Biology Exam. For each correct answer you’ll receive one point and you will not lose any points for each incorrect answer.

Although you won’t lose any points for wrong answers, you should guess aggressively by getting rid of the incorrect answer choices. The moment you’ve eliminated a couple of answer choices, your odds of getting the question right, even if you guess, are far greater. If you can eliminate as many as two answer choices, your odds improve enough that it’s in your best interest to guess.

WORD ASSOCIATIONS

Another way to rack up the points on the AP Biology Exam is by using word associations in tandem with your POE skills. Make sure that you memorize the words in the Key Terms lists throughout this book. Know them backward and forward. As you learn them, make sure you group them by association, since the testing board is bound to ask about them on the AP Biology Exam. What do we mean by “word associations?” Let’s take the example of mitosis and meiosis.

You’ll soon see from our review that there are several terms associated with mitosis and meiosis. Synapsis, crossing-over, and tetrads, for example, are words associated with meiosis but not mitosis. We’ll explain what these words mean later in this book. For now, just take a look.

This might seem like a difficult problem. But let’s think about the associations we just discussed. The question asks us about mitosis. However, (A), (B), and (C) all mention events that we’ve associated with meiosis. Therefore, they are out. Without even racking your brain, you’ve managed to find the correct answer: (D). Not bad!

Once again, don’t worry about the science for now. We’ll review it later. What is important to recognize is that by combining the associations we’ll offer throughout this book and your aggressive POE techniques, you’ll be able to rack up points on problems that might have seemed difficult at first.

MNEMONICS—OR THE BIOLOGY NAME GAME

One of the big keys to simplifying biology is the organization of terms into a handful of easily remembered packages. The best way to accomplish this is by using mnemonics. Biology is all about names: the names of chemical structures, processes, theories, and so on. How are you going to keep them all straight? A mnemonic, as you may already know, is a convenient device for remembering something.

For example, one important issue in biology is taxonomy, that is, the classification of life-forms, or organisms. Organisms are classified in a descending system of similarity, leading from domains (the broadest level) to species (the most specific level). The complete order runs: domain, kingdom, phylum, class, order, family, genus, and species. Don’t freak out yet. Look how easy it becomes with a mnemonic:

King Philip of Germany decided to walk to America. What do you think happened?

Learn the mnemonic and you’ll never forget the science!

Mnemonics can be as goofy as you like, as long as they help you remember. Throughout this book, we’ll give you mnemonics for many of the complicated terms we’ll be seeing. Use ours, if you like them, or feel free to invent your own. Be creative! Remember: the important thing is that you remember the information, not how you remember it.

IDENTIFYING EXCEPT QUESTIONS

About 10 percent of the multiple-choice questions in Section I are EXCEPT/NOT/LEAST questions. With this type of question, you must remember that you’re looking for the wrong (or the least correct) answer. The best way to go about these is by using POE.

More often than not, the correct answer is a true statement, but is wrong in the context of the question. However, the other three tend to be pretty straightforward. Cross off the three that apply, and you’re left with the one that does not. Here’s a sample question.

If you don’t remember anything about gametes and gametogenesis, or the production of gametes, this might be a particularly difficult problem. We’ll see these again later on, but for now, remember that gametes are the sex cells of sexually reproducing organisms. As such, we know that they are haploid and are produced in the sexual organs. We also know that they come together to create offspring.

From this very basic review, we know immediately that (A) and (B) are not our answers. Both of these are accurate statements, so we eliminate them. That leaves us with (C) and (D). If you have no idea what (D) means, focus on (C). In sexual reproduction, each parent contributes one gamete, or half the genetic complement of the offspring. This definitely helps vary the genetic makeup of the offspring. Choice (C) is a true statement, so it can be eliminated. The correct answer is (D).

Don’t sweat it if you don’t recall the biology. We’ll be reviewing it in detail soon enough. For now, remember that the best way to answer these types of questions is to spot all the right statements and cross them off. You’ll wind up with the wrong statement, which happens to be the correct answer.

SOLVING GRID-IN QUESTIONS

Part B of the multiple-choice section requires you to answer six grid-in questions. Unlike the questions in Part A, you will not be able to use Process of Elimination. However, there are strategies you can use to increase your chances of efficiently getting these questions correct. First, identify what the question is actually asking for. Are you being asked to find a value on a graph or chart? Perhaps they are having you calculate the frequency of an allele using Hardy-Weinberg equilibrium. If you have no idea how to find out what they are asking you, take a quick educated guess and move on. For instance, if they are asking for a frequency, try guessing a decimal between 0 and 1, such as 0.25. However, if you do know how to find the answer, then write down the question number and any work (notes, calculations, etc.) that you would need to answer the question neatly. Before filling in your answer, make sure that you haven’t made any mistakes on interpreting data or making calculations. Be sure not to forget to bubble in your answers.

Although these grid-in questions require calculations, fear not! The College Board provides you with a handy formula sheet, which you can find at the end of this book. You can expect to be given this sheet as part of the exam, so you do not need to memorize these equations. However, it will be important for you to practice using them and familiarizing yourself with the formula sheet prior to the exam. Keep this page handy as you review and practice problems so that you will be accustomed to using it on the day of the exam.

Chapter 2

How to Approach Free-Response Questions

THE ART OF THE FREE-RESPONSE ESSAY

On Section II of the exam, you are given two long-form free-response questions and six short-form free-response questions to answer in 80 minutes. You will also have a 10-minute reading period, which means you have a total of 90 minutes to complete Section II. The best way to rack up points on this section is to give the readers what they’re looking for. Fortunately, we know precisely what that is.

The readers, or graders, have a checklist of key terms and concepts that they use to assign points. We like to call these “hot button” terms. Simply put, for each hot button term that you include in a response, you will receive a predetermined number of points. For example, if the question deals with the function of enzymes, the graders are instructed to give two points for a mention of the “lock-and-key theory of enzyme specificity.”

Naturally, you can’t just compose a “laundry list” of scientific terms. Otherwise, it wouldn’t be an essay. What you can do, however, is organize your free-response essays around a handful of these key points. The most effective and efficient way to do this is by using the 10-minute reading period to brainstorm and come up with the scientific terms. Then outline your response before you begin to write, using your hot buttons as your guide.

READ THE QUESTIONS CAREFULLY

The testing board gives you 10 minutes to read the questions and organize your thoughts before you begin writing. The first thing you should do is take less than a minute to skim all of the questions and put them into your own personal order of difficulty from easiest to toughest. Once you’ve decided the order in which you will answer the questions (easiest first, hardest last), you can begin to formulate your responses. Your first step should be a more detailed assessment of each question.

The most important advice we can give you is to read each question at least twice. As you read the question, focus on key words, especially “direction words.” Almost every essay question begins with a direction word. These words are often in bold, so they are easy to spot. Some examples of direction words are discuss, define, explain, describe, compare, and contrast. If a question asks you to discuss a particular topic, you should give a viewpoint and support it with examples. If a question asks you to compare two things, you should discuss how the two things are similar. On the other hand, if the question asks you to contrast two things, you need to show how these things are different.

Many students lose points on their essays because they either misread the question or fail to do what’s asked of them.

BRAINSTORM

Your next objective during the 10-minute reading period should be to organize your thoughts.

Once you’ve read the questions, you need to brainstorm. Jot down as many key terms and concepts as you can. Don’t forget, the test readers assign points on the basis of these key concepts. For each one that you mention and/or explain, you get a point.

How many do you need? You won’t need all of them, that’s for sure. However, you will need enough to get you the maximum number of points for that question. Most of these can be pulled directly from your reading in this book. At the end of each chapter is a Key Terms list which is full of terms that you should incorporate into your free responses. In addition to this list, you can feel free to create your own thorough lists of terms for your own use.

Don’t spend more than about 2 minutes per question brainstorming. Once your 10-minute reading period is up, you should be ready to start writing your essays.

OUTLINE YOUR RESPONSE

Have you ever written yourself into a corner? You’re halfway through your essay when you suddenly realize that you have no idea whatsoever where you’re going with your train of thought. To avoid this (and the panic that accompanies it), take a few minutes to draft an outline.

Your outline should incorporate as many of the hot buttons as you need in order to maximize your score. In other words, if a question asks for two examples, choose only those two with which you are most comfortable. In your outline, make notes about the crucial points to mention with regard to each topic or key word. Once your outline is complete, you’re ready to move on to writing the actual essay.

All of this preparation may seem time-consuming. However, it should take no more than two minutes per long question and one minute per short question. What’s more, it will greatly simplify the whole essay-writing process. So while you lose a little time at the outset, you’ll more than make up for it when it comes time to actually write your answer.

DEVELOP YOUR IDEAS IN EACH RESPONSE

Now you can use your outline to write your essay. Most students can come up with key terms or phrases that concern a particular biology topic. What separates a high-scoring student from a low-scoring student is how the student develops his or her thoughts in each essay. Besides giving the hot buttons, you’ll need to elaborate on your thoughts and ideas. For example, don’t just throw out a list of terms that pertain to meiosis and mitosis (such as synapsis, crossing-over, and gametes). Go one step further. Make sure you mention the significance of meiosis (it produces genetic variability). This extra piece of information will earn you an extra point.

Generally, you’ll need to write about two to four paragraphs, depending on the number of parts contained in each essay question. In addition, be sure to give the appropriate number of examples for each essay. If the question asks for three examples, give only three examples. If you present more than is required, the test readers won’t even read them or count them toward your score. The bottom line is this: stick to the question.

ANSWER EACH PART OF THE QUESTION SEPARATELY

The more parts there are to a free-response question, the more important it is to pace yourself. For each question, you’re better off writing a little bit for each part than you are spending all your time on any one part of a question. Why? Even if you were to write the perfect answer to one part of a question, there’s a limit to the number of points the test readers can assign to that part.

As you address each part of the question, make sure you break your response into paragraphs to make the test reader’s job easier. When test readers have an easy time reading your essay, they’re more likely to award points: your writing comes across as clearer and more organized. Readers have also requested that students label each part of their essay answers, so write “Part (a),” “Part (b),” and so on, accordingly in your response.

Finally, don’t spend too much time writing a fancy introduction. You won’t get brownie points for beautifully written openings like, “It was the best of experiments, it was the worst of experiments.” Just leap right into the essay. And don’t worry too much about grammar or spelling errors. Your grammar can hurt only if it’s so bad that it seriously impairs your ability to communicate.

INCORPORATE ELEMENTS OF AN EXPERIMENTAL DESIGN

Since one of the free-response questions will be experimentally based, you’ll need to know how to design an experiment. Most of these questions require that you present an appropriately labeled diagram or graph. Otherwise, you’ll only get partial credit for your work.

There are two things you must remember when designing experiments on the AP Biology Exam: (1) always label your figures, and (2) include controls in all experiments. Let’s take a closer look at these two points.

Know How to Label Diagrams and Figures

Let’s briefly discuss the important elements in setting up a graph. The favorite type of graph on the AP Biology Exam is the coordinate graph. The coordinate graph has a horizontal axis (x-axis) and a vertical axis (y-axis).

The x-axis usually contains the independent variable—the thing that’s being manipulated or changed. The y-axis contains the dependent variable—the thing that’s affected when the independent variable is changed.

Now let’s look at what happens when you put some points on the graph. Every point on the graph represents both an independent variable and a dependent variable.

Once you draw both axes and label the axes as x and y, you can plot the points on the graph. Let’s look at the following question.

For now, let’s discuss only (b), which asks us to design an experiment. Let’s set up a graph that shows the results of an experiment examining the relationship between pH and enzyme activity. Notice that we’ve chosen only one factor here, pH. We could have chosen any of the three. Why did we choose pH and not temperature or substrate concentration? Well, perhaps it’s the one we know the most about.

What is the independent variable? It is pH. In other words, pH is being manipulated in the experiment. We’ll therefore label the x-axis with pH values from 0 through 14.

What is the dependent variable? It’s the enzyme activity—the thing that’s affected by pH. Let’s label the y-axis “Rate of Reaction.” Now we’re ready to plot the values on the graph. Based on our knowledge of enzymes, we know that for most enzymes the functional range of pH is narrow, with optimal performance occurring at or around a pH of 7.

Now you should interpret your graph. If the pH level decreases from a neutral pH of 7, the reaction rate of the enzyme will decrease. If the pH level increases, the rate of reaction will also decrease. Don’t forget to include a simple explanation of your graph.

Additional quantitative and graphing skills will be discussed at length in a later chapter of this text. There you will learn how to include statistics and hypothesis testing in your free-response questions and how best to present data using graphs.

INCLUDE CONTROLS IN YOUR EXPERIMENTS

Almost every experiment will have at least one group that represents the normal/unchanged/neutral version of the independent variable. This is called the control. A control is simply a standard of comparison. What does a control do? It enables the biologist to verify that the outcome of the study is due to changes in the independent variable and nothing else.

Let’s say the principal of your school thinks that students who eat breakfast do better on the AP Biology Exam than those who don’t eat breakfast. He gives a group of 10 students from your class free breakfast every day for a year. When the school year is over, he administers the AP Biology Exam and they all score brilliantly! Did they do well because they ate breakfast every day? We don’t know for sure. Maybe those kids were the smartest kids in the class and would have scored well anyway.

In this case, the best way to be sure that eating breakfast made a difference is to have a control group. In other words, he would need to also follow for a year a group of students of equal intelligence to the first group, BUT who are known to never eat breakfast. At the end of that year, he could have them take the AP Biology Exam. If they do just as well as the group of similar intelligence that ate breakfast, then we can probably conclude that eating breakfast wasn’t necessarily leading to higher AP scores. The group of students that didn’t eat breakfast is called the control group because those students were not “exposed” to the variable of interest—in this case, breakfast. Control groups are generally any group that you include just for the sake of comparison.

Chapter 3

Using Time Effectively to Maximize Points

BECOMING A BETTER TEST TAKER

Very few students stop to think about how to improve their test-taking skills. Most assume that if they study hard, they will test well and that if they do not study, they will do poorly. Most students continue to believe this even after experience teaches them otherwise. Have you ever studied really hard for an exam and then blown it on test day? Have you ever aced an exam for which you thought you weren’t well prepared? Most students have had one, if not both, of these experiences. The lesson should be clear: factors other than your level of preparation influence your final test score. This chapter will provide you with some insights that will help you perform better on the AP Biology Exam and on other exams as well.

PACING AND TIMING

A big part of scoring well on an exam is working at a consistent pace. The worst mistake made by inexperienced or less savvy test takers is that they come to a question that stumps them and rather than just skip it, they panic and stall. Time seems to stand still when you’re working on a question you cannot answer, and it is not unusual for students to waste five minutes on a single question (especially a question involving a graph or the word EXCEPT) because they are too stubborn to cut their losses. It is important to be aware of how much time you have spent on a given question and section. There are several ways to improve your pacing and timing for the test:

Remember, when all the questions on a test are of equal value, no one question is that important, and your overall goal for pacing is to get the most questions correct. Finally, you should set a realistic goal for your final score. In the next section, we will break down how to achieve your desired score and how to pace yourself to do so.

GETTING THE SCORE YOU WANT

Depending on the score you need, it may be in your best interest not to try to work through every question. Check with the schools to which you are applying to find out what scores they will accept for credit.

AP Exams in all subjects no longer include a “guessing penalty” of a quarter of a point for every incorrect answer. Instead, students are assessed only on the total number of correct answers. A lot of AP materials, even those you receive in your AP class, may not include this information. It’s really important to remember that if you are running out of time, you should fill in all the bubbles before the time for the multiple-choice section is up. Even if you don’t plan to spend a lot of time on every question or even if you have no idea what the correct answer is, you need to fill something in.

TEST ANXIETY

Everybody experiences anxiety before and during an exam. To a certain extent, test anxiety can be helpful. Some people find that they perform more quickly and efficiently under stress. If you’ve ever pulled an all-nighter to write a paper and ended up doing good work, you know the feeling.

However, too much stress is definitely a bad thing. Hyperventilating during the test, for example, almost always leads to a lower score. If you find that you stress out during exams, here are a few preemptive actions you can take:

The best way to avoid stress is to study both the test material and the test itself. Congratulations! By reading this book, you are taking a major step toward a stress-free AP Biology Exam.

REFLECT

Respond to the following questions:

Part V

Content Review for the AP Biology Exam

Chapter 4

Chemistry of Life

ELEMENTS

Although organisms exist in many diverse forms, they all have one thing in common: they are all made up of matter. Matter is made up of elements. Elements, by definition, are substances that cannot be broken down into simpler substances by chemical means.

THE ESSENTIAL ELEMENTS OF LIFE

Although there are 92 natural elements, 96% of the mass of all organisms is made up of just four of them: oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). Other elements such as calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), Chlorine (Cl), and magnesium (Mg) are also present, but in smaller quantities. These elements make up most of the remaining four percent of an organism’s weight. Some elements are known as trace elements because they are only required by an organism in very small quantities. Trace elements include iron (Fe), iodine (I), and copper (Cu).

SUBATOMIC PARTICLES

If you break down an element into smaller pieces, you’ll eventually come to the atom—the smallest unit of an element that retains its characteristic properties. Atoms are the building blocks of the physical world.

Within atoms, there are even smaller subatomic particles called protons, neutrons, and electrons. Let’s take a look at a typical atom.

Protons and neutrons are particles that are packed together in the core of an atom called the nucleus. You’ll notice that protons are positively charged (+) particles, whereas neutrons are uncharged particles.

Electrons, on the other hand, are negatively charged (–) particles that spin around the nucleus. Electrons are pretty small compared to protons and neutrons. In fact, for our purposes, electrons are considered massless. Most atoms have the same number of protons and electrons, making them electrically neutral. Some atoms have the same number of protons but differ in the number of neutrons in the nucleus. These atoms are called isotopes.

COMPOUNDS

When two or more different types of atoms are combined in a fixed ratio, they form a chemical compound. You’ll sometimes find that a compound has different properties from those of its elements. For instance, hydrogen and oxygen exist in nature as gases. Yet when they combine to make water, they often pass into a liquid state. When hydrogen atoms get together with oxygen atoms to form water, we’ve got a chemical reaction.

The atoms of a compound are held together by chemical bonds, which may be ionic bonds, covalent bonds, or hydrogen bonds.

An ionic bond is formed between two atoms when one or more electrons are transferred from one atom to the other. In this reaction, one atom loses electrons and becomes positively charged, and the other atom gains electrons and becomes negatively charged. The charged forms of the atoms are called ions. An ionic bond results from the attraction between two oppositely charged ions. For example, when Na reacts with Cl, the charged ions Na⁺ and Cl^– are formed.

A covalent bond is formed when electrons are shared between atoms. If the electrons are shared equally between the atoms, the bond is called nonpolar covalent. If the electrons are shared unequally, the bond is called polar covalent. When one pair of electrons is shared between two atoms, the result is a single covalent bond. When two pairs of electrons are shared, the result is a double covalent bond. When three pairs of electrons are shared, the result is a triple covalent bond.

WATER: THE VERSATILE MOLECULE

One of the most important substances in nature is water. Water is considered a unique molecule because it plays an important role in chemical reactions.

Let’s take a look at one of the properties of water. Water has two hydrogen atoms joined to an oxygen atom.

In water molecules, the hydrogen atoms have a partial positive charge and the oxygen atom has a partial negative charge. Molecules that have partially positive and partially negative charges are said to be polar. Water is therefore a polar molecule. The positively-charged ends of the water molecules strongly attract the negatively-charged ends of other polar compounds (including water). Likewise, the negatively-charged ends strongly attract the positively-charged ends of polar compounds. These forces are most readily apparent in the tendency of water molecules to stick together, as in the formation of water beads or raindrops.

These types of intermolecular attractions are called hydrogen bonds. Hydrogen bonds are weak chemical bonds that form when a hydrogen atom that is covalently bonded to one electronegative atom is also attracted to another electronegative atom. Water molecules are held together by hydrogen bonds.

Although hydrogen bonds are individually weak, they are strong when present in large numbers. Because water reacts well with other polar substances, it makes a great solvent; it can dissolve many kinds of substances. The hydrogen bonds that hold water molecules together contribute to a number of special properties, including cohesion, adhesion, heat capacity, and expansion on freezing.

Cohesion and Adhesion

As mentioned above, water molecules have a strong tendency to stick together. That is, water exhibits cohesive forces. These forces are extremely important to life. For instance, during transpiration water molecules evaporate from a leaf, “pulling” on neighboring water molecules. These, in turn, draw up the molecules immediately behind them, and so on, all the way down the plant vessels. The resulting chain of water molecules enables water to move up the stem. Water also has a high surface tension because of the cohesiveness of its molecules.

The strong cohesion of water molecules leads to high surface tension, which is the tension on the surface of water from water molecules huddling together tightly to minimize contact with the air.

Water molecules also like to stick to other substances—that is, they’re adhesive. Have you ever tried to separate two glass slides stuck together by a film of water? They’re difficult to separate because of the water sticking to the glass surfaces.

These two forces taken together—cohesion and adhesion—account for the ability of water to rise up the roots, trunks, and branches of trees. Since this phenomenon occurs in thin vessels, it’s called capillary action.

Heat Capacity

Another remarkable property of water is its high heat capacity. What’s heat capacity? Your textbook will give you a definition something like this: “heat capacity is the quantity of heat required to change the temperature of a substance by 1 degree.” What does that mean? In plain English, heat capacity refers to the ability of a substance to resist temperature changes. For example, when you heat up an iron kettle, it gets hot pretty quickly. Why? Because it has a low specific heat. It doesn’t take much heat to increase the temperature of the kettle. Water, on the other hand, has a high heat capacity. You have to add a lot of heat to get an increase in temperature. Water’s ability to resist temperature changes is one of the things that helps keep the temperature in our oceans fairly stable. It’s also why organisms that are mainly made up of water, like us, are able to keep a constant body temperature.

Expansion on Freezing

Perhaps one of the most important properties of water is yet another result of hydrogen bonding. When four water molecules are bound in a solid lattice of ice, the hydrogen bonds actually cause solid water to expand on freezing. In most materials, when the molecules lose kinetic energy and cool from liquid to solid, the molecules get more dense, moving closer together. However, in liquid water, the molecules are slightly more dense than in solid water. Because water expands on freezing, becoming slightly less dense than liquid water, ice can crack lead pipes in the winter, or a soda can will pop if it is left in your cold car. The important consequence of this property of water is that ice floats on the top of lakes or streams, allowing animal life to live underneath the ice. If ice was denser than water, it would sink to the bottom, freezing the body of water solid. All aquatic life would be unable to survive.

So let’s review the unique properties of water:

THE ACID TEST

We just said that water is important because most reactions occur in watery solutions. Well, there’s one more thing to remember: reactions are also influenced by whether the solution in which they occur is acidic, basic, or neutral.

What makes a solution acidic or basic? A solution is acidic if it contains a lot of hydrogen ions (H⁺). That is, if you dissolve an acid in water, it will release a lot of hydrogen ions. When you think about acids, you usually think of substances with a sour taste, like lemons. For example, if you squeeze a little lemon juice into a glass of water, the solution will become acidic. That’s because lemons contain citric acid.

Bases, on the other hand, do not release hydrogen ions when added to water. They release a lot of hydroxide ions (OH^–). These solutions are said to be alkaline (the fancy name for a basic solution). Bases usually have a slippery consistency. Common soap, for example, is composed largely of bases.

The acidity or alkalinity of a solution can be measured using a pH scale. The pH scale is numbered from 1 to 14. The midpoint, 7, is considered neutral pH. The concentration of hydrogen ions in a solution will indicate whether it is acidic, basic, or neutral. If a solution contains a lot of hydrogen ions, then it will be acidic and have a low pH. Here’s the trend:

Therefore, as the concentration of H⁺ ions increases by a factor of 10, the pH becomes one number smaller. For example, stomach acid has a pH of 2, and if we use the equation, we discover that the concentration of H⁺ ions in stomach acid is 10^–2 M. This is pretty high when you consider the other extreme is lye, which has a pH of 14, a concentration of H⁺ ions around 10^–14 M! Use your calculator to double check that these numbers are correct.

You’ll notice from the scale below that stronger acids have lower pHs. If a solution has a low concentration of hydrogen ions, it will have a high pH.

One more thing to remember: The pH scale is not a linear scale—it’s logarithmic. That is, a change of one pH number actually represents a tenfold change in hydrogen ion concentration. For example, a pH of 3 is actually ten times more acidic than a pH of 4. This is also true in the reverse direction: A pH of 4 represents a tenfold decrease in acidity compared to a pH of 3.

The equation for pH is listed on the AP Biology Equations and Formulas sheet. However, you will not be expected to perform calculations using this equation. Instead, you should understand how the equation works and when pH calculations are useful.

ORGANIC MOLECULES

Now that we’ve discussed chemical compounds in general, let’s talk about a special group of compounds. Most of the chemical compounds in living organisms contain a skeleton of carbon atoms. These molecules are known as organic compounds. By contrast, molecules that do not contain carbon atoms are called inorganic compounds. For example, salt (NaCl) is an inorganic compound.

Carbon is important for life because it is a versatile atom, meaning that it not only has the ability to bind with other carbons but also with a number of other elements including nitrogen, oxygen, and hydrogen. The resulting molecules are key in carrying out the activities necessary for life.

To recap:

Now let’s focus on the following four classes of organic compounds central to life on Earth:

Most macromolecules are chains of building blocks, called polymers. The individual building blocks of a polymer are called monomers.

Carbohydrates

Organic compounds that contain carbon, hydrogen, and oxygen are called carbohydrates. They usually contain these three elements in a ratio of appoximately 1:2:1, respectively. We can represent the proportion of elements within carbohydrate molecules by the formula C_nH_2nO_n^, which can be simplified as (CH₂O)_n.

Most carbohydrates are categorized as either monosaccharides, disaccharides, or polysaccharides. The term saccharides is a fancy word for “sugar.” The prefixes mono-, di-, and poly- refer to the number of sugars in the molecule. Mono- means “one,” di- means “two,” and poly- means “many.” A monosaccharide is therefore a carbohydrate made up of a single sugar molecule.

Monosaccharides: The Simplest Sugars

Monosaccharides, the simplest sugars, serve as an energy source for cells. The two most common sugars are (1) glucose and (2) fructose.

Both of these monosaccharides are six-carbon sugars with the chemical formula C₆H₁₂O₆. Glucose, the most abundant monosaccharide, is the most popular sugar around. Glucose is an important part of the food we eat and it is the favorite food made by plants during photosynthesis. This glucose can be broken down to give us (and plants) energy. Fructose, the other monosaccharide you need to know for the test, is a common sugar in fruits.

Glucose and fructose can be depicted as either “straight” or “rings.” Both of them are pretty easy to spot; just look for the carbon molecules with a lot of OHs and Hs attached to them.

Here are the two different forms.

Disaccharides

What happens when two monosaccharides are brought together? The hydrogen (–H) from one sugar molecule combines with the hydroxyl group (–OH) of another sugar molecule. What do H and OH add up to? Water (H₂O)!

Maltose is an example of a disaccharide.

This process is called dehydration synthesis, or condensation, because during this process, a water molecule is lost. When two monosaccharides are joined, the bond is called a glycosidic linkage, and the resulting sugar is called a disaccharide. The resulting sugar is maltose if a disaccharide formed from two glucose molecules.

Now, what if you want to break up the disaccharide and form two monosaccharides again? Just add water. That’s called hydrolysis, which means “water” (hydro-) and “breaking” (-lysis). The water breaks the bond between the two monomers. Hydrolysis is a common reaction in biology.

Polysaccharides

Polysaccharides are made up of many repeated units of monosaccharides. The most common polysaccharides you’ll need to know for the test are starch, cellulose, and glycogen. Animals store glucose molecules in the form of glycogen in the liver and muscle cells. Plants “stockpile” α-glucose in the form of starch in structures called plastids. Cellulose, on the other hand, is made up of β-glucose and is a major part of the cell walls in plants. Its function is to lend structural support. Chitin, a polymer of β-glucose molecules, serves as a structural molecule in the walls of fungus and in the exoskeletons of arthropods.

Here’s an AP question that may come up on the test: why can’t humans digest cellulose? This is because the bonds joining the glucose subunits in cellulose are different than those in starch. Starch is composed of α-glucose subunits held together by 1,4 glycosidic linkages, while cellulose contains β-glucose subunits held together by 1,4 linkages. Humans cannot digest the β-linkages; however, humans can digest polysaccharides that have α-linkages, like starch and glycogen.

Proteins

Amino acids are organic molecules that serve as the building blocks of proteins. They contain carbon, hydrogen, oxygen, and nitrogen atoms. There are twenty different amino acids commonly found in proteins. Fortunately, you don’t have to memorize the twenty amino acids. But you do have to remember that every amino acid has four important parts: an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen, and an R group.

Here’s a typical amino acid.

Amino acids differ only in the R group, which is also called the side chain. The R group associated with an amino acid could be as simple as a hydrogen atom (as in the amino acid glycine) or as complex as a charged carbon skeleton (as in the amino acid arginine).

When it comes to spotting an amino acid, simply keep an eye out for the amino group (NH₂), then look for the carboxyl molecule (COOH). The side chains for each amino acid vary greatly. You don’t have to memorize the structures of the side chains for individual amino acids, but you should know a few key characteristics they can have.

Polypeptides

When two amino acids join they form a dipeptide. The carboxyl group of one amino acid combines with the amino group of another amino acid. Here’s an example:

This is the same dehydration synthesis process we saw earlier. Why? Because a water molecule is removed to form a bond. By the way, the bond between two amino acids has a special name—a peptide bond. If a group of amino acids are joined together in a “string,” the resulting organic compound is called a polypeptide. Once a polypeptide chain twists and folds on itself, it forms a three-dimensional structure called a protein.

Higher Protein Structure

The polypeptide has to go through several changes before it can officially be called a protein. Proteins can have four levels of structure. The linear sequence of the amino acids is called the primary structure of a protein. Now the polypeptide begins to twist, forming either a coil (known as an alpha helix) or zigzagging pattern (known as beta-pleated sheets). These are examples of proteins’ secondary structures.

A polypeptide folds and twists because the different R-groups of the amino acids are interacting with each other. Remember, each R-group is unique and has a particular size, shape, charge, etc. that allows it to react to things around it. Depending on which amino acids are in a protein and the order that they are in, the protein can twist and fold in very different ways. This is why proteins can form so many different shapes.

The secondary structure is formed by amino acids that interact with other amino acids closeby in the primary structure. However, after the secondary structure reshapes the polypeptide, amino acids that were far away in the primary structure arrangement can now also interact with each other. This is called the tertiary structure. Sometimes, two cysteine amino acids can react with each other to form a covalent disulfide bond that stabilizes the tertiary structure.

Lastly, several different polypeptide chains sometimes interact with each other to form a quaternary structure. Only proteins that have folded correctly into their specific three-dimensional structure can perform their function properly. Mistakes in the amino acid chain can create nonfunctional proteins.

One more thing: In some cases, the folding of proteins involves other proteins known as chaperone proteins (or chaperonins). They help the protein fold properly and make the process more efficient.

Lipids

Like carbohydrates, lipids consist of carbon, hydrogen, and oxygen atoms, but not in the 1:2:1 ratio typical of carbohydrates. The most common examples of lipids are triglycerides, phospholipids, and steroids.

Triglycerides

Our fat stores in the body are filled with lipids called triglycerides. Each triglyceride is made of a glycerol molecule with three fatty acid chains attached to it.

Let’s take a look.

To make a triglyceride, each of the carboxyl groups (–COOH) of the three fatty acids must react with one of the three hydroxyl groups (–OH) of the glycerol molecule. This happens by the removal of a water molecule. So, the creation of a fat requires the removal of three molecules of water. Once again, what have we got? You probably already guessed it—dehydration synthesis! The linkage now formed between the glycerol molecule and the fatty acids is called an ester linkage. A fatty acid can be saturated, which means it has a single covalent bond between each pair of carbon atoms, or it can be unsaturated, which means adjacent carbons are joined by double bonds instead of single bonds. A polyunsaturated fatty acid has many double bonds within the fatty acid.

Lipids are important because they function as structural components of cell membranes, sources of insulation, and a means of energy storage.

Phospholipids

Another special class of lipids is known as phospholipids. Phospholipids contain two fatty acid “tails” and one negatively charged phosphate “head.” Take a look at a typical phospholipid.

Phospholipids are extremely important, mainly because of some unique properties they possess, particularly with regard to water.

The two fatty acid tails are hydrophobic (“water-hating”). In other words, just like oil and vinegar, fatty acids and water don’t mix. The reason for this is that fatty acid tails are nonpolar, and nonpolar substances don’t mix well with polar ones, such as water.

On the other hand, the phosphate “head” of the lipid is hydrophilic (“water- loving”), meaning that it does mix well with water. Why? It carries a negative charge, and this charge draws it to the positively charged end of a water molecule. Since a phospholipid has both a hydrophilic region and a hydrophobic region, it is an amphipathic molecule. One side of a phospholipid loves to hang out with water, and the other side hates to.

Thus, the two fatty acid chains orient themselves away from water, while the phosphate portion orients itself toward the water. Keep these properties in mind. We’ll see later how this orientation of phospholipids in water relates to the structure and function of cell membranes.

Cholesterol

Cholesterol is another important type of lipid. Cholesterol is a a four-ringed molecule that is found in membranes. It affects membrane fluidity by preventing it from freezing or melting. Cholesterol is also important for making certain types of hormones and for making vitamin D.

Nucleic Acids

The fourth class of organic compounds are the nucleic acids. Like proteins, nucleic acids contain carbon, hydrogen, oxygen, and nitrogen, but nucleic acids also contain phosphorus. Nucleic acids are molecules that are made up of simple units called nucleotides. For the AP Biology Exam, you’ll need to know about two kinds of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

DNA is important because it contains the hereditary “blueprints” of all life. RNA is important because it’s essential for protein synthesis. We’ll discuss DNA and RNA in greater detail when we discuss heredity. The following table summarizes the important macromolecules discussed here.

ORIGINS OF THE EARTH

We’ve just seen the organic compounds that are essential for life. But where did they come from in the first place? This is still a hotly debated topic among scientists. Most scientists believe that the earliest precursors of life arose from nonliving matter (basically gases) in the primitive oceans of the earth. But this theory didn’t take shape until the 1920s. Two scientists, Alexander Oparin and J. B. S. Haldane, proposed that the primitive atmosphere contained the following gases: methane (CH₄), ammonia (NH₃), hydrogen (H₂), and water (H₂O). Interestingly enough, there was almost no free oxygen (O₂) in this early atmosphere. They believed that these gases collided, producing chemical reactions that eventually led to the organic molecules we know today.

This theory didn’t receive any substantial support until 1953. In that year, Stanley Miller and Harold Urey simulated the conditions of primitive Earth in a laboratory. They put the gases theorized to be abundant in the early atmosphere into a flask, struck them with electrical charges in order to mimic lightning, and organic compounds similar to amino acids appeared!

But how do we make the leap from simple organic molecules to more complex compounds and life as we know it? Since no one was around to witness the process, no one knows for sure how (or when) it occurred. It is likely that the original life-forms were simply molecules of RNA. This is called the RNA-world hypothesis. RNA can take many shapes because it is not restricted to be a double helix. It is possible that RNA molecules capable of replicating and thus passing along themselves (their genome) were the first life-forms. Complex organic compounds (such as proteins) must have formed via dehydration synthesis. Simple cells then used organic molecules as their source of food. Over time, simple cells evolved into complex cells.

Now let’s throw in a few new terms. Living organisms that rely on organic molecules for food are called heterotrophs (or consumers). For example, we’re heterotrophs, but the earliest heterotrophs were simple unicellular life-forms. Eventually, some life-forms found a way to make their own food; most commonly through photosynthesis. These organisms are called autotrophs (or producers). Early autotrophs (most likely cyanobacteria) are responsible for Earth’s oxygenated atmosphere.

KEY TERMS

elements

oxygen

carbon

hydrogen

nitrogen

trace elements

atom

protons

neutrons

electrons

nucleus

isotopes

radiometric dating

compound

chemical reaction

chemical bond

ionic bond

covalent bond

hydrogen bond

ions

nonpolar covalent

polar covalent

polar

cohesion

adhesion

heat capacity

expansion on freezing

capillary action

acidic

basic

neutral

alkaline

pH scale

organic compounds

inorganic compounds

polymer

monomer

carbohydrates

monosaccharides

disaccharides

polysaccharides

glucose

fructose

dehydration synthesis (or condensation)

glycosidic bond

hydrolysis

starch

cellulose

glycogen

plastids

amino acids

amino group

carboxyl group

R group

side chain

dipeptide

peptide bond

polypeptide

protein

primary structure

secondary structure

tertiary structure

quaternary structure

chaperone proteins

lipids

triglycerides

cholesterol

phospholipids

steroids

glycerol

ester linkage

saturated

unsaturated

polyunsaturated

hydrophobic

hydrophilic

amphipathic

nucleic acids

nucleotides

deoxyribonucleic acid (DNA)

ribonucleic acid (RNA)

Alexander Oparin and J. B. S. Haldane

Stanley Miller and Harold Urey

RNA-world hypothesis

heterotrophs (or consumers)

autotrophs (or producers)

Summary

Chapter 4 Drill

Answers and explanations can be found in Chapter 16.

Questions 4-6 refer to the following paragraph and diagram.

In 1953, Stanley Miller and Harold Urey performed an experiment at the University of Chicago to test the hypothesis that the conditions of the early Earth would have favored the formation of larger, more complex organic molecules from basic precursors. The experiment, as shown below, consisted of sealing basic organic chemicals (representing the atmosphere of the primitive Earth) in a flask, which was exposed to electric sparks (to simulate lightning) and water vapor.

After one day of exposure, the mixture in the flask had turned pink in color, and later analysis showed that at least 10% of the carbon had been transformed into simple and complex organic compounds including at least 11 different amino acids and some basic sugars. No nucleic acids were detected in the mixture.

REFLECT

Respond to the following questions:

Chapter 5

Cells

LIVING THINGS

All living things are composed of cells. According to the cell theory, the cell is life’s basic unit of structure and function. This simply means that the cell is the smallest unit of living material that can carry out all the activities necessary for life.

It may seem strange that we are still made of tiny little cells. Why not just be a living thing that is one giant cell?

One reason for this is because compartments allow more specialization. As we will see, compartment­alization is an important part of the organization of unicellular and multicellular organisms.

The second reason we can’t just be giant cells is the surface area-to-volume ratio. There is always lots of exchange going on between the inside of things and the outside. This ratio must be kept small so that there is lots of space to do these exchanges.

Therefore, even the largest things are still made of cells.

TYPES OF CELLS AND ORGANELLES

For centuries, scientists have known about cells. However, it wasn’t until the development of the electron microscope that scientists were able to figure out what cells do. We now know that there are two distinct types of cells: prokaryotic cells and eukaryotic cells.

A prokaryotic cell, which is a lot smaller than a eukaryotic cell, is relatively simple. Bacteria, for example, are prokaryotic cells. The inside of the cell is filled with a substance called cytoplasm. The genetic material in a prokaryote is one continuous, circular DNA molecule that is found free in the cell in an area called the nucleoid (this is not the same as a nucleus!). Most prokaryotes have a cell wall composed of peptidoglycans that surrounds a lipid layer called the plasma membrane. Prokaryotes also have ribosomes (though smaller than those found in eukaryotic cells), and they may also have one or more flagella, which are long projections used for motility (movement). Eukaryotic cells are more complex than prokaryotic cells. Fungi, protists, plants, and animals are eukaryotes.

Eukaryotic cells are more complex than prokaryotic cells. Fungi, protists, plants, and animals are eukaryotes. Eukaryotic cells are organized into many smaller structures called organelles. Some of these organelles are the same structures seen in prokaryotic cells, but many are uniquely eukaryotic. A good way to remember the difference is that prokaryotes do not have any membrane-bound organelles. Their only membrane is the plasma membrane.

Organelles

A eukaryotic cell is like a microscopic factory. It’s filled with organelles, each of which has its own special tasks. Let’s take a tour of a eukaryotic cell and focus on the structure and function of each organelle. Here’s a picture of a typical animal cell and its principal organelles.

Plasma Membrane

The cell has an outer envelope known as the plasma membrane. Although the plasma membrane appears to be a simple, thin layer surrounding the cell, it’s actually a complex, double-layered structure made up of phospholipids and proteins. The hydrophobic fatty acid tails face inward and the hydrophilic phosphate heads face outward. It is called a phospholipid bilayer since two lipid layers are forming a hydrophobic sandwich.

The plasma membrane is important because it regulates the movement of substances into and out of the cell. The membrane itself is semipermeable, meaning that only certain substances, namely small hydrophobic molecules (such as O₂ and CO₂), pass through it unaided. Anything large and/or hydrophilic can only pass through the membrane via special tunnels (discussed more later in this chapter).

Many proteins are associated with the cell membrane. Some of these proteins are loosely associated with the lipid bilayer (peripheral proteins). They are located on the inner or outer surface of the membrane. Others are firmly bound to the plasma membrane (integral proteins). These proteins are amphipathic, which means that their hydrophilic regions extend out of the cell or into the cytoplasm, while their hydrophobic regions interact with the tails of the membrane phospholipids. Some integral proteins extend all the way through the membrane (transmembrane proteins).

This arrangement of phospholipids and proteins is known as the fluid-mosaic model. This means that each layer of phospholipids is flexible, and it is a mosaic because it is peppered with different proteins and carbohydrate chains. Remember, anything hydrophilic should not go through the hydrophobic interior. This means that the phospholipids on one side should never flip-flop to the other side of the membrane (because that would require their polar heads to pass through the hydrophobic area).

Why should the plasma membrane need so many different proteins? It’s because of the number of activities that take place in or on the membrane. Generally, plasma membrane proteins fall into several broad functional groups. Some membrane proteins form junctions between adjacent cells (adhesion proteins). Others serve as docking sites for arrivals at the cell, such as hormones (receptor proteins). Some proteins form pumps that use ATP to actively transport solutes across the membrane (transport proteins). Others form channels that selectively allow the passage of certain ions or molecules (channel proteins). Finally, some proteins, such as glycoproteins, are exposed on the extracellular surface and play a role in cell recognition and adhesion (recognition and adhesion proteins).

Attached to the surface of some proteins are carbohydrate side chain. They are found only on the outer surface of the plasma membrane. As mentioned above, cholesterol molecules are also found in the phospholipid bilayer because they help stabilize membrane fluidity in animal cells.

The Nucleus

The nucleus, which is usually the largest organelle, is the control center of the cell. The nucleus not only directs what goes on in the cell, it is also responsible for the cell’s ability to reproduce. It’s the home of the hereditary information—DNA—which is organized into large structures called chromosomes. The most visible structure within the nucleus is the nucleolus, which is where rRNA is made and ribosomes are assembled.

Ribosomes

The ribosomes are the sites of protein synthesis. Their job is to manufacture all the proteins required by the cell or secreted by the cell. Ribosomes are round structures composed of two subunits. The structure is composed of RNA and proteins. Ribosomes can be either free floating in the cell or attached to another structure called the endoplasmic reticulum (ER).

Endoplasmic Reticulum (ER)

The endoplasmic reticulum (ER) is a continuous channel that extends into many regions of the cytoplasm. The region of the ER that is attached to the nucleus and “studded” with ribosomes is called the rough ER (RER). Proteins generated in the rough ER are trafficked to or across the plasma membrane, or they are used to build Golgi bodies, lysosomes, or the ER. The region of the ER that lacks ribosomes is called the smooth ER (SER). The smooth ER makes lipids, hormones, and steroids and breaks down toxic chemicals.

Golgi Bodies

The Golgi bodies, which look like stacks of flattened sacs, also participate in the processing of proteins. Once the ribosomes on the rough ER have completed synthesizing proteins, the Golgi bodies modify, process, and sort the products. They’re the packaging and distribution centers for materials destined to be sent out of the cell. They package the final products in little sacs called vesicles, which carry the products to the plasma membrane. Golgi bodies are also involved in the production of lysosomes.

Mitochondria

Another important organelle is the mitochondrion. The mitochondria are often referred to as the “powerhouses” of the cell. They’re power stations responsible for converting the energy from organic molecules into useful energy for the cell. The energy molecule in the cell is adenosine triphosphate (ATP).

The mitochondrion is usually an easy organelle to recognize because it has a unique oblong shape and a characteristic double membrane consisting of an inner portion and an outer portion. The inner mitochondrial membrane forms folds known as cristae and separates the innermost area called the matrix from the intermembrane space. The outer membrane separates the intermembrane space from the cytoplasm. As we’ll see later, most of the production of ATP is done on the cristae.

Lysosomes

Throughout the cell are small, membrane-bound structures called lysosomes. These tiny sacs carry digestive enzymes, which they use to break down old, worn-out organelles, debris, or large ingested particles. Lysosomes make up the cell’s clean up crew, helping to keep the cytoplasm clear of unwanted flotsam. Lysosomes contain hydrolytic enzymes that only function at acidic pH, which is enclosed inside the lumen of the lysosome.

Centrioles

The centrioles are small, paired, cylindrical structures that are often found within microtubule organizing centers (MTOCs). Centrioles are most active during cellular division. When a cell is ready to divide, the centrioles produce microtubules, which pull the replicated chromosomes apart and move them to opposite ends of the cell. Although centrioles are common in animal cells, they are not found in most types of plant cells.

Vacuoles

In Latin, the term vacuole means “empty cavity.” But vacuoles are far from empty. They are fluid-filled sacs that store water, food, wastes, salts, or pigments.

Peroxisomes

Peroxisomes are organelles that detoxify various substances, producing hydrogen peroxide (H₂O₂) as a byproduct. They also contain enzymes that break down hydrogen peroxide into oxygen and water. In animals, they are common in the liver and kidney cells.

Cytoskeleton

Have you ever wondered what actually holds the cell together and enables it to keep its shape? The shape of a cell is determined by a network of fibers called the cytoskeleton. The most important fibers you’ll need to know are microtubules and microfilaments.

Microtubules, which are made up of the protein tubulin, participate in cellular division and movement. These small fibers are an integral part of three structures: centrioles, cilia, and flagella. We’ve already mentioned that centrioles help chromosomes separate during cell division. Cilia and flagella are threadlike structures best known for their locomotive properties in single-celled organisms. The beating motion of cilia and flagella structures propels these organisms through their watery environments.

The two classic examples of organisms with these structures are the Euglena, which gets about using its whiplike flagellum, and the Paramecium, which is covered in cilia. The rhythmic beating of the Paramecium’s cilia enables it to motor about in waterways, ponds, and microscope slides in your biology lab. You’ve probably already checked these out in lab, but here’s what they look like.

Though we usually associate such structures with microscopic organisms, they aren’t the only ones with cilia and flagella. As you probably know, these structures are also found in certain human cells. For example, the cells lining your respiratory tract possess cilia that sweep constantly back and forth (beating up to twenty times per second), helping to keep dust and unwanted debris from descending into your lungs. And every sperm cell has a type of flagellum, which enables it to swim through the female reproductive organs to fertilize the waiting ovum.

Microfilaments, like microtubules, are important for movement. These thin, rodlike structures are composed of the protein actin. Actin monomers are joined together and broken apart as needed to allow microfilaments to grow and shrink. Microfilaments assist during cytokinesis, muscle contraction, and formation of pseudopodia extensions during cell movement.

Plant Cells Versus Animal Cells

Plant cells contain most of the same organelles and structures seen in animal cells, with several key exceptions. Plant cells, unlike animal cells, have a protective outer covering called the cell wall (made of cellulose). A cell wall is a rigid layer just outside of the plasma membrane that provides support for the cell. It is found in plants, protists, fungi, and bacteria. (In fungi, the cell wall is usually made of chitin, a modified polysaccharide. Chitin is also a principle component of an arthropod’s exoskeleton.) In addition, plant cells possess chloroplasts (organelles involved in photosynthesis). Chloroplasts contain chlorophyll, the light-capturing pigment that gives plants their characteristic green color. Another difference between plant and animal cells is that most of the cytoplasm within a plant cell is usually taken up by a large vacuole that crowds the other organelles. In mature plants, this vacuole contains the cell sap. A full vacuole in a plant is a sign that it is not dehydrated. Dehydrated plants cannot fill their vacuoles and they wilt. Plant cells also differ from animal cells in that plant cells do not contain centrioles.

To help you remember the differences among prokaryotes, plant cells, and animal cells, we’ve put together this simple table. Make sure you learn it! The testing board is bound to ask you which cells contain which structures:

Why do we need to know about the structure of cells? Because biological structure is often closely related to function. (Watch out for this connection: it’s a favorite theme for the AP Biology Exam.) And, more importantly, because the testing board likes to test you on it!

Transport: The Traffic Across Membranes

We’ve talked about the structure of cell membranes; now let’s discuss how molecules and fluids pass through the plasma membrane. What are some of the patterns of membrane transport? The ability of molecules to move across the cell membrane depends on two things: (1) the semipermeability of the plasma membrane and (2) the size and charge of particles that want to get through.

Since the plasma membrane is composed primarily of phospholipids, lipid-soluble substances cross the membrane without any resistance. Why? Because “like dissolves like.” The lipid bilayer is a hydrophobic sandwich, and only hydrophobic things can pass that zone. If a substance is hydrophilic, the bilayer won’t let it pass without assistance, called facilitated transport.

Facilitated transport depends upon a number of proteins that act as tunnels through the membrane. Channels are very specialized types of tunnels that only let certain things through.

The most famous of these are aquaporins, which are water-specific channels. Although water is polar, there are typically sufficient aquaporins for water to traverse the membrane whenever it wishes without forming traffic jams. However, without aquaporins, no water would be able to cross the membrane.

Passive Transport: Simple and Facilitated Diffusion

Now we know how things cross the membrane, but let’s talk about why they cross the membrane. The simple answer is: “To get to the other side.” If there is a high concentration of something in one area, it will move to spread out and diffuse into an area with a lower concentration, even if that means entering or exiting a cell. In other words, the substance moves down a concentration gradient. This is called diffusion. When the molecule that is diffusing is hydrophobic, the diffusion is called simple diffusion. When the diffusion requires the help of a channel-type protein, it is called facilitated diffusion. Anytime that a substance is moving by diffusion, it is called passive transport because there is no outside energy required to cause the movement. It’s like riding a bicycle downhill. The molecules are just “going with the flow.”

Osmosis

When the molecule that is diffusing is water, the process is called osmosis. Water always wants to move from an area where it is most concentrated to an area where it is least concentrated. Water is not usually pure water, but since it is so great at dissolving things, it usually exists as a solution. A solution is made when a liquid solvent dissolves solute particles. So, if we rethink water moving down its concentration gradient, this is the same as saying that it wants to go from where there is less solute (ie. watery solution) to where there is more solute (ie. concentrated solution). It’s as if the water is moving to dilute the concentrated solute particles.

Often, situations discussing osmosis set it up so that there are two areas and the water can flow freely, but the solute cannot. For example, if a chamber containing water and a chamber containing a sucrose solution are connected by a semipermeable membrane that allows water but not sucrose to cross, diffusion of sucrose between the chambers cannot occur. In this case, osmosis draws water into the sucrose chamber to reduce the sucrose concentration. This will reduce the total volume of the water chamber. Water will flow into the sucrose chamber until the concentration is the same across the membrane.

In both diffusion and osmosis, the final result is that solute concentrations are the same on both sides of the membrane. The only difference is that in diffusion the membrane is permeable to solute, and in osmosis it is not.

The term tonicity is used to describe osmotic gradients. If the environment is isotonic to the cell, the solute concentration is the same inside and outside. A hypertonic solution has more total dissolved solutes than the cell, while a hypotonic solution has less. The tendency of water to move down its concentration gradient (into cells) can be a powerful force; it can cause cells to explode and can overcome gravity. You may also hear the terms isosmotic, hyperosmotic, and hyposmotic. These words are usually used when comparing two solutions, while tonicity terms are used when comparing a solution to a cell. Other than this, the definitions are similar; isotonic and isosmotic both describe situations where the concentration is the same on either side of a membrane, for example. The only difference is what type of membrane.

Water potential (Ψ) is the measure of potential energy in water and describes the eagerness of water to flow from an area of high water potential to an area of low water potential. It is affected by two factors: pressure potential (Ψ_p) and solute potential (Ψ_s). The equation for solute (or osmotic) potential is listed on the AP Biology Equations and Formulas sheet and describes the effect of solute concentration on water flow. Adding a solute lowers the water potential of a solution, causing water to be less likely to leave this solution and more likely to flow into it. This makes sense because the added solute makes the solution more concentrated, and the water is now unlikely to diffuse away. The more solute molecules present, the more negative the solute potential is.

A red blood cell dropped into a hypotonic solution (such as distilled water) will expand because water will move into the cell, an area of lower water potential. Eventually, the red blood cell will pop. If a similar experiment is done with a plant cell, water will still move into the cell, but the cell wall will exert pressure, increasing the water potential and limiting the gain of water. Water potential also explains how water moves from soil into plant roots and how plants transport water from roots to leaves to support photosynthesis.

The concentration of a solution can be calculated by dividing the number of moles of solute by the volume (in liters) of solution. Highly concentrated (or stock) solutions can be diluted to make less concentrated solutions. The equation to do this is on the AP Biology Equations and Formulas sheet.

This equation tells you how much (V_i) of a concentrated solution (at C_i) is required to make a more dilute solution (C_f) of a certain volume (V_f). The amount of solvent added will be the final volume of the solution (V_f) minus whatever amount of stock solution you need to add. For example, if you have a bottle of 2 M solution of Tris buffer and would like to make 50 mL of 0.1M Tris.

Thus, you would add 2.5 mL of the concentrated (or stock) Tris solution to a new tube or bottle and then add water (the solvent) up to a final volume of 50 mL. In other words, you should add 47.5 mL of water.

Active Transport

Suppose a substance wants to move in the opposite direction—from a region of lower concentration to a region of higher concentration. A transport protein can help usher the substance across the plasma membrane, but it’s going to need energy to accomplish this. This time it’s like riding a bicycle uphill. Compared with riding downhill, riding uphill takes a lot more work. Movement against the natural flow is called active transport.

But where does the protein get this energy? Some proteins in the plasma membrane are powered by ATP. The best example of active transport is a special protein called the sodium-potassium pump. It ushers out three sodium ions (Na⁺) and brings in two potassium ions (K⁺) across the cell membrane. These pumps depend on ATP to get ions across that would otherwise remain in regions of higher concentration. Primary active transport occurs when ATP is directly utilized to transport something. Secondary active transport occurs when something is actively transported using the energy captured from the movement of another substance flowing down its concentration gradient.

We’ve now seen that small substances can cross the cell membrane by:

Endocytosis

When the particles that want to enter a cell are just too large, the cell uses a portion of the cell membrane to engulf the substance. The cell membrane forms a pocket, pinches in, and eventually forms either a vacuole or a vesicle. This is called endocytosis.

Three types of endocytosis exist: pinocytosis, phagocytosis, and receptor- mediated endocytosis. In pinocytosis, the cell ingests liquids (“cell-drinking”). In phagocytosis, the cell takes in solids (“cell-eating”). A special type of endocytosis, receptor-mediated endocytosis, involves cell surface receptors that work in tandem with a endocytic pits that are lined with a protein called clathrin. When a particle, or ligand, binds to one of these receptors, the ligand is brought into the cell by the invagination or “folding in” of the cell membrane. A vesicle then forms around the incoming ligand and carries it into the cell’s interior.

Bulk Flow

Other substances move by bulk flow. Bulk flow is the one-way movement of fluids brought about by pressure. For instance, the movement of blood through a blood vessel or movement of fluids in xylem and phloem of plants are examples of bulk flow.

Dialysis

Dialysis is the diffusion of solutes across a selectively permeable membrane. Special membranes that have holes of a certain size within them can be used to sort substances by using the process of diffusion. Kidney dialysis is a specialized process by which the blood is filtered using machines and concentration gradients. Things present at high levels will naturally diffuse out of the blood; dialysis just gives them the opportunity.

Exocytosis

Sometimes large particles are transported out of the cell. In exocytosis, a cell ejects waste products or specific secretion products, such as hormones, by the fusion of a vesicle with the plasma membrane. Think of it as reverse endocytosis.

Cell Junctions

When cells come in close contact with each other, they develop specialized intercellular junctions that involve their plasma membranes as well as other components. These structures may allow neighboring cells to form strong connections with each other, prevent passage of materials, or establish rapid communication between adjacent cells. There are three types of intercellular contacts in animal cells: desmosomes, gap junctions, and tight junctions.

Desmosomes hold adjacent animal cells tightly to each other, like a rivet. They consist of a pair of discs associated with the plasma membrane of adjacent cells, plus the intercellular protein filaments that cross the small space between them. Intermediate filaments within the cells are also attached to the discs (see figure on the next page).

Gap junctions are protein complexes that form channels in membranes and allow communication between the cytoplasm of adjacent animal cells for the transfer of small molecules and ions. Gap junctions are found in the heart and in compact bone and smooth muscle.

Tight junctions are tight connections between the membranes of adjacent animal cells. They’re so tight that there is no space between the cells. Cells connected by tight junctions seal off body cavities and prevent leaks. Tight junctions are found in the small intestine.

Cell Communication

Communication is important for organisms and involves transduction of stimulatory or inhibitory signals from other cells, organisms, or the environment. Unicellular organisms detect and respond to environmental signals. For example, they can use cell communication to locate a suitable mate, adapt metabolism rates in response to changes in nutrient availability, or make their numbers known to other members of their species (a phenomenon known as quorum sensing).

Taxis is the movement of an organism in response to a stimulus and can be positive (towards the stimulus) or negative (away from the stimulus). Taxes are innate behavioral responses, or instincts. Chemotaxis is movement in response to chemicals. For example, bacteria can control flagella rotation to direct their motion, thus avoiding repellents (such as poisons), or helping them find favorable locations with high concentrations of attractants (such as food). In our bodies, neutrophils use chemotaxis to respond to an infection and are the first responders to inflammation.

The cells of multi-celled organisms must communicate with one another to coordinate the activities of the organism as a whole. Signaling can be short-range (affecting only nearby cells) or long-range (affecting cells throughout the organism). It can be done by cell junctions or signaling molecules called ligands that bind to receptors and trigger a response. Hormones and neurotransmitters are common signaling molecules, and they will be covered in Chapter 11.

Signal transduction is the process by which an external signal is transmitted to the inside of a cell. It usually involves the following three steps:

Hydrophobic signaling molecules, like cholesterol-based steroid hormones, can diffuse across the plasma membrane. These molecules can bind receptors inside the cell and often travel to the nucleus where they regulate gene expression.

For signaling molecules that cannot enter the cell, a plasma membrane receptor is required. Plasma membrane receptors form an important class of integral membrane proteins that transmit signals from the extracellular space into the cytoplasm. Each receptor binds a particular molecule in a highly specific way. There are three classes of membrane receptors.

Signal transduction in eukaryotic cells usually involves many steps and complex regulation. In contrast, bacterial cells usually use a simpler two-component regulatory system in transduction pathways.

CELL COMMUNICATION IN PLANTS

Plants do not have a nervous system but can produce several proteins found in animal nervous systems, such as certain neurotransmitter receptors. Plants can also generate electrical signals in response to environmental stimuli, and this can affect flowering, respiration, photosynthesis, and wound healing. Light receptors are common in plants and help link environmental cues to biological processes such as seed germination, the timing of flowering, and chlorophyll production. Some plants can also use chemicals to communicate with nearby plants. For example, wounded tomatoes produce a volatile chemical as an alarm signal. This warns nearby plants and allows them to prepare a defense or immune response.

TROPISMS

Plants need light. Notice that all the plants in your house tip toward the windows. This movement toward the light is known as phototropism. As you also know, plants generally grow up and down: the branches grow upward, while the roots grow downward into the soil, seeking water. This tendency to grow toward or away from the earth is called gravitropism. All of these tropisms are examples of behavior in plants.

 

A tropism is a turning response to a stimulus. Tropisms are different from taxes, which are changes in motility. Remember, plants are immobile.

There are four basic tropisms in plants. They’re easy to remember because their prefixes indicate the stimuli to which plants react.

KEY TERMS

cells

light microscopes

electron microscopes

eukaryotic cells

prokaryotic cells

cytoplasm

nucleoid

plasma membrane

flagella

organelles

phosholipid bilayer

peripheral proteins

integral proteins

transmembrane proteins

fluid-mosaic model

adhesion proteins

receptor proteins

transport proteins

channel proteins

recognition and adhesion proteins

carbohydrate side chains

chromosomes

nucleolus

ribosomes

endoplasmic reticulum (ER)

rough ER

smooth ER

Golgi bodies

vesicles

mitochondria

adenosine triphosphate (ATP)

lysosomes

centrioles

microtubule organizing centers (MTOCs)

vacuoles

peroxisomes

cytoskeleton

microtubules

microfilaments

tubulin

cilia

Euglena

Paramecium

cell wall

chitin

chloroplasts

cell sap

facilitated transport

aquaporins

simple diffusion

facilitated diffusion

passive transport

simple diffusion (or passive transport)

osmosis

tonicity

isotonic

hypertonic

hypotonic

water potential

solute potential

solutes

channel proteins

active transport

sodium-potassium pump

endocytosis

pinocytosis

phagocytosis

receptor-mediated endocytosis

bulk flow

dialysis

exocytosis

intercellular junctions

desmosomes

gap junctions

tight junctions

ligands

receptors

signal transduction

ligand-gated ion channel

catalytic receptor

G-protein-linked receptor

phototropism

gravitropism

thigmotropism

photoperiodism

Summary

Chapter 5 Drill

Answers and explanations can be found in Chapter 16.

Question 4 is based on the information and table below.

A new unicellular organism has recently been identified living in thermal pools in Yellowstone National Park. The thermal pools have average temperatures of 45°C, a pH of approximately 3.2, and high concentrations of sulfur-containing compounds. To identify the organism, a microbiologist performs a series of tests to evaluate its structural organization. The table below summarizes the microscopy data of the newly identified organism.

                                               

Cellular Structure	Analysis
Plasma Membrane	Present
Cell Wall	Present, very thick
Mitochondria	Absent
Ribosomes	Present, highly abundant
Flagella	Present, peritrichous organization

Question 5 represents a question requiring a numeric answer.

REFLECT

Respond to the following questions:

Chapter 6

Cellular Energetics

BIOENERGETICS

In Chapter 4, we discussed some of the more important organic molecules. But what makes these molecules so important? Glucose, starch, and fat are all energy-rich. However, the energy is packed in the chemical bonds holding the molecules together. To carry out the processes necessary for life, cells must find a way to release the energy in these bonds when they need it and store it away when they don’t. The study of how cells accomplish this is called bioenergetics. Generally, bioenergetics is the study of how energy from the sun is transformed into energy in living things.

During chemical reactions, such bonds are either broken or formed. This process involves energy, no matter in which direction we go. Every chemical reaction involves a change in energy.

ADENOSINE TRIPHOSPHATE (ATP)

We’ve all heard the expression “nothing in life is free.” The same holds true in nature. Here’s a fundamental principle of energy that it is necessary to address.

This rule is called the first law of thermodynamics. As a result, the cell cannot take energy out of thin air. Rather, it must harvest it from somewhere.

The second law of thermodynamics states that energy transfer leads to less organization. That means the universe tends toward disorder (or entropy).

TYPES OF REACTIONS

Exergonic reactions are those in which the products have less energy than the reactants. Simply put, energy is given off during the reaction.

Let’s look at an example. The course of a reaction can be represented by an energy diagram. Here’s an energy diagram for an exergonic reaction.

You’ll notice that energy is represented along the y-axis. Based on the diagram, we see our reaction released energy. An example of an exergonic reaction is when food is oxidized in mitochondria of cells and then releases the energy stored in the chemical bonds.

Reactions that require an input of energy are called endergonic reactions. You’ll notice that the products have more energy than the reactants.

The products gained energy in the form of heat. An example is when plants use carbon dioxide and water to form sugars.

GIBBS FREE ENERGY

A practical way to discuss thermodynamics is the mathematical notion of Gibbs free energy.

This equation is on the AP Biology Equations and Formulas sheet. T denotes temperature, H denotes enthalpy (the measure of energy in a thermodynamic system), and S denotes entropy. The change in the Gibbs free energy of a reaction determines whether the reaction is favorable (spontaneous, negative ∆G) or unfavorable (nonspontaneous, positive ∆G). In other words, this equation can be used to figure out if the reactants will stay as they are or be converted to products.

Spontaneous reactions, ones that occur without a net addition of energy, have ∆G < 0. They occur with energy to spare. Reactions with a negative ∆G are exergonic (energy exits the system); reactions with a positive ∆G are endergonic. Endergonic reactions only occur if energy is added. In the lab, energy is added in the form of heat; in the body, endergonic reactions are driven by reaction coupling to exergonic or favorable reactions.

Activation Energy

Even though exergonic reactions release energy, the reaction might not occur naturally without a little bit of energy to get things going. This is because the reactants must first turn into an intermediate state, called the transition state, before turning into the products. The transition state is sort of a reactants-products hybrid state that is difficult to achieve. In order to reach this transition state, a certain amount of energy is required. This is called the activation energy.

You’ll notice that we needed a little energy to get us going. That’s because chemical bonds must be broken before new bonds can form. This energy barrier—the hump in the graph—is called the activation energy. Once a set of reactants has reached its activation energy, the reaction can occur much faster than it would in the absence of the enzyme.

Enzymes

A catalyst is something that speeds something up. Enzymes are biological catalysts that speed up reactions. They accomplish this by lowering the activation energy and helping the transition state to form. Thus, the reaction can occur more quickly because the tricky transition state is not as much of a hurdle to overcome. Enzymes do NOT change the energy of the starting point or the ending point of the reaction. They only lower the activation energy.

Enzyme Specificity

Most of the crucial reactions that occur in the cell require enzymes. Yet enzymes themselves are highly specific—in fact, each enzyme catalyzes only one kind of reaction. This is known as enzyme specificity. Because of this, enzymes are usually named after the molecules they target. In enzymatic reactions, the targeted molecules are known as substrates. For example, maltose, a disaccharide, can be broken down into two glucose molecules. Our substrate, maltose, gives its name to the enzyme that catalyzes this reaction: maltase.

Many enzymes are named simply by replacing the suffix of the substrate with –ase. Using this nomenclature, maltose becomes maltase.

Enzyme-Substrate Complex

Enzymes have a unique way of helping reactions along. As we just saw, the reactants in an enzyme-assisted reaction are known as substrates. During a reaction, the enzyme’s job is to bring the transition state about by helping the substrate(s) get into position. It accomplishes this through a special region on the enzyme known as an active site.

The enzyme temporarily binds one or more of the substrates to its active site and forms an enzyme-substrate complex. Let’s take a look:

Once the reaction has occurred and the product is formed, the enzyme is released from the complex and restored to its original state. Now the enzyme is free to react again with another bunch of substrates.

By binding and releasing substrates over and over again, the enzyme speeds the reaction along, enabling the cell to release much-needed energy from various molecules. Here is a quick review on the function of enzymes.

Enzymes Do:

Enzymes Don’t:

Induced Fit

However, scientists have discovered that enzymes and substrates don’t fit together quite so seamlessly. It appears that the enzyme has to change its shape slightly to accommodate the shape of the substrates. This is called induced fit. Sometimes certain factors are involved in activating the enzyme and making it capable of binding the substrate. Because the fit between the enzyme and the substrate must be perfect, enzymes only operate under a strict set of biological conditions.

Enzymes Don’t Always Work Alone

Enzymes sometimes need a little help in catalyzing a reaction. Those factors are known as cofactors. Cofactors can either be organic molecules called coenzymes or they can be inorganic molecules or ions. The inorganic cofactors are usually metal ions (Fe²⁺, Mg²⁺). Vitamins are examples of organic coenzymes. Your daily dose of vitamins is important for just this reason: the vitamins are active and necessary participants in crucial chemical reactions.

Factors Affecting Reaction Rates

Enzymatic reactions can be influenced by a number of factors, such as temperature, pH, and the relative amounts of enzyme and substrate.

Temperature

The rate of a reaction increases with increasing temperature, up to a point, because an increase in the temperature of a reaction increases the chance of collisions among the molecules. But too much heat can damage an enzyme. If a reaction is conducted at an excessively high temperature (above 42°C), the enzyme loses its three-dimensional shape and becomes inactivated. Enzymes damaged by heat and deprived of their ability to catalyze reactions are said to be denatured.

Here’s one thing to remember: all enzymes operate at an ideal temperature. For most human enzymes, this temperature is body temperature, 37°C.

Not all organisms have a constant body temperature. For example, ectotherms depend on the environment to control their varying body temperatures. Q₁₀ is a measure of temperature sensitivity of a physiological process or enzymatic reaction rate. The equation for Q₁₀ is included on the AP Biology Equations and Formulas sheet.

The temperature unit must be in either Celsius or Kelvin, and the same unit must be used for T₁ and T₂. The two reaction rates (k₁ and k₂) must also have the same unit. Q₁₀ has no unit; it is the factor by which the rate of a reaction increases. The more temperature-dependent a reaction is, the higher Q₁₀ will be. Reactions with Q₁₀ = 1 are temperature independent.

pH

Enzymes also function best at a particular pH. For most enzymes, the optimal pH is at or near a pH of 7.

Other enzymes operate at a low pH. For instance, pepsin, the digestive enzyme found in the stomach, is most effective at an extremely acidic pH of 2.

Enzyme Regulation

We know that enzymes control the rates of chemical reactions. But what regulates the activity of enzymes? It turns out that a cell can control enzymatic activity by regulating the conditions that influence the shape of the enzyme. Enzymes can be turned on/off by things that bind to them. Sometimes these things can bind at the active site, and sometimes they bind at other sites, called allosteric sites.

If the substance has a shape that fits the active site of an enzyme (i.e., similar to the substrate), it can compete with the substrate and block the substrate from getting into the active site. This is called competitive inhibition. If there was enough substrate available, the substrate would out-compete the inhibitor and the reaction would occur. You can always tell a competitive inhibitor based on what happens when you flood the system with lots of substrate. If the inhibitor binds to an allosteric site, it is an allosteric inhibitor and it is noncompetitive inhibition. A noncompetitive inhibitor generally distorts the enzyme shape so that it cannot function. The substrate can still bind, but the enzyme will not be able to catalyze the reaction.

REACTION COUPLING

As we just saw, almost everything an organism does requires energy. How, then, can the cell acquire the energy it needs without becoming a major mess? Fortunately, it’s through adenosine triphosphate (ATP).

ATP, as the name indicates, consists of a molecule of adenosine bonded to three phosphates. The great thing about ATP is that an enormous amount of energy is packed into those phosphate bonds, particularly the third bond.

When a cell needs energy, it takes one of these potential-packed molecules of ATP and splits off the third phosphate, forming adenosine diphosphate (ADP) and one loose phosphate (P_i ), while releasing energy in the process.

The energy released from this reaction can then be put to whatever use the cell pleases. Of course, this doesn’t mean that the cell is above the laws of thermodynamics. But within those constraints, ATP is the best source of energy the cell has available. It is relatively neat (only one bond needs to be broken to release that energy) and relatively easy to form. Organisms can use exergonic processes that increase energy, like breaking down ATP, to power endergonic reactions, like building organic macromolecules.

Sources of ATP

But where does all this ATP come from? It can be formed in several ways, but the bulk of it comes from a process called cellular respiration. Cellular respiration is a process of breaking down glucose and making ATP.

In autotrophs, the sugar is made during photosynthesis. In heterotrophs, the glucose comes from the food we eat. We will start by going over photosynthesis, since in plants it is a precursor to cellular respiration.

PHOTOSYNTHESIS

Plants and algae are producers. All they do is bask in the sun, churning out the glucose necessary for life.

As we discussed earlier, photosynthesis is the process by which light energy is converted to chemical energy. Here’s an overview of photosynthesis.

You’ll notice from this equation that carbon dioxide and water are the raw materials plants use to manufacture simple sugars. But remember, there’s much more to photosynthesis than what’s shown in the simple reaction above. We’ll soon see that this beautifully orchestrated process occurs thanks to a whole host of special enzymes and pigments. But before we turn to the stages in photosynthesis, let’s talk about where photosynthesis occurs.

The leaves of plants contain lots of chloroplasts, which are the primary sites of photosynthesis.

Now let’s look at an individual chloroplast. If you split the membrane of a chloroplast, you’ll find a fluid-filled region called the stroma. Inside the stroma are structures that look like stacks of coins. These structures are the grana.

The many disk-like structures that make up the grana are called the thylakoids. They contain chlorophyll, the light-absorbing pigment that drives photosynthesis, as well as enzymes involved in the process.

There are two stages in photosynthesis: the light reactions (also called the light-dependent reactions) and the dark reactions (also called the light-independent reactions). The whole process begins when the photons (or “energy units”) of sunlight strike a leaf, activating chlorophyll and exciting electrons. The activated chlorophyll molecule then passes these excited electrons down to a series of electron carriers, ultimately producing ATP and NADPH. The whole point of the light reaction is to produce two things: (1) energy in the form of ATP and (2) electron carriers, specifically NADPH. Both of these products, along with carbon dioxide, are then used in the dark reaction (light-independent) to make carbohydrates.

THE LIGHT REACTION

The Pigments

Many light-absorbing pigments participate in photosynthesis. Some of the more important ones are chlorophyll a, chlorophyll b, and carotenoids. These pigments are clustered in the thylakoid membrane into units called antenna complexes.

All of the pigments within a unit are able to “gather” light, but they’re not able to “excite” the electrons. Only one special molecule—located in the reaction center— is capable of transforming light energy to chemical energy. In other words, the other pigments, called antenna pigments, “gather” light and “bounce” the energy to the reaction center.

There are two types of reaction centers: photosystem I (PS I) and photosystem II (PS II). The principal difference between the two is that each reaction center has a specific type of chlorophyll—chlorophyll a—that absorbs a particular wavelength of light. For example, P680, the reaction center of photosystem II, has a maximum absorption at a wavelength of 680 nanometers. The reaction center for photosystem I—P700—best absorbs light at a wavelength of 700 nanometers.

When light energy is used to make ATP, it is called photophos­phorylation. Autotrophs are using light (that’s photo) and ADP and phosphates (that’s phosphorylation) to produce ATP.

An absorption spectrum shows how well a certain pigment absorbs electromagnetic radiation. Light absorbed is plotted as a function of radiation wavelength. This spectrum is the opposite of an emission spectrum, which gives information on which wavelengths are emitted by a pigment. The absorption spectrum for chlorophyll a, chlorophyll b and carotenoids is below. You can see that chlorophyll a and chlorophyll b absorb blue and red light quite well but do not absorb light in the green part of the spectrum. Light in the green range of wavelengths is reflected, and this is why chlorophyll and many plants are green. Carotenoids absorb light on the blue-green end of the spectrum, but not on the other end. This is why plants rich in carotenoids are yellow, orange or red.

Capturing Energy

When a leaf captures sunlight, the energy is sent to P680, the reaction center for photosystem II. The activated electrons are trapped by P680 and passed to a molecule called the primary acceptor, and then they are passed down to carriers in the electron transport chain and eventually enter photosystem I.

Some of the energy dissipates as electrons move along the chain of acceptors and will be used to “pump” protons across the membrane into the thylakoid lumen. To replenish the electrons in the thylakoid, when the reaction center P680 absorbs light, it also splits water into oxygen, hydrogen ions, and electrons. That process is called photolysis. The electrons from photolysis replace the missing electrons in photosystem II.

Here’s how it works: Hydrogen ions accumulate inside the thylakoids when photolysis occurs. A proton gradient is established. As the hydrogen ions move through ATP synthase, ADP and P_i produce ATP.

After the electrons leave photosystem II, they go to photosystem I. The electrons are passed through a second electron transport chain until they reach the final electron acceptor NADP⁺ to make NADPH.

The light-dependent reactions occur in the grana of chloroplasts, where the thylakoids are found. Remember: the light-absorbing pigments and enzymes for the light-dependent reactions are found within the thylakoids.

THE LIGHT-INDEPENDENT REACTION

Now let’s turn to the dark reaction. The dark reaction uses the products of the light reaction—ATP and NADPH—to make sugar. We now have energy to make glucose, but what do plants use as their carbon source? CO₂, of course. You’ve probably heard of the term carbon fixation. All this means is that CO₂ from the air is converted into carbohydrates. This step occurs in the stroma of the leaf. The dark reactions are also called the Calvin-Benson Cycle (or just Calvin cycle).

Let’s summarize the important facts about the dark reaction:

CAM Photosynthesis

In some plants, the stomates are closed during the day to reduce excessive water loss from transpiration. You might think that this would prevent these plants from carrying out photosynthesis during the day. However, desert plants have evolved a way to perform photosynthesis when their stomates are closed; it’s called CAM (crassulacean acid metabolism) photosynthesis. In CAM photosynthesis, a process similar to C₄ photosynthesis, PEP carboxylase is used to fix CO₂ to oxaloacetate, but oxaloacetate is converted to malic acid instead of malate (an ionized form of malate) and sent to the cell’s vacuole. During the day, malic acid is converted back to oxaloacetate, and carbon dioxide is released for photosynthesis. CO₂ then enters the Calvin cycle.

The following table summarizes the stages of photosynthesis:

CELLULAR RESPIRATION: THE SHORTHAND VERSION

In the shorthand version, cellular respiration looks something like this.

Notice that we’ve taken a sugar, perhaps a molecule of glucose, and combined it with oxygen to produce carbon dioxide, water, and energy in the form of our old friend, ATP. However, as you probably already know, the actual picture of what really happens is far more complicated.

Generally speaking, we can break cellular respiration down into two different approaches: aerobic respiration or anaerobic respiration. If ATP is made in the presence of oxygen, we call it aerobic respiration. If oxygen isn’t present, we call it anaerobic respiration. Let’s jump right in with aerobic respiration.

AEROBIC RESPIRATION

Aerobic respiration consists of four stages:

In the first three stages, glucose is broken down, and energy molecules are made. Some of these are ATP, and others are special electron carriers called NADH and FADH₂. In the fourth stage, the electron carriers unload their electrons, and the energy is eventually used to make even more ATP.

Stage 1: Glycolysis

The first stage begins with glycolysis, the splitting (-lysis) of glucose (glyco-). Glucose is a six-carbon molecule that is broken into two three-carbon molecules called pyruvic acid. This breakdown of glucose also results in the net production of two molecules of ATP.

Although we’ve written glycolysis as if it were a single reaction, this process doesn’t occur in one step. In fact, it requires a sequence of enzyme-catalyzed reactions.

If you take a good look at the reaction above, you’ll see two ATPs are needed to produce four ATP. You’ve probably heard the expression, “You have to spend money to make money.” In biology, you have to invest ATP to make ATP: our investment of two ATP yielded four ATP, for a net gain of two. The ATP molecules generated in glycolysis are created from combining ADP and an inorganic phosphate with the help of an enzyme.

Glycolysis also creates two NADH, which result from the transfer of electrons to the carrier NAD⁺, which then becomes NADH. NAD⁺ and NADH are constantly being turned into each other as electrons are being carried and then unloaded.

There are four important tidbits to remember regarding glycolysis:

Stage 2: Formation of Acetyl-CoA

Pyruvic acid is transported to the mitochondrion. Each pyruvic acid (a three-carbon molecule) is converted to acetyl coenzyme A (a two-carbon molecule, usually just called acetyl-CoA) and CO₂ is released.

Are you keeping track of our carbons? We’ve now gone from two three-carbon molecules to two two-carbon molecules. The extra carbons leave the cell in the form of CO₂. Once again, two molecules of NADH are also produced. This process of turning pyruvic acid into acetyl-CoA is called the pyruvate dehydrogenase complex.

Stage 3: The Krebs Cycle

The next stage is the Krebs cycle, also known as the citric acid cycle. Each of the two acetyl coenzyme A molecules will enter the Krebs cycle, one at a time, and all the carbons will ultimately be converted to CO₂. This stage occurs in the matrix of the mitochondria.

The Krebs cycle begins with each molecule of acetyl-CoA produced from the second stage of aerobic respiration combining with oxaloacetate, a four-carbon molecule, to form a six-carbon molecule, citric acid or citrate (hence its name, the citric acid cycle).

Citrate gets turned into several other things, and because the cycle begins with a four-carbon molecule, oxaloacetate, it eventually gets turned back into oxaloacetate to maintain the cycle by joining with the next acetyl-CoA coming down the pipeline.

With each turn of the cycle, three types of energy are produced:

To figure out the total number of products per molecule of glucose, we simply double the number of products—after all, we started off the Krebs cycle with two molecules of acetyl-CoA for each molecule of glucose!

Now we’re ready to tally up the number of ATP produced.

So far, we’ve made only four ATP—two ATP from glycolysis and two ATP from the Krebs cycle.

Although that seems like a lot of work for only four ATP, we have also produced hydrogen carriers in the form of 10NADH and 2FADH₂. These molecules will, in turn, produce lots of ATP.

Stage 4: Oxidative Phosphorylation

Electron Transport Chain

As electrons (and the hydrogen atoms to which they belong) are removed from a molecule of glucose, they carry with them much of the energy that was originally stored in their chemical bonds. These electrons—and their accompanying energy—are then transferred to readied hydrogen carrier molecules. In the case of cellular respiration, these charged carriers are NADH and FADH₂.

Let’s see how many “loaded” electron carriers we’ve produced. We now have:

That gives us 12 altogether.

These electron carriers—NADH and FADH₂—“shuttle” electrons to the electron transport chain, the resulting NAD+ and FADH can be recycled to be used as carriers again, and the hydrogen atoms are split into hydrogen ions and electrons.

Then, two interesting things occur. First, the high-energy electrons from NADH and FADH₂ are passed down a series of protein carrier molecules that are embedded in the cristae, thus it is called the electron transport chain. Some of the carrier molecules in the electron transport chain are NADH dehydrogenase and cytochrome C.

Each carrier molecule hands down the electrons to the next molecule in the chain. The electrons travel down the electron transport chain until they reach the final electron acceptor, oxygen. Oxygen combines with these electrons (and some hydrogens) to form water. This explains the “aerobic” in aerobic respiration. If oxygen weren’t available to accept the electrons, they wouldn’t move down the chain at all, thereby shutting down the whole process of electron transport.

CHEMIOSMOSIS

At the same time that electrons are being passed down the electron transport chain, another mechanism is at work. Remember those hydrogen ions (also called protons) that split off from the original hydrogen atom? The energy released from the electron transport chain is used to pump hydrogen ions across the inner mitochondrial membrane from the matrix into the intermembrane space. The pumping of hydrogen ions into the intermembrane space creates a pH gradient, or proton gradient. The hydrogen ions really want to diffuse back into the matrix. The potential energy established in this gradient is responsible for the production of ATP. This pumping of ions and diffusion of ions to create ATP is chemiosmosis.

These hydrogen ions can diffuse across the inner membrane only by passing through channels called ATP synthase. Meanwhile, ADP and P_i are on the other side of these protein channels. The flow of protons through these channels produces ATP by combining ADP and P_i on the matrix side of the channel. Overall, this process is called oxidative phosphorylation because when electrons are given up it is called “oxidation” and then ADP is “phosphorylated” to make ATP.

You’re also expected to know the following two things for the AP Biology Exam:

For the AP Biology Exam, all you need to remember are the big steps and the overall outcome.

ANAEROBIC RESPIRATION

When oxygen is not available, the anaerobic version of respiration occurs. The electron transport chain stops working, and the electron carriers have nowhere to drop their electrons. The mitochondrial production of acetyl-CoA and the Krebs cycle cease too.

Glycolysis, however, can continue to run. This means that glucose can be broken down to pyruvate to give net two ATP. Only two instead of 30!

Glycolysis also gives two NADH. The pyruvate and the NADH make a deal with each other, and the pyruvate helps the NADH get recycled back into NAD+ and takes its electrons. This creates either lactic acid (in muscles) or ethanol (in yeast). Since these two things are toxic, fermentation is only done in emergencies. Aerobic respiration is a better option. Organisms carry out a process called fermentation. Under anaerobic conditions, pyruvic acid is converted to either lactic acid or ethyl alcohol (or ethanol) and carbon dioxide.

What types of organisms undergo fermentation?

Your Muscle Cells Can Ferment

Although human beings are aerobic organisms, they can actually carry out fermentation in their muscle cells. Have you ever had a cramp? If so, that cramp was possibly the consequence of anaerobic respiration.

When you exercise, your muscles require a lot of energy. To get this energy, they convert enormous amounts of glucose to ATP. But as you continue to exercise, your body doesn’t get enough oxygen to keep up with the demand in your muscles. This creates an oxygen debt. What do your muscle cells do? They switch over to anaerobic respiration. Pyruvic acid produced from glycolysis is converted to lactic acid. As a consequence, the lactic acid causes your muscles to ache.

KEY TERMS

bioenergetics

1st Law of Thermodynamics

2nd Law of Thermodynamics

entropy

exergonic reaction

endergonic reaction

Gibbs free energy

enthalpy

transition state

activation energy

enzymes

enzyme specificity

substrates

active site

enzyme-substrate complex

induced fit

coenzymes

cofactors

denatured

Q₁₀

allosteric sites

competitive inhibition

noncompetitive inhibition

allosteric inhibitor

cellular respiration

photosynthesis

stroma

grana

thylakoids

light-dependent reactions

light-independent reactions

photons

chlorophyll a and b

carotenoids

reaction center

antenna pigments

photosystem I

photosystem II

p680

p700

photophos­phorylation

absorption spectrum

emission spectrum

photolysis

NADPH

carbon fixation

Calvin-Benson Cycle

CAM photosynthesis

aerobic respiration

NADH

FADH₂

anaerobic respiration

glycolysis

pyruvic acid

matrix

acetyl coenzyme A (acetyl-CoA)

Krebs cycle (or citric acid cycle)

oxaloacetate

citric acid

Electron Transport Chain

Chemiosmosis

cytochromes

pH gradient (or proton gradient)

ATP synthase

oxidative phosphorylation

fermentation

lactic acid

ethyl alcohol (or ethanol)

Summary

Chapter 6 Drill

Answers and explanations can be found in Chapter 16.

Questions 4-6 refer to the following diagram and paragraph.

Glycolysis (shown below) is a critical metabolic pathway that is utilized by nearly all forms of life. The process of glycolysis occurs in the cytoplasm of the cell and converts 1 molecule of glucose into 2 molecules of pyruvic acid.

REFLECT

Respond to the following questions:

Chapter 7

Molecular Biology

DNA: THE BLUEPRINT OF LIFE

All living things possess an astonishing degree of organization. From the simplest single-celled organism to the largest mammal, millions of reactions and events must be coordinated precisely for life to exist. This coordination is directed by DNA, which is the hereditary blueprint of the cell.

THE MOLECULAR STRUCTURE OF DNA

DNA is made up of repeated subunits of nucleotides. Each nucleotide has a five-carbon sugar, a phosphate, and a nitrogenous base. Take a look at the nucleotide below.

The name of the pentagon-shaped sugar in DNA is deoxyribose. Hence, the name deoxyribonucleic acid. Notice that the sugar is linked to two things: a phosphate and a nitrogenous base. A nucleotide can have one of four different nitrogenous bases:

Any of these four bases can attach to the sugar. As we’ll soon see, this is extremely important when it comes to the message of the genetic code in DNA.

The nucleotides can link up in a long chain to form a single strand of DNA. Here’s a small section of a DNA strand.

The nucleotides themselves are linked together by phosphodiester bonds between the sugars and the phosphates. This is called the sugar-phosphate backbone of DNA that serves as a scaffold for the bases.

Two DNA Strands

Each DNA molecule consists of two strands that wrap around each other to form a long, twisted ladder called a double helix. The structure of DNA was brilliantly deduced in 1953 by three scientists: Watson, Crick, and Franklin.

Now let’s look at the way two DNA strands get together. Again, think of DNA as a ladder. The sides of the ladder consist of alternating sugar and phosphate groups, while the rungs of the ladder consist of pairs of nitrogenous bases.

The nitrogenous bases pair up in a particular way. Adenine in one strand always binds to thymine (A–T or T–A) in the other strand. Similarly, guanine always binds to cytosine (G–C or C–G). This predictable matching of the bases is known as base pairing.

The two strands are said to be complementary. This means that if you know the sequence of bases in one strand, you’ll know the sequence of bases in the other strand. For example, if the base sequence in one DNA strand is A–T–C, the base sequence in the complementary strand will be T–A–G.

The two DNA strands run in opposite directions. You’ll notice from the figure above that each DNA strand has a 5’ end and a 3’ end, so-called for the carbon that ends the strand (i.e., the fifth carbon in the sugar ring is at the 5’ end, while the third carbon is at the 3’ end). The 5’ end has a phosphate group, and the 3’ end has an OH, or “hydroxyl,” group. The 5’ end of one strand is always opposite to the 3’ end of the other strand. The strands are therefore said to be antiparallel.

The DNA strands are linked by hydrogen bonds. Two hydrogen bonds hold adenine and thymine together, and three hydrogen bonds hold cytosine and guanine together.

Before we go any further, let’s review the base pairing in DNA:

GENOME STRUCTURE

The order of the four base pairs in a DNA strand is the genetic code. Like a special alphabet in our cells, these four nucleotides spell out thousands of recipes. Each recipe is called a gene. The human genome has around 20,000 genes.

The recipes of the genes are spread out among the millions of nucleotides of DNA, and all of the DNA for a species is called its genome. Each separate chunk of DNA in a genome is called a chromosome.

Prokaryotes have one circular chromosome, and eukaryotes have linear chromosomes. In eukaryotes, the DNA is further structured, likely since linear chromosomes are more likely to get tangled. To keep it organized, the DNA is wrapped around proteins called histones, and then the histones are bunched together in groups called a nucleosome. Not all DNA is wound-up equally, because it must be unwound in order to be read. How tightly DNA is packaged depends on the section of DNA and also what is going on in the cell at that time. Humans have 23 different chromosomes and they have two copies of each, so each human cell has 46 linear chromosome segments in the nucleus. The DNA of a cell is contained in structures called chromosomes. Chromosomes consist of DNA wrapped around proteins called histones. When the genetic material is in a loose form in the nucleus it is called euchromatin, and its genes are active, or available for transcription. When the genetic material is fully condensed into coils, it is called heterochromatin, and its genes are generally inactive. Situated in the nucleus, chromosomes contain the recipe for all the processes necessary for life, including passing themselves and their information on to future generations. In this chapter, we’ll look at precisely how they accomplish this.

DNA REPLICATION

We said in the beginning of this chapter that DNA is the hereditary blueprint of the cell. By directing the manufacture of proteins, DNA serves as the cell’s blueprint. But how is DNA inherited? For the information in DNA to be passed on, it must first be copied. This copying of DNA is known as DNA replication.

Because the DNA molecule is twisted over on itself, the first step in replication is to unwind the double helix by breaking the hydrogen bonds. This is accomplished by an enzyme called helicase. The exposed DNA strands now form a y-shaped replication fork.

Now each strand can serve as a template for the synthesis of another strand. DNA replication begins at specific sites called origins of replication. Because the DNA helix twists and rotates during DNA replication, another class of enzymes, called DNA topoisomerases, cuts and rejoins the helix to prevent tangling. The enzyme that performs the actual addition of nucleotides alongside the naked strand is DNA polymerase. But DNA polymerase, oddly enough, can only add nucleotides to the 3’ end of an existing strand. Therefore, to start off replication at the 5’ end, an enzyme called RNA primase adds a short strand of RNA nucleotides called an RNA primer. The primer is later degraded by enzymes, and the space is filled with DNA.

One strand is called the leading strand, and it is made continuously. That is, the nucleotides are steadily added one after the other by DNA polymerase. The other strand—the lagging strand—is made discontinuously. Unlike the leading strand, the lagging strand is made in pieces of nucleotides known as Okazaki fragments. Why is the lagging strand made in small pieces?

Normally, nucleotides are added only in the 5’ to 3’ direction since nucleotides can only be added to the 3’ end of the growing chain. However, when the double-helix is “unzipped,” one of the two strands is oriented in the opposite direction—3’ to 5’. Because DNA polymerase doesn’t work in this direction, nucleotides—the Okazaki fragments—need to be added in pieces. You can see in the figure below that the leading strand is being created towards the opening of the helix and the helix continually opens ahead of it to accommodate it. The lagging strand is built in the opposite direction of the way the helix is opening, so it can only build until it hits a previously built stretch. Once the helix unwinds a bit more, it can build another okazaki fragment, and so on. These fragments are eventually linked together by the enzyme DNA ligase to produce a continuous strand. Finally, hydrogen bonds form between the new base pairs, leaving two identical copies of the original DNA molecule.

When DNA is replicated, we don’t end up with two entirely new molecules. Each new molecule has half of the original molecule. Because DNA replicates in a way that conserves half of the original molecule in each of the two new ones, it is said to be semiconservative.

An interesting problem is that a few bases at the very end of a DNA molecule cannot be replicated because the DNA polymerase needs to bind. This means that every time replication occurs, the chromosome loses a few base pairs. The genome has compensated for this over time, by putting bits of unimportant (or at least less important) DNA at the ends of a molecule. These ends are called telomeres. They get shorter and shorter over time.

Many enzymes and proteins are involved in DNA replication. The ones you’ll need to know for the AP Biology Exam are DNA helicase, DNA polymerase, DNA ligase, topoisomerase, and RNA primase:

Key History

The reason that we know that the DNA is the inheritable material is because of several key experiments. The first turning point was achieved by Avery, MacLeod, and McCarty. They isolated various cellular components from a dead virulent strain of bacteria. Then they followed up on a previous experiment by Griffiths and added each of these cellular components to a stain of living non-virulent bacteria. Only the DNA component of the deadly bacteria was able to change the second bacteria into a deadly strain capable of reproducing. This means that the DNA must be responsible for passing traits and it is inheritable.

The next important experiment was done by Hershey-Chase. They used bacterophages, which are a special type of virus. They labelled the protein parts of some viruses with radiolabelled sulfur and they labelled the DNA parts of other viruses with radiolabelled phosphorus. When the viruses infected bacteria, only the labelled DNA was inside, but they were still able to replicate and make progeny viruses. Thus they proved that only DNA is required to pass on information. The protein was not required.

Central Dogma

DNA’s main role is directing the manufacture of molecules that actually do the work in the body. DNA is just the recipe book, not the chef or the meal. When a DNA recipe is used, scientists say that that DNA is expressed.

The first step of DNA expression is to turn it into RNA. The RNA is then sent out into the cell to perform its job. Often, the job of an RNA is to get turned into a protein. Proteins are the biggest group of “worker-molecules,” and most expressed DNA turns into proteins. These proteins, in turn, regulate everything that occurs in the cell.

The process of making an RNA from DNA is called transcription, and the process of making a protein from an RNA is called translation. Transcription takes place in the nucleus (where the DNA is kept), and translation takes place in the cytoplasm.

Obviously, in prokaryotes, both occur in the cytoplasm because prokaryotes don’t contain a nucleus; this allows transcription and translation to occur at the same time.

The flow of genetic information, the “Central Dogma” of Biology, is therefore:

RNA

Before we discuss transcription of RNA, let’s talk about its structure. Although RNA is also made up of nucleotides, it differs from DNA in three ways.

Here’s a table to compare DNA and RNA. Keep these differences in mind—the testing board loves to test you on them.

                                   

DIFFERENCES BETWEEN DNA AND RNA
	DNA (double-stranded)	RNA (single-stranded)
Sugar:	deoxyribose	ribose
Bases:	adenine  guanine  cytosine  thymine	adenine  guanine  cytosine  uracil

There are three main types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). All three types of RNA are key players in the synthesis of proteins:

There is also another class of RNA, called interfering RNAs, or RNAi. These are small snippets of RNA that are naturally made in the body or intentionally created by humans. These interfering RNAs, called siRNA and miRNA, can bind to specific sequences or RNA and mark them for destruction. This will be discussed more later in this chapter. Now that we know about the different types of RNA, let’s see how they direct the synthesis of proteins.

Transcription

Transcription involves making an RNA copy of a bit of DNA code. The initial steps in transcription are similar to the initial steps in DNA replication. The obvious difference is that, whereas in replication we end up with a complete copy of the cell’s DNA, in transcription we end up with only a specific section copied into an mRNA. This is because only the bit of DNA that needs to be expressed will be transcribed. If you wanted to make a cake, but your cookbook couldn’t leave your vault (AKA the nucleus), you wouldn’t copy the entire cookbook! You would only copy down the recipe for the cake.

Since each recipe is a gene, transcription occurs as-needed on a gene-by-gene basis.

The exception to this is prokaryotes because they will transcribe a recipe that can be used to make several proteins. This is called a polycistronic transcript. Eukaryotes tend to have one gene that gets transcribed to one mRNA and translated into one protein. Our transcripts are monocistronic.

Transcription involves three phases: initiation, elongation, and termination. As in DNA replication, the first initiation step in transcription is to unwind and unzip the DNA strands using helicase. Transcription begins at special sequences of the DNA strand called promoters. You can think of a promoter as a docking site or a runway. We will talk about how promoters are involved in regulating transcription later in the chapter.

Because RNA is single-stranded, we have to copy only one of the two DNA strands. The strand that serves as the template is known as the antisense strand, the non-coding strand, or the template strand. The other strand that lies dormant is the sense strand, or the coding strand.

Just as DNA polymerase builds DNA, RNA polymerase builds RNA, and just like DNA polymerase, RNA polymerase only adds nucleotides to the 3’ side (5’ to 3’). This means that the RNA polymerase must bind to the 3’ end of the template strand (which would be the 5’ end of future mRNA).

RNA polymerase doesn’t need a primer, so it can just start transcribing the DNA right off the bat. The promoter region is considered to be “upstream” of the actual coding part of the gene. This way the polymerase can get set up before the bases it needs to transcribe, like a staging area before an official parade starting point. The official starting point is called the start site.

When transcription begins, RNA polymerase travels along and builds an RNA that is complementary to the template strand of DNA. It is just like DNA replication except when DNA has an adenine, the RNA can’t add a thymine since RNA doesn’t have thymine. Instead the RNA adds a uracil to pair with adenine.

Once the mRNA finishes adding on nucleotides and reaches the termination sequence, it separates from the DNA template, completing the process of transcription. The new RNA has now transcribed, or “copied,” the sequence of nucleotide bases directly from the exposed DNA strand. Note that the freshly synthesized RNA is complementary to the template strand, but it is identical to the coding strand (with the substitution of uracil for thymine).

RNA Processing

In prokaryotes, the mRNA is now complete, but in eukaryotes the RNA must be processed before it can leave the nucleus.

In eukaryotes, the freshly transcribed RNA in called an hnRNA (heterogeneous nuclear RNA) and it contains both coding regions and noncoding regions. The regions that express the code that will be turned into protein are exons. The noncoding regions in the mRNA are introns.

The introns—the intervening sequences—must be removed before the mRNA leaves the nucleus. This is called splicing and it is accomplished by an RNA-protein complex called a spliceosome.

In addition to splicing, a poly(A) tail is added to the 3’ end and a 5’ GTP cap is added to the 5’ end. This process produces a final mRNA that is shorter than the transcribed RNA.

Translation

Translation is the process of turning an mRNA into a protein. Remember, each protein is made of amino acids. The order of the mRNA nucleotides will be read in the ribosome in groups of three. Three nucleotides is called a codon. Each codon corresponds to a particular amino acid. The genetic code is redundant, meaning that certain amino acids are specified by more than one codon.

The mRNA attaches to the ribosome to initiate translation and “waits” for the appropriate amino acids to come to the ribosome. That’s where tRNA comes in. A tRNA molecule has a unique three-dimensional structure that resembles a four-leaf clover:

One end of the tRNA carries an amino acid. The other end, called an anticodon, has three nitrogenous bases that can complementarily base pair with the codon in the mRNA. Usually, the normal rules of base pairing are set in stone, but tRNA anticodons can be a bit flexible when they bind with a codon on an mRNA, especially the 3 nucleotide in an anticodon. The third position is said to experience wobble pairing. Things that don’t normally bind will pair up, like guanine and uracil.

Transfer RNAs are the “go-betweens” in protein synthesis. Each tRNA becomes charged and enzymatically attaches to an amino acid in the cell’s cytoplasm and “shuttles” it to the ribosome. The charging enzymes involved in forming the bond between the amino acid and tRNA require ATP.

Translation also involves three phases: initiation, elongation, and termination. Initiation begins when a ribosome attaches to the mRNA.

What does the ribosome do? It helps the process along by holding everything in place while the tRNAs assist in assembling polypeptides.

Initiation

Ribosomes contain three binding sites: an A site, a P site, and an E site. The mRNA will shuffle through from A to P to E. As the mRNA codons are read, the polypeptide will be built. In all organisms the start codon for the initiation of protein synthesis is A–U–G, which codes for the amino acid methionine. Proteins can have AUGs in the rest of the protein that code for methionine as well, but the special first AUG of an mRNA is the one that will kick off translation. The tRNA with the complementary anticodon, U–A–C, is methionine’s personal shuttle; when the AUG is read on the mRNA, it delivers the methionine to the ribosome.

Elongation

The addition of amino acids is called elongation. Remember that the mRNA contains many codons, or “triplets,” of nucleotide bases. As each amino acid is brought to the mRNA, it is linked to its neighboring amino acid by a peptide bond. When many amino acids link up, a polypeptide is formed.

Termination

How does this process know when to stop? The synthesis of a polypeptide is ended by stop codons. A codon doesn’t always code for an amino acid; there are three that serve as a stop codon. Termination occurs when the ribosome runs into one of these three stop codons.

How about a little review?

Gene Regulation

What controls gene transcription, and how does an organism express only certain genes? Regulation of gene expression can occur at different times. The largest point is before transcription, or pre-transcriptional regulation. It can also occur post-transcriptionally or post-translationally.

The start of transcription requires the DNA to be unwound and RNA polymerase to bind at the promoter. The process is usually a bit more complicated than that because transcription factors can either encourage or inhibit this from happening. This is often accomplished by making it easier or more difficult for the RNA polymerase to bind or to move to the start site.

The following examples are famous models of regulation. You do not need to memorize them, but you should be familiar with the big picture of how things can come together to regulate transcription. Most of what we know about gene regulation comes from our studies of E. coli. In bacteria, the region of bacterial DNA that regulates gene expression is called an operon. One of the best-understood operons is the lac operon, which controls expression of the enzymes that break down lactose.

The operon consists of four major parts: structural genes, the regulatory gene, the promoter gene, and the operator:

The following two diagrams show the lac operon when lactose is absent (A) and when lactose is present (B).

Other operons, such as the trp operon, operate in a similar manner except that this mechanism is continually “turned on” and is only “turned off” in the presence of high levels of the amino acid, tryptophan. Tryptophan is a product of the pathway that codes for the trp operon. When tryptophan combines with the trp repressor protein, it causes the repressor to bind to the operator, which turns the operon “off,” thereby blocking transcription. In other words, a high level of tryptophan acts to repress the further synthesis of tryptophan.

The following two diagrams show the trp operon when tryptophan is absent (C) and when tryptophan is present (D).

Post-transcriptional regulation occurs when the cell creates an RNA, but then decides that it should not be translated into a protein. This is where RNAi comes into play. RNAi molecules can bind to an RNA via complementary base pairing. This creates a double-stranded RNA (remember RNA is usually single stranded). When a double-stranded RNA is formed, this signals to some special destruction machinery that the RNA should be destroyed. This would prevent it from going on to be translated.

Post-translational regulation can also occur. This would be if a cell has already made a protein, but it doesn’t need to use the protein yet. This is especially common regulation for enzymes because when the cell needs them, it needs them ASAP. It is easier to make them ahead of time and then just turn them on or off as needed. This can involve binding with other proteins, phosphorylation, pH, cleavage, etc. Remember, even if a protein is made, it might need other things to be made (or not made) in order for the protein to be functional.

MUTATIONS

A mutation is a error in the genetic code. Mutations can occur because DNA is damaged and cannot be repaired or because DNA damage is repaired incorrectly. Damage can be caused by chemicals or radiation. It can also occur when a DNA polymerase or an RNA polymerase makes a mistake. DNA polymerases have proofreading abilities, but RNA polymerases do not. This is because RNA is only a temporary molecule and if a mistake is made, it is not as problematic. DNA is important now and in the future since it is passed on from cell to cell in somatic cells and from parent to offspring. If the mistake occurs in a germline cell, that will become a gamete. Mistakes in DNA can last forever.

It is important to know that just having an error in the DNA is not a problem unless that gene is expressed AND the error causes a change in the gene product (RNA or protein). Think of it like an error in a recipe in a cookbook; an error won’t harm anyone unless the recipe is actually made AND the error causes a big change in the recipe. As we will see, a mutation can cause different types of effects.

Base Substitution

Base substitution (point) mutations result when a single nucleotide base is substituted for another. Point mutations can be:

Gene Rearrangements

Gene rearrangements involve DNA sequences that have deletions, duplications, inversions, and translocations.

BIOTECHNOLOGY

Recombinant DNA

Scientists have learned how to harness the central dogma in order to research and cure diseases. Recombinant DNA is generated by combining DNA from multiple sources to create a unique DNA molecule that is not found in nature. A common application of recombinant DNA technology is the introduction of a eukaryotic gene of interest (such as insulin) into a bacterium for production. Bacteria can be hijacked and put to work as little protein factories. This branch of technology that produces new organisms or products by transferring genes between cells is called genetic engineering.

Polymerase Chain Reaction (PCR)

A few years ago, it would take weeks of tedious experiments to identify and study specific genes. Today, thanks to polymerase chain reaction (PCR), we are able to make billions of identical copies of genes within a few hours. To do PCR, the process of DNA replication is slightly modified. In a small PCR tube, DNA, primers, a powerful DNA polymerase, and lots of DNA nucleotides (A’s, C’s, G’s, and T’s) are mixed together.

In a PCR machine, or thermocycler, the tube is heated, cooled, and warmed many times. Each time the machine is heated, the hydrogen bonds break, separating the double-stranded DNA. As it is cooled, the primers bind to the sequence flanking the region of the DNA we want to copy. When it is warmed, the polymerase binds to the primers on each strand and adds nucleotides on each template strand. After this first cycle is finished, there are two identical double-stranded DNA molecules. When the second cycle is completed, these two double-stranded DNA segments will have been copied into four. The process repeats itself over and over, creating as much DNA as needed.

Transformation

Insulin, the protein hormone that lowers blood sugar levels, can now be made for medical purposes by bacteria. Yes, bacteria can be induced to use the universal DNA code to transcribe and translate a human gene! The process of giving bacteria foreign DNA is called transformation.

Genes of interest are first placed into a small circular DNA molecule called a plasmid. Often, a plasmid is pre-designed to have some special helpful genes in it, and together, these are called a vector. Plasmid vectors often contain genes for antibiotic resistance and restriction sites. Plasmids and the gene of interest are cut with the same restriction enzyme (restriction enzymes cut DNA at very specific pre-determined sequences), creating compatible sticky ends. When placed together, the gene is inserted into the plasmid creating recombinant DNA.

The bacteria are then transformed (given the recombinant DNA to take up). In most AP Biology courses, this is done by the heat shock method.

Not all the bacteria will be transformed, but the ones that did not take up the plasmid are not needed. This is where the antibiotic resistance gene on the vector comes in. By growing all the bacteria in the presence of an antibiotic, only those with the resistance gene (AKA those that have been transformed) will survive.

This laboratory technique has not only been used to safely mass-produce important proteins used for medicine, such as insulin, it also plays an important role in the study of gene expression. A technique similar to transformation is transfection, which is putting a plasmid into a eukaryotic cell, rather than a bacteria cell. This is a bit trickier than transformation. Because eukaryotic cells do not grow like bacteria do, transfection is not as useful for making large quantities of something, but sometimes it is important to use eukaryotic cells.

Gel Electrophoresis

An important part of DNA technology is the ability to observe differences in different preparations of DNA.

The DNA fragments can be separated according to their molecular weight using gel electrophoresis. Because DNA and RNA are negatively charged, they migrate through the gel toward the positive pole of the electrical field. The smaller the fragments, the faster they move through the gel. Restriction enzymes are also used to create a molecular fingerprint. The patterns created after cutting with restriction enzymes are unique for each person because each person’s DNA is slightly different. Some people might have sequences that are cut many times, resulting in many tiny fragments, and others might have sequences that are cut infrequently, producing a few large fragments. When restriction fragments between individuals of the same species are compared, the fragments differ in length because of polymorphisms, which are slight differences in DNA sequences. These fragments are called restriction fragment length polymorphisms, or RFLPs. In DNA fingerprinting, RFLPs produced from DNA left at a crime scene are compared to RFLPs from the DNA of suspects.

KEY TERMS

nucleotide

five-carbon sugar

phosphate

nitrogenous base

deoxyribose

adenine

guanine

cytosine

thymine

phosphodiester bonds

double helix

Watson, Crick, and Franklin

base pairing

complementary

antiparallel

hydrogen bonds

gene

genome

chromosome

nucleosome

euchromatin

heterochromatin

DNA replication

helicase

replication fork

origins of replication

topoisomerase

DNA polymerase

RNA primase

RNA primer

leading strand

lagging strand

Okazaki fragments

DNA ligase

semiconservative replication

telomeres

Avery, MacLeod, and McCarty

Hershey-Chase

transcription

translation

Central Dogma

ribose

uracil

messenger RNA (mRNA)

ribosomal RNA (rRNA)

transfer RNA (tRNA)

RNA interference (RNAi)/silencing RNA (siRNA)

polycistronic

monocistronic

promoter

antisense/non-coding/template strand

sense/coding strand

RNA polymerase

start site

exons

introns

spliceosome

poly(A) tail

5’ GTP cap

codon

anticodon

wobble pairing

Initiation

Elongation

Termination

A site, P site, E site

start codon

stop codons

pre-transcriptional regulation

transcription factors

operon

structural genes

promoter genes

operator site

regulatory gene

post-transcriptional regulation

post-translational regulation

mutation

base substitution

nonsense mutation

missense mutation

silent mutation

insertions

deletions

frameshift mutation

duplications

inversions

translocations

recombinant DNA

genetic engineering

polymerase chain reaction (PCR)

transformation

plasmid

vector

restriction enzyme

sticky end

transfection

gel electrophoresis

restriction fragment length polymorphism (RFLPs)

DNA fingerprinting

Summary

Chapter 7 Drill

Answers and explanations can be found in Chapter 16.

REFLECT

Respond to the following questions:

Chapter 8

Cell Reproduction

CELL DIVISION

Every second, thousands of cells are dying throughout our bodies. Fortunately, the body replaces them at an amazing rate. In fact, epidermal cells, or skin cells, die off and are replaced so quickly that the average 18-year-old grows an entirely new skin every few weeks. The body keeps up this unbelievable rate thanks to the mechanisms of cell division.

This chapter takes a closer look at how cells divide. But remember, cell division is only a small part of the life cycle of a cell. Most of the time, cells are busy carrying out their regular activities. There are also some types of cells that are nondividing. Often, these are highly specialized cells that are created from a population of less specialized cells. The body continually makes them as needed, but they do not directly replicate themselves. Red blood cells are nondividing cells. Other cells are just temporarily nondividing. They enter a phase called G₀, where they hang out until they get a signal to re-enter the normal cell cycle.

THE CELL CYCLE

Every cell has a life cycle—the period from the beginning of one division to the beginning of the next. The cell’s life cycle is known as the cell cycle. The cell cycle is divided into two periods: interphase and mitosis. Take a look at the cell cycle of a typical cell.

INTERPHASE: THE GROWING PHASE

Interphase is the time span from one cell division to another. We call this stage interphase (inter- means between) because the cell has not yet started to divide. Although biologists sometimes refer to interphase as the “resting stage,” the cell is definitely not inactive. This phase is when the cell carries out its regular activities. All the proteins and enzymes it needs to grow are produced during interphase.

The Three Stages of Interphase

Interphase can be divided into three stages: G₁, S, G₂.

The most important phase is the S phase. That’s when the cell replicates its genetic material. The first thing a cell has to do before undergoing mitosis is to duplicate all of its chromosomes, which contain the organism’s DNA “blueprint.” During interphase, every single chromosome in the nucleus is duplicated.

You’ll notice that the original chromosome and its duplicate are still linked, like conjoined twins. These identical strands of DNA are now called sister chromatids. The chromatids are held together by a structure called the centromere. You can think of each chromatid as a chromosome, but because they remain attached they are called chromatids instead. Chromosomes need to have their own centromere. Once the chromatids separate they will be full-fledged chromosomes.

Cell Cycle Regulation

We’ve already said that replication occurs during the S phase of interphase, so what happens during G₁ and G₂? During these stages, the cell produces proteins and enzymes. For example, during G₁ the cell produces all of the enzymes required for DNA replication (DNA helicase, DNA polymerase, and DNA ligase, as we learned in Chapter 7). By the way, G stands for “gap,” but we can also associate it with “growth.” These three phases are highly regulated by checkpoints and special proteins called cyclins and cyclin-dependent kinases (CDKs).

Cell cycle checkpoints are control mechanisms that make sure cell division is happening properly in eukaryotic cells. They monitor the cell to make sure it is ready to progress through the cell cycle and stop progression if it is not. In eukaryotes, checkpoint pathways function mainly at phase boundaries (such as the G₁/S transition and the G₂/M transition). Checkpoint pathways are an example of an important cell signaling pathway inside of cells.

For example, if the DNA genome has been damaged in some way, the cell should not divide. If it does, damaged DNA will be passed onto daughter cells, which can be disastrous. When damaged DNA is found, checkpoints are activated and cell cycle progression stops. The cell uses the extra time to repair damage in DNA. If the DNA damage is so extensive that it cannot be repaired, the cell can undergo apoptosis, or programmed cell death. Apoptosis cannot stop once it has begun, so it is a highly regulated process. It is an important part of normal cell turnover in multicellular organisms.

Cell cycle checkpoints control cell cycle progression by regulating two families of proteins: cyclin-dependent kinases (CDKs) and cyclins. To induce cell cycle progression, an inactive CDK binds a regulatory cyclin. Once together, the complex is activated, can affect many proteins in the cell, and causes the cell cycle to continue. To inhibit cell cycle progression, CDKs and cyclins are kept separate. CDKs and cyclins were first studied in yeast, unicellular eukaryotic fungi. Budding yeast and fission yeast were good model organisms because they have only one CDK protein each and a few different cyclins. This relatively simple system allowed biologists to figure out how cell cycle progression is controlled. Their findings were then used to figure out how more complex eukaryotes (such as mammals) control the cell cycle.

Cancer

A cell losing control of the cell cycle can have disastrous consequences. For example, a mutation in a protein that normally controls progression through the cell cycle can result in unregulated cell division and cancer. Cancer means “crab,” as in the zodiac sign. The name comes from the observation that malignant tumors grow into surrounding tissue, embedding themselves like clawed crabs. Cancer occurs when normal cells start behaving and growing very abnormally and spread to other parts of the body.

Mutated genes that induce cancer are called oncogenes (“onco-” is a prefix denoting cancer). Normally, these genes are required for proper growth of the cell and regulation of the cell cycle. Oncogenes, then, are genes that can convert normal cells into cancerous cells. Often these are abnormal or mutated versions of normal genes. The normal healthy version is called a proto-oncogene.

Tumor suppressor genes produce proteins that prevent the conversion of normal cells into cancer cells. They can detect damage to the cell and work with CDK/cyclin complexes to stop cell growth until the damage can be repaired. They can also trigger apoptosis if the damage is too severe to be repaired.

Cell cycle checkpoints and apoptosis have been intimately linked with cancer. In order for a normal cell to become a cancer cell, it must override cell cycle checkpoints and grow in an unregulated way. It must also avoid cell death. Tumors often accumulate DNA damage. Cancer treatments target these changes, because they are what make a cancer cell different from a normal cell.

Let’s recap:

MITOSIS: THE DANCE OF THE CHROMOSOMES

Once the chromosomes have replicated, the cell is ready to begin mitosis. Mitosis is the period when the cell divides. Mitosis consists of a sequence of four stages: prophase, metaphase, anaphase, and telophase. It is not important to memorize the name of each phase, but it is important that you know the basic order of operations for mitosis.

Stage 1: Prophase: Prep (the cell prepares to divide)

One of the first signs of prophase is the disappearance of the nucleolus (ribosome making area) and the nuclear envelope. In prophase, the chromosomes thicken, forming coils upon coils, and become visible, the dense chromosomes are called chromatin. (During interphase, the chromosomes are not visible.)

Now the cell has plenty of room to “sort out” the chromosomes. Remember centrioles? During prophase, these cylindrical bodies found within microtubule organizing centers (MTOCs) start to move away from each other, toward opposite ends of the cell. The centrioles will spin out a system of microtubules known as the spindle fibers. These spindle fibers will attach to a structure on each chromatid called a kinetochore. The kinetochores are part of the centromere.

Stage 2: Metaphase: Middle (chromosomes align in the middle)

The next stage is called metaphase. The chromosomes now begin to line up along the equatorial plane, or the metaphase plate, of the cell. That’s because the spindle fibers are attached to the kinetochore of each chromatid.

Stage 3: Anaphase: Apart (the chromatids are pulled apart)

During anaphase, the sister chromatids of each chromosome separate at the centromere and migrate to opposite poles. The chromatids are pulled apart by the microtubules, which begin to shorten. Each half of a pair of sister chromatids now moves to opposite poles of the cell. Non-kinetochore microtubules elongate the cell.

Stage 4: Telophase: Two (the cell completes splitting in two)

The final phase of mitosis is telophase. A nuclear membrane forms around each set of chromosomes and the nucleoli reappear.

The nuclear membrane is ready to divide. Now it’s time to split the cytoplasm in a process known as cytokinesis. Look at the figure below and you’ll notice that the cell has begun to split along a cleavage furrow (which is produced by actin microfilaments).

A cell membrane forms about each cell, and the cells split into two distinct daughter cells. The division of the cytoplasm yields two daughter cells.

Here’s one thing to remember: cytokinesis occurs differently in plant cells. The cell doesn’t form a cleavage furrow. Instead, a partition called a cell plate forms down the middle region.

Stage 5: Interphase

Once the daughter cells are produced, they reenter the initial phase—interphase—and the whole process starts over. The cell goes back to its original state. Once again, the chromosomes become invisible, and the genetic material is called chromatin again.

But How Will I Remember All That?

For mitosis, you may already have your own mnemonic. If not, here’s a table with a mnemonic we created for you.

                                             

IPMAT
Interphase	I is for Interlude
Prophase	P is for Prepare
Metaphase	M is for Middle
Anaphase	A is for Apart
Telophase	T is for Two

Purpose of Mitosis

Mitosis has two purposes:

For our purposes, we can say that mitosis occurs in just about every cell except sex cells. When you think of mitosis, remember: “Like begets like.” Hair cells “beget” other hair cells, skin cells “beget” other skin cells, and so on. Mitosis is involved in growth, repair, and asexual reproduction.

HAPLOIDS VERSUS DIPLOIDS

Every organism has a certain number of unique chromosomes. For example, fruit flies have four chromosomes, humans have twenty-three chromosomes, and dogs have thirty-nine chromosomes. It turns out that most eukaryotic cells in fact have two full sets of chromosomes—one set from each parent. Humans, for example, have two sets of twenty-three chromosomes, giving us our grand total of forty-six.

A cell that has two sets of chromosomes is a diploid cell, and the zygotic chromosome number is given as “2n.” That means we have two copies of each chromosome. In humans, for example, the diploid number of chromosomes is forty-six.

If a cell has only one set of chromosomes, we call it a haploid cell. This kind of cell is given the symbol n. For example, we would say that the haploid number of chromosomes for humans is twenty-three.

Remember:

Why do we need to know the terms haploid and diploid? Because they are extremely important when it comes to sexual reproduction. As we’ve seen, forty-six is the normal diploid number for human beings, but there are only twenty-three different chromosomes. The duplicate versions of each chromosome are called homologous chromosomes. The homologous chromosomes that make up each pair are similar in size and shape and express similar traits. This is the case in all sexually reproducing organisms. In fact, this is the essence of sexual reproduction: each parent donates half its chromosomes to its offspring.

Gametes

Although most cells in the human body are diploid, there are special cells that are haploid. These haploid cells are called sex cells, or gametes. Why do we have haploid cells?

As we’ve said, an offspring has one set of chromosomes from each of its parents. A parent, therefore, contributes a gamete with one set that will be paired with the set from the other parent to produce a new diploid cell, or zygote. This produces offspring that are a combination of their parents.

AN OVERVIEW OF MEIOSIS

Meiosis is the production of gametes. Since sexually reproducing organisms need only haploid cells for reproduction, meiosis is limited to sex cells in special sex organs called gonads. In males, the gonads are the testes, while in females they are the ovaries. The special cells in these organs—also known as germ cells—produce haploid cells (n), which then combine to restore the diploid (2n) number during fertilization.

When it comes to genetic variation, meiosis is a big plus. Variation, in fact, is the driving force of evolution. The more variation there is in a population, the more likely it is that some members of the population will survive extreme changes in the environment. Meiosis is far more likely to produce these sorts of variations than is mitosis, which therefore confers selective advantage on sexually reproducing organisms. We’ll come back to this theme in Chapter 10.

A Closer Look at Meiosis

Meiosis actually involves two rounds of cell division: meiosis I and meiosis II.

Before meiosis begins, the diploid cell goes through interphase. Just as in mitosis, double-stranded chromosomes are formed during this phase.

Meiosis I

Meiosis I consists of four stages: prophase I, metaphase I, anaphase I, and telophase I.

Prophase I

Prophase I is a little more complicated than regular prophase. As in mitosis, the nuclear membrane disappears, the chromosomes become visible, and the centrioles move to opposite poles of the nucleus. But that’s where the similarity ends.

The major difference involves the movement of the chromosomes. In meiosis, the chromosomes line up side-by-side with their counterparts (homologs). This event is known as synapsis.

Synapsis involves two sets of chromosomes that come together to form a tetrad (or a bivalent). A tetrad consists of four chromatids. Synapsis is followed by crossing-over, the exchange of segments between homologous chromosomes.

What’s unique in prophase I is that pieces of chromosomes are exchanged between the homologous partners. This is one of the ways organisms produce genetic variation. By the end of prophase I, the chromosomes will have exchanged regions containing several alleles, or different forms of the same gene. This means that each chromosome might have a different mix of alleles than it began with. Remember, the two homologous chromosomes are the versions that came from the person’s mother and father. So, a chromosome that has experienced crossing-over will now be a mix of alleles from the mother and father versions.

Metaphase I

As in mitosis, the chromosome pairs—now called tetrads—line up at the metaphase plate. By contrast, you’ll recall that in regular metaphase, the chromosomes line up individually. One important concept to note is that the alignment during metaphase is random, so the copy of each chromosome that ends up in a daughter cell is random. Therefore, the gamete will be created with a mixture of genetic information from the person’s father and mother. This means that the offspring created would be a combination of all four grandparents.

Anaphase I

During anaphase I, one of each pair of chromosomes within a tetrad separates and moves to opposite poles. Notice that the chromatids do not separate at the centromere. The homologs separate with their centromeres intact.

The chromosomes now go on to their respective poles.

Telophase I

During telophase I, the nuclear membrane forms around each set of chromosomes.

Finally, the cells undergo cytokinesis, leaving us with two daughter cells. Notice that at this point the nucleus contains the haploid number of chromosomes, but each chromosome is a duplicated chromosome.

Meiosis II

The purpose of the second meiotic division is to separate the sister chromatids, and the process is virtually identical to mitosis. Let’s run through the steps in meiosis II.

During prophase II, the chromosomes once again condense and become visible. In metaphase II, the chromosomes move toward the metaphase plate. This time they line up single file, not as pairs. During anaphase II, the chromatids of each chromosome split at the centromere, and each chromatid is pulled to opposite ends of the cell. At telophase II, a nuclear membrane forms around each set of chromosomes and a total of four haploid cells are produced.

Gametogenesis

Meiosis is also known as gametogenesis. If sperm cells are produced, then meiosis is called spermatogenesis. During spermatogenesis, four sperm cells are produced for each diploid cell. If an egg cell or an ovum is produced, this process is called oogenesis.

Oogenesis is a little different from spermatogenesis. Oogenesis produces only one ovum, not four. The other three cells, called polar bodies, get only a tiny amount of cytoplasm and eventually degenerate. Why does oogenesis produce only one ovum? Because the female wants to conserve as much cytoplasm as possible for the surviving gamete, the ovum.

Here’s a summary of the major differences between mitosis and meiosis.

                                               

MITOSIS	MEIOSIS
• Occurs in somatic (body) cells	• Occurs in germ (sex) cells
• Produces identical cells	• Produces gametes
• Diploid cell → diploid cells	• Diploid cell → haploid cells
• 1 cell becomes 2 cells	• 1 cell becomes 4 cells
• Number of divisions: 1	• Number of divisions: 2

Meiotic Errors

Sometimes, a set of chromosomes has an extra or a missing chromosome. This occurs because of nondisjunction—the chromosomes failed to separate properly during meiosis. This error, which produces the wrong number of chromosomes in a cell, usually results in miscarriage or severe genetic defects. For example, humans typically have two copies of each chromosome, but individuals with Down syndrome have three—instead of two—copies of the twenty-first chromosome.

Chromosomal abnormalities also occur if one or more segments of a chromosome break and are either lost or reattach to another chromosome. The most common example is translocation (a segment of a chromosome moves to another chromosome).

Here’s an example of a translocation.

Fortunately, in most cases, damaged DNA can usually be repaired with special repair enzymes.

KEY TERMS

cell division

cell cycle

interphase

mitosis

G₀ phase

G₁ phase

G₂ phase

S phase

sister chromatids

centromere

cyclins

cyclin-dependent kinases (CDKs)

cell cycle checkpoints

apoptosis

cancer

oncogene

tumor suppressor gene

prophase

metaphase

anaphase

telophase

chromatin

spindle fibers

kinetochores

metaphase plate

cytokinesis

cleavage furrow

cell plate

diploid cell

haploid cell

homologous chromosomes

sex cells (or gametes)

meiosis

gonads

testes

ovaries

germ cells

meiosis I

meiosis II

synapsis

tetrad (or bivalent)

crossing-over (or recombination)

alleles

gametogenesis

spermatogenesis

oogenesis

polar bodies

ovum

nondisjunction

Down syndrome

translocation

Summary

Chapter 8 Drill

Answers and explanations can be found in Chapter 16.

Questions 2 and 3 refer to the following graph and paragraph.

An experiment is performed to evaluate the amount of DNA present during a complete cell cycle. All of the cells were synced prior to the start of the experiment. During the experiment, a fluorescent chemical was applied to cells, which would only fluoresce when bound to DNA. The results of the experiment are shown above. Differences in cell appearance by microscopy or changes in detected DNA were determined to be phases of the cell cycle and are labeled with the letters A–D.

Question 4 represents a question requiring a numeric answer. Calculate the correct answer for each question.

REFLECT

Respond to the following questions:

Chapter 9

Heredity

GREGOR MENDEL: THE FATHER OF GENETICS

What is genetics? In its simplest form, genetics is the study of heredity. It explains how certain characteristics are passed on from parents to children. Much of what we know about genetics was discovered by the monk Gregor Mendel in the 19th century. Since then, the field of genetics has vastly expanded. But before we get ahead of ourselves, let’s study the basic rules of genetics.

Let’s begin then with some of the fundamental points of genetics:

                                       

Name	Genotype	Phenotype
homozygous dominant	TT	Tall
homozygous recessive	tt	Short
heterozygous	Tt	Tall

One of the major ways the testing board likes to test genetic information is by having you do crosses. Crosses involve the mating of hypothetical organisms with specific phenotypes and genotypes. We’ll look at some examples in a moment, but for now, keep these test-taking tips in mind:

Now let’s look at some basic genetic principles.

MENDELIAN GENETICS

One of Mendel’s hobbies was to study the effects of cross-breeding on different strains of pea plants. Mendel worked exclusively with true-breeder pea plants. This means the plants he used were genetically pure and consistently produced the same traits. For example, tall plants always produced tall plants; short plants always produced short plants. Through his work, he came up with three principles of genetics: the law of dominance, the law of segregation, and the law of independent assortment.

The Law of Dominance

Mendel crossed two true-breeding plants with contrasting traits: tall pea plants and short pea plants.

To his surprise, when Mendel mated these plants, the characteristics didn’t blend to produce plants of average height. Instead, all the offspring were tall.

Mendel recognized that one trait must be masking the effect of the other trait. This is called the law of dominance. The dominant tall allele, T, somehow masked the presence of the recessive short allele, t. Consequently, all a plant needs is one tall allele to make it tall.

Monohybrid Cross

A monohybrid cross is when two individuals that are heterozygous for two traits are crossed. However, in order to be sure that you have heterozygotes, the first step is to cross true-breeding plants of allele #1 with true-breeding plants of allele #2. Follow along as these plants are crossed.

A simple way to represent a cross is to set up a Punnett square. Punnett squares are used to predict the results of a cross. Let’s construct a Punnett square for the cross between Mendel’s tall and short pea plants. Let’s first designate the alleles for each plant. As we saw earlier, we can use the letter “T” for the tall dominant allele and “t” for the recessive short allele.

Since one parent was a pure, tall pea plant, we’ll give it two dominant alleles (TT homozygous dominant). The other parent was a pure, short pea plant, so we’ll give it two recessive alleles (tt homozygous recessive). Let’s put the alleles for one of the parents across the top of the box and the alleles for the other parent along the side of the box.

Now we can fill in the four boxes by matching the letters. What are the results for the F1 generation?

Each offspring received one allele from each parent. They all received one T and one t. They’re all Tt! Our parents had duplicate copies of single alleles, TT and tt, respectively. We could therefore refer to them as homozygous. The offspring, on the other hand, are heterozygous: they possess one copy of each allele.

Let’s compare the results of this cross with what we already know about meiosis. From meiosis, we know that when gametes are formed, the chromosomes separate so that each cell gets one copy of each chromosome. We now know that chromosomes are made up of genes, and genes consist of alleles. We’ve just seen that alleles also separate and recombine. We can say, therefore, that each allele on the edge of a Punnett square also “represents” a gamete.

When fertilization occurs, chromosomes—along with the alleles they carry—get paired up in a new combination.

The Law of Segregation

Next, Mendel took the offspring and self-pollinated them. Let’s use a Punnett square to spell out the results. This time we’re mating the offspring of the first generation—F1. Take a look at the results:

One of the offspring could be a short pea plant! The short-stemmed trait reappeared in the F2 generation. How could that happen? Once again, the alleles separated and recombined, producing a new combination for this offspring. The cross resulted in one offspring with a pair of recessive alleles, tt. Because there is no T (dominant) allele around to mask the expression of the recessive short allele, our new plant could wind up short.

Although all of the F1 plants appear to be tall, the alleles separate and recombine during the cross. This is an example of the Law of Segregation. It just means that each gamete only gets one of the two copies of a gene. Gametes are haploid.

What about the genotype and phenotype for this cross? Remember, genotype refers to the genetic makeup of an organism, whereas phenotype refers to the appearance of the organism. Using the results of our Punnett square, what is the ratio of phenotypes and genotypes in the offspring?

Let’s sum up the results. We have four offspring with two different phenotypes: three of the offspring are tall, whereas one of them is short. On the other hand, we have three genotypes: 1 TT, 2 Tt, and 1 tt.

Here’s a summary of the results:

The Law of Independent Assortment

So far, we have looked at only one trait: tall versus short. What happens when we study two traits at the same time? The two traits also segregate randomly. This is an example of independent assortment. For example, let’s look at two traits in pea plants: height and color. When it comes to height, a pea plant can be either tall or short. As for color, the plant can be either green or yellow, with green being dominant. Each gene comes in two alleles, so this gives us four alleles total. By the Law of Independent Assortment, these four alleles can combine to give us four different gametes.

In other words, each allele of the height gene can be paired with either allele of the color gene. The reason alleles segregate independently is because chromosomes segregate independently. During meiosis I, each pair of homologous chromosomes is split, and which one aligns left or right during metaphase I is different for each pair.

Dihybrid Cross

Now that we know that different genes assort independently, let’s look at a cross of two traits. The dihybrid cross is just like the monohybrid, but it is when two heterozygotes for two genes are crossed. Keep in mind that the uppercase letter refers to the dominant allele. Therefore, T refers to tall and G refers to green, whereas t refers to short and g refers to yellow. Now let’s set up a cross between plants differing in two characteristics—called a dihybrid cross—using these four gametes and see what happens.

Each trait will act independently, meaning that a plant that is tall can be either green or yellow. Similarly, a green plant can be either tall or short.

Here is the Punnett Square for a cross between two double heterozygotes (Tt Gg).

This is an example of the Law of Independent Assortment. Each of the traits segregated independently. Don’t worry about the different combinations in the cross—you’ll make yourself dizzy with all those letters. Simply memorize the phenotype ratio of the pea plants. For the 16 offspring there are:

That’s 9:3:3:1, but don’t forget the circumstances that this applies. It is only when two heterozygotes for two genes are crossed. It is not just a magic ratio that always works.

The Punnett square method works well for monohybrid crosses and helps us visualize the possible combinations. However, a better method for predicting the likelihood of certain results from a dihybrid cross is to apply the law of probability. For dihybrid ratios, the law states that the probability that two or more independent events will occur simultaneously is equal to the product of the probability that each will occur independently. To illustrate the product rule, let’s consider again the cross between two identical dihybrid tall, green plants with the genotype TtGg. To find the probability of having a tall, yellow plant, simply multiply the probabilities of each event. If the probability of being tall is and the probability of being yellow is , then the probability of being tall and yellow is × = .

Let’s summarize Mendel’s three laws.

                                     

SUMMARY OF MENDEL’S LAWS
Laws	Definition
Law of dominance	One trait masks the effects of another trait.
Law of segregation	Each gamete only gets one of the copies of each gene.
Law of independent assortment	Each pair of homologous chromosomes splits independently, so the alleles of different genes can mix and match

Test Cross

Suppose we want to know if a tall plant is homozygous (TT) or heterozygous (Tt). Its physical appearance doesn’t necessarily tell us about its genetic makeup. The only way to determine its genotype is to cross the plant with a recessive, short plant, tt. This is known as a test cross, or back cross. Using the recessive plant, there are only two possibilities: (1) TT × tt or (2) Tt × tt. Let’s take a look.

If none of the offspring is short, our original plant must have been homozygous, TT. If, however, even one short plant appears in the bunch, we know that our original pea plant was heterozygous, Tt. In other words, it wasn’t a pure-breeding plant. A test cross uses a recessive organism to determine the genotype of an organism of unknown genotype.

BEYOND MENDELIAN GENETICS

Not all patterns of inheritance obey the principles of Mendelian genetics. In fact, many traits we observe are due to a combined expression of alleles. Here are a couple of examples of non-Mendelian forms of inheritance:

Since linked genes are found on the same chromosome, they cannot segregate independently. This violates the Law of Independent Assortment.

Let’s pretend that the height and color genes we looked at in the dihybrid cross are linked. A heterozygote for both traits still has two alleles for height (T and t) and two alleles for color (G and g). However, because height and color are located on the same chromosome, the allele for height and the allele for color are physically linked. For example, maybe the heterozygote has one chromsome with Tg and one chromosome with tG. When gametes are formed, the T and g will travel together, and the t and G will travel together and be packaged into a gamete together. So, in the unlinked dihybrid shown earlier there were four possible gamete combinations (TG, Tg, tG, tg), but now there are only two (Tg and tG). The only way to physically separate linked alleles is by crossing over. If a crossover event occurs between the linked genes then recombinant gametes can occur.

If the genes were unlinked then the the four gametes (TG, Tg, tG, tg) would be equally likely. If certain combinations of alleles are found more often in offspring (are likely appearing more often in gametes), then this is a sign of possible linkage.

Look at the example below from a cross of TtGg and ttgg. If you draw out the punnett square you should get equal numbers of each phenotype occurring if the genes are assumed to be unlinked.

There are more Green/short and yellow/Tall offspring. This is a sign that these alleles are linked on a chromosome.

The percentage of recombination (or recombination frequency) can be determined by adding up the recombinants and dividing by the total number of offspring.

This percentage can also be used as a measure of how far apart the genes are. The distance on a chromosome is measured in map units or centimorgans.

The frequency of crossing-over between any two linked alleles is proportional to the distance between them. That is, the farther apart two linked alleles are on a chromosome, the more often the chromosome will cross over between them. This finding led to recombination mapping—mapping of linkage groups with each map unit being equal to 1 percent recombination. For example, if two linked genes, A and B, recombine with a frequency of 15 percent, and B and C recombine with a frequency of 9 percent, and A and C recombine with a frequency of 24 percent, what is the sequence and the distance between them?

The sequence and the distance of A-B-C is

If the recombination frequency between A and C had been 6 percent instead of 24 percent, the sequence and distance of A-B-C would instead be

SEX-LINKED TRAITS

We already know that humans contain twenty-three pairs of chromosomes. Twenty-two of the pairs of chromosomes are called autosomes. They code for many different traits. The other pair contains the sex chromosomes. This pair determines the sex of an individual. A female has two X chromosomes. A male has one X and one Y chromosome—an X from his mother and a Y from his father. Some traits, such as color blindness and hemophilia, are carried on sex chromosomes. These are called sex-linked traits. Most sex-linked traits are found on the X chromosome and are more properly referred to as “X-linked.”

Since males have one X and one Y chromosome, what happens if a male has a defective X chromosome? Unfortunately, he’ll express the sex-linked trait, even if it is recessive. Why? Because his one and only X chromosome is defective. He doesn’t have another X to mask the effect of the bad X. However, if a female has only one defective X chromosome, she won’t express a recessive sex-linked trait. For her to express the trait, she has to inherit two defective X chromosomes. A female with one defective X is called a carrier. Although she does not exhibit the trait, she can still pass it on to her children.

You can also use the Punnett square to figure out the results of sex-linked traits. Here’s a classic example: a male who has normal color vision and a woman who is a carrier for color blindness have children. How many of the children will be color-blind? To figure out the answer, let’s set up a Punnett square.

Notice that we placed a bar above any defective X to indicate the presence of a defective allele. And now for the results. The couple have one son who is color-blind, a son who sees color normally, a daughter who is a carrier, and a daughter who sees color normally. The color-blind child is a son.

Barr Bodies

A look at the cell nucleus of normal females will reveal a dark-staining body known as a Barr body. A Barr body is an X chromosome that is condensed and visible. In every female cell, one X chromosome is activated and the other X chromosome is deactivated during embryonic development. Surprisingly, the X chromosome destined to be inactivated is randomly chosen in each cell. Therefore, in every tissue in the adult female one X chromosome remains condensed and inactive. However, this X chromosome is replicated and passed on to a daughter cell. X-inactivation is why it is okay that females have two X chromosomes and males only have one. After X-inactivation, it is like everyone has one copy.

Other Sex-Linked Diseases

KEY TERMS

Gregor Mendel

trait

genes

locus

homologous chromosomes

alleles

homozygous

heterozygous

phenotype

genotype

dominant

recessive

parent, or P1 generation

filial, or F1 generation

F2 generation

law of dominance

law of segregation

law of independent assortment

monohybrid cross

Punnett square

dihybrid cross

test cross

incomplete dominance

codominance

polygenetic inheritance

multiple alleles

non-nuclear inheritance

linked genes

map units

autosomes

sex chromosomes

color blindness

hemophilia

sex-linked traits

carrier

Barr body

Summary

Chapter 9 Drill

Answers and explanations can be found in Chapter 16.

REFLECT

Respond to the following questions:

Chapter 10

Evolutionary Biology

All of the organisms we see today arose from earlier organisms. This process, known as evolution, can be described as a change in a population over time. Interestingly, however, the driving force of evolution, natural selection, operates on the level of the individual. In other words, evolution is defined in terms of populations but occurs in terms of individuals.

NATURAL SELECTION

What is the basis of our knowledge of evolution? Much of what we now know about evolution is based on the work of Charles Darwin. Darwin was a nineteenth-century British naturalist who sailed the world in a ship named the HMS Beagle. Darwin developed his theory of evolution based on natural selection after studying animals in the Galápagos Islands and other places.

He observed that there were similar animals on the various islands, but the beaks varied in length on the finches and the necks varied in length on the tortoises. There must be a reason why animals in different areas had different traits. Darwin concluded that it was impossible for the finches and tortoises of the Galápagos simply to “grow” longer beaks or necks as needed. Rather, those traits were inherited and passed on from generation to generation. So, he decided there must be a way for populations to evolve and change their traits (i.e., a population of finches developing longer beaks).

He decided that there must have been a variety of beak lengths originally, but only the longest one was particularly helpful. Since those finches could eat better, survive better, and reproduce better, they were more likely to contribute offspring to the next generation. Over many years, the long-beak finches became more and more plentiful with each generation until long beaks were the “norm.” In another example, on the first island Darwin studied, there must once have been short-necked tortoises. Unable to reach the higher vegetation, these tortoises eventually died off, leaving only those tortoises with longer necks. Consequently, evolution has come to be thought of as “the survival of the fittest”: Only those organisms most fit to survive will survive and reproduce.

Darwin elaborated his theory in a book entitled On the Origin of Species. In a nutshell, here’s what Darwin observed:

Lamarck and the Long Necks

Darwin was not the first to propose a theory explaining the variety of life on Earth. One of the most widely accepted theories of evolution in Darwin’s day was that proposed by Jean-Baptiste de Lamarck.

In the eighteenth century, Lamarck had proposed that acquired traits were inherited and passed on to offspring. For example, in the case of our giraffes, Lamarck’s theory said that the giraffes had long necks because they were constantly reaching for higher leaves while feeding. This theory is referred to as the “law of use and disuse,” or, as we might say now, “use it or lose it.” According to Lamarck, giraffes have long necks because they constantly use them.

We know now that Lamarck’s theory was wrong: acquired changes—that is, changes at a “macro” level in somatic (body) cells—cannot be passed on to germ cells. For example, if you were to lose one of your fingers, your children would not inherit this trait.

Evidence for Evolution

In essence, nature “selects” which living things survive and reproduce. Today, we find support for the theory of evolution in several areas:

COMMON ANCESTRY

By using the evidence mentioned above, scientists can get a good handle on how evolution of certain species occurred. It all comes down to who has common ancestors. Life started somewhere. Some original life-form is the common ancestor to all life, but where things went from there can become quite convoluted.

Scientists use charts called phylogenetic trees, or cladograms, to study the relationships between organisms. They always begin with the common ancestor and then branch out. Anytime there is a fork in the road, it is called a common ancestor node. These common ancestors likely do not exist anymore, but they are the point at which evolution went in two directions. One direction eventually led to one species, and the other eventually led to the other species.

For example, we have a common ancestor with chimps. This doesn’t mean that our great-great…great-grandfather was a chimp. It means that chimps and we have the same great-great…great-grandfather, who was neither a human nor a chimp. Instead, he was some other species completely, and a speciation event must have occurred where his species was split and evolved in different directions. One lineage became chimps, and the other linage became humans.

This is an example of a phylogenetic tree.

In this tree, the three main domains of life are seen. You can see that plants, animals, and fungi are much more closely related to each other than they are to bacteria. The archaea and the eukarya have a common ancestor with bacteria, and then they also have another common ancestor that bacteria doesn’t have.

GENETIC VARIABILITY

As you know, no two individuals are identical. The differences in each person are known as genetic variability. All this means is that no two individuals in a population have identical sets of alleles (except, of course, identical twins). In fact, the survival of a species is dependent on this genetic variation; it allows a species to survive in a changing environment. If a population were all the same then they would have the same weaknesses and the same strengths. Natural selection only occurs if some individuals have more evolutionary fitness and can be selected. The more variations there are among a population, the more likely that a trait will exist that might be the perfect lifesaver. The most famous example is Rudolph the Red-Nosed Reindeer. His red nose was a random mutation, but under the right conditions, it became the best nose to have. A more diverse population is more likely to survive and evolve when things are constantly changing around them.

How did all this wonderful variation come about? Well, the simple answer is that random mutations are occurring all the time. This can be because of errors by the DNA polymerase, changes to the DNA caused by transposons, or other types of DNA damage. Either way, mutations create new variations and alleles.

However, just the mutations occurring does not account for the great amount of genetic variation among a population. The mixing of genes through sexual reproduction contributes to genetic variation. During meiosis, crossing-over mixes the alleles among homologous chromosomes, and the independent assortment when chromosomes are packaged further adds to the genetic uniqueness of each gamete.

In bacteria, a process called conjugation increases the genetic variation, even though they are asexual reproducers. Additionally, viruses can pass around chunks of genome during infection. This process is called transduction. Each of these processes will be covered more in Chapter 11.

It might be hard to think of it in this way, but genetic variation is the very foundation of evolution, as we’ll soon see. Now that we’ve reintroduced genes, we can refine our definition of evolution. More specifically:

The Peppered Moths

Let’s take an example. During the 1850s in England, there was a large population of peppered moths. In most areas, exactly half of them were dark or carried alleles for dark coloring. The other half carried the alleles for light coloring. This 1:1 ratio of phenotypes was observed until air pollution, due primarily to the burning of coal, changed the environment. What happened?

Imagine two different cities: City 1 (in the south) and City 2 (in the north). Prior to the Industrial Revolution, both of these cities had unpolluted environments. In both of these environments, dark moths and light moths lived comfortably side by side. For simplicity’s sake, let’s say our proportions were a perfect fifty-fifty, half dark and half light. However, at the height of the Industrial Revolution, City 2, our northern city, was heavily polluted, whereas City 1, our southern city, was unchanged. In the north, where all the trees and buildings were covered with soot, the light moths didn’t stand a chance. They were impossible for a predator to miss! As a result, the predators gobbled up light-colored moths just as fast as they could reproduce, sometimes even before they reached an age in which they could reproduce. However, the dark moths were just fine. With all the soot around, the predators couldn’t even see them; the dark moths continued doing their thing—above all, reproducing. And when they reproduced, they had more and more offspring carrying the dark allele.

After a few generations, the peppered moth gene pool in City 2 changed. Although our original moth gene pool was 50 percent light and 50 percent dark, excessive predation changed the population’s genetic makeup. By about 1950, the gene pool reached 90 percent dark and only 10 percent light. This occurred because the light moth didn’t stand a chance in an environment where it was so easy to spot. The dark moths, on the other hand, multiplied just as fast as they could.

In the southern city, you’ll remember, there was very little pollution. What happened there? Things remained pretty much the same. The gene pool was unchanged, and the population continued to have roughly equal proportions of light moths and dark moths.

CAUSES OF EVOLUTION

Natural selection, the evolutionary mechanism that “selects” which members of a population are best suited to survive and which are not, works both “internally” and “externally”: internally through random mutations and externally through environmental pressures.

To see how this process unfolds in nature, let’s return to the moth case. Why did the dark moths in the north survive? Because they were dark-colored. But how did they become dark-colored? The answer is, through random mutation. One day, a moth was born with dark-colored wings. As long as a mutation does not kill an organism before it reproduces (most mutations, in fact, do), it may be passed on to the next generation. Over time, this one moth had offspring. These, too, were dark. The dark- and the light-colored moths lived happily side by side until something from the outside—in our example, the environment—changed all that.

The initial variation came about by chance. This variation gave the dark moths an edge. However, that advantage did not become apparent until something made it apparent. In our case, that something was the intensive pollution from coal burning. The abundance of soot made it easier for predators to spot the light-colored moths, thus effectively removing them from the population. Therefore, dark color is an adaptation, a variation favored by natural selection.

Eventually, over long stretches of time, these two different populations might change so much that they could no longer reproduce together. At that point, we would have two different species, and we could say, definitively, that the moths had evolved. Evolution occured as a consequence of random mutation and the pressure put on the population by an environmental change. Catastrophic events can speed up natural selection and adaptation. When the rules change, sometimes the odd variations are selected for. Earth has undergone several mass extinction events. The tree of life would look much different if these events had not occurred.

Types of Selection

The situation with our moths is an example of directional selection. One of the phenotypes was favored at one of the extremes of the normal distribution.

In other words, directional selection “weeds out” one of the phenotypes. In our case, dark moths were favored, and light moths were practically eliminated. Here’s one more thing to remember: directional selection can happen only if the appropriate allele—the one that is favored under the new circumstances—is already present in the population. Two other types of selection are stabilizing selection and disruptive selection.

Stabilizing selection means that organisms in a population with extreme traits are eliminated. This type of selection favors organisms with common traits. It “weeds out” the phenotypes that are less adaptive to the environment. A good example is birth weight in human babies. An abnormally small baby has a higher chance of having birth defects; conversely an abnormally large baby will have a challenge in terms of a safe birth delivery.

Disruptive selection, on the other hand, does the reverse. It favors both the extremes and selects against common traits. For example, females are “selected” to be small and males are “selected” to be large in elephant seals. You’ll rarely find a female or male of intermediate size.

SPECIES

A dog and a bumblebee obviously cannot produce offspring. Therefore, they are different species. However, a poodle and a Great Dane can reproduce (at least in theory). We would not say that they are different species; they are merely different breeds. In order for these to become different species of dogs, they would have to become reproductively isolated from each other. This would then allow the two groups to undergo natural selection and evolve differently. With different variation and different environmental pressures, they could each change in different ways and no longer be able to mate. This is called divergent evolution.

Species often originate from a common ancestor. More often than not, the “engine” of evolution is cataclysmic environmental change, such as pollution in the case of the moths. Geographic barriers, new stresses, disease, and dwindling resources are all factors in the process of evolution. Pre- and post-zygotic barriers also prevent organisms of two different species from mating to produce viable offspring. Pre-zygotic barriers prevent fertilization. Examples of this kind of barrier include temporal isolation, or when two species reproduce at different times of the year. A post-zygotic barrier is related to the inability of the hybrid to produce offspring. For example, a horse and a donkey can mate to produce a mule, but mules are sterile and therefore cannot produce a second generation. Often plants undergo speciation due to polyploidy, which occurs when they get doubles of their chromosomes.

Convergent evolution is the process by which two unrelated and dissimilar species come to have similar (analogous) traits, often because they have been exposed to similar selective pressures. Examples of convergent evolution include aardvarks, anteaters, and pangolins. They all have strong, sharp claws and long snouts with sticky tongues to catch insects, yet they evolved from three completely different mammals.

There are two types of speciation: allopatric speciation and sympatric speciation. Allopatric speciation simply means that a population becomes separated from the rest of the species by a geographic barrier so that the two populations can’t interbreed. An example would be a mountain that separates two populations of ants. In time, the two populations might evolve into different species. If, however, new species form without any geographic barrier, it is called sympatric speciation. This type of speciation is common in plants. Two species of plants may evolve in the same area without any geographic barrier.

POPULATION GENETICS

Mendel’s laws can also extend to the population level. Suppose you caught a bunch of fruit flies—about 1,000. Let’s say that 910 of them were red-eyed and 90 were green-eyed. If you allowed the fruit flies to mate and counted the next generation, we’d see that the ratio of red-eyed to green-eyed fruit flies would remain the same: 91 percent red-eyed and 9 percent green-eyed. That is, the allele frequency would remain constant. At first glance you may ask, how could that happen?

The Hardy-Weinberg law states that even with all the shuffling of genes that goes on, the relative frequencies of genotypes in a population still prevail over time. The alleles don’t get lost in the shuffle. The dominant gene doesn’t become more prevalent, and the recessive gene doesn’t disappear.

Hardy-Weinberg Equilibrium

The Hardy-Weinberg law says that a population will be in genetic equilibrium only if it meets these five conditions: (1) a large population, (2) no mutations, (3) no immigration or emigration, (4) random mating, and (5) no natural selection.

When these five conditions are met, the gene pool in a population is pretty stable. Any departure from them results in changes in allele frequencies in a population. For example, if a small group of your fruit flies moved to a new location, the allele frequency may be altered and result in evolutionary changes. That’s an example of genetic drift called the founder effect. In other words, the gene frequency may differ from the original gene pool. Genetic drift often occurs in new colonies with small populations. You can think of genetic drift as changes to the alleles in a population due to random luck rather than natural selection. Things that really change the population size are called bottleneck events. If most of a species is killed by some crazy weather event, whichever individuals are left now make up the new gene pool, even if they were not previously being selected for.

Hardy-Weinberg Equations

Let’s say that the allele for red eyes, R, is dominant over the allele for green eyes, r. Red-eyed fruit flies include homozygous dominants, RR, and heterozygous, Rr. The green-eyed fruit flies are recessive, rr. The frequency of each allele is described in the equation below. The allele must be either R or r. Let “p” represent the frequency of the R allele and “q” represent the frequency of the other allele in the population.

This sum of the frequencies must add up to one. If you know the value of one of the alleles, then you’ll also know the value of the other allele. This makes sense because Hardy-Weinberg ONLY works for populations with 2 alleles that have normal dominant-recessive behavior. So, if you know there are only 2 alleles possible and you know that 70% are the dominant allele, then the remaining 30% must be the recessive allele.

We can also determine the frequency of the genotypes in a population using the following equation.

In this equation, p² represents the homozygous dominants, 2pq represents the heterozygotes, and q² represents the homozygous recessives.

Both of these equations are listed on the AP Biology Equations and Formulas sheet. But how do you use them? Use the proportions in the population to figure out both the allele and genotype frequencies. Let’s calculate the frequency of the genotype for green-eyed fruit flies. If 9 percent of the fruit flies are green-eyed, then the genotype frequency, q², is 0.09. You can now use this value to figure out the frequency of the recessive allele in the population. The allele frequency for green eyes is equal to the square root of 0.09—that’s 0.3. If the recessive allele is 0.3, the dominant allele must be 0.7. That’s because 0.3 + 0.7 equals 1.

Using the second equation, you can calculate the genotypes of the homozygous dominants and the heterozygotes. The frequency for the homozygous dominants, p², is 0.7 × 0.7, which equals 0.49. The frequency for the heterozygotes, 2pq, is 2 × 0.3 × 0.7, which equals 0.42. If you include the frequency of the recessive genotype—0.09—the numbers once again add up to 1.

KEY TERMS

evolution

natural selection

Charles Darwin

Jean-Baptiste de Lamarck

paleontology

biogeography

flora

fauna

embryology

comparative anatomy

homologous structures

analogous structures

molecular biology

common ancestor

phylogenetic tree

genetic variability

conjugation

transduction

Peppered moths

environmental pressure

random mutation

adaptation

directional selection

stabilizing selection

disruptive selection

species

speciation

reproductively isolated

divergent evolution

pre-zygotic barriers

post-zygotic barriers

convergent evolution

allopatric speciation

sympatric speciation

Hardy-Weinberg law

genetic drift

Summary

Chapter 10 Drill

Answers and explanations can be found in Chapter 16.

Questions 2-5 refer to the following graph and paragraph.

During the industrial revolution, a major change was observed in many insect species due to the mass production and deposition of ash and soot around cities and factories. One of the most famous instances was within the spotted moth population. An ecological survey was performed where the number of spotted moths and longtail moths were counted in 8 different urban settings over a square kilometer in 1802. A repeat experiment was performed 100 years later in 1902. The results of the experiment are shown below.

Question 6 represents a question requiring a numeric answer.

Questions 8 and 9 refer to the following scenario.

A cruise ship with 500 people on board crashes on a deserted island. They like the island so much that they decide to stay. There is a small number of people on board with red hair, an autosomal recessive trait.

REFLECT

Respond to the following questions:

Chapter 11

Animal Structure and Function

THE STRUCTURE AND FUNCTION OF ORGANISMS

To carry on with the business of life, higher organisms must all contend with the same basic challenges: obtaining nutrients, distributing them throughout their bodies, voiding wastes, responding to their environments, and reproducing. To accomplish these basic tasks, nature has come up with solutions.

Unicellular and multicellular organisms alike meet these challenges through organization and specialization. We already learned about the organelles within a cell allowing compartment­alization. Each organelle does it own task, and they work together to keep the cell alive. In many animals and humans, there are higher levels of organization.

Homeostasis

All living things have a “steady-state” that they try to maintain. This is helpful because the structures and processes within living things are sensitive to things like temperature, pH, pressure, salinity, osmotic pressure, and many other things. There is a set range of conditions that living things can live in successfully, called homeostasis. The body is constantly working to maintain this state by taking measurements and then responding appropriately. That might mean shivering if it is cold or releasing the hormone insulin if blood glucose is high. Depending on the condition, the body will respond accordingly.

Many of these responses are controlled by negative or positive feedback pathways. A negative feedback pathway (also called feedback inhibition) works by turning itself off using the end product of the pathway. The end-product inhibits the process beginning again, shutting down the pathway. This is a common strategy to conserve energy. If plenty of X is made, then the pathway to make X can be turned off. Sometimes, a very distant end product will turn off a process occuring several steps back. For example, ATP turns off the beginning stages of glycolysis, although ATP is not made until much later in cellular respiration.

A positive feedback pathway also involves an end-product playing a role, but instead of inhibiting the pathway, it further stimulates it. For example, once X is made, it tells the pathway to make even more X. This is less common, but it occurs during fruit ripening and labor and delivery, which ramps up and up as it proceeds.

DEVELOPMENT

For the AP test, it is important to have a general idea of how the body works. Let’s start at the beginning.

Embryonic Development

How does a tiny, single-celled egg develop into a complex, multicellular organism? By dividing, of course. The cell changes shape and organization many times by going through a succession of stages. This process is called morphogenesis.

When an egg is fertilized by a sperm, it forms a diploid cell called a zygote.

Fertilization triggers the zygote to go through a series of divisions. As these occur, the embryo becomes increasingly differentiated, or specialized. An undifferentiated cell is like a blank slate—it can become any type of cell. Once a cell begins to specialize, it is limited in its future options.

In order for a cell to differentiate, it must change. Certain genes will be expressed, and other genes might be turned off. Cells called organizers release signals that let each cell know how they should develop. As an over-simplified example, a cell destined to become a muscle might have an increase in things that make it flexible, while something destined to become bone might have a decrease in those things. Once the change has been made, the future muscle cell can’t change its mind and become a bone cell.

The early genes that turn certain cells in the early embryo into future-this or future-that are called homeotic genes. A subset of homeotic genes are called Hox genes. The timing is essential for the induction of these genes. Exactly the right bit of the embryo must be modified at exactly the right time, or the embryo may develop with the brain in the wrong place or too many limbs or only limbs on one side of the body. Severely damaged embryos will stop developing.

An interesting additional tool that the developing embryo uses is apoptosis, or programmed cell death. Certain bits of the developing embryo are used as a scaffold for development (like those between your fingers and toes), and when they are no longer necessary, those cells commit suicide. Think of it like an eraser coming along and erasing the webbing tissue between fingers and toes.

BODY SYSTEMS

Once the embryo develops into a fully formed organism, it is highly specialized. Groups of cells that all perform the same function are called a tissue, and several tissues can come together to form specialized structures called organs. Several organs then come together to form body systems.

Fortunately, you only need to know details about the immune system, the nervous system, and the endocrine system. Here is a brief list of other major systems so you get the gist of their function:

Circulatory: Blood vessels (arteries, capillaries, and veins) carry blood around the body to transport chemical signals and to bring supplies to cells and carry waste away. The blood flow is controlled by the heart, which pumps the blood through the blood vessels.

Respiratory: The lungs are responsible for gas exchange (O₂ and CO₂), also helps maintain pH levels in the blood.

Digestive: The esophagus, stomach, small intestine, large intestine, pancreas, liver, and gall bladder work together to break food down and absorb nutrients. The stomach does mixing and breakdown. The small intestine does most of the absorption. The pancreas makes lots of enzymes.

Excretory: The kidneys filter the blood and reabsorb things that the body wants to keep and get rid of the rest in urine.

Reproductive: The male and female systems are largely controlled by hormones and allow the production of gametes and the ability to reproduce.

Muscular and Skeletal: The body has skeletal muscle and smooth muscles that each contract by action potential signals from the nervous system. The skeletal system provides structure, protection, and calcium storage.

THE IMMUNE SYSTEM

The immune system is the body’s defense system. It is a carefully and closely coordinated system of specialized cells, each of which plays a specific role in the war against bodily invaders. Let’s take a brief sidetrack and talk a bit about these invaders. Pathogens are disease-causing biological agents that can generally be divided into bacteria, viruses, fungi, and parasites.

Bacteria

We have been talking on and off about bacteria already. They are prokaryotes that come in many shapes and sizes. They can infect many things, and sometimes they cause harm and sometimes they do not. You may have heard of “gut bacteria” before; this is a special colony of bacteria that lives inside each one of us. It helps us with some digestion and makes some things we need. We have a mutualistic relationship with our gut bacteria.

Bacteria divide by fission; however, this does not increase their genetic diversity. Instead, they can perform conjugation with other bacterial cells and swap some of their DNA. Genetic variety among bacteria is leading to increased antibiotic resistance. As we mentioned in Chapter 10, an increase in genetic variation increases the likelihood that a population will survive a catastrophic event.

VIRUSES

Viruses are nonliving agents capable of infecting cells. Why are viruses considered nonliving? They require a host cell’s machinery in order to replicate. A virus consists of two main components: a protein capsid and genetic material made of DNA or RNA, depending on the virus. Viruses are all very specific in which type of cells they infect, and the thing infected by a virus is called a host.

Viruses have one goal: replicate/spread. In order to do this, a virus needs to make more genome and make more capsid. They then assemble together into new viral particles.

The viral genome carries the genes for building the capsid and anything else the virus needs that the host cannot provide. Sometimes, if two viruses infect the same cell, there will be mixing of he genomes, especially if the viruses that have genomes split between several chromosome-like segments. A new virus particle might emerge that is a blend of the two viruses.

A commonly studied virus is a bacteriophage (a virus that infects bacteria). Bacteriophages undergo two different types of replication cycles, the lytic cycle and the lysogenic cycle. In the lytic cycle, the virus immediately starts using the host cell’s machinery to replicate the genetic material and create more protein capsids. These spontaneously assemble into mature viruses and cause the cell to lyse, or break open, releasing new viruses into the environment. In the lysogenic cycle, the virus incorporates itself into the host genome and remains dormant until it is triggered to switch into the lytic cycle. A virus can hide in the genome of a bacteria cell for a very long time. During this time, the cell may divide and replicate the virus as well. By the time the lytic cycle is triggered the virus may have been replicated many many times as the cell hosting it divides.

When a virus excises from a host genome (becomes unintegrated), it sometimes accidentally takes some of the bacterial cell’s DNA with it. Then, that gets replicated and packaged into new viral particles with the viral genome. The next cell that gets infected is not only getting infected with the viral genome, but also with that chunk of bacterial DNA. If that chunk held a gene for something like antibiotic resistance, the next cell that gets infected will gain that trait. The transfer of DNA from a virus to a bacterial cell is called transduction.

Viruses that infect animals do not have to break their way out of the cell the same way that a bacteriophage does. Since animals cells don’t have a cell wall, the viruses often just “bud” out of the membrane like exocytosis. When a virus does this, it becomes enveloped by a chunk of cell membrane that it takes with it. Viruses with a lipid envelope are called enveloped viruses.

Retroviruses like the HIV virus are RNA viruses that use an enzyme called reverse transcriptase to convert their RNA genomes into DNA so that they can be inserted into a host genome. RNA viruses have extremely high rates of mutation because they lack proofreading mechanisms when they replicate their genomes of mutation. This high rate of mutation will create lots of variety, which makes these viruses difficult to treat. As was discussed in Chapter 10, they evolve quickly as drug-resistant mutations become naturally selected. New drugs must constantly be identified to treat the resistance.

Foreign molecules—be they viral, bacterial, or chemical—that can trigger an immune response are called antigens. Humans and other vertebrates have two types of immune responses: the innate immune response and the adaptive/specific immune response. The innate is more of a general anti-invader response. The body recognizes certain things that are common of foreign things and destroys them. The adaptive response carefully catalogs and handles each antigen in a particular way. It also has a memory component that helps it fight repeat attackers very efficiently.

THE TWO IMMUNE RESPONSES

The Innate Immune System

The body’s first line of defense against foreign substances is the skin and the mucous lining of the respiratory and digestive tracts. If these defenses are not sufficient, other nonspecific defense mechanisms are activated. These include phagocytes such as macrophages (which engulf antigens), complement proteins (which lyse the cell wall of the antigen), interferons (which inhibit viral replication and activate surrounding cells that have antiviral actions), and inflammatory response (a series of events in response to antigen invasion or physical injury). Activation of these defenses requires immune cells to recognize the foreign substance (usually via receptor binding) and activate intracellular signaling pathways. This is another example of how important cell communication is to survival. These first line defenses are called the innate immune system, and many organisms have this level of defense. The specifics vary with organism structure, but there are several common themes. For example, a thick outer surface usually protects the organism, such as the skin of a human, the cell wall of a bacteria, or the cuticle of a plant. In all organisms, cell communication pathways are essential to recognize “self” cells, recognize foreign substances, and initiate immune responses when under attack by a pathogen (a disease-causing agent) or chemical.

The Adaptive/Specific Immune Response

Lymphocytes are the primary cells of the immune system. They are found mostly in the blood and lymph nodes and are a type of white blood cell (or leukocyte). There are two types of lymphocytes: B-cells and T-cells. When an individual becomes infected by a pathogen, B- and T-lymphocytes get activated.

B-lymphocytes mature in bone marrow and are involved in the humoral response, which defends the body against pathogens present in extracellular fluids, such as lymphatic fluid or blood. Each B-cell has a special receptor on its surface that can only bind to foreign things. If a pathogen arrives that fits the receptor, the B-cell becomes activated (with the help of a T-cell). The B-cell will begin to replicate and seek out more of the pathogens. Some B-cells become memory B-cells that remain in circulation, allowing the body to mount a quicker response if a second exposure to the same pathogen should occur. Other B-cells become plasma cells that produce antibodies, which are specific proteins that bind to antigens on the surface of pathogens that originally activated them. The antibody that is made by each B-cell is identical to the the surface receptor that caught the antigen. Each B-cell has a unique receptor/antibody that it makes.

Antibodies all have the same basic monomer structure that is shaped like the letter Y. The stem of the Y is always the same and can interact with other cells in the immune response. The arms of the Y are always unique because this is where the antibody binds antigen. On each antibody, both arms bind the same shape so that it can hold two antigens at once. As mentioned, this Y shape is just the monomer of an antibody. Sometimes antibodies can have one, two, or five Y-monomers with the stem parts attaching and the arms facing outward. Antibodies are typically made only when the appearance of antigens in the body stimulates a defense mechanism, but they will linger around after an infection. When an antibody binds to the antigen it is made for, it marks the antigen for destruction. Antibodies can also combat the antigen just by binding to it because this alone can wreak havoc for the pathogen.

T-lymphocytes, maturing in the thymus, are involved in cell-mediated immunity; this branch of the immune system is responsible for monitoring “self” cells to make sure they are still healthy. The plasma membrane of cells has major histocompatibility complex (MHC) markers that allow T-cells to get a glimpse of what is happening inside each cell. T-cells have special antigen-recognizing receptors just like B-cells, and if the receptors see something foreign, the T-cells jump into action.

MHC I are on all nucleated cells. They take peptides that have been found inside the cell and hold them up on the surface so that a type of circulating T-cell called a cytotoxic T-cell can inspect them. If they decide the cell is infected or is a tumor cell, they signal for it to be destroyed by apoptosis, which is a careful self-destruct program.

MHC II are on special immune cells, like B-cells and macrophages, that identify and engulf antigens. These types of cells are called antigen-presenting cells. They hold up a chunk of whatever antigen the immune cell has picked-up and let a type of T-cell called a helper T-cell inspect it. If the T-cell agrees that it is something foreign, it helps activate the immune cell. Think of the helper T-cell as a double-checker. This interaction between different branches of the immune system requires B-cells and T-cells to recognize each other and coordinate an immune attack—another process tightly controlled by cell signaling and communication pathways.

A lymph node is a mass of tissue found along a lymph vessel. A lymph node contains a large number of lymphocytes. Because lymphocytes are important in fighting infection, they multiply rapidly when they come in contact with an antigen. As a consequence, lymph nodes swell when they’re fighting an infection. That’s why when you have a sore throat, one of the first things a doctor does is touch the sides of your throat to see if your lymph nodes are swollen, a probable sign of infection.

One thing to remember about immune cells and blood cells: all blood cells, white and red, are produced in the bone marrow. However, red blood cells (or erythrocytes) play no role in the immune system; instead, they help transport oxygen throughout the body. They are full of hemoglobin.

Vaccines

After an infection, the adaptive immune response keeps around groups of cells called memory B-cell and memory T-cells. They act as a militia and keep their eyes peeled for the same antigens they have seen before. The second time that you are infected with a pathogen, you will usually fight it off very quickly. You might not even know you were even infected because your body destroys it so fast. Vaccines are tiny doses of antigen that have been modified so they are not dangerous. Your immune system is introduced to them and prepares a militia, but you don’t ever get the “real” infection. If you do come into contact with the real version, your body will fight it off ASAP. In a nutshell, getting vaccinated is getting a tiny harmless dose now so you don’t get knocked off your feet by the big, bad version later.

AIDS

AIDS, or “acquired immunodeficiency syndrome,” is a devastating disease that interferes with the body’s immune system. AIDS is caused by the specific infection of helper T-cells by human immunodeficiency virus (HIV). The virus essentially wipes out helper T-cells, preventing the body from defending itself. Those afflicted with AIDS do not die of AIDS itself, but rather of infections that they can no longer fight off, due to their compromised immune systems.

Auto-Immunity

The B-cells and T-cells are carefully created so that they do not react to “self” and only react to foreign things. However, sometimes mistakes happen and the immune system begins to think that “self” is dangerous. These attacks cause auto-immune diseases such as Type I diabetes, rheumatoid arthritis, lupus, and celiac disease.

THE NERVOUS SYSTEM

All organisms must be able to react to changes in their environment. As a result, organisms have evolved systems that collect and process information from the outside world. The task of coordinating this information falls to the nervous system. The simplest nervous system is found in the hydra. It has a nerve net made up of a network of nerve cells, which sends impulses in both directions. As animals became more complex, they developed clumps of nerve cells called ganglia. These cells are like primitive brains. More complex organisms, like humans, have a brain with specialized cells called neurons.

Neurons

The functional unit in the nervous system is a neuron. Neurons receive and send the neural impulses that trigger organisms’ responses to their environments. Let’s talk about the parts of a neuron. A neuron consists of a cell body, dendrites, and an axon.

The cell body contains the nucleus and all the usual organelles found in the cytoplasm. Dendrites are short extensions of the cell body that receive stimuli. The axon is a long, slender extension that transmits an impulse from the cell body to another neuron or to an organ. A nerve impulse begins at the top of the dendrites, passes through the dendrites to the cell body, and moves down the axon.

How Neurons Communicate

Within a neuron, the signal is called an action potential, which is a wave of positive charge that sweeps down the axon. In order for the signal to be clear, the cell must have a “normal,” non-positive state. Nearly all cells in the body have a natural resting state that is negative. The natural charge of a cell is called the resting membrane potential, which represents the difference in charge from inside the cell to outside the cell.

The resting potential arises from two activities:

Both the Na⁺K⁺-ATPase pump and the leaky channels cause a potential difference between the inside of the neuron and the surrounding interstitial fluid. The resting membrane potential is always negative inside the cell, and the neuronal membrane is said to be polarized. In humans, the negative charge is –70mV.

Action Potential

Here’s what a neuron does in response to a stimulus. If a stimulus has enough intensity to excite a neuron, the cell reaches its threshold—the minimum amount of stimulus a neuron needs to respond. When the threshold is reached, the cell “fires” an action potential. The action potential is an all-or-none response—it doesn’t fire “part way.”

 

(1) Reaching threshold: An outside stimulus causes a slight influx of positive charge in the neuron. When this influx causes the cell body of the neuron to reach −50mV, threshold is reached.

 

(2) Sodium channels open: The −50mV voltage causes the opening of many voltage-gated sodium channels near where the axon meets the cell body. Remember, the sodium potassium pump is actively pumping sodium out of the cell. This means that it is pumping sodium against the concentration gradient, meaning there is already a lot of sodium outside the cell. Therefore, the sodium wants to flow into the cell. When these channels are opened at threshold, a ton of sodium rushes into the cell. This causes the inside of the cell to become very positive (since sodium is positively charged). This is called depolarization. When the cell reaches +35mV inside, these sodium channels close again.

 

(3) Potassium channels open: As the sodium channels close, the potassium channels open. Potassium flows the opposite direction of sodium, out of the cell. This outflux of positives causes the cell to become negative again. This is called repolarization. When the voltage reaches arond −90mV, the potassium channels close, and the cell returns to resting membrane potential.

The Refractory Period

The period after an action potential is known as the refractory period. There are two different refractory periods. The first is caused because the sodium channels are unable to open again right away. There are in lockdown mode for a short time. The second is caused because the cell dips down below the resting membrane potential and is super negative. A greater stimulus is required to reach the threshold, so it is more difficult to initiate another action potential.

To summarize:

Passing Along the Signal

When one small area is depolarized, it causes a “domino effect.” The action potential spreads to the rest of the axon. The impulse is transmitted down the axonal membrane until it reaches the end of the axon called the axon bulb. Let’s discuss how the neuron manages to pass the impulse to the next neuron.

When an impulse reaches the end of an axon, the axon releases a chemical called a neurotransmitter into the space between the two neurons. This space is called a synapse. The cell before the synapse is called the presynaptic cell, and the cell after the synapse is called the postsynaptic cell. The neurotransmitter diffuses across the synaptic cleft and binds to receptors on the dendrites of the next neuron.

This will trigger an action potential in the second neuron if the postsynaptic membrane is excited. However, sometimes the signal will cause the postsynaptic membrane to become negatively charged (inhibited). Now the impulse moves along the second neuron from dendrites to axon.

There are many neurotransmitters, but the most important one for the AP Biology Exam is called acetylcholine. Acetylcholine is a neurotransmitter that:

The extra acetylcholine in the synaptic cleft is broken down by the enzyme acetylchol­inesterase.

Other important neurotransmitters include norepinephrine and GABA. Norepinephrine is a peptide neurotransmitter that is released between neurons within the central nervous system. GABA is secreted in the central nervous system and acts as an inhibitor.

Speed of an Impulse

Sometimes a neuron has supporting cells that wrap around its axon. These cells are called Schwann cells. Schwann cells produce a substance called the myelin sheath, which insulates the axon.

As you can see from the illustration above, the whole axon isn’t covered with myelin sheaths. The spaces between myelin sheaths—the exposed regions of the axon—are called the nodes of Ranvier. Myelin sheaths speed up the propagation of an impulse. Instead of the standard “domino effect” that occurs during an action potential, the impulse can now jump from node to node. It is almost as if there are giant dominoes which can skip sections of the neuron. This form of conduction is called saltatory conduction.

Thanks to the myelin sheath, the neuron can transmit an impulse down the axon far more rapidly than it could without its help.

Parts of the Nervous System

Central Nervous System

All of the neurons within the brain and spinal cord make up the central nervous system. All of the other neurons lying outside the brain and the spinal cord—in our skin, our organs, and our blood vessels—are collectively part of the peripheral nervous system. Although both of these systems are really part of one system, we still use the terms central and peripheral. The brain has many regions and parts that each have specific functions, but you do not need to know the details of the different sections.

So keep the following in mind:

The Stimulus-Decision-Response Pathway

Neurons can be classified into three groups: sensory (affector) neurons, interneurons, and motor (effector) neurons. Sensory neurons receive impulses from the environment and bring them to the body. For example, sensory neurons in your hand are stimulated by touch. They transmit the message about the touch stimulus to the brain and the spinal cord. Once there, interneurons will make the decision about what to do about the stimulus. Then, motor neurons transmit the decision from the brain to muscles or glands to produce a response. The muscle will respond by contracting, or the gland will respond by secreting a substance (such as a hormone).

So, the basic function of the nervous system is to detect a stimulus and transmit it to the central nervous system, which makes a decision and then sends that decision out to the body to respond to the stimulus.

Reflexes

As mentioned, the central nervous system is composed of the brain and the spinal cord. Usually, the brain is the part that makes the decisions, so most stimuli are sent to the brain. However, in certain instances, the spinal cord is capable of making the decision. This is what happens in reflexes. A quick decision is required to prevent injury, and reflex arcs are pre-determined decisions that the spinal cord is set up to execute. The spinal cord may make a decision to withdraw a hand because of pain or to relax a muscle when its opposite contracts to prevent injury.

THE ENDOCRINE SYSTEM

Like the nervous system, the endocrine system is an excellent example of signaling. It is responsible for maintaining homeostasis and for coordinating responses to many stimuli in the body. Chemical messengers can be produced in one region of the body to act on target cells in another region. These chemicals, known as hormones, are produced in specialized organs called endocrine glands. Hormones have a number of functions including regulating growth, behavior, development, and reproduction. Other chemical messengers are used for communication. For example, pheromones help animals to communicate with members of their species and attract the opposite sex.

Endocrine glands release hormones directly into the bloodstream, which carries them throughout the body. Take a look at the endocrine glands in the human body.

Although hormones flow in your blood, they affect only specific cells. The cells that a hormone affects are known as the target cells. Suppose, for example, that gland X makes hormone Y. Hormone Y, in turn, has some effect on organ Z. We would then say that organ Z is the target organ of hormone Y.

Hormones also operate by a negative feedback system. That is, an excess of the hormone will signal the endocrine gland to temporarily shut down production. For example, when hormone Y reaches a peak level in the bloodstream, the organ secreting the hormone, gland X, will get a signal to stop producing hormone Y. Once the levels of hormone Y decline, the gland can resume production of the hormone. Now we will go through a few examples of hormone regulation.

The Pancreas

The pancreas secretes two well-known hormones, glucagon and insulin, both of which are produced in clusters of cells called the islets of Langerhans. The target organs for these hormones are the liver and muscle cells. Glucagon, produced by α cells, stimulates the liver to convert glycogen into glucose and to release that glucose into the blood. Glucagon therefore increases the levels of glucose in the blood. Insulin has precisely the opposite effect that glucagon does.

When the blood has too much glucose floating around, insulin, produced by β cells, allows body cells to remove glucose from the blood. Consequently, insulin decreases the level of glucose in the blood. Insulin is particularly effective on muscle and liver cells. In short:

Sex Hormones

There are three key hormones involved in the reproductive system: estrogen, progesterone, and testosterone. Estrogen and progesterone are hormones released by the ovaries that regulate the menstrual cycle. Testosterone is the male hormone responsible for promoting spermatogenesis, the production of sperm. In addition, these hormones maintain secondary sex characteristics.

How Hormones Work

How do hormones trigger the activities of their target cells? That all depends on whether the hormone is a steroid (lipid soluble) or a protein, peptide, or amine (not lipid soluble). If the hormone is a steroid, then the hormone can diffuse across the membrane of the target cell. It then binds to a receptor protein in the nucleus and regulates transcription of the DNA, which in turn effects production of proteins.

However, if the hormone is a protein, peptide, or amine, it can’t get into the target cell by means of simple diffusion. Remember: only hydrophobic things can pass through the membrane. The hormone binds to a receptor protein on the cell membrane of the target cell. This often causes a signal cascade whereby the signal is transduced into the cell without the actual hormone itself ever entering the cell.

Here’s a summary of the hormones and their effects on the body.

While the nervous system and the endocrine system work in close coordination, there are significant differences between the two:

KEY TERMS

homeostasis

negative feedback pathway (feedback inhibition)

positive feedback pathway

embryonic development

morphogenesis

zygote

fertilization

homeotic genes/Hox genes

tissue

organ

body systems

Immune System

pathogen

bacteria

conjugation

viruses

host

bacteriophage

lytic cycle

lysogenic cycle

enveloped virus

retrovirus

reverse transcriptase

antigen

innate immune system

adaptive and specific immune response

phagocytes

macrophages

complement proteins

interferons

inflammatory response

lymphocytes

B-lymphocytes

humoral response

memory B-cell

plasma cell

antibody

T-lymphocytes

cell-mediated immunity

major histocompatibility complex (MHC) markers

cytotoxic T-cell

apoptosis

helper T-cell

lymph node

AIDS

Nervous System

nerve net

ganglia

neurons

cell body

dendrites

axon

action potential

resting membrane potential

Na⁺/K⁺ ATPase pump

polarized

threshold

all-or-none response

depolarization

refractory period

axon bulb

neurotransmitter

synapse

acetylcholine

aceytlcholi­nesterase

norepinephrine

GABA

Schwann cells

myelin sheath

nodes of Ranvier

saltatory conduction

central nervous system

peripheral nervous system

sensory (effector) neurons

interneurons

motor (affector) neurons

reflexes

Endocrine System

hormones

endocrine glands

pheromones

target cells

glucagon (alpha cell)

insulin

islets of Langerhans

glycogen

estrogen

progesterone

testosterone

Summary

Chapter 11 Drill

Answers and explanations can be found in Chapter 16.

Questions 2-4 refer to the following chart and paragraph.

A scientist wishes to test the efficacy and immunogenicity of a newly developed, live-attenuated virus vaccine strain. To test for immunogenicity, the scientist acquires 100 healthy volunteers and exposes them to either the vaccine strain or a placebo strain (consisting of isotonic saline solution). Twelve days following the initial primary exposure, the serum antibody concentration is determined by an ELISA analysis. A follow-up exposure to test for existing immunity is performed on day 60 using the same 100 individuals. Serum antibody titers are determined for the secondary challenge on day 72. These data are shown in the chart above.

REFLECT

Respond to the following questions:

Chapter 12

Behavior and Ecology

In the preceding chapters, we looked at individual organisms and the ways they solve life’s many problems: acquiring nutrition, reproducing, and so on. Now let’s turn to how organisms deal with their environments. We can divide the discussion of organisms and their environments into two general categories: behavior and ecology.

BEHAVIOR

Some animals behave in a programmed way to specific stimuli, while others behave according to some type of learning. We humans can do both. For the AP Biology Exam, you’ll have to know a little about the different types of behavior.

All behavior means, basically, is how organisms cope with their environments. This chapter looks at the general types of "Ahead1" id="calibre_link-108">INSTINCT  

Instinct is an inborn, unlearned behavior. Sometimes the instinctive behavior is triggered by environmental signals called releasers. The releaser is usually a small part of the environment that is perceived. For example, when a male European robin sees another male robin, the sight of a tuft of red feathers on the male is a releaser that triggers fighting behavior. In fact, because instinct underlies all other behavior, it can be thought of as the circuitry that guides behavior.

For example, hive insects, such as bees and termites, never learn their roles; they are born knowing them. On the basis of this inborn knowledge, or instinct, they carry out all their other behaviors: a worker carries out “worker tasks,” a drone “drone tasks,” and a queen “queen tasks.” Another example is the “dance” of the honey bee, which is used to communicate the location of food to other members of the beehive.

There are other types of instinct that last for only a part of an animal’s life and are gradually replaced by “learned” behavior. For example, human infants are born with an ability to suck from a nipple. If it were not for this instinctual behavior, the infant would starve. Ultimately, however, the infant will move beyond this instinct and learn to feed itself. What exactly, then, is instinct?

For our purposes:

A particular type of innate behavior is a fixed action pattern. These behaviors are not simple reflexes, and yet they are not conscious decisions. An example is the egg-rolling behavior exhibited by a graylag goose. If the egg is removed from the goose, it will continue to make the same movements. That is, the innate movements are independent of the environment.

Learning

Another form of behavior is learning. Learning refers to a change in a behavior brought about by an experience (which is what you’re doing this very moment). Animals learn in a number of ways. For the AP Biology Exam, we’ll take a look at the key types of learning.

Imprinting

Have you ever seen a group of goslings waddling along after their mother? How is it that they recognize her? Well, the mother arrives and gives out a call that the goslings recognize. The goslings, hearing the call, know that this is their mother and follow her around until they are big enough to head out on their own.

Now imagine the same goslings, newly hatched. If the mother is absent, they will accept the first moving object they see as their mother. This process is known as imprinting.

Animals undergo imprinting within a few days after birth in order to recognize members of their own species. While there are different types of imprinting, including parent, sexual, and song imprinting, they all occur during a critical period—a window of time when the animal is sensitive to certain aspects of the environment.

Remember:

Classical Conditioning

If you have a dog or a cat, you know that every time you hit the electric can opener, your cat or dog comes running. This is a form of classical conditioning. To feed your pet, you need to open its can of food. For your pet, the sound of the opener has come to be associated with eating: every time it hears the opener, it thinks that it is about to be fed. We can say that your pet has been “conditioned” to link the buzz of the can opener with its evening meal.

This type of learning is now known as associative learning.

Operant Conditioning

Another type of associative learning is operant conditioning (or trial-and-error learning).

In operant conditioning, an animal learns to perform an act in order to receive a reward.

If the behavior is not reinforced, the conditioned response will be lost. This is called extinction. Here’s one thing to remember:

Habituation is another form of learning. It occurs when an animal learns not to respond to a stimulus. For example, if an animal encounters a stimulus over and over again without any consequences, the response to it will gradually lessen and may altogether disappear.

To recap, there are four basic types of learning:

Internal Clocks: The Circadian Rhythm

There are other instinctual behaviors that occur in both animals and plants. One such behavior deals with time. Have you ever wondered how roosters always know when to start crowing? The first thought that comes to mind is that they’ve caught a glimpse of the sun. Yet many crow even before the sun has risen.

Roosters do have internal alarm clocks. Plants have them as well. These internal clocks, or cycles, are known as circadian rhythms.

Watch out though: seasonal changes, like the loss of leaves by deciduous trees or the hibernation of mammals, are not examples of circadian rhythms. Circadian refers only to daily rhythms. Need a mnemonic? Just think how bad your jet lag would be after a trip around the world. In other words: Circling the globe screws up your circadian rhythm.

HOW ANIMALS COMMUNICATE

Some animals use signals as a way of communicating with members of their species. These signals, which can be chemical, visual, electrical or tactile, are often used to influence mating and social behavior.

Chemical signals are one of the most common forms of communication among animals. Pheromones, for instance, are chemical signals between members of the same species that stimulate olfactory receptors and ultimately affect behavior. For example, when female insects give off their pheromones, they attract males from great distances.

Visual signals also play an important role in the behavior observed among members of a species. For example, fireflies produce pulsed flashes that can be seen by other fireflies far away. The flashes are sexual displays that help male and female fireflies identify and locate each other in the dark.

Other animals use electrical channels to communicate. For example, some fish generate and receive weak electrical fields. Finally, tactile signals are found in animals that have mechanoreceptors in their skin to detect prey. For instance, cave-dwelling fishes use mechanoreceptors in their skin for communicating with other members and detecting prey.

Social Behavior

Many animals are highly social species, and they interact with each other in complex ways. Social behaviors can help members of the species survive and reproduce more successfully. Several behavioral patterns for animal societies are summarized below:

Symbiotic Relationships

Many organisms that coexist exhibit some type of symbiotic relationship. These include remoras, or “sucker fish,” which attach themselves to the backs of sharks, and lichen—the fuzzy, mold-like stuff that grows on rocks. Lichen appears to be one organism, when in fact it is two organisms—a fungus and an alga, or photosynthetic bacterium—living in a complex symbiotic relationship.

Overall, there are three basic types of symbiotic relationships:

There are many special types of relationships between multicellular organisms and unicellular organisms. One important example is bacteria living inside the guts of many mammals. We have a mutualistic relationship. Humans and other mammals provide them a nice home with nutrients, and they help us in many ways by breaking things down and helping us make things. It is also good that we are filled with “good” bacteria because otherwise we might be susceptible to dangerous pathogenic bacteria.

PLANT BEHAVIOR

Plants have also evolved specific ways to respond to their environment. The plant behaviors covered on the AP Biology Exam are photoperiodism and tropisms. Plants flower in response to changes in the amount of daylight and darkness they receive. This is called photoperiodism. Although you’d think that plants bloom based on the amount of sunlight they receive, they actually flower according to the amount of uninterrupted darkness.

Tropisms

Plants need light. Notice that all the plants in your house tip toward the windows. This movement of plants toward the light is known as phototropism. As you know, plants generally grow up and down: the branches grow upward, while the roots grow downward into the soil, seeking water. This tendency to grow toward or away from the earth is called gravitropism. All of these tropisms are examples of behavior in plants.

A tropism is a turning in response to a stimulus.

There are three basic tropisms in plants. They’re easy to remember because their prefixes the stimuli to which plants react:

ECOLOGY

The study of the interactions between living things and their environments is known as ecology. We’ve spent most of our time discussing individual organisms. However, in the real world, organisms are in constant interaction with other organisms and the environment. The best way for us to understand the various levels of ecology is to progress from the big picture, the biosphere, down to the smallest ecological unit, the population.

There is a hierarchy within the world of ecology. Each of the following terms represents a different level of ecological interaction:

Biosphere

The biosphere can be divided into large regions called biomes. Biomes are massive areas that are classified mostly on the basis of their climates and plant life. Because of the different climates and terrains on the earth, the distribution of living organisms varies.

Remember that biomes tend to be arranged along particular latitudes. For instance, if you hiked from Alaska to Kansas, you would pass through the following biomes: tundra, taiga, temperate deciduous forests, and grasslands.

Ecosystem

Ecosystems are self-contained regions that include both living and nonliving factors. Living factors are called biotic factors and nonliving factors are called abiotic factors. Abiotic factors include water, humidity, temperature, soil/atmosphere composition, light, and radiation. For example, a lake, its surrounding forest, the atmosphere above it, and all the organisms that live in or feed off of the lake would be considered an ecosystem. As you probably know, there is an exchange of materials between the components of an ecosystem.

Take a look at the flow of carbon through a typical ecosystem.

You’ll notice how carbon is recycled throughout the ecosystem—this is called the carbon cycle. In other words, carbon flows through ecosystems. Other substances have similar cycles. The interactions between the biotic and the abiotic factors are crucial for the balance of the ecosystem.

Community

The next smaller level is the community. A community refers to a group of interacting plants and animals that show some degree of interdependence. For instance, you, your dog, and the fleas on your dog are all members of the same community.

Each organism has its own niche—its position or function in a community. Because every species occupies a niche, it’s going to have an impact on all the other organisms. When two organisms occupy the same niche, they will compete for the resources within that niche. If a species can occupy an unoccupied niche, it will usually thrive without competition. These connections are shown in the food chain. A food chain describes the way different organisms depend on one another for food. There are basically four levels to the food chain: producers, primary consumers, secondary consumers, and tertiary consumers.

Producers (autotrophs)

Producers, or autotrophs, have all of the raw building blocks to make their own food. From water and the gases that abound in the atmosphere and with the aid of the sun’s energy, autotrophs convert light energy to chemical energy. They accomplish this through photosynthesis.

Primary productivity is the rate at which autotrophs convert light energy into chemical energy in an ecosystem. There are two types of primary productivity:

Autotrophs produce all of the available food. They make up the first trophic (feeding) level. They possess the highest biomass (the total weight of all the organisms in an area) and the greatest numbers. Did you know that plants make up about 99 percent of the earth’s total biomass?

Consumers (heterotrophs)

Consumers, or heterotrophs, are forced to find their energy sources in the outside world. Basically, heterotrophs digest the carbohydrates of their prey into carbon, hydrogen, and oxygen and use these molecules to make organic substances.

The bottom line is that heterotrophs, or consumers, get their energy from the things they consume.

Primary consumers are organisms that directly feed on producers. A good example is a cow. These organisms are also known as herbivores. They make up the second trophic level.

The next level consists of organisms that feed on primary consumers. They are the secondary consumers, and they make up the third trophic level. Above these are tertiary consumers.

Decomposers

All organisms at some point must finally yield to decomposers. Decomposers are the organisms that break down organic matter into simple products. Generally, fungi and bacteria are the decomposers. They serve as the “garbage collectors” in our environment.

Keystone Species

Sometimes one organism is particularly important to an ecosystem. Maybe they are the only producer or maybe they are the only thing that keeps a particularly deadly predator in check. Important species like this are called keystone species. If a keystone species is removed from the ecosystem, the whole balance can be undone very quickly.

The 10% Rule

In a food chain, only about 10 percent of the energy is transferred from one level to the next—this is called the 10% rule. The other 90 percent is used for things like respiration, digestion, running away from predators—in other words, it’s used to power the organism doing the eating! As a level, the producers have the most energy in an ecosystem; the primary consumers have less energy than producers; the secondary consumers have less energy than the primary consumers; and the tertiary consumers will have the least energy of all.

The energy flow, biomass, and numbers of members within an ecosystem can be represented in an ecological pyramid. Organisms that are higher up on the pyramid have less biomass and energy, and they are fewer in number.

Build-up of Toxins

The downside of food pyramids is that when the consumers at the top eat something beneath them it is like they are eating that thing AND the thing that thing ate AND and the thing that thing ate, etc. So, if there is a toxin in the environment, the consumers at the top are getting the most of it because it becomes more concentrated at each level.

This simply means that if a toxin is introduced into an ecosystem, the animals most likely to be affected are those at the top of the pyramid. This occurs because of the increasing concentration of such toxins. The classic example of this phenomenon is DDT, an insecticide initially used to kill mosquitoes. Although the large-scale spraying of DDT resulted in a decrease in the mosquito population, it also wound up killing off ospreys.

Ospreys are aquatic birds whose diet consists primarily of fish. The fish that ospreys consumed had, in turn, been feeding on contaminated insects (bioaccumulation). Because fish eat thousands of insects, and ospreys hundreds of fish, the toxins grew increasingly concentrated (biomagnification). Though the insecticide seemed harmless enough, it resulted in the near-extinction of certain osprey populations. What no one knew was that in sufficient concentrations, DDT weakened the eggshells of ospreys. Consequently, eggs broke before they could hatch, killing the unborn ospreys.

Such environmental tragedies still occur. All ecosystems, small or great, are intricately woven, and any change in one level invariably results in major changes at all the other levels.

Disrupting the Balance

Ecosystems are never exactly stable, existing in a precarious balance. Many things can disrupt the balance. If the biomass at any level changes, this will affect the surrounding levels and spread throughout the ecosystem. Geological changes, weather changes, new species, diseases, lack of resources, new resources, and many other things can disrupt the balance.

Population Ecology

Population ecology is the study of how populations change. Whether these changes are long-term or short-term, predictable or unpredictable, we’re talking about the growth and distribution patterns of a population.

When studying a population, you need to examine four things: the size (the total number of individuals), the density (the number of individuals per area), the distribution patterns (how individuals in a population are spread out), and the age structure.

For example, the graph below shows there is a high death rate among the young of oysters, but those that survive do well. On the other hand, there is a low death rate among the young of humans, but, after age sixty, the death rate is high.

The growth of a population can be represented as the number of crude births minus the number of crude deaths divided by the size of the population.

Population growth can also be calculated in the following way:

= Birth Rate – Death Rate

Each population has a carrying capacity—the maximum number of individuals of a species that a habitat can support. Most populations, however, don’t reach their carrying capacity because they’re exposed to limiting factors.

One important factor is population density. The factors that limit a population are either density-independent or density-dependent. Density-independent factors are factors that affect the population, regardless of the density of the population. Some examples are severe storms and extreme climates. On the other hand, density-dependent factors are those with effects that depend on population density. Resource depletion, competition, and predation are all examples of density-dependent factors. In fact, these effects become even more intense as the population density increases.

Exponential Growth

The growth rates of populations also vary greatly. There are two types of growth: exponential growth and logistic growth. Equations for both are included on the AP Biology Equations and Formulas sheet. Exponential growth occurs when a population is in an ideal environment. Growth is unrestricted because there are lots of resources, space, and no disease or predation. Here’s an example of exponential growth. Notice that the curve arches sharply upward—the exponential increase.

Exponential growth occurs very quickly, resulting in a J-shaped curve. A good example of exponential growth is the initial growth of bacteria in a culture. There’s plenty of room and food, so they multiply rapidly.

However, as the bacterial population increases, the individual bacteria begin to compete with each other for resources. When the resources become limited, the population reaches its carrying capacity, and the curve levels off.

The population becomes restricted in size because of limited resources. This is referred to as logistic growth. Notice that the growth forms an S-shaped curve.

These growth patterns are associated with two kinds of life-history strategies: r-selected species and k-selected species.

R-strategists tend to thrive in areas that are barren or uninhabited. Once they colonize an area, they reproduce as quickly as possible. Why? They know they’ve got to multiply before competitors arrive on the scene! The best way to ensure their survival is to produce lots of offspring. Typical examples are common weeds, dandelions, and bacteria.

At the other end of the spectrum are the k-strategists. These organisms are best suited for survival in stable environments. They tend to be large animals, such as elephants, with long lifespans. Unlike r-strategists, they produce few offspring. Given their size, k-strategists usually don’t have to contend with competition from other organisms.

ECOLOGICAL SUCCESSION

Communities of organisms don’t just spring up on their own; they develop gradually over time. Ecological succession refers to the predictable procession of plant communities over a relatively short period of time (decades or centuries).

Centuries may not seem like a short time to us, but if you consider the enormous stretches of time over which evolution occurs, hundreds of thousands or even millions of years, you’ll see that it is pretty short.

The process of ecological succession in which no previous organisms have existed is called primary succession.

The Pioneers

How does a new habitat full of bare rocks eventually turn into a forest? The first stage of the job usually falls to a community of lichens. Lichens are hardy organisms. They can invade an area, land on bare rocks, and erode the rock surface, over time turning it into soil. Lichens are considered pioneer organisms.

Once lichens have made an area more habitable, they’ve set the stage for other organisms to settle in. Communities establish themselves in an orderly fashion. Lichens are replaced by mosses and ferns, which in turn are replaced by tough grasses, then low shrubs, then evergreen trees, and, finally, the deciduous trees. Why are lichens replaced? Because they can’t compete with the new plants for sunlight and minerals.

The entire sequence is called a sere. The final community is called the climax community. The climax community is the most stable. In our example, the deciduous trees are part of the climax community.

Now what happens when a forest is devastated by fire? The same principles apply, but the events occur much more rapidly. The only exception is that the first invaders are usually not lichens, but grasses, shrubs, saplings, and weeds. When a new community develops where another community has been destroyed or disrupted, this event is called secondary succession.

HUMAN IMPACT ON THE ENVIRONMENT

Unfortunately, humans have disturbed the existing ecological balance, and the results are far-reaching. Soils have been eroded and various forms of pollution have increased. The potential consequences on the environment are summarized below.

KEY TERMS

behavior

ecology

instinct

fixed action pattern

learning

imprinting

critical period

classical conditioning

associative learning

operant conditioning (or trial-and-error learning)

habituation

circadian rhythms

pheromones

agonistic behavior

dominance hierarchy

territoriality

altruistic behavior

symbiotic relationship

mutualism

commensalism

parasitism

photoperiodism

tropism

phototropism

gravitropism

thigmotropism

biosphere

ecosystem

community

population

biomes

abiotic factors

biotic factors

carbon cycle

niche

food chain

producers

primary productivity

primary consumers

herbivores

secondary consumers

tertiary consumers

decomposer

keystone species

10% rule

ecological pyramid

population growth

carrying capacity

population density

density-independent factors

density-dependent factors

exponential growth

logistic growth

r-strategists

k-strategists

ecological succession

primary succession

pioneer organisms

sere

climax community

secondary succession

greenhouse effect

ozone depletion

acid rain

desertification

deforestation

pollution

biomagnification

reduction in biodiversity

Summary

Chapter 12 Drill

Answers and explanations can be found in Chapter 16.

Questions 4-6 refer to the following table, chart and paragraph.

Table 1: Minimum pH Tolerance of Common Aquatic Organisms

                                                               

Animal	pH Minimum
Brook Trout	4.9
American Bullfrog	3.8
Yellow Perch	4.6
Tiger Salamander	4.9
Crayfish	5.4
Snails	6.1
Clams	6.0

Over the period of 1980 to 2000, the average pH in Richard Creek changed drastically. An ecological survey was performed to evaluate the effect of detectable decreases in pH on the aquatic life of the creek. Four times a year, ecological surveys were performed to identify the amount of snails (a primary consumer), crayfish (a secondary consumer), and brook trout (a tertiary consumer) present at five different locations. The percent change relative to 1980 is shown in Chart 1 above. Many aquatic organisms cannot live in low pH conditions. The minimum pH necessary for common aquatic organisms to sustain life is shown in Table 1.

Question 8 refers to the following graph.

REFLECT

Respond to the following questions:

Chapter 13

Quantitative Skills and Biostatistics

There will be six designated quantitative questions on the exam, but this does not mean that the multiple-choice and the free-response questions will not be quantitative. These types of questions pop up all over the place. Even if think you are a whiz, check out the formula page at the back of this book. Expect at least a couple questions using formulas from this sheet.

It is often easy to see patterns in data, but it is not always easy to determine if a pattern is valid or significant. Quantitative data analysis is the first step in figuring this out. In this chapter, we will review how data can be summarized, presented, and tested for validity. This depends on what kind of question was being asked at the beginning of the experiment. When you’re reading this chapter, pay attention to which techniques are used when. On the AP Biology Exam, you should be able to justify which techniques are best.

This list is a good reference for the types of quantitative questions you should be able to tackle. We will not walk though all of these in detail, but you will find some examples in the end-of-chapter drill and in the practice tests. Use the formula sheet to familiarize yourself with these concepts.

SUMMARIZING AND PRESENTING DATA

Instead of presenting raw data, scientists use descriptive statistics and graphs to summarize large datasets, present patterns in data, and communicate results. Descriptive statistics summarize and show variation in the data. There are many types of descriptive statistics, including measures of central tendency (such as mean, median, and mode) and measures of variability (such as standard deviation, standard error, and range). The AP Biology Equations and Formulas sheet contains definitions for mean, median, mode and range, and equations for mean, standard deviation, and standard error. That said, you will not need to calculate standard deviation or standard error. Instead, focus on understanding how these values are used.

Descriptive statistics are used to summarize the data collected from samples, but may also describe the entire population you’re trying to study. Experiments are designed to include a sample, which is a subset of the population being studied. The best experiments use random sampling, which makes sure there is no bias when picking which individuals from the population will be included in the sample. It is important that the sample is big enough that the data from the experiment are a good representation of what would happen if the whole population were measured.

Graphs are visual representations of data and are often used to reveal trends that might not be obvious by looking at a table of numbers. There are six types of graphs you should be familiar with:

Each is described below. Pay attention to which graph is used when. On the AP Biology Exam, you may need to decide which graph is best and then create it. You may also have to analyze graphs given to you on the exam.

A good graph must include the following things:

TYPES OF DATA

Data can be quantitative (based on numbers or amounts that can be measured or counted) or qualitative (data that is descriptive, subjective, or difficult to measure). For example, behavioral observations are qualitative. Most data on the AP Biology Exam will be quantitative, with either counts or measurements.

Count data

Count data are generated by counting how many of an item fit into a category. For example, you could count the number of organisms with a particular phenotype or the number of animals in one habitat versus another. Count data also include data that is collected as percentages or the results of a genetic cross. This type of data is usually summarized using a bar graph or a pie graph. For example, suppose a mixed population of E. coli were plated on growth plates. Some cells contained a β-galactosidase marker and grew in blue colonies, while others did not contain the marker and grew in white colonies. The colonies were counted after twenty-four hours of growth.

In another example, suppose fly populations were monitored in northern Maine to determine if population size varies over the warm months of the year.

Count data can be analyzed using hypothesis testing, which will be described later in this chapter.

Measurements

Measurements are continuous, meaning there is an infinite number of potential measurements over a given range. Size, height, temperature, weight, and response rate are all measurements. There are two types of measurement data: parametric and nonparametric.

Normal or Parametric Data

Normal or parametric data are measurement data that fit a normal curve or distribution, usually when a large sample size is used. For example, if you took a large sample of seventeen-year-olds in America and graphed the frequency of heights, the results will be normally distributed.

Several descriptive statistics can be used to summarize normal data.

The sample size (n) is how many members of the population are included in the study. Sample size is an important consideration when you’re trying to determine how well the data in the study represents a population. Large sample sizes are always better, but for technical reasons, experiments can’t be infinitely large.

The mean (x) is the average of the sample, calculated by adding all of the individual values and dividing by the number of values you have. The mean is not necessarily a number provided in the sample. You should be able to recognize what the mean of a given dataset is and be able to calculate the mean using the equation on the AP Biology Equations and Formulas sheet. One limitation of mean is that it is influenced by outliers, or numerical observations that are far removed from the rest of the observations.

The standard deviation (s) can determine if numbers are packed together or dispersed because it is a measure of how much each individual number differs from the mean. A low standard deviation means the data points are all similar and close to the mean, while a high standard deviation means the data are more spread out. Here is the relationship between a normal distribution and standard deviation (or SD).

This means that about 70 percent of the data is within one standard deviation of the mean in a normally distributed dataset. Standard error (SE) can also be used to report how much a given dataset varies and is calculated by dividing the standard deviation by the square root of the sample size.

Nonparametric Data

Nonparametric data often include large outliers and do not fit a normal distribution. In order to determine if data is parametric or not, you can construct a histogram or frequency diagram. These graphs give information on the spread of the data and the central tendencies. Making a histogram is like setting up bins, or intervals with the same range, that cover the entire dataset (the x-axis). The number of measurements in each bin are graphed on the y-axis. For example, suppose you counted the number of pine needles on each branch of a Pinus strobus tree. A histogram of this data may look like this.

This dataset does not match a normal distribution, meaning it is a nonparametric dataset. Keep in mind that even if a certain dataset is not normal, the population itself could be. There could have been sampling bias or errors in the data collection, which can lead to sample data that doesn’t match population data. The best way to fix this is usually to increase the sample size. Histograms differ from bar graphs in that they show ranges instead of just categories.

Nonparametric data requires a different set of descriptive statistics than parametric data.

The median is the middle number in a dataset and is determined by putting the numbers in consecutive order and finding the middle number. If there is an odd number of numbers, there will be a single number that is the median. If there is an even number of numbers, the median is determined by averaging the two middle numbers. Therefore, the median is not necessarily one of the numbers in the dataset. The median is useful in gauging the midpoint of the data, but will not necessarily tell you much about outliers.

The mode is the most frequently recurring number in the dataset. If there are no numbers tha-t occur more than once, there is no mode. If there are multiple numbers that occur most frequently, each of those numbers is a mode. The mode must be one of the numbers in the sample, and modes are never averaged.

The range is the difference between the smallest and largest number in a sample. This value is less useful than standard deviation, because it does not give any information on individual values or the majority of values.

Example 1: Eleven male laboratory mice were weighed at thirty-two weeks of age. The data collected was: 32 g, 28 g, 29 g, 34 g, 30 g, 28 g, 32 g, 31 g, 30 g, 32 g, 33 g. What is the mean, median and mode of this dataset?

Solution: Let’s start by putting the 11 numbers in the dataset in order, from smallest value to largest value: 28 g, 28 g, 29 g, 30 g, 30 g, 31 g, 32 g, 32 g, 32 g, 33 g, 34 g. The mean is

The median is the middle value, or 31 g. The mode is the most frequent number, or 32 g.

Example 2: In the following set of values, what is the range?

Solution: The smallest value in the set above is −5, and the largest is 14. The difference between these two is the range, which is 19.

TYPES OF EXPERIMENTS OR QUESTIONS

You will be tested on scientific experiments and the scientific reasoning behind different aspects of the experiments a LOT. You should be clear with the steps of the scientific method and know how to properly design an experiment and recognize a poorly designed experiment. The following list should remind you:

Most biological experiments do one of three things:

How you present and summarize data depends on what kind of experiment you perform.

Time-Course Experiments

These experiments look at how something changes over time. A line graph is usually used to present this type of data. Several lines can be plotted on the same graph, but these must be clearly labeled. Also, each dot on a line graph could represent one data point or a mean of values. If mean values are plotted, standard deviation or standard error can also be shown. More generally, line graphs can also be used to compare how a dependent variable (y-axis) changes with an independent variable (x-axis).

When making line graphs, the intervals on the axes must be consistent. Also make sure it is clear whether the data start at the origin (0, 0) or not. The same guidelines apply to scatterplots, which will be discussed below.

Data points should be connected with a solid line. You can extrapolate (or continue) the line past the data points, but then must use a broken line. Finally, the slope on a line graph tells you the rate of change.

Suppose we want to determine how stress hormone levels change after the end of an important exam. If we measure cortisol and epinephrine in the serum of several people every hour for five hours after the end of an exam, we would have several values for each time point. We could plot the mean of each measurement and also show data variance using standard error bars. In this example, the distance above the data point is the standard error, and the distance below the data point is the standard error. We call this “±SE.”

Comparative Experiments

These experiments compare populations, groups, or events. There are several options for graphing data from these experiments:

In order to conclude that the samples or groups being compared are different or not, hypothesis testing should be performed. This will be discussed later in this chapter.

Association Experiments

These experiments look for associations between variables. They attempt to determine if two variables are correlated, and additional tests can demonstrate causation. Scatterplots are used to present data from association experiments. Each data point is plotted as a dot. Suppose different substrate concentrations are used in an enzymatic reaction (using the enzyme Kozmase III), and the enzyme efficiency is measured (in percent of maximum). The data could be presented like this.

If the relationship looks linear, a linear regression line can be added. There are a few common shapes of scatterplots you should be familiar with:

PROBABILITY

You already saw an introduction to probability calculations in Chapter 8 of this book. The probability (P) that an event will occur is the number of favorable cases (a) divided by the total number of possible cases (n).

This can be determined experimentally by observation (such as when population data is being collected) or by the nature of the event. For example, the probability of getting a two when rolling a die is 1/6, since there are six sides on a die.

Example 3: What is the probability of drawing the nine of hearts from a deck of cards?

Solution: Since there are 52 cards in a deck and this question is asking about one particular card, P = 1/52.

Combining Probabilities

Many genetics problems involve several probabilities, all being considered together to answer a larger biological question. There are three rules that are often used.

Product Rule

This rule is used for independent events and is also called the “AND rule.” The probability of independent events occurring together is the product of their separate probabilities. This rule is used when the order of the events matters.

Example 4: What is the probability of drawing a heart and a spade consecutively from a deck of cards if the first draw was replaced before the second draw?

Solution:

Sum Rule

This rule is used when studying two mutually exclusive events, and can be thought of as the “EITHER/OR″ rule.” The probability of either of two events occurring is the sum of their individual probabilities. This rule is used when the order of the events matters.

Example 5: What is the probability of drawing a diamond or a heart from a deck of cards?

Solution:

HYPOTHESIS TESTING

t-test and p-values

Many experiments involve comparing two datasets or two groups, and a t-test can be used to calculate whether the means of two groups are significantly different from each other. This test is most often applied to datasets that are normally distributed. A p-value equal to or below 0.05 is considered significant in most biology-related fields. T-test calculations involve comparing each data point to the group’s mean and also take standard deviation and sample size into consideration.

Understanding mathematically how p-values are calculated and t-tests are done is not important here. Instead, it’s important that you understand how these values are used to interpret data.

Let’s work through an example to demonstrate how common statistics are used in biological labs: A researcher has sections of two different types of skin cancers from human patients. She stains them for the protein CD31, which is a marker of endothelial cells. She then takes digital pictures of the immunofluorescent sections and counts how many blood vessels are present in each picture. She takes five pictures of each slide.

Solutions:

Chi-Square (x²) Tests

A chi square test is a statistical tool used to measure the difference between observed and expected data. For example, suppose you roll a die 120 times. You would expect a 1:1:1:1:1:1 ratio between all the numbers that come up. In other words, you would expect to see each side 20 times. However, because this is an experiment and the sample size is only 120, you will probably see some variation in the data. If you rolled 24 sixes for example, the disagreement between observed (24) and expected (20) is small, and could have occurred by chance. If you rolled 40 sixes however, there is a large disagreement from the expected. Maybe it is a weighted die. The region in between these two values is trickier. Where is the line drawn between expected/normal variations and results that are so different that they must tell a different story altogether.

Chi-square tests are one way to make this decision. They start with a null hypothesis (H_o), which represents a set numerical outcome that you want to compare your data with. The chi-square test will determine if your actual data is close to the null hypothesis outcome and could have occurred due to a fluke (i.e., rolling a six 24 times) or if it is so different that it is probably not a fluke (i.e., 40 rolled sixes) and the null hypothesis outcome must not correctly describe what is occurring. In the dice case, rolling a six 40 times would cause the null hypothesis of expecting a 1:1:1:1:1:1 to be rejected and the die can be considered to be weighted. In the calculations, expected results if the null hypothesis were true are compared to the actual values, and an x² value is calculated. This value is compared to a critical value, and a decision is made to reject or accept the null hypothesis.

For example, suppose data was collected from 100 families with three children each. Fourteen families had three female children, 36 families had two females and a male, 30 families had one female and two males, and 20 families had three male children. We would expect offspring sex to segregate independently. In other words, the sex of a given child shouldn’t be affected by the sex of previous children. Let’s test whether this is true for this dataset.

Since we expect sex to segregate independently, this is the null hypothesis (H_o). Each family has three children, so there are four possible outcomes for each family:

Using some advanced math (that you don’t need to worry about), the probabilities for each of these is:

Because there are 100 families, we expect 12.5 to have three females, 37.5 to have two females and a male, 37.5 to have one female and two males, and 12.5 to have three males. This can be calculated by multiplying the probability of each event by the total (100 in this case).

Next, we compare this expected data (E) to what actually happened (the observed data, O). Note that the total numbers for observed and expected columns must be the same. To calculate a x² value, the formula (O – E)²/E is calculated for each row of the table, and summed.

The calculated x² value is 6.24. Next, this value needs to be compared to a critical value (CV). This is obtained from a table like this one.

This chart is included on the AP Biology Equations and Formulas sheet. In order to use this table, you must know the degrees of freedom (DF), which represent the number of independent variables in the data. In most cases, this is the number of possibilities being compared minus one. In this example, DF = 4 – 1, because we are comparing four different family types.

You also need a reference p-value. This is the probability of observing a deviation from the expected results due to chance. For most biological tests, a p-value of 0.05 is used.

Since we are using DF = 3 and p = 0.05, the critical value is 7.82 (using the chart above). Next, the critical value is compared to the x² value; if x² < CV, you accept H_o. If x² > CV, you reject H_o. We calculated a x² value of 6.24, which is smaller than 7.82. Since x² < CV, we accept H_o and conclude that offspring sex could, indeed, be segregating independently in this dataset.

KEY TERMS

descriptive statistics

sample

population

quantitative data

qualitative data

bar graph

pie graph

normal or parametric data

normal distribution

sample size

mean

outliers

standard deviation

standard error

nonparametric data

histogram or frequency diagram

median

mode

range

hypothesis

dependent variable

independent variable

contants (contolled variables)

controls

statistical significance

line graph

bra graph

box and whisker plot

scatterplot

probability

product rule

sum rule

t-test

p-value

chi-square test

null hypothesis

critical value

degrees of freedom

Summary

Chapter 13 Drill

Answers and explanations can be found in Chapter 16.

REFLECT

Respond to the following questions: