Introduction to AP Biology
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TABLE OF CONTENTS Preface........................................................................................................ 1 Chapter One: Chemistry of Life ................................................................... 4 The Structure of Water .................................................................................................... 4 Water Properties that are Unique about this Solvent ..................................................... 6 Hydrogen Bonding and Other Bond Types ..................................................................... 9 Covalent Bonds .............................................................................................................. 12 Ionic Bonds .................................................................................................................... 12 Elements of Life ............................................................................................................. 12 Basics of Biological Macromolecules ............................................................................. 15 Properties and Function of Carbohydrates ................................................................... 19 Properties and Function of Lipids ................................................................................. 22 Structure and Function of Proteins ............................................................................... 28 Structure and Function of Nucleic Acids ....................................................................... 32 Key Takeaways ............................................................................................................... 35 Chapter One: Quiz ......................................................................................................... 36 Chapter Two: Cell Structure and Function ................................................ 39 Cell Structure and Subcellular Components ................................................................. 39 Prokaryotic Cell Structure ............................................................................................. 39 Eukaryotic Cell Structure Basics ................................................................................... 43 Details about the Eukaryotic Cell Structures and Function .......................................... 46 Cell Size and Shape ........................................................................................................ 55 Plasma Membranes........................................................................................................ 55
Membrane Permeability ................................................................................................ 59 Plasma Membrane Transport Mechanisms .................................................................. 59 Tonicity and Osmoregulation ........................................................................................ 65 Mechanisms of Transport inside the Cell ...................................................................... 68 Cell Compartmentalization ............................................................................................ 69 Origins of Cell Organelles .............................................................................................. 69 Key Takeaways ................................................................................................................71 Chapter Two: Quiz ......................................................................................................... 73 Chapter Three: Cellular Energetics ........................................................... 76 Enzyme Structure .......................................................................................................... 76 Enzyme Catalysis ........................................................................................................... 79 Environmental Impacts on Enzyme Function .............................................................. 81 Eukaryotic Cellular Metabolism .................................................................................... 82 Glycolysis ....................................................................................................................... 83 Krebs Cycle ..................................................................................................................... 87 Oxidative Phosphorylation or the Electron Transport Chain ....................................... 91 Bacterial Metabolism ..................................................................................................... 95 Photosynthesis ............................................................................................................... 97 Key Takeaways ............................................................................................................. 100 Chapter Three: Quiz ......................................................................................................101 Chapter Four: Cell Communication and the Cell Cycle ............................ 104 Cell Communication .................................................................................................... 104 Signal Transduction and Second Messengers .............................................................. 115 Cell Signaling Feedback ............................................................................................... 120
Cell Cycle ...................................................................................................................... 122 Regulation of the Cell Cycle ......................................................................................... 126 Apoptosis of Cells ......................................................................................................... 128 Key Takeaways ............................................................................................................. 130 Chapter Four: Quiz ....................................................................................................... 131 Chapter Five: Heredity ............................................................................ 134 Meiosis ......................................................................................................................... 134 Meiosis and Genetic Diversity ..................................................................................... 140 Mendelian Genetics ...................................................................................................... 141 Non-Mendelian Genetics ............................................................................................. 146 Environmental Effects on Phenotype .......................................................................... 149 Chromosomal Theory of Inheritance .......................................................................... 152 Key Takeaways ..............................................................................................................155 Chapter Five: Quiz ....................................................................................................... 156 Chapter Six: Gene Expression and Regulation......................................... 159 DNA and RNA Structure.............................................................................................. 159 Replication ................................................................................................................... 163 Transcription and RNA Processing ............................................................................. 166 Translation ................................................................................................................... 170 Post-translational Protein Modification...................................................................... 176 Regulation of Gene Expression..................................................................................... 177 Gene Expression and Cell Specialization .................................................................... 180 Mutations ..................................................................................................................... 182 Biotechnology............................................................................................................... 184
Key Takeaways ............................................................................................................. 187 Chapter Six: Quiz ......................................................................................................... 188 Chapter Seven: Natural Selection ............................................................. 191 Natural Selection .......................................................................................................... 191 Artificial Selection ........................................................................................................ 194 Population Genetics ..................................................................................................... 196 Hardy-Weinberg Equilibrium ..................................................................................... 198 Evidence of Evolution .................................................................................................. 199 Common Ancestry........................................................................................................202 Continuing Evolution................................................................................................... 203 Phylogeny .....................................................................................................................204 Speciation .................................................................................................................... 208 Extinction ..................................................................................................................... 210 Variations in Population ............................................................................................... 211 Origin of Life on Earth .................................................................................................. 211 Key Takeaways ............................................................................................................. 213 Chapter Seven: Quiz..................................................................................................... 214 Chapter Eight: Ecology ............................................................................. 217 Responses to the Environment .....................................................................................217 Energy Flow through Ecosystems ............................................................................... 221 Population Ecology ...................................................................................................... 225 Effect of Density of Populations .................................................................................. 226 Community Ecology ..................................................................................................... 227 Biodiversity .................................................................................................................. 230
Disruptions to Ecosystems .......................................................................................... 233 Key Takeaways ............................................................................................................. 236 Chapter Eight: Quiz ..................................................................................................... 237 Summary ................................................................................................ 240 Course Quizzes ....................................................................................... 243 Answer Key to Quizzes ............................................................................ 286 Answer Key: Chapter One ............................................................................................ 286 Answer Key: Chapter Two ........................................................................................... 287 Answer Key: Chapter Three .........................................................................................288 Answer Key: Chapter Four........................................................................................... 289 Answer Key: Chapter Five............................................................................................290 Answer Key: Chapter Six ............................................................................................. 291 Answer Key: Chapter Seven ......................................................................................... 292 Answer Key: Chapter Eight.......................................................................................... 293 Answer Key: Course Quizzes ....................................................................................... 294
PREFACE If you have decided to take this AP Biology course, you probably want to know what the advanced high school student studying biology will need to know in order to be successful when it comes to understanding the biological processes of life. This course will deliver that information to you and much more. As you listen to this course, you will understand how living things work on a cellular level and how this translates into the ecology of living things in general. You will start with the basics, such as the chemistry of water, which is the basic solvent of all life forms. Gradually, you should build your knowledge to include the different molecules in living things, the way these molecules form cellular components, how cells work, the genetics and hereditary patterns seen in nature, and what we understand about natural selection and ecology in general. When you finish the course, you should feel confident that your knowledge of advanced biology is greatly enhanced. Chapter one in the course introduces AP biology in an extremely basic way. Before you can understand the more complex topics you will later learn in the course, you need to know the biochemistry behind it. Water is the basic solvent of life, capable of hydrogen bonding so important to many aspects of biology in general. There are certain elements and macromolecules that are a natural part of living things. In this chapter, you will know what these are and will be able to understand biology from the perspective of the molecules involved. Chapter two is everything you ever wanted to know about the cell. There are different types of cells, including plant cells and animal cells that have similarities and differences between one another. In this chapter, we will talk about the different intracellular structures and what they do as well as the structure and function of the cell membrane. Cell membranes are crucial to the life of the cell itself because they allow molecules to enter and exit the cell in specific ways and define the boundaries of the cell. After you have studied this chapter, you will feel confident that you know what the cell looks like and what the different parts of the cell do.
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In chapter three in the course, we will discuss how cells get the energy they need in order to run every day processes. There are some differences in how animal cells do this compared to how plant cells do this. We will talk about enzymes and how they allow most of the biochemical processes of the cell to happen so quickly. There are specific ways that cells use glucose as an energy source under different circumstances, which will be covered as well. These are complex processes that you should understand as best you can. In addition, we will talk about the process of photosynthesis and how this contributes to plant cell energetics. The focus of chapter four will be to study the ways a cell can communicate with other cells or with its environment. There are different ways that cell can do this. There are often receptors that trigger events in the cell through what’s called signal transduction. We will also talk about the cell cycle and how it is regulated. There are processes a cell goes through from the time it becomes a daughter cell until it dies that we will discuss in this chapter. In chapter five of the course, we take a look at heredity as it applies to biological systems and organisms. On a small scale, heredity involves the process of meiosis, which is how most eukaryotic organisms pass on genetic information from one generation to the next with the ability to have genetic diversity in the subsequent generation. We will also discuss genetics in general, including Mendelian genetics first identified by Gregor Mendel in the late 1800s. There is also non-Mendelian genetics, which doesn’t follow typical Mendelian rules. There are also environmental effects on an organism’s phenotype that have nothing to do with inheritance. Finally, we will talk about chromosomal inheritance patterns, which involve larger effects on the organism because more than one or a few genes are involved in the passage of traits to the offspring. Chapter six expands on the study of genes and genetics to involve the molecular basis of nucleic acids, including how they are used to make new copies of a cell or make proteins for the cell using process like DNA replication, transcription, and translation. These are well-understood by biologists as part of the study of molecular biology. You will also learn about the regulation of gene expression and how gene expression gets used to create specialized cells in a multicellular organism. We will talk about mutations and
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how they affect an organism’s genotype and phenotype and will discuss ways biotechnology is using the study of genes and gene mutations for a variety of purposes. In chapter seven of the course, we will talk about the biological basis of natural selection, which is the main way that the process of evolution occurs. Animal breeders and plant breeders use artificial selection in order to get what they want out of the offspring organism rather than using any natural selection process. This will lead us to talk about the principles of population genetics and how it is believed that evolution occurs over long or short stretches of time. New species are created and made extinct all the time, which we will discuss. We will also talk about how life originated on earth and how there is variation even within members of the same species. Chapter eight studies ecology or the environment and how it relates to the populations that live in it. All organisms respond to their environment in some way and have the potential to affect it. In this chapter, we will talk about energy flow in the environment and issues related to population ecology, community ecology, and the effect of increases in density on the ecosystem. There are other disruptions of the ecosystem that are occurring all the time, which will be discussed in the chapter. Finally, we will talk about biodiversity and why it is important to the ecosystems on earth.
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CHAPTER ONE: CHEMISTRY OF LIFE This chapter introduces AP biology in an extremely basic way. Before you can understand the more complex topics you will later learn in the course, you need to know the biochemistry behind it. Water is the basic solvent of life, capable of hydrogen bonding so important to many aspects of biology in general. There are certain elements and macromolecules that are a natural part of living things. In this chapter, you will know what these are and will be able to understand biology from the perspective of the molecules involved.
THE STRUCTURE OF WATER Water is a very simple molecule but it is so important to the study of biology. There really isn’t much water in the universe overall but on planet Earth, this just isn’t the case and water is everywhere. All biological processes depend on water to some degree. As you will learn soon, there are some unique properties of water that make it so good for the biology of this planet. Water is found on earth in all of its physical forms. It is found frozen as ice, liquid in all of the oceans, rivers, and lakes on the planet, and gaseous as part of the gases in the atmosphere. Each phase change from one to another involves transformation of the water to a different energy state. Figure 1 shows what the basic molecule of water looks like:
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Figure 1.
If you have studied any chemistry at all, you will recognize that water or H2O is a small molecule made from one atom of oxygen that is covalently bound to two molecules of hydrogen. Covalent bonds in chemistry are very strong and separation of the parts is difficult. Because oxygen is called electronegative, meaning it likes to attract negatively charged electrons, it carries a slight negative charge compared to the hydrogen atoms, which are slightly more positively charged than they would be if they were by themselves. This unequal sharing of electrons creates what is called a dipole moment between each hydrogen and oxygen atom. These dipole moments create a tiny magnetic force that attracts each hydrogen atom to an oxygen atom in a nearby water molecule. This is what keeps liquid water so likely to attract to itself. This attraction between two water molecules from hydrogen to oxygen is called hydrogen bonding. We will talk more about that in a minute. Hydrogen bonds by themselves are quite weak. They are so weak that we do not call them bonds but rather that they are considered a type of attractive force. While each hydrogen bond is weak, putting a lot of these hydrogen bonds together makes a collection of water in liquid form very hard to separate. It’s this type of attraction between water molecules that makes water so unique as a solvent.
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WATER PROPERTIES THAT ARE UNIQUE ABOUT THIS SOLVENT One of the unique properties of water that you don’t often see with other solvents is that it floats or becomes less dense as it freezes. This is not true of most other solvents. When liquid water turns to ice, the kinetic energy of the liquid water is lessened. Low kinetic energy is the same as being low in temperature because temperature and kinetic energy are closely related. With water, the molecules form a stable lattice where the molecules of water do not move. Most other solvents will have the molecules closer together and denser when they freeze. With water, though, the hydrogen bonds and unique shape of the water molecule means that the solid form is less dense. In fact, the dipole ends will actually repel each other into a fixed lattice shape that looks like that seen in figure 2:
Figure 2.
This decreased density of the molecules of water in the frozen state is what makes ice float above its liquid state. This is important in biology because it means that when a lake freezes, the life forms like fish and other underwater creatures will remain alive under the ice surface.
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Water is such a good solvent that it is often called the universal solvent. This is because so many solutes or substances will dissolve in it. Because water is so polar and has dipole moments, it will easily dissolve any polar molecule plus ions. Ions, as you may remember from chemistry class, are substances that have so much of a difference in electronegativity between the atoms that they separate into different parts in water. Sodium chloride, potassium hydroxide, and hydrochloric acid are all ionic molecules that easily dissolve in water. Nonpolar substances, like waxes, oils, and fats, do not easily dissolve in water. This is why these types of molecules are called hydrophobic or water-hating. Most biological molecules, except for lipids, dissolve in water—even those that are very large. All sugars, DNA, vitamins, and almost all proteins are polar enough to dissolve in water. This is why water is so vital to life in general. A great portion of our bodies are made from water and water is the solvent inside all cells. Water is also great for dissolving most gases, such as carbon dioxide and oxygen, which circulate freely in the human body in our plasma. There is a molecule called hemoglobin in humans that helps oxygen to travel through the bloodstream but it also dissolves by itself. Oxygen or O2 is not polar but because water is polar, it pulls the double oxygen gas molecule into a dipole so that it is soluble in water as a solvent. This is crucial for aquatic life on earth. Another unique property is its degree of cohesion. Cohesion is how a molecule sticks to other molecules of the same type. It’s basically because of the hydrogen bonding or attraction between the molecules of water that make it so cohesive. It is the most cohesive non-metallic liquid known. Cohesion is stronger at the surface of something. The cohesion at the surface of water is called its surface tension. Water has a high surface tension compared to other liquids. It is the high surface tension of water that allows a leaf or spider to sit in the surface without sinking. Water has a high degree of adhesion. When you drink a glass of water and set it down, drops will remain on the side of the glass as droplets, gradually getting pulled downward as a result of gravity. This adhesion involves the ability of water molecules to stick to other molecules, such as the glass you drank the water from. Any surface with a high
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negative charge will adhere to water molecules to a greater degree. Glass has a negative charge but things like wax do not have this negative charge so you will see less of this phenomenon. Another interesting thing you will see related to cohesion is called capillary action. This is seen as the tendency of water to be more cohesive when in contact with another surface. In a capillary tube, you will see a rise in the water level at the edges and a sinking in the middle. If you have a thin enough tube, water will rise against gravity, which is what is known as capillary action. It works better with glass tubes because the glass is so negative in its own charge. This is also seen in the meniscus of water. The meniscus is the upper layer of a solvent in a narrow tube. With nonpolar solvents, you will see a flat meniscus because there is no adhesion to the sides of the tube. With water, though, you will see a concave meniscus, which is what you’ll see in figure 3:
Figure 3.
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As you will learn later, it’s this amazing property of cohesion and the phenomenon of capillary action that keeps plants watered internally. Water rises from the roots to the upper plant parts by capillary action of water inside the circulatory system of the plant.
HYDROGEN BONDING AND OTHER BOND TYPES In case you need some brushing up on your chemistry skills, we will talk now about the different bonding types and how they apply to biological systems. The three main types of bonds in biology are covalent bonds, ionic bonds, and what you can call attractive forces, of which hydrogen bonding is just one of these. Hydrogen bonding is what takes place between water molecules as you have just discovered. It requires that a hydrogen atom be at least one component of the attractive force or bond. In nearly all cases, the attraction involves a hydrogen atom being attracted to some other atom that is itself already attached to a larger molecule covalently. Hydrogen best bonds to those atoms that are the most electronegative, such as chlorine, oxygen, or fluorine but it will bond with others as well. An example of hydrogen bonding within the same molecule is how it is used to zip together two DNA strands in the nucleus. Proteins also can retain their shape because of hydrogen bonding between atoms within the same molecule. Figure 4 shows the periodic table and the degree of electronegativity within the table itself:
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Figure 4.
As you will see later, hydrogen bonding is sometimes included as a type of van der Waals force in a molecule. Van der Waals forces are attractive forces that don’t have to involve hydrogen and are weaker than hydrogen bonds. As was just said earlier, hydrogen bonding depends entirely on the dipole to dipole interaction between some electronegative atom and any hydrogen atom that is itself bound covalently to some other molecule. Water is often that molecule. These are weak forces that are only about five percent of the strength of a typical covalent bond. It is the slight positive charge on the bonded hydrogen atom in a molecule that allows for this type of bonding to happen. Hydrogen bonds are extremely important in all aspects of biology. They help the transcription factors bind to DNA during DNA transcription and help antigens and antibodies pair up together. Proteins will gain their shape with hydrogen bonding and DNA strands are held together using these bonds.
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Figure 6.
Lipids are another form of major biomolecule or biological molecule. These are generally made from a combination of fatty acids attached to a glycerol molecule to make a triglyceride molecule of varying sizes. These molecules are the long-term storage form of energy in biological systems, often used when sugars are used up or are unavailable. There are several other forms of lipids besides triglycerides, such as steroids, phospholipids, waxes, grease, and oils. Figure 7 shows what a triglyceride looks like as well as what cholesterol, a steroid lipid, looks like: 16
Figure 68.
Figure 7.
Figure 19.
Figure 23.
COURSE QUIZZES 1.
You are trying to dissolve a substance in water. Which substance will least likely dissolve in water? A. Benzene B. Ethanol C. Hydrochloric acid D. Potassium chloride
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What major property of water accounts for the fact that a leaf will remain on its surface? A. Heat of vaporization B. Capillary action C. Decreased solid density compared to liquid density D. High surface tension
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When looking at a tube of water in a narrow tube, what shape will the meniscus be? A. Convex B. Concave C. Flat D. Undulant
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Hydrogen bonding is best done between hydrogen and an electronegative atom. According to the periodic table showing electronegativity, which molecule would best form a hydrogen bond with a hydrogen atom? A. Carbon B. Oxygen C. Chlorine D. Fluorine
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Which element inside living organisms is found to be the most prevalent by weight? A. Hydrogen B. Carbon C. Oxygen D. Nitrogen
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According to the number of atoms, which element is seen most commonly inside living organisms? A. Hydrogen B. Carbon C. Oxygen D. Nitrogen
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Which biological molecule is most responsible for creating and defining the genetics of the cell itself? A. Lipids B. Carbohydrates C. Proteins D. Nucleic acids
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Which biological molecule is most likely to be an enzyme? A. Lipids B. Carbohydrates C. Proteins D. Nucleic acids
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Which biological molecule is used as a rapid source of energy for the cell? A. Lipids B. Carbohydrates C. Proteins D. Nucleic acids
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ANSWER KEY: CHAPTER EIGHT 1. Answer: c. Living things put energy into the environment, naturally disrupting a natural downward trend that results in decreased chaos and decreased entropy in the system. 2. Answer: a. Sunlight puts energy into the ecosystem, allowing plants to grow and add to their structure, which would decrease the entropy of the environment. The other choices are decaying or destroying forces that would increase entropy. 3. Answer: d. Wind will spread pollen and seeds that will tend to scatter them and increase the biodiversity of many parts of the world. 4. Answer: a. Directional selection involves the favoring of an extreme or the fittest of the organisms being at one extreme end of the spectrum. 5. Answer: a. An ecological pyramid is a pyramid that shows the different trophic levels with things like energy levels, biomass, and numbers of organisms represented per level. 6. Answer: c. The tertiary consumer at the top of the pyramid is most affected because of issues like biological magnification that affects higher-order consumers the greatest. 7. Answer: b. Each of these is an untrue statement about human population density except that, because of rising density in humans, there is increasing strain on the population. 8. Answer: d. Each of these is a negative impact on the population as the density of human population gets greater. 9. Answer: b. With mutualism, the interaction between both species is positive so that both benefit from the relationship. 10. Answer: c. With commensalism, one organism benefits but the other neither benefits or is harmed because of the disparity between the two types of interactions between species members.
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ANSWER KEY: COURSE QUIZZES 1. Answer: a. Each of these is a polar molecule that will easily dissolve in water with the exception of benzene. Benzene is not polar and therefore will not dissolve well in water as its solvent. 2. Answer: d. It is the high surface tension of water that most contributes to the fact that a leaf or perhaps a spider will sit on the surface of the water rather than sinking. 3. Answer: a. The meniscus will be concave with rising of the edges of the water surface near the edges of the tube where the water adheres to the surface of the tube, causing it to rise above the water in the middle of the tube. 4. Answer: d. Fluorine is the most electronegative atom so it would be the atom that will best participate in hydrogen bonding with a hydrogen atom. 5. Answer: c. These represent the most prevalent elements inside the human body but, if you go by weight, oxygen is considered the most prevalent by weight in the body. 6. Answer: a. Hydrogen atoms are very small but the molecule itself is very prevalent in living systems, being the most prevalent atom by number of atoms in living systems. 7. Answer: d. The genetics of the cell involve the nucleic acids, which in most living things involves the DNA polymer. 8. Answer: c. Almost all enzymes in the cell are made from polypeptides or proteins. 9. Answer: b. Carbohydrates, mainly simple sugars, are used as rapid sources of energy in the cell. Sugar is the main molecule used to create the energy molecules of the cell through various biochemical pathways. 10. Answer: a. Each of these is considered a monosaccharide except for sucrose, which is a typical disaccharide, often referred to as table sugar. 11. Answer: a. Starch is a polymer of glucose that is made by plants and used by animals of all types in order to be used for animal cellular energy. It comes from the glucose molecules made in the photosynthetic process. 12. Answer: c. Glycogen is the form of glucose storage polymer found in humans and in most animals. It is found in the liver and muscles where glucose can be released from it when glucose levels are low or when glucose is most rapidly needed.
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