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Chapter 5 | 117 5 | PHOTOSYNTHESIS

Figure 5.1 This sage thrasher’s diet, like that of almost all , depends on photosynthesis. (credit: modification of work by Dave Menke, U.S. Fish and Wildlife Service)

Chapter Outline

5.1: Overview of Photosynthesis 5.2: The Light-Dependent Reactions of Photosynthesis 5.3: The Calvin Cycle

Introduction No matter how complex or advanced a machine, such as the latest cellular phone, the device cannot function without energy. Living things, similar to machines, have many complex components; they too cannot do anything without energy, which is why humans and all other organisms must “eat” in some form or another. That may be common knowledge, but how many people realize that every bite of every meal ingested depends on the process of photosynthesis? 5.1 | Overview of Photosynthesis

By the end of this section, you will be able to: • Summarize the process of photosynthesis • Explain the relevance of photosynthesis to other living things • Identify the reactants and products of photosynthesis • Describe the main structures involved in photosynthesis

All living organisms on earth consist of one or more cells. Each cell runs on the chemical energy found mainly in carbohydrate (food), and the majority of these molecules are produced by one process: photosynthesis. Through photosynthesis, certain organisms convert solar energy (sunlight) into chemical energy, which is then used to build carbohydrate molecules. The energy used to hold these molecules together is released when an breaks down food. Cells then use this energy to perform work, such as cellular respiration. 118 Chapter 5 | Photosynthesis

The energy that is harnessed from photosynthesis enters the ecosystems of our planet continuously and is transferred from one organism to another. Therefore, directly or indirectly, the process of photosynthesis provides most of the energy required by living things on earth. Photosynthesis also results in the release of into the atmosphere. In short, to eat and breathe, humans depend almost entirely on the organisms that carry out photosynthesis.

Click the following link (http://openstaxcollege.org/l/photosynthesis2) to learn more about photosynthesis.

Solar Dependence and Food Production Some organisms can carry out photosynthesis, whereas others cannot. An autotroph is an organism that can produce its own food. The Greek roots of the word autotroph mean “self” (auto) “feeder” (troph). Plants are the best-known autotrophs, but others exist, including certain types of bacteria and algae (Figure 5.2). Oceanic algae contribute enormous quantities of food and oxygen to global food chains. Plants are also photoautotrophs, a type of autotroph that uses sunlight and from to synthesize chemical energy in the form of carbohydrates. All organisms carrying out photosynthesis require sunlight.

Figure 5.2 (a) Plants, (b) algae, and (c) certain bacteria, called , are photoautotrophs that can carry out photosynthesis. Algae can grow over enormous areas in , at times completely covering the surface. (credit a: Steve Hillebrand, U.S. Fish and Wildlife Service; credit b: "eutrophication&hypoxia"/Flickr; credit c: NASA; scale-bar data from Matt Russell)

Heterotrophs are organisms incapable of photosynthesis that must therefore obtain energy and carbon from food by consuming other organisms. The Greek roots of the word mean “other” (hetero) “feeder” (troph), meaning that their food comes from other organisms. Even if the food organism is another animal, this food traces its origins back to autotrophs and the process of photosynthesis. Humans are , as are all animals. Heterotrophs depend on autotrophs, either directly or indirectly. Deer and wolves are heterotrophs. A deer obtains energy by eating plants. A wolf eating a deer obtains energy that originally came from the plants eaten by that deer. The energy in the plant came from photosynthesis, and therefore it is the only autotroph in this example (Figure 5.3). Using this reasoning, all food eaten by humans also links back to autotrophs that carry out photosynthesis.

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Figure 5.3 The energy stored in carbohydrate molecules from photosynthesis passes through the food chain. The predator that eats these deer is getting energy that originated in the photosynthetic vegetation that the deer consumed. (credit: Steve VanRiper, U.S. Fish and Wildlife Service)

Photosynthesis at the Grocery Store

Figure 5.4 Photosynthesis is the origin of the products that comprise the main elements of the human diet. (credit: Associação Brasileira de Supermercados)

Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle contains hundreds, if not thousands, of different products for customers to buy and consume (Figure 5.4). Although there is a large variety, each item links back to photosynthesis. Meats and dairy products link to photosynthesis because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from grains, which are the seeds of photosynthetic plants. What about desserts and drinks? All of these products contain sugar—the basic carbohydrate produced directly from photosynthesis. The photosynthesis connection applies to every meal and every food a person consumes.

Main Structures and Summary of Photosynthesis Photosynthesis requires sunlight, carbon dioxide, and water as starting reactants (Figure 5.5). After the process is complete, photosynthesis releases oxygen and produces carbohydrate molecules, most commonly . These sugar molecules contain the energy that living things need to survive. 120 Chapter 5 | Photosynthesis

Figure 5.5 Photosynthesis uses solar energy, carbon dioxide, and water to release oxygen and to produce energy- storing sugar molecules.

The complex reactions of photosynthesis can be summarized by the chemical equation shown in Figure 5.6.

Figure 5.6 The process of photosynthesis can be represented by an equation, wherein carbon dioxide and water produce sugar and oxygen using energy from sunlight.

Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex, as in the way that the reaction summarizing cellular respiration represented many individual reactions. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the physical structures involved. In plants, photosynthesis takes place primarily in leaves, which consist of many layers of cells and have differentiated top and bottom sides. The process of photosynthesis occurs not on the surface layers of the leaf, but rather in a middle layer called the mesophyll (Figure 5.7). The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata. In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a . In plants, chloroplast- containing cells exist in the mesophyll. have a double (inner and outer) membrane. Within the chloroplast is a third membrane that forms stacked, disc-shaped structures called . Embedded in the membrane are molecules of chlorophyll,apigment (a molecule that absorbs light) through which the entire process of photosynthesis begins. Chlorophyll is responsible for the green color of plants. The thylakoid membrane encloses an internal space called the thylakoid space. Other types of pigments are also involved in photosynthesis, but chlorophyll is by far the most

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important. As shown in Figure 5.7, a stack of thylakoids is called a granum, and the space surrounding the granum is called (not to be confused with stomata, the openings on the leaves).

Figure 5.7 Not all cells of a leaf carry out photosynthesis. Cells within the middle layer of a leaf have chloroplasts, which contain the photosynthetic apparatus. (credit "leaf": modification of work by Cory Zanker)

On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

The Two Parts of Photosynthesis Photosynthesis takes place in two stages: the light-dependent reactions and the Calvin cycle. In the light-dependent reactions, which take place at the thylakoid membrane, chlorophyll absorbs energy from sunlight and then converts it into chemical energy with the use of water. The light-dependent reactions release oxygen from the hydrolysis of water as a byproduct. In the Calvin cycle, which takes place in the stroma, the chemical energy derived from the light-dependent reactions drives both the capture of carbon in carbon dioxide molecules and the subsequent assembly of sugar molecules. The two reactions use carrier molecules to transport the energy from one to the other. The carriers that move energy from the light-dependent reactions to the Calvin cycle reactions can be thought of as “full” because they bring energy. After the energy is released, the “empty” energy carriers return to the light-dependent reactions to obtain more energy. 122 Chapter 5 | Photosynthesis

5.2 | The Light-Dependent Reactions of Photosynthesis

By the end of this section, you will be able to: • Explain how plants absorb energy from sunlight • Describe how the wavelength of light affects its energy and color • Describe how and where photosynthesis takes place within a plant

How can light be used to make food? It is easy to think of light as something that exists and allows living organisms, such as humans, to see, but light is a form of energy. Like all energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is transformed into chemical energy, which autotrophs use to build carbohydrate molecules. However, autotrophs only use a specific component of sunlight (Figure 5.8).

Figure 5.8 Autotrophs can capture light energy from the sun, converting it into chemical energy used to build food molecules. (credit: modification of work by Gerry Atwell, U.S. Fish and Wildlife Service)

Visit this site (http://openstaxcollege.org/l/light_reaction2) and click through the animation to view the process of photosynthesis within a leaf.

What Is Light Energy? The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy, which is referred to as “visible light.” The manner in which solar energy travels can be described and measured as

This OpenStax book is available for free at http://cnx.org/content/col11487/1.9 Chapter 5 | Photosynthesis 123 waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the distance between two consecutive, similar points in a series of waves, such as from crest to crest or trough to trough (Figure 5.9).

Figure 5.9 The wavelength of a single wave is the distance between two consecutive points along the wave.

Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun. The electromagnetic spectrum is the range of all possible wavelengths of radiation (Figure 5.10). Each wavelength corresponds to a different amount of energy carried.

Figure 5.10 The sun emits energy in the form of electromagnetic radiation. This radiation exists in different wavelengths, each of which has its own characteristic energy. Visible light is one type of energy emitted from the sun.

Each type of electromagnetic radiation has a characteristic range of wavelengths. The longer the wavelength (or the more stretched out it appears), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy. The sun emits (Figure 5.10) a broad range of electromagnetic radiation, including X-rays and ultraviolet (UV) rays. The higher-energy waves are dangerous to living things; for example, X-rays and UV rays can be harmful to humans. Absorption of Light Light energy enters the process of photosynthesis when pigments absorb the light. In plants, pigment molecules absorb only visible light for photosynthesis. The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal these colors to the human eye. The visible light portion of the electromagnetic spectrum is perceived by the human eye as a rainbow of colors, with violet and blue having shorter wavelengths and, therefore, higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy. 124 Chapter 5 | Photosynthesis

Understanding Pigments Different kinds of pigments exist, and each absorbs only certain wavelengths (colors) of visible light. Pigments reflect the color of the wavelengths that they cannot absorb. All photosynthetic organisms contain a pigment called chlorophyll a, which humans see as the common green color associated with plants. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not from green. Because green is reflected, chlorophyll appears green. Other pigment types include chlorophyll b (which absorbs blue and red-orange light) and the carotenoids. Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is its absorption spectrum. Many photosynthetic organisms have a mixture of pigments; between them, the organism can absorb energy from a wider range of visible-light wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity decreases with depth, and certain wavelengths are absorbed by the water. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees block most of the sunlight (Figure 5.11).

Figure 5.11 Plants that commonly grow in the shade benefit from having a variety of light-absorbing pigments. Each pigment can absorb different wavelengths of light, which allows the plant to absorb any light that passes through the taller trees. (credit: Jason Hollinger) How Light-Dependent Reactions Work The overall purpose of the light-dependent reactions is to convert light energy into chemical energy. This chemical energy will be used by the Calvin cycle to fuel the assembly of sugar molecules. The light-dependent reactions begin in a grouping of pigment molecules and proteins called a photosystem. Photosystems exist in the membranes of thylakoids. A pigment molecule in the photosystem absorbs one photon, a quantity or “packet” of light energy, at a time. A photon of light energy travels until it reaches a molecule of chlorophyll. The photon causes an electron in the chlorophyll to become “excited.” The energy given to the electron allows it to break free from an of the chlorophyll molecule. Chlorophyll is therefore said to “donate” an electron (Figure 5.12). To replace the electron in the chlorophyll, a molecule of water is split. This splitting releases an electron and results in the + formation of oxygen (O2) and (H ) in the thylakoid space. Technically, each breaking of a water molecule releases a pair of electrons, and therefore can replace two donated electrons.

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Figure 5.12 Light energy is absorbed by a chlorophyll molecule and is passed along a pathway to other chlorophyll molecules. The energy culminates in a molecule of chlorophyll found in the reaction center. The energy “excites” one of its electrons enough to leave the molecule and be transferred to a nearby primary electron acceptor. A molecule of water splits to release an electron, which is needed to replace the one donated. Oxygen and hydrogen ions are also formed from the splitting of water.

The replacing of the electron enables chlorophyll to respond to another photon. The oxygen molecules produced as byproducts find their way to the surrounding environment. The hydrogen ions play critical roles in the remainder of the light-dependent reactions. Keep in mind that the purpose of the light-dependent reactions is to convert solar energy into chemical carriers that will be used in the Calvin cycle. In eukaryotes and some prokaryotes, two photosystems exist. The first is called photosystem II, which was named for the order of its discovery rather than for the order of the function. After the photon hits, photosystem II transfers the free electron to the first in a series of proteins inside the thylakoid membrane called the electron transport chain. As the electron passes along these proteins, energy from the electron fuels membrane pumps that actively move hydrogen ions against their concentration gradient from the stroma into the thylakoid space. This is quite analogous to the process that occurs in the mitochondrion in which an electron transport chain pumps hydrogen ions from the mitochondrial stroma across the inner membrane and into the intermembrane space, creating an electrochemical gradient. After the energy is used, the electron is accepted by a pigment molecule in the next photosystem, which is called (Figure 5.13). 126 Chapter 5 | Photosynthesis

Figure 5.13 From photosystem II, the electron travels along a series of proteins. This electron transport system uses the energy from the electron to pump hydrogen ions into the interior of the thylakoid. A pigment molecule in photosystem I accepts the electron. Generating an Energy Carrier: ATP In the light-dependent reactions, energy absorbed by sunlight is stored by two types of energy-carrier molecules: ATP and NADPH. The energy that these molecules carry is stored in a bond that holds a single atom to the molecule. For ATP, it is a atom, and for NADPH, it is a hydrogen atom. Recall that NADH was a similar molecule that carried energy in the mitochondrion from the to the electron transport chain. When these molecules release energy into the Calvin cycle, they each lose to become the lower-energy molecules ADP and NADP+. The buildup of hydrogen ions in the thylakoid space forms an electrochemical gradient because of the difference in the concentration of protons (H+) and the difference in the charge across the membrane that they create. This potential energy is harvested and stored as chemical energy in ATP through chemiosmosis, the movement of hydrogen ions down their electrochemical gradient through the transmembrane ATP synthase, just as in the mitochondrion. The hydrogen ions are allowed to pass through the thylakoid membrane through an embedded protein complex called ATP synthase. This same protein generated ATP from ADP in the mitochondrion. The energy generated by the hydrogen stream allows ATP synthase to attach a third phosphate to ADP, which forms a molecule of ATP in a process called . The flow of hydrogen ions through ATP synthase is called chemiosmosis, because the ions move from an area of high to low concentration through a semi-permeable structure. Generating Another Energy Carrier: NADPH The remaining function of the light-dependent reaction is to generate the other energy-carrier molecule, NADPH. As the electron from the electron transport chain arrives at photosystem I, it is re-energized with another photon captured by chlorophyll. The energy from this electron drives the formation of NADPH from NADP+ and a hydrogen ion (H+). Now that the solar energy is stored in energy carriers, it can be used to make a sugar molecule. 5.3 | The Calvin Cycle

By the end of this section, you will be able to: • Describe the Calvin cycle • Define • Explain how photosynthesis works in the energy cycle of all living organisms

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After the energy from the sun is converted and packaged into ATP and NADPH, the cell has the fuel needed to build food in the form of carbohydrate molecules. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? The carbon atoms used to build carbohydrate molecules comes from carbon dioxide, the gas that animals exhale with each breath. The Calvin cycle is the term used for the reactions of photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other carbohydrate molecules. The Interworkings of the Calvin Cycle

In plants, carbon dioxide (CO2) enters the chloroplast through the stomata and diffuses into the stroma of the chloroplast—the site of the Calvin cycle reactions where sugar is synthesized. The reactions are named after the scientist who discovered them, and reference the fact that the reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery (Figure 5.14).

Figure 5.14 Light-dependent reactions harness energy from the sun to produce ATP and NADPH. These energy- carrying molecules travel into the stroma where the Calvin cycle reactions take place.

The Calvin cycle reactions (Figure 5.15) can be organized into three basic stages: fixation, reduction, and regeneration. In the stroma, in addition to CO2, two other chemicals are present to initiate the Calvin cycle: an enzyme abbreviated RuBisCO, and the molecule ribulose bisphosphate (RuBP). RuBP has five atoms of carbon and a phosphate group on each end.

RuBisCO catalyzes a reaction between CO2 and RuBP, which forms a six-carbon compound that is immediately converted into two three-carbon compounds. This process is called carbon fixation, because CO2 is “fixed” from its inorganic form into organic molecules. ATP and NADPH use their stored energy to convert the three-carbon compound, 3-PGA, into another three-carbon compound called G3P. This type of reaction is called a reduction reaction, because it involves the gain of electrons. A reduction is the gain of an electron by an atom or molecule. The molecules of ADP and NAD+, resulting from the reduction reaction, return to the light-dependent reactions to be re-energized. One of the G3P molecules leaves the Calvin cycle to contribute to the formation of the carbohydrate molecule, which is commonly glucose (C6H12O6). Because the carbohydrate molecule has six carbon atoms, it takes six turns of the Calvin cycle to make one carbohydrate molecule (one for each carbon dioxide molecule fixed). The remaining G3P molecules regenerate RuBP, which enables the system to prepare for the carbon-fixation step. ATP is also used in the regeneration of RuBP. 128 Chapter 5 | Photosynthesis

Figure 5.15 The Calvin cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic molecule. In stage 2, the organic molecule is reduced. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the cycle can continue.

In summary, it takes six turns of the Calvin cycle to fix six carbon atoms from CO2. These six turns require energy input from 12 ATP molecules and 12 NADPH molecules in the reduction step and 6 ATP molecules in the regeneration step.

The following is a link (http://openstaxcollege.org/l/calvin_cycle2) to an animation of the Calvin cycle. Click Stage 1, Stage 2, and then Stage 3 to see G3P and ATP regenerate to form RuBP.

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Photosynthesis The shared evolutionary history of all photosynthetic organisms is conspicuous, as the basic process has changed little over eras of time. Even between the giant tropical leaves in the rainforest and tiny cyanobacteria, the process and components of photosynthesis that use water as an electron donor remain largely the same. Photosystems function to absorb light and use electron transport chains to convert energy. The Calvin cycle reactions assemble carbohydrate molecules with this energy. However, as with all biochemical pathways, a variety of conditions leads to varied adaptations that affect the basic pattern. Photosynthesis in dry-climate plants (Figure 5.16) has evolved with adaptations that conserve water. In the harsh dry heat, every drop of water and precious energy must be used to survive. Two adaptations have evolved in such plants. In one form, a more efficient use of CO2 allows plants to photosynthesize even when CO2 is in short supply, as when the stomata are closed on hot days. The other adaptation performs preliminary reactions of the Calvin cycle at night, because opening the stomata at this time conserves water due to cooler temperatures. In addition, this adaptation has allowed plants to carry out low levels of photosynthesis without opening stomata at all, an extreme mechanism to face extremely dry periods.

Figure 5.16 Living in the harsh conditions of the desert has led plants like this cactus to evolve variations in reactions outside the Calvin cycle. These variations increase efficiency and help conserve water and energy. (credit: Piotr Wojtkowski)

Photosynthesis in Prokaryotes The two parts of photosynthesis—the light-dependent reactions and the Calvin cycle—have been described, as they take place in chloroplasts. However, prokaryotes, such as cyanobacteria, lack membrane-bound organelles. Prokaryotic photosynthetic autotrophic organisms have infoldings of the plasma membrane for chlorophyll attachment and photosynthesis (Figure 5.17). It is here that organisms like cyanobacteria can carry out photosynthesis. 130 Chapter 5 | Photosynthesis

Figure 5.17 A photosynthetic prokaryote has infolded regions of the plasma membrane that function like thylakoids. Although these are not contained in an organelle, such as a chloroplast, all of the necessary components are present to carry out photosynthesis. (credit: scale-bar data from Matt Russell) The Energy Cycle Living things access energy by breaking down carbohydrate molecules. However, if plants make carbohydrate molecules, why would they need to break them down? Carbohydrates are storage molecules for energy in all living things. Although energy can be stored in molecules like ATP, carbohydrates are much more stable and efficient reservoirs for chemical energy. Photosynthetic organisms also carry out the reactions of respiration to harvest the energy that they have stored in carbohydrates, for example, plants have mitochondria in addition to chloroplasts. You may have noticed that the overall reaction for photosynthesis:

6CO2 + 6H2 O ⎯→ C6 H12 O6 + 6O2 is the reverse of the overall reaction for cellular respiration:

6O2 +C6 H12 O6 → 6CO2 + 6H2 O Photosynthesis produces oxygen as a byproduct, and respiration produces carbon dioxide as a byproduct. In nature, there is no such thing as waste. Every single atom of matter is conserved, recycling indefinitely. Substances change form or move from one type of molecule to another, but never disappear (Figure 5.18).

CO2 is no more a form of waste produced by respiration than oxygen is a waste product of photosynthesis. Both are byproducts of reactions that move on to other reactions. Photosynthesis absorbs energy to build carbohydrates in chloroplasts, and aerobic cellular respiration releases energy by using oxygen to break down carbohydrates. Both organelles use electron transport chains to generate the energy necessary to drive other reactions. Photosynthesis and cellular respiration function in a biological cycle, allowing organisms to access life-sustaining energy that originates millions of miles away in a star.

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Figure 5.18 In the , the reactions of photosynthesis and cellular respiration share reciprocal reactants and products. (credit: modification of work by Stuart Bassil) 132 Chapter 5 | Photosynthesis

KEY TERMS absorption spectrum the specific pattern of absorption for a substance that absorbs electromagnetic radiation

autotroph an organism capable of producing its own food

Calvin cycle the reactions of photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other carbohydrate molecules

carbon fixation the process of converting inorganic CO2 gas into organic compounds

chlorophyll the green pigment that captures the light energy that drives the reactions of photosynthesis

chlorophyll a the form of chlorophyll that absorbs violet-blue and red light

chlorophyll b the form of chlorophyll that absorbs blue and red-orange light

chloroplast the organelle where photosynthesis takes place

electromagnetic spectrum the range of all possible frequencies of radiation

granum a stack of thylakoids located inside a chloroplast

heterotroph an organism that consumes other organisms for food

light-dependent reaction the first stage of photosynthesis where visible light is absorbed to form two energy-carrying molecules (ATP and NADPH)

mesophyll the middle layer of cells in a leaf

photoautotroph an organism capable of synthesizing its own food molecules (storing energy), using the energy of light

photon a distinct quantity or “packet” of light energy

photosystem a group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb light energy and convert it into chemical energy

pigment a molecule that is capable of absorbing light energy

stoma the opening that regulates gas exchange and water regulation between leaves and the environment; plural: stomata

stroma the fluid-filled space surrounding the grana inside a chloroplast where the Calvin cycle reactions of photosynthesis take place

thylakoid a disc-shaped membranous structure inside a chloroplast where the light-dependent reactions of photosynthesis take place using chlorophyll embedded in the membranes

wavelength the distance between consecutive points of a wave CHAPTER SUMMARY 5.1 Overview of Photosynthesis

The process of photosynthesis transformed life on earth. By harnessing energy from the sun, photosynthesis allowed living things to access enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy, allowing them to evolve new structures and achieve the biodiversity that is evident today. Only certain organisms, called autotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that can absorb light and convert light energy into chemical energy. Photosynthesis uses carbon dioxide and water to assemble carbohydrate molecules (usually glucose) and releases oxygen into the air. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place.

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5.2 The Light-Dependent Reactions of Photosynthesis

In the first part of photosynthesis, the light-dependent reaction, pigment molecules absorb energy from sunlight. The most common and abundant pigment is chlorophyll a. A photon strikes photosystem II to initiate photosynthesis. Energy travels through the electron transport chain, which pumps hydrogen ions into the thylakoid space. This forms an electrochemical gradient. The ions flow through ATP synthase from the thylakoid space into the stroma in a process called chemiosmosis to form molecules of ATP, which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule, another energy carrier for the Calvin cycle reactions.

5.3 The Calvin Cycle

Using the energy carriers formed in the first stage of photosynthesis, the Calvin cycle reactions fix CO2 from the environment to build carbohydrate molecules. An enzyme, RuBisCO, catalyzes the fixation reaction, by combining CO2 with RuBP. The resulting six-carbon compound is broken down into two three-carbon compounds, and the energy in ATP and NADPH is used to convert these molecules into G3P. One of the three-carbon molecules of G3P leaves the cycle to become a part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be formed back into RuBP, which is ready to react with more CO2. Photosynthesis forms a balanced energy cycle with the process of cellular respiration. Plants are capable of both photosynthesis and cellular respiration, since they contain both chloroplasts and mitochondria.

ART CONNECTION QUESTIONS 1. Figure 5.7 On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

REVIEW QUESTIONS 2. What two products result from photosynthesis? a. ATP b. glucose a. water and carbon dioxide c. chlorophyll b. water and oxygen d. water c. glucose and oxygen 7. Plants produce oxygen when they photosynthesize. d. glucose and carbon dioxide Where does the oxygen come from? 3. Which statement about thylakoids in eukaryotes is not a. splitting water molecules correct? b. ATP synthesis a. Thylakoids are assembled into stacks. c. the electron transport chain b. Thylakoids exist as a maze of folded d. chlorophyll membranes. 8. Which color(s) of light does chlorophyll a reflect? c. The space surrounding thylakoids is called stroma. a. red and blue d. Thylakoids contain chlorophyll. b. green 4. From where does a heterotroph directly obtain its c. red energy? d. blue a. the sun 9. Where in plant cells does the Calvin cycle take place? b. the sun and eating other organisms c. eating other organisms a. thylakoid membrane d. simple chemicals in the environment b. thylakoid space 5. What is the energy of a photon first used to do in c. stroma photosynthesis? d. granum a. split a water molecule 10. Which statement correctly describes carbon fixation? b. energize an electron c. produce ATP a. the conversion of CO2 to an d. synthesize glucose b. the use of RUBISCO to form 3-PGA 6. Which molecule absorbs the energy of a photon in c. the production of carbohydrate molecules from photosynthesis? G3P 134 Chapter 5 | Photosynthesis

d. the formation of RuBP from G3P molecules a. ADP e. the use of ATP and NADPH to reduce CO2 b. G3P c. RuBP 11. What is the molecule that leaves the Calvin cycle to be d. 3-PGA converted into glucose?

CRITICAL THINKING QUESTIONS 12. What is the overall purpose of the light reactions in 15. Which part of the Calvin cycle would be affected if a photosynthesis? cell could not produce the enzyme RuBisCO? 13. Why are carnivores, such as lions, dependent on 16. Explain the reciprocal nature of the net chemical photosynthesis to survive? reactions for photosynthesis and respiration. 14. Describe the pathway of energy in light-dependent reactions.

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ANSWER KEY

Chapter 1

1 Figure 1.8 B 3 C 5 A 7 Researchers can approach biology from the smallest to the largest, and everything in between. For instance, an ecologist may study a population of individuals, the population’s community, the community’s ecosystem, and the ecosystem’s part in the biosphere. When studying an individual organism, a biologist could examine the cell and its organelles, the tissues that the cells make up, the organs and their respective organ systems, and the sum total—the organism itself. Chapter 2

1 Figure 2.3 Potassium-39 has twenty neutrons. Potassium-40 has twenty one neutrons. 2 A 4 A 6 C 8 D 10 A 12 Hydrogen bonds and van der Waals interactions form weak associations between different molecules. They provide the structure and shape necessary for proteins and DNA within cells so that they function properly. Hydrogen bonds also give water its unique properties, which are necessary for life. 14 Water molecules are polar, meaning they have separated partial positive and negative charges. Because of these charges, water molecules are able to surround charged particles created when a substance dissociates. The surrounding layer of water molecules stabilizes the ion and keeps differently charged ions from reassociating, so the substance stays dissolved. 16 A change in gene sequence can lead to a different amino acid being added to a polypeptide chain instead of the normal one. This causes a change in protein structure and function. For example, in sickle cell anemia, the hemoglobin β chain has a single amino acid substitution. Because of this change, the disc-shaped red blood cells assume a crescent shape, which can result in serious health problems. Chapter 3

1 Figure 3.7 Plant cells have plasmodesmata, a cell wall, a large central vacuole, chloroplasts, and plastids. Animal cells have lysosomes and centrosomes. 3 Figure 3.22 No, it must have been hypotonic, as a hypotonic solution would cause water to enter the cells, thereby making them burst. 4 C 6 D 8 D 10 A 12 C 15 The advantages of light microscopes are that they are easily obtained, and the light beam does not kill the cells. However, typical light microscopes are somewhat limited in the amount of detail that they can reveal. Electron microscopes are ideal because you can view intricate details, but they are bulky and costly, and preparation for the microscopic examination kills the specimen. Transmission electron microscopes are designed to examine the internal structures of a cell, whereas a scanning electron microscope only allows visualization of the surface of a structure. 17 “Form follows function” refers to the idea that the function of a body part dictates the form of that body part. As an example, organisms like birds or fish that fly or swim quickly through the air or water have streamlined bodies that reduce drag. At the level of the cell, in tissues involved in secretory functions, such as the salivary glands, the cells have abundant Golgi. 19 Water moves through a semipermeable membrane in osmosis because there is a concentration gradient across the membrane of solute and solvent. The solute cannot effectively move to balance the concentration on both sides of the membrane, so water moves to achieve this balance. Chapter 4

1 Figure 4.6 A compost pile decomposing is an exergonic process. A baby developing from a fertilized egg is an endergonic process. Tea dissolving into water is an exergonic process. A ball rolling downhill is an exergonic process. 3 Figure 4.16 The illness is caused by lactic acid build-up. Lactic acid levels rise after exercise, making the symptoms worse. Milk sickness is rare today, but was common in the Midwestern United States in the early 1800s. 4 D 6 C 8 D 10 C 12 B 14 Physical exercise involves both anabolic and catabolic processes. Body cells break down sugars to provide ATP to do the work necessary for exercise, such as muscle contractions. This is catabolism. Muscle cells also must repair muscle tissue damaged by exercise by building new muscle. This is . 16 Most vitamins and minerals act as cofactors and coenzymes for enzyme action. Many require the binding of certain cofactors or coenzymes to be able to catalyze their reactions. Since enzymes catalyze many important reactions, it is critical to obtain sufficient vitamins and minerals from diet and supplements. Vitamin C (ascorbic acid) is a coenzyme necessary for the action of enzymes that build collagen. 18 The oxygen we inhale is the final electron acceptor in the electron transport chain and allows aerobic respiration to proceed, which is the most efficient pathway for harvesting energy in the form of ATP from food molecules. The carbon dioxide we breathe out is formed during the citric acid cycle when the bonds in carbon compounds are broken. 20 They are very economical. The substrates, intermediates, and products move between pathways and do so in response to finely tuned feedback inhibition loops that keep overall on an even keel. Intermediates in one pathway may occur in another, and they can move from one pathway to another fluidly in response to the needs of the cell. Chapter 5

1 Figure 5.7 Levels of carbon dioxide (a reactant) will fall, and levels of oxygen (a product) will rise. As a result, the rate of photosynthesis will slow down. 2 C 4 C 6 C 8 B 10 A 12 To convert solar energy into chemical energy that cells can use to do work. 14 The energy is present initially as light. A photon of light hits chlorophyll, causing an electron to be energized. 600 Answer Key

The free electron travels through the electron transport chain, and the energy of the electron is used to pump hydrogen ions into the thylakoid space, transferring the energy into the electrochemical gradient. The energy of the electrochemical gradient is used to power ATP synthase, and the energy is transferred into a bond in the ATP molecule. In addition, energy from another photon can be used to create a high-energy bond in the molecule NADPH. 16 Photosynthesis takes the energy of sunlight and combines water and carbon dioxide to produce sugar and oxygen as a waste product. The reactions of respiration take sugar and consume oxygen to break it down into carbon dioxide and water, releasing energy. Thus, the reactants of photosynthesis are the products of respiration, and vice versa. Chapter 6

1 Figure 6.4 D. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. The kinetochore breaks apart and the sister chromatids separate. The nucleus reforms and the cell divides. 2 C 4 B 6 A 8 C 10 C 12 Human somatic cells have 46 chromosomes, including 22 homologous pairs and one pair of nonhomologous sex chromosomes. This is the 2n, or diploid, condition. Human gametes have 23 chromosomes, one each of 23 unique chromosomes. This is the n, or haploid, condition. 14 If one of the genes that produce regulator proteins becomes mutated, it produces a malformed, possibly non-functional, cell-cycle regulator. This increases the chance that more mutations will be left unrepaired in the cell. Each subsequent generation of cells sustains more damage. The cell cycle can speed up as a result of loss of functional checkpoint proteins. The cells can lose the ability to self-destruct. 16 The common components of eukaryotic cell division and binary fission are DNA duplication, segregation of duplicated chromosomes, and the division of the cytoplasmic contents. Chapter 7

1 Figure 7.2 Yes, it will be able to reproduce asexually. 2 C 4 B 6 D 8 B 10 D 12 The offspring of sexually reproducing organisms are all genetically unique. Because of this, sexually reproducing organisms may have more successful survival of offspring in environments that change than asexually reproducing organisms, whose offspring are all genetically identical. In addition, the rate of adaptation of sexually reproducing organisms is higher, because of their increased variation. This may allow sexually reproducing organisms to adapt more quickly to competitors and parasites, who are evolving new ways to exploit or outcompete them. 14 Random alignment leads to new combinations of traits. The chromosomes that were originally inherited by the gamete-producing individual came equally from the egg and the sperm. In metaphase I, the duplicated copies of these maternal and paternal homologous chromosomes line up across the center of the cell to form a tetrad. The orientation of each tetrad is random. There is an equal chance that the maternally derived chromosomes will be facing either pole. The same is true of the paternally derived chromosomes. The alignment should occur differently in almost every meiosis. As the homologous chromosomes are pulled apart in anaphase I, any combination of maternal and paternal chromosomes will move toward each pole. The gametes formed from these two groups of chromosomes will have a mixture of traits from the individual’s parents. Each gamete is unique. 16 The problems caused by trisomies arise because the genes on the chromosome that is present in three copies produce more product than genes on chromosomes with only two copies. The cell does not have a way to adjust the amount of product, and the lack of balance causes problems in development and the maintenance of the individual. Each chromosome is different, and the differences in survivability could have to do with the numbers of genes on the two chromosomes. Chromosome 21 may be a smaller chromosome, so there are fewer unbalanced gene products. It is also possible that chromosome 21 carries genes whose products are less sensitive to differences in dosage than chromosome 18. The genes may be less involved in critical pathways, or the differences in dosage may make less of a difference to those pathways. Chapter 8

1 Figure 8.9 You cannot be sure if the plant is homozygous or heterozygous as the data set is too small: by random chance, all three plants might have acquired only the dominant gene even if the recessive one is present. 3 Figure 8.16 Half of the female offspring would be heterozygous (XWXw) with red eyes, and half would be homozygous recessive (XwXw) with white eyes. Half of the male offspring would be hemizygous dominant (XWY) with red eyes, and half would be hemizygous recessive (XwY) with white eyes. 4 B 6 A 8 C 10 D 12 C 14 The garden pea has flowers that close tightly during self-pollination. This helps to prevent accidental or unintentional fertilizations that could have diminished the accuracy of Mendel’s data. 16 The Punnett square will be 2 × 2 and will have T and t along the top and T and t along the left side. Clockwise from the top left, the genotypes listed within the boxes will be TT, Tt, Tt, and tt. The genotypic ratio will be 1TT:2Tt:1tt. 18 Yes this child could have come from these parents. The child would have inherited an i allele from each parent and for this to happen the type A parent had to have genotype IAi and the type b parent had to have genotype IBi. Chapter 9

1 Figure 9.10 Ligase, as this enzyme joins together Okazaki fragments. 2 A 4 B 6 A 8 C 10 D 12 The DNA is wound around proteins called histones. The histones then stack together in a compact form that creates a fiber that is 30-nm thick. The fiber is further coiled for greater compactness. During metaphase of mitosis, the chromosome is at its most compact to facilitate chromosome movement. During interphase, there are denser areas of chromatin, called heterochromatin, that contain DNA that is not expressed, and less dense euchromatin that contains DNA that is expressed. 14 Telomerase has an inbuilt RNA template

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anaerobic, 292, 319 autosome, 170 INDEX anaerobic cellular respiration, autosomes, 165 113 autotroph, 118, 132, 563 A analogous structure, 270, 283, autotrophs, 535 absorption spectrum, 124, 132 288 axial skeleton, 426, 440 abyssal zone, 556, 563 analogous structures, 253 axon, 433, 440 acellular, 450, 472 anaphase, 140, 149 acetyl CoA, 104, 113 aneuploid, 165, 170 B anion, 51 acid, 51 B cell, 472 anions, 31 Acid rain, 547 B cells, 460 anneal, 245 acid rain, 563 Basal angiosperms, 348 annealing, 229 Acids, 38 basal angiosperms, 351 Annelida, 378, 395 acoelomate, 395 basal ganglia, 436, 440 anoxic, 292, 319 acoelomates, 360 base, 51 anther, 344, 351 Actinopterygii, 387, 395 bases, 38 Anthophyta, 347, 351 action potential, 432, 440 Basic science, 22 Anthropoids, 393 activation energy, 97, 113 basic science, 24 anthropoids, 395 active immunity, 461, 472 Basidiomycota, 314 antibody, 461, 472 active site, 98, 113 basidiomycota, 319 antigen, 460, 472 Active transport, 81 benthic realm, 555, 563 antigen-presenting cell (APC), active transport, 85 bicuspid valve, 417, 440 462, 472 adaptation, 253, 270 Bilateral symmetry, 359 Anura, 388, 395 Adaptive immunity, 460 bilateral symmetry, 395 anus, 411, 440 adaptive immunity, 472 Bile, 410 aorta, 417, 440 adaptive radiation, 264, 270 bile, 440 apex consumer, 563 adhesion, 37, 51 binary fission, 145, 149 apex consumers, 531 adrenal gland, 440 binomial nomenclature, 276, aphotic zone, 555, 563 adrenal glands, 423 288 apical meristem, 329, 351 Age structure, 512 biodiversity, 568, 590 Apoda, 388, 395 age structure, 525 biodiversity hotspot, 586, 590 apoptosis, 453, 472 algal bloom, 560, 563 bioenergetics, 92, 113 appendicular skeleton, 428, 440 allele, 194 biofilm, 294, 319 applied science, 22, 24 alleles, 178 biogeochemical cycle, 537, 563 Archaeplastida, 306, 319 allergy, 469, 472 Biology, 5 Arctic tundra, 553 Allopatric speciation, 262 biology, 24 arctic tundra, 563 allopatric speciation, 270 Biomagnification, 536 Arteries, 419 allosteric inhibition, 100, 113 biomagnification, 563 artery, 440 alternation of generations, 155, biomarker, 243, 245 Arthropoda, 371, 395 170 biome, 531, 563 Ascomycota, 314, 319 alternative RNA splicing, 219, bioremediation, 301, 319 Asexual reproduction, 478 220 biosphere, 12, 24 asexual reproduction, 495 alveoli, 415 , 225 Asymmetrical, 358 alveolus, 440 biotechnology, 245 asymmetrical, 395 amino acid, 51 birth rate, 505, 525 atom, 9, 24 Amino acids, 46 Black Death, 297, 319 atomic number, 28, 51 amniote, 395 blastocyst, 483, 495 ATP, 102, 113 amniotes, 389 body plan, 356, 395 ATP synthase, 107, 113 amoebocyte, 395 bolus, 409, 440 atrium, 417, 440 Amoebocytes, 362 bones, 391 attenuation, 455, 472 Amoebozoa, 306, 319 boreal forest, 552, 563 auditory ossicles, 427, 440 Amphibia, 388, 395 bottleneck effect, 256, 270 autoantibody, 470, 472 ampulla of Lorenzini, 395 botulism, 299, 319 Autoimmunity, 470 ampullae of Lorenzini, 387 brachiation, 393, 395 autoimmunity, 472 amygdala, 437, 440 brainstem, 437, 440 autonomic nervous system, 437, amylase, 409, 440 branch point, 279, 288 anabolic, 93, 113 440 606 Index

bronchi, 415, 440 chaetae, 379 complete digestive system, 370, bronchiole, 440 channel, 561, 563 396 bronchioles, 415 chaparral, 550, 563 concentration gradient, 77, 85 budding, 363, 395, 495 chelicerae, 373, 395 cone, 351 Budding, 479 , 51 cones, 339 buffer, 51 chemical bonds, 31 conifer, 351 Buffers, 38 chemical diversity, 569, 590 Conifers, 341 bulbourethral gland, 486, 495 chemiosmosis, 107, 113 conjugation, 296, 319 Bush meat, 578 chemoautotroph, 563 Continuous variation, 174 bush meat, 590 chemoautotrophs, 535 continuous variation, 194 chiasmata, 158, 170 control, 20, 24 C chitin, 41, 51, 370, 395 convergent evolution, 253, 270 chlorophyll, 120, 132 coral reef, 563 caecilian, 395 chlorophyll a, 124, 132 Coral reefs, 557 Caecilians, 389 chlorophyll b, 124, 132 corolla, 344, 351 Calvin cycle, 127, 132 chloroplast, 85, 120, 132 corpus callosum, 435, 441 calyx, 344, 351 Chloroplasts, 69 corpus luteum, 487, 495 canopy, 548, 563 choanocyte, 362, 395 cotyledon, 351 capillaries, 419 Chondrichthyes, 386, 395 cotyledons, 347 capillary, 440 Chordata, 382, 395 covalent bond, 32, 51 capsid, 451, 472 Chromalveolata, 306, 319 craniate, 396 capsule, 295, 319 chromosome inversion, 168, craniates, 385 carbohydrate, 51 170 Crocodilia, 390, 396 Carbohydrates, 40 chyme, 410, 441 crossing over, 158, 170 carbon fixation, 127, 132 chytridiomycosis, 580, 590 cryptofauna, 558, 563 cardiac cycle, 418, 440 Chytridiomycota, 314, 319 ctenidia, 375, 396 Cardiac muscle tissue, 430 cilia, 64 cutaneous respiration, 388, 396 cardiac muscle tissue, 440 cilium, 85 cyanobacteria, 292, 319 carpel, 344, 351 citric acid cycle, 105, 113 cycad, 351 carrying capacity, 505, 525 clade, 288 Cycads, 341 cartilaginous joint, 440 clades, 285 cytokine, 457, 472 Cartilaginous joints, 428 cladistics, 285, 288 Cytokinesis, 140 catabolic, 93, 113 class, 276, 288 cytokinesis, 149 cation, 51 cleavage furrow, 140, 149 cytopathic, 453, 472 cations, 31 climax community, 524, 525 cytoplasm, 63, 85 cell, 10, 24 clitellum, 380, 395 cytoskeleton, 63, 85 cell cycle, 137, 149 clitoris, 487, 495 , 63, 85 cell cycle checkpoints, 142, 149 cloning, 228, 245 cytotoxic T lymphocyte (TC), cell plate, 140, 149 closed circulatory system, 417, 472 cell wall, 69, 85 441 cell-mediated immune club moss, 351 D response, 460, 472 club mosses, 335 Cellulose, 41 Cnidaria, 363, 395 dead zone, 544, 563 cellulose, 51 cnidocyte, 395 death rate, 505, 525 central nervous system (CNS), cnidocytes, 363 Deductive reasoning, 19 435, 440 codominance, 186, 194 deductive reasoning, 24 central vacuole, 70, 85 codon, 214, 220 demography, 500, 525 centriole, 149 coelom, 360, 395 denaturation, 46, 51 centrioles, 138 cohesion, 36, 51 dendrite, 441 Cephalochordata, 383, 395 colon, 411, 441 Dendrites, 432 cephalothorax, 373, 395 commensalism, 302, 319 dendritic cell, 462, 472 cerebellum, 437, 441 community, 12, 24 density-dependent, 508 cerebral cortex, 435, 441 competitive exclusion principle, density-dependent regulation, cerebrospinal fluid (CSF), 435, 518, 525 525 441 competitive inhibition, 99, 113 density-independent, 508 chaeta, 395 complement system, 459, 472

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density-independent regulation, ectotherms, 404 eutherian mammal, 396 525 effector cell, 472 Eutherian mammals, 393 deoxyribonucleic acid (DNA), effector cells, 464 eutrophication, 542, 564 49, 51 electrocardiogram (ECG), 419, evaporation, 35, 51 deoxyribose, 200, 220 441 evolution, 12, 24 depolarization, 432, 441 electrochemical gradient, 81, 85 Excavata, 306, 319 Descriptive, 19 electromagnetic spectrum, 123, exergonic, 113 descriptive science, 24 132 exergonic reactions, 96 desmosome, 85 electron, 28, 51 exocrine gland, 441 desmosomes, 72 electron transfer, 31, 51 Exocrine glands, 421 detrital food web, 534, 563 electron transport chain, 105, Exocytosis, 83 Deuteromycota, 319 113 exocytosis, 85 deuterostome, 396 element, 51 exon, 220 Deuterostomes, 360 elements, 28 exons, 212 diaphragm, 415, 441 Emergent vegetation, 562 Exotic species, 579 diastole, 418, 441 emergent vegetation, 563 exotic species, 590 dicot, 351 Endemic species, 571 exponential growth, 504, 525 dicots, 348 endemic species, 590 external fertilization, 481, 495 Diffusion, 77 endergonic, 113 extinction, 570, 590 diffusion, 85 endergonic reactions, 96 extinction rate, 590 dihybrid, 183, 194 endocrine gland, 441 extinction rates, 584 dioecious, 371, 396 endocrine glands, 421 extracellular digestion, 365, 396 diphyodont, 396 Endocytosis, 82 extracellular matrix, 70, 85 diphyodonts, 392 endocytosis, 85 extremophile, 319 diploblast, 396 endomembrane system, 64, 85 extremophiles, 294 diploblasts, 359 endoplasmic reticulum (ER), 65, diploid, 136, 149 85 F diploid-dominant, 155, 170 endosymbiosis, 319 F , 175, 194 Diplontic, 327 endosymbiotic theory, 303 1 diplontic, 351 endotherm, 404, 441 F2, 175, 194 disaccharide, 51 environmental disturbance, 525 facilitated transport, 78, 85 Disaccharides, 41 environmental disturbances, fallout, 546, 564 discontinuous variation, 174, 523 falsifiable, 20, 24 194 enzyme, 51, 113 family, 276, 288 dispersal, 263, 270 Enzymes, 45 fat, 43, 51 divergent evolution, 253, 270 enzymes, 97 Feedback inhibition, 102 DNA ligase, 205, 220 epidemic, 319 feedback inhibition, 113 DNA polymerase, 205, 220 epidemics, 297 fermentation, 108, 113 domain, 288 epidermis, 364, 396 fern, 351 domains, 276 epigenetic, 216, 220 ferns, 336 Dominant, 177 epistasis, 192, 194 fertilization, 157, 170 dominant, 194 Equilibrium, 531 fibrous joint, 441 dorsal hollow nerve cord, 382, equilibrium, 563 fibrous joints, 428 396 esophagus, 408, 441 filament, 344, 351 double helix, 201, 220 essential nutrient, 441 Fission, 478 down feather, 396 essential nutrients, 413 fission, 495 down feathers, 391 estrogen, 491, 495 Flagella, 64 down-regulation, 422, 441 Estuaries, 559 flagellum, 85 estuary, 563 fluid mosaic model, 74, 85 E eucoelomate, 396 follicle stimulating hormone eucoelomates, 360 (FSH), 490, 495 Echinodermata, 380, 396 eudicots, 347, 351 food chain, 531, 564 ecosystem, 12, 24, 530, 563 eukaryote, 24 food web, 533, 564 ecosystem diversity, 569, 590 eukaryotes, 10 foodborne disease, 299, 319 ecosystem services, 560, 563 eukaryotic cell, 60, 85 Foundation species, 521 ectotherm, 441 euploid, 165, 170 foundation species, 525 608 Index

founder effect, 257, 270 gestation period, 493, 495 homosporous, 327, 351 fragmentation, 363, 396, 495 gingkophyte, 351 homozygous, 178, 194 Fragmentation, 479 ginkgophyte, 342 hormone, 51, 441 frog, 396 glia, 432, 441 hormone receptors, 421 Frogs, 389 Glomeromycota, 314, 319 Hormones, 45, 421 frontal lobe, 436, 441 Glycogen, 41 hornwort, 351 FtsZ, 147, 149 glycogen, 51 hornworts, 333 , 103 horsetail, 351 G glycolysis, 113 Horsetails, 335 glycoprotein, 451, 472 host, 519, 525 G phase, 141, 149 0 gnathostome, 396 human beta chorionic G1 phase, 137, 149 Gnathostomes, 386 gonadotropin (β-HCG), 493, 495 G2 phase, 138, 149 gnetophyte, 351 humoral immune response, 460, gallbladder, 411, 441 Gnetophytes, 342 472 gametangia, 327 Golgi apparatus, 66, 86 hybridization, 194 gametangium, 351 gonadotropin-releasing hybridizations, 175 gamete, 149 hormone (GnRH), 490, 495 hydrogen bond, 33, 51 gametes, 136 Gram-negative, 295, 319 hydrophilic, 34, 52 gametophyte, 170, 327, 351 Gram-positive, 295, 319 hydrophobic, 34, 52 gametophytes, 157 granum, 121, 132 hydrosphere, 537, 564 gap junction, 85 grazing food web, 534, 564 hydrothermal vent, 293, 319 Gap junctions, 72 gross primary productivity, 535, hyoid bone, 427, 441 gastrodermis, 364, 396 564 hypersensitivity, 469, 472 gastrovascular cavity, 365, 396 gymnosperm, 351 hypertonic, 79, 86 gastrulation, 484, 495 Gymnosperms, 339 hypha, 312, 319 Gel electrophoresis, 226 gynoecium, 344, 351 hypothalamus, 437, 441 gel electrophoresis, 245 hypothesis, 18, 24 gemmule, 396 H hypothesis-based science, 19, gemmules, 363 24 habitat heterogeneity, 572, 590 gene, 149 hypotonic, 79, 86 gene expression, 216, 220 hagfish, 396 gene flow, 257, 270 Hagfishes, 385 I gene pool, 254, 270 haplodiplontic, 327, 351 Gene therapy, 233 haploid, 136, 149 immune tolerance, 468, 473 gene therapy, 245 haploid-dominant, 155, 170 Immunodeficiency, 469 genes, 136 Haplontic, 327 immunodeficiency, 473 genetic code, 214, 220 haplontic, 351 incomplete dominance, 186, Genetic diversity, 569 heat energy, 94, 113 194 genetic diversity, 590 helicase, 205, 220 Inductive reasoning, 18 genetic drift, 255, 270 helper T lymphocyte (TH), 472 inductive reasoning, 24 genetic engineering, 232, 245 hemizygous, 189, 194 inferior vena cava, 417, 441 genetic map, 236, 245 hemocoel, 371, 396 inflammation, 457, 473 genetic testing, 245 herbaceous, 349, 351 inheritance of acquired genetically modified organism, Hermaphroditism, 480 characteristics, 250, 270 232 hermaphroditism, 495 inhibin, 491, 495 genetically modified organism heterodont teeth, 392, 396 Innate immunity, 456 (GMO), 245 heterosporous, 327, 351 innate immunity, 473 genome, 136, 149 heterotroph, 132 inner cell mass, 483, 495 , 236, 245 Heterotrophs, 118 interferon, 457, 473 genotype, 178, 194 heterozygous, 179, 194 interkinesis, 161, 170 genus, 276, 288 hippocampus, 436, 441 internal fertilization, 481, 495 germ cell, 170 homeostasis, 8, 24 interphase, 137, 149 germ cells, 155 homologous chromosomes, interstitial cell of Leydig, 495 germ layer, 396 136, 149 interstitial cells of Leydig, 485 germ layers, 359 homologous structure, 270 interstitial fluid, 406, 441 gestation, 493, 495 homologous structures, 253 intertidal zone, 555, 564

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intracellular, 421 life sciences, 18 meiosis I, 157, 170 intracellular digestion, 362, 396 life table, 525 Meiosis II, 157 intracellular hormone receptor, life tables, 500 meiosis II, 170 441 light-dependent reaction, 132 membrane potential, 442 intraspecific competition, 506, light-dependent reactions, 121 memory cell, 464, 473 525 limbic system, 437, 442 meninges, 435, 442 intron, 220 line, 387 menstrual cycle, 491, 495 introns, 212 linkage, 191, 194 mesoglea, 364, 397 ion, 31, 52 Lipids, 42 mesohyl, 362, 397 ionic bond, 32, 52 lipids, 52 mesophyll, 120, 132 Island , 521 litmus, 37 metabolism, 92, 114 island biogeography, 525 litmus paper, 52 Metagenomics, 240 isotonic, 80, 86 liver, 411, 442 metagenomics, 245 , 52 liverwort, 352 metamerism, 379, 397 , 29 Liverworts, 333 metaphase, 140, 149 locus, 136, 149 metaphase plate, 140, 149 J logistic growth, 505, 525 MHC class II molecule, 461 Lophotrochozoa, 374, 397 , 293, 320 J-shaped growth curve, 505, luteinizing hormone (LH), 490, microevolution, 254, 270 525 495 microscope, 56, 86 joint, 428, 442 Lymph, 466 microsporocyte, 352 K lymph, 473 microsporocytes, 339 lymphocyte, 458, 473 migration, 255, 270 K-selected species, 510, 525 lysosome, 86 mimicry, 516, 525 karyogram, 164, 170 lysosomes, 66 mineral, 442 karyotype, 164, 170 Minerals, 413 keystone species, 522, 525 M mismatch repair, 208, 220 kidney, 442 Mitochondria, 68 macroevolution, 254, 270 kidneys, 406 mitochondria, 86 macromolecule, 24, 52 kinetic energy, 95, 113 mitosis, 138, 149 macromolecules, 9, 39 kinetochore, 140, 149 mitotic, 137, 138 macrophage, 457, 473 kingdom, 276, 288 mitotic phase, 149 madreporite, 381, 397 mitotic spindle, 149 major histocompatibility class L model organism, 245 (MHC) I, 473 model organisms, 238 major histocompatibility class labia majora, 487, 495 model system, 174, 194 (MHC) I molecules, 458 labia minora, 487, 495 modern synthesis, 254, 270 major histocompatibility class lagging strand, 205, 220 mold, 320 (MHC) II molecule, 473 lamprey, 396 molds, 313 mammal, 397 Lampreys, 386 molecular , 284, 288 Mammals, 392 lancelet, 396 molecule, 9, 24 mammary gland, 397 Lancelets, 384 Mollusca, 374, 397 Mammary glands, 392 large intestine, 411, 442 monocot, 352 mantle, 375, 397 larynx, 415, 442 monocots, 347 mark and recapture, 501, 525 lateral, 387 monocyte, 457, 473 marsupial, 397 lateral line, 397 monoecious, 363, 397 Marsupials, 392 law of dominance, 179, 194 monohybrid, 180, 194 mass number, 28, 52 law of independent assortment, monophyletic group, 285, 288 mast cell, 473 183, 194 monosaccharide, 52 Mast cells, 457 law of segregation, 181, 194 Monosaccharides, 40 Matter, 28 leading strand, 205, 220 monosomy, 165, 170 matter, 52 lichen, 319 monotreme, 397 maximum parsimony, 287, 288 Lichens, 317 monotremes, 392 medusa, 364, 397 life cycle, 170 mortality rate, 502, 525 megasporocyte, 339, 352 life cycles, 154 moss, 352 meiosis, 154, 170 life science, 24 mosses, 334 610 Index

mRNA, 210, 220 nucleotide excision repair, 208, paper, 37 MRSA, 320 220 parasite, 320, 519, 525 mutation, 209, 220 nucleotides, 49 parasites, 305 mutualism, 519, 525 nucleus, 28, 52, 65, 86 parasympathetic nervous mycelium, 312, 320 system, 439, 442 Mycorrhiza, 316 O parathyroid gland, 442 mycorrhiza, 320 parathyroid glands, 423 occipital lobe, 436, 442 mycoses, 315 parietal lobe, 436, 442 oceanic zone, 556, 564 mycosis, 320 Parthenogenesis, 480 octet rule, 31, 52 myelin sheath, 433, 442 parthenogenesis, 496 oil, 52 myofibril, 442 passive immune, 461 oils, 44 myofibrils, 430 passive immunity, 473 Okazaki fragments, 205, 220 myofilament, 442 Passive transport, 77 oncogene, 150 myofilaments, 431 passive transport, 86 oncogenes, 143 Myxini, 385, 397 pathogen, 296, 320 one-child policy, 513, 525 pectoral girdle, 428, 442 oogenesis, 488, 495 N peer-reviewed article, 24 open circulatory system, 442 Peer-reviewed articles, 23 nacre, 376, 397 Open circulatory systems, 417 pelagic realm, 555, 564 nasal cavity, 415, 442 Opisthokonta, 306, 320 pellicle, 320 natural killer (NK) cell, 458, 473 oral cavity, 409, 442 pellicles, 305 natural science, 24 order, 276, 288 pelvic girdle, 428, 442 natural sciences, 18 organ, 24 penis, 485, 496 Natural selection, 251 organ system, 10, 24 pepsin, 410, 442 natural selection, 270 organelle, 24, 86 peptidoglycan, 295, 320 nematocyst, 397 organelles, 10, 60 of elements, 29, nematocysts, 363 organism, 24 52 Nematoda, 370, 397 Organisms, 10 peripheral nervous system nephron, 442 organogenesis, 484, 496 (PNS), 437, 442 nephrons, 407 Organs, 10 peristalsis, 408, 442 neritic zone, 556, 564 origin, 145, 150 permafrost, 553, 564 Net primary productivity, 535 osculum, 362, 397 peroxisome, 86 net primary productivity, 564 osmolarity, 79, 86 Peroxisomes, 68 neuron, 442 Osmoregulation, 406 petal, 352 neurons, 432 osmoregulation, 442 Petals, 344 neutron, 52 Osmosis, 79 Petromyzontidae, 386, 397 Neutrons, 28 osmosis, 86 pH scale, 37, 52 neutrophil, 458, 473 osmotic balance, 406, 442 Phagocytosis, 83 nitrogenous base, 200, 220 Osteichthyes, 387, 397 phagocytosis, 86 non-renewable resource, 541, ostracoderm, 397 Pharmacogenomics, 240 564 ostracoderms, 385 pharmacogenomics, 245 noncompetitive inhibition, 100, ovarian cycle, 491, 496 pharyngeal slit, 397 114 ovary, 344, 352 Pharyngeal slits, 382 nondisjunction, 164, 170 oviduct, 496 pharynx, 415, 442 nonpolar covalent bond, 52 oviducts, 487 phase, 137 Nonpolar covalent bonds, 32 oviparity, 482, 496 phenotype, 178, 194 nontemplate strand, 211, 220 ovoviparity, 482, 496 , 334, 352 nonvascular plant, 352 ovulation, 492, 496 phosphate group, 200, 220 nonvascular plants, 331 oxidative , 105, phospholipid, 52 notochord, 382, 397 114 Phospholipids, 45 nuclear envelope, 65, 86 photic zone, 555, 564 nucleic acid, 52 P photoautotroph, 132, 564 nucleic acids, 49 P, 175, 194 photoautotrophs, 118, 535 nucleolus, 65, 86 pancreas, 411, 423, 442 photon, 124, 132 nucleotide, 52 pandemic, 320 photosystem, 124, 132 pandemics, 297 phototroph, 320

This OpenStax book is available for free at http://cnx.org/content/col11487/1.9 Index 611

phototrophs, 292 prokaryotic cell, 59, 86 resistance, 531 phylogenetic tree, 14, 24, 279, prometaphase, 139, 150 resistance (ecological), 564 288 promoter, 210, 221 restriction enzyme, 245 phylogeny, 276, 288 prophase, 139, 150 restriction enzymes, 229 phylum, 276, 288 Prosimians, 393 reverse , 232, 245 physical map, 245 prosimians, 398 Rhizaria, 306, 320 Physical maps, 236 prostate gland, 486, 496 ribonucleic acid (RNA), 49, 52 physical science, 24 protein, 52 ribosome, 86 physical sciences, 18 protein signature, 243, 245 Ribosomes, 68 pigment, 120, 132 Proteins, 45 RNA polymerase, 211, 221 pinocytosis, 83, 86 proteomics, 243, 245 rooted, 279, 288 pioneer species, 524, 526 proto-oncogene, 150 rough endoplasmic reticulum pistil, 344, 352 proto-oncogenes, 143 (RER), 65, 86 pituitary gland, 422, 443 proton, 28, 52 rRNA, 213, 221 placenta, 493, 496 protostome, 398 planktivore, 564 Protostomes, 360 S planktivores, 558 pseudocoelomate, 398 S phase, 138, 150 plasma membrane, 63, 86 pseudocoelomates, 360 S-shaped curve, 505 plasmid, 228, 245 pseudopeptidoglycan, 296, 320 S-shaped growth curve, 526 plasmodesma, 86 pulmonary circulation, 417, 443 salamander, 398 Plasmodesmata, 71 Punnett square, 180, 194 salamanders, 388 plastid, 303, 320 salivary gland, 443 pneumatic, 391 Q salivary glands, 409 pneumatic bone, 397 quadrat, 501, 526 saprobe, 320 polar covalent bond, 32, 52 quiescent, 150 saprobes, 310 Polymerase chain reaction sarcolemma, 430, 443 (PCR), 227 R sarcomere, 431, 443 polymerase chain reaction Sarcopterygii, 387, 398 (PCR), 245 r-selected species, 510, 526 saturated fatty acid, 52 polyp, 364, 397 radial symmetry, 358, 398 Saturated fatty acids, 44 polypeptide, 46, 52 radioactive isotope, 52 savanna, 564 polyploid, 167, 170 radioactive isotopes, 29 Savannas, 549 polysaccharide, 41, 52 radula, 374, 398 Science, 17 population, 12, 24 receptor-mediated endocytosis, science, 19, 25 population density, 500, 526 83, 86 scientific law, 25 population genetics, 254, 270 Recessive, 177 scientific laws, 18 population size, 500, 526 recessive, 195 scientific method, 18, 25 Porifera, 361, 397 reciprocal cross, 177, 195 scientific theory, 18, 25 post-anal tail, 383, 397 recombinant, 158, 170 scrotum, 485, 496 post-transcriptional, 217, 220 recombinant DNA, 230, 245 sebaceous gland, 398 post-translational, 217, 220 recombinant protein, 245 Sebaceous glands, 392 potential energy, 95, 114 recombinant proteins, 230 secondary consumer, 564 primary bronchi, 415 recombination, 191, 195 Secondary consumers, 531 primary bronchus, 443 rectum, 411, 443 secondary immune response, primary consumer, 564 reduction division, 162, 170 465, 473 primary consumers, 531 Relative species abundance, secondary plant compound, 590 primary immune response, 464, 521 secondary plant compounds, 473 relative species abundance, 526 572 primary succession, 523, 526 renal artery, 407, 443 secondary succession, 523, 526 Primates, 393, 397 renal vein, 407, 443 selectively permeable, 77, 86 primer, 205, 221 replication fork, 221 Semen, 485 producer, 564 replication forks, 205 semen, 496 producers, 531 Reproductive cloning, 230 semiconservative replication, progesterone, 491, 496 reproductive cloning, 245 205, 221 prokaryote, 24 resilience, 531 seminal vesicle, 496 Prokaryotes, 10 resilience (ecological), 564 612 Index

seminal vesicles, 486 , 41 Temperate forests, 552 seminiferous tubule, 496 starch, 53 temperate grassland, 565 seminiferous tubules, 485 start codon, 214, 221 Temperate grasslands, 551 sensory-somatic nervous stereoscopic vision, 393, 398 Temperature, 35 system, 437, 443 steroid, 53 temperature, 53 sepal, 352 steroids, 45 template strand, 211, 221 sepals, 344 stigma, 344, 352 temporal lobe, 436, 443 septum, 145, 150, 313, 320 stoma, 132 tertiary consumer, 565 Sertoli cell, 496 stomach, 410, 443 Tertiary consumers, 531 Sertoli cells, 485 stomata, 120 test cross, 181, 195 set point, 404, 443 stop codon, 221 testes, 485, 496 sex determination, 481, 496 stop codons, 214 Testosterone, 490 sexual reproduction, 478, 496 Strobili, 335 testosterone, 496 shared ancestral character, 286, strobili, 352 Testudines, 391, 398 288 stroma, 121, 132 tetrad, 171 shared derived character, 286, stromatolite, 293, 320 tetrads, 158 288 style, 344, 352 Tetrapod, 383 sister taxa, 279, 288 subduction, 541, 564 tetrapod, 398 Skeletal muscle tissue, 430 substrate, 114 thalamus, 437, 443 skeletal muscle tissue, 443 substrates, 98 thallus, 312, 320 skull, 427, 443 subtropical desert, 564 Thermodynamics, 93 small intestine, 410, 443 Subtropical deserts, 549 thermodynamics, 114 smooth endoplasmic reticulum sudoriferous gland, 398 thoracic cage, 428, 444 (SER), 66, 86 Sudoriferous glands, 392 threshold of excitation, 432, 444 Smooth muscle tissue, 430 superior vena cava, 417, 443 thylakoid, 132 smooth muscle tissue, 443 surface tension, 36, 53 thylakoids, 120 solute, 79, 86 survivorship curve, 503, 526 thymus, 424, 444 solvent, 36, 53 swim bladder, 387, 398 thyroid gland, 423, 444 somatic cell, 157, 170 sympathetic nervous system, tight junction, 72, 87 source water, 561, 564 438, 443 tissue, 25 speciation, 262, 270 Sympatric speciation, 262 tissues, 10 species, 276, 288 sympatric speciation, 270 Tonicity, 79 species distribution pattern, 501, synapse, 443 tonicity, 87 526 synapses, 432 trachea, 398, 415, 444 Species richness, 520 synapsis, 158, 170 tracheae, 371 species richness, 526 synaptic cleft, 435, 443 tragedy of the commons, 578, species-area relationship, 584, syngamy, 327, 352 590 590 Synovial joints, 428 trait, 176, 195 spermatogenesis, 488, 496 synovial joints, 443 trans-fat, 44, 53 Sphenodontia, 391, 398 systematics, 276, 288 transcription bubble, 210, 221 spicule, 398 systemic circulation, 417, 443 transduction, 296, 320 spicules, 362 systole, 418, 443 transformation, 296, 320 spinal cord, 443 transgenic, 232, 245 spindle, 138 T Transgenic, 235 spiracle, 398 translocation, 171 T cell, 473 spiracles, 371 translocations, 164 T cells, 460 splicing, 212, 221 tricuspid valve, 417, 444 tadpole, 389, 398 spongocoel, 362, 398 triglyceride, 53 taxon, 276, 288 sporangia, 327 triglycerides, 43 , 276 sporangium, 352 triploblast, 398 taxonomy, 288 sporophyll, 352 triploblasts, 359 telomerase, 206, 221 sporophylls, 335 trisomy, 165, 171 telomere, 221 sporophyte, 157, 170, 327, 352 tRNA, 221 telomeres, 206 Squamata, 391, 398 tRNAs, 213 telophase, 140, 150 stamen, 352 trophic level, 531, 565 temperate forest, 564 stamens, 344 trophoblast, 483, 496

This OpenStax book is available for free at http://cnx.org/content/col11487/1.9 Index 613 tropical rainforest, 565 Whole genome sequencing, 238 Tropical rainforests, 548 whole genome sequencing, 245 tumor suppressor gene, 150 wild type, 187, 195 Tumor suppressor genes, 144 tunicate, 398 X tunicates, 383 X inactivation, 166, 171 U X-linked, 188, 195 Xylem, 334 unified cell theory, 59, 87 xylem, 352 unsaturated fatty acid, 44, 53 up-regulation, 422, 444 Y ureter, 407, 444 yeast, 320 urethra, 407, 444 yeasts, 312 urinary bladder, 407, 444 Urochordata, 383, 398 Z Urodela, 388, 398 uterus, 487, 496 zero population growth, 505, 526 V zona pellucida, 483, 496 Zygomycota, 314, 320 vaccine, 455, 473 vacuole, 87 vacuoles, 67 vagina, 487, 496 van der Waals interaction, 53 van der Waals interactions, 33 variable, 20, 25 variation, 252, 270 vascular plant, 352 Vascular plants, 331 vein, 444 Veins, 420 ventricle, 417, 444 vertebral column, 382, 398, 428, 444 vesicle, 87 Vesicles, 67 vestigial structure, 270 vestigial structures, 259 vicariance, 263, 270 viral envelope, 451, 473 virion, 451, 473 vitamin, 444 Vitamins, 413 viviparity, 482, 496 W water vascular system, 380, 398 wavelength, 123, 132 wetland, 565 Wetlands, 562 whisk fern, 352 whisk ferns, 336 white blood cell, 457, 473 white-nose syndrome, 580, 590