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biology_how_why_corpus

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[ "The plasma membrane is the edge of life, the boundary that separates the living cell from its surroundings. A remarkable film only about 8 nm thick: it would take over 8,000 plasma membranes to equal the thickness of this page: the plasma membrane controls traffic into and out of the cell it surrounds. Like all biological membranes, the plasma membrane exhibits selective permeability; that is, it allows some substances to cross it more easily than others. One of the earliest episodes in the evolution of life may have been the formation of a membrane that enclosed a solution different from the surrounding solution while still permitting the uptake of nutrients and elimination of waste products. The ability of the cell to discriminate in its chemical exchanges with its environment is fundamental to life, and it is the plasma membrane and its component molecules that make this selectivity possible. Figure 7.1 How do cell membrane proteins help regulate chemical traffic? In this chapter, \nyou will learn how cellular membranes control the passage of substances. The image in Figure 7.1 shows the elegant structure of a eukaryotic plasma membrane protein that plays a crucial role in nerve cell signaling. This protein provides a channel for a stream of potassium ions (K+) to exit a nerve cell at a precise moment after nerve stimulation, restoring the cell's ability to fire again. (The orange ball in the center represents one potassium ion moving through the channel. ) In this way, the plasma membrane and its proteins not only act as an outer boundary but also enable the cell to carry out its functions. The same applies to the many varieties of internal membranes that partition the eukaryotic cell: The molecular makeup of each membrane allows compartmentalized specialization in cells." ]

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[ "Figure 8.21 Feedback inhibition in isoleucine synthesis. When ATP allosterically inhibits an enzyme in an ATP-generating pathway, as we discussed earlier, the result is feedback inhibition, a common mode of metabolic control. In feedback inhibition, a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway. Figure 8.21 shows an example of this control mechanism operating on an anabolic pathway. Certain cells use this five-step pathway to synthesize the amino acid isoleucine from threonine, another amino acid. As isoleucine accumulates, it slows down its own synthesis by allosterically inhibiting the enzyme for the first step of the pathway. Feedback inhibition thereby prevents the cell from wasting chemical resources by making more isoleucine than is necessary." ]

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[ "Basic principles of supply and demand regulate the metabolic economy. The cell does not waste energy making more of a particular substance than it needs. If there is a glut of a certain amino acid, for example, the anabolic pathway that synthesizes that amino acid from an intermediate of the citric acid cycle is switched off. The most common mechanism for this control is feedback inhibition: The end product of the anabolic pathway inhibits the enzyme that catalyzes an early step of the pathway (see Figure 8.21). This prevents the needless diversion of key metabolic intermediates from uses that are more urgent." ]

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[ "Metabolic control occurs on two levels, as shown for the synthesis of tryptophan in Figure 18.2. First, cells can adjust the activity of enzymes already present. This is a fairly fast response, which relies on the sensitivity of many enzymes to chemical cues that increase or decrease their catalytic activity (see Chapter 8). The activity of the first enzyme in the tryptophan synthesis pathway is inhibited by the pathway's end product (Figure 18.2a). Thus, if tryptophan accumulates in a cell, it shuts down the synthesis of more tryptophan by inhibiting enzyme activity. Such feedback inhibition, typical of anabolic (biosynthetic) pathways, allows a cell to adapt to short-term fluctuations in the supply of a substance it needs." ]

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[ "EVOLUTION The role of glycolysis in both fermentation and respiration has an evolutionary basis. Ancient prokaryotes are thought to have used glycolysis to make ATP long before oxygen was present in Earth's atmosphere. The oldest known fossils of bacteria date back 3.5 billion years, but appreciable quantities of oxygen probably did not begin to accumulate in the atmosphere until about 2.7 billion years ago. Cyanobacteria produced this O2 as a by-product of photosynthesis. Therefore, early prokaryotes may have generated ATP exclusively from glycolysis. The fact that glycolysis is today the most widespread metabolic pathway among Earth's organisms suggests that it evolved very early in the history of life. The cytosolic location of glycolysis also implies great antiquity; the pathway does not require any of the membrane-bounded organelles of the eukaryotic cell, which evolved approximately 1 billion years after the prokaryotic cell. Glycolysis is a metabolic heirloom from early cells \nthat continues to function in fermentation and as the first stage in the breakdown of organic molecules by respiration." ]

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[ "In some plant species, alternate modes of carbon fixation have evolved that minimize photorespiration and optimize the Calvin cycle: even in hot, arid climates. The two most important of these photosynthetic adaptations are C4 photosynthesis and crassulacean acid metabolism (CAM)." ]

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[ "The C4 plants are so named because they preface the Calvin cycle with an alternate mode of carbon fixation that forms a four-carbon compound as its first product. Several thousand species in at least 19 plant families use the C4 pathway. Among the C4 plants important to agriculture are sugarcane and corn, members of the grass family. Figure 10.20 C4 leaf anatomy and the C4 pathway. The structure and biochemical functions of the leaves of C4 plants are an evolutionary adaptation to hot, dry climates. This adaptation maintains a CO2 concentration in the bundle sheath that favors photosynthesis over photorespiration. A unique leaf anatomy is correlated with the mechanism of C4 photosynthesis (Figure 10.20; compare with Figure 10.4). In C4 plants, there are two distinct types of photosynthetic cells: bundle-sheath cells and mesophyll cells. Bundle-sheath cells are arranged into tightly packed sheaths around the veins of the leaf. Between the bundle sheath and the leaf surface are the more \nloosely arranged mesophyll cells. The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells. However, the Calvin cycle is preceded by incorporation of CO2 into organic compounds in the mesophyll cells. See the numbered steps in Figure 10.20, which are also described here: The first step is carried out by an enzyme present only in mesophyll cells called PEP carboxylase. This enzyme adds CO2 to phosphoenolpyruvate (PEP), forming the four-carbon product oxaloacetate. PEP carboxylase has a much higher affinity for CO2 than does rubisco and no affinity for O2. Therefore, PEP carboxylase can fix carbon efficiently when rubisco cannot: that is, when it is hot and dry and stomata are partially closed, causing CO2 concentration in the leaf to fall and O2 concentration to rise. After the C4 plant fixes carbon from CO2, the mesophyll cells export their four-carbon products (malate in the example shown in Figure 10.20) to bundle-sheath cells through plasmodesmata (see Figure 6.31). Within the bundle-\nsheath cells, the four-carbon compounds release CO2, which is reassimilated into organic material by rubisco and the Calvin cycle. The same reaction regenerates pyruvate, which is transported to mesophyll cells. There, ATP is used to convert pyruvate to PEP, allowing the reaction cycle to continue; this ATP can be thought of as the \"price\" of concentrating CO2 in the bundle-sheath cells. To generate this extra ATP, bundle-sheath cells carry out cyclic electron flow, the process described earlier in this chapter (see Figure 10.16). In fact, these cells contain PS I but no PS II, so cyclic electron flow is their only photosynthetic mode of generating ATP. In effect, the mesophyll cells of a C4 plant pump CO2 into the bundle sheath, keeping the CO2 concentration in the bundle-sheath cells high enough for rubisco to bind carbon dioxide rather than oxygen. The cyclic series of reactions involving PEP carboxylase and the regeneration of PEP can be thought of as a CO2-concentrating pump that is powered by ATP. In \nthis way, C4 photosynthesis minimizes photorespiration and enhances sugar production. This adaptation is especially advantageous in hot regions with intense sunlight, where stomata partially close during the day, and it is in such environments that C4 plants evolved and thrive today. Since the Industrial Revolution began in the 1800s, human activities such as the burning of fossil fuels have drastically increased the concentration of CO2 in the atmosphere. The resulting global climate change, including an increase in average temperatures around the planet, may have far-reaching effects on plant species. Scientists are concerned that increasing CO2 concentration and temperature may affect C3 and C4 plants differently, thus changing the relative abundance of these species in a given plant community. Which type of plant would stand to gain more from increasing CO2 levels? Recall that in C3 plants, the binding of O2 rather than CO2 by rubisco leads to photorespiration, lowering the efficiency of photosynthesis. \nC4 plants overcome this problem by concentrating CO2 in the bundle-sheath cells at the cost of ATP. Rising CO2 levels should benefit C3 plants by lowering the amount of photorespiration that occurs. At the same time, rising temperatures have the opposite effect, increasing photorespiration. (Other factors such as water availability may also come into play. ) In contrast, many C4 plants could be largely unaffected by increasing CO2 levels or temperature. In different regions, the particular combination of these two factors is likely to alter the balance of C3 and C4 plants in varying ways. The effects of such a widespread and variable change in community structure are unpredictable and thus a cause of legitimate concern." ]

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[ "A second photosynthetic adaptation to arid conditions has evolved in many succulent (water-storing) plants, numerous cacti, pineapples, and representatives of several other plant families. These plants open their stomata during the night and close them during the day, just the reverse of how other plants behave. Closing stomata during the day helps desert plants conserve water, but it also prevents CO2 from entering the leaves. During the night, when their stomata are open, these plants take up CO2 and incorporate it into a variety of organic acids. This mode of carbon fixation is called crassulacean acid metabolism, or CAM, after the plant family Crassulaceae, the succulents in which the process was first discovered. The mesophyll cells of CAM plants store the organic acids they make during the night in their vacuoles until morning, when the stomata close. During the day, when the light reactions can supply ATP and NADPH for the Calvin cycle, CO2 is released from the organic acids \nmade the night before to become incorporated into sugar in the chloroplasts. Figure 10.21 C4 and CAM photosynthesis compared. Both adaptations are characterized by ➊ preliminary incorporation of CO2 into organic acids, followed by ➋ transfer of CO2 to the Calvin cycle. The C4 and CAM pathways are two evolutionary solutions to the problem of maintaining photosynthesis with stomata partially or completely closed on hot, dry days. Notice in Figure 10.21 that the CAM pathway is similar to the C4 pathway in that carbon dioxide is first incorporated into organic intermediates before it enters the Calvin cycle. The difference is that in C4 plants, the initial steps of carbon fixation are separated structurally from the Calvin cycle, whereas in CAM plants, the two steps occur at separate times but within the same cell. (Keep in mind that CAM, C4, and C3 plants all eventually use the Calvin cycle to make sugar from carbon dioxide. )" ]

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[ "Recall that the universe is really equivalent to \"the system\" plus \"the surroundings. \" In 1878, J. Willard Gibbs, a professor at Yale, defined a very useful function called the Gibbs free energy of a system (without considering its surroundings), symbolized by the letter G. We'll refer to the Gibbs free energy simply as free energy. Free energy is the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell." ]

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[ "As we saw in the previous section, when a process occurs spontaneously in a system, we can be sure that deltaG is negative. Another way to think of deltaG is to realize that it represents the difference between the free energy of the final state and the free energy of the initial state: deltaG = Gfinal state -' Ginitial state Thus, deltaG can be negative only when the process involves a loss of free energy during the change from initial state to final state. Because it has less free energy, the system in its final state is less likely to change and is therefore more stable than it was previously. Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change. Unstable systems (top) are rich in free energy, G. They have a tendency to change spontaneously to a more stable state (bottom), and it is possible to harness this \"downhill\" change to perform work. We can think of free energy as a measure of a system's instability: its tendency to change to a more \nstable state. Unstable systems (higher G) tend to change in such a way that they become more stable (lower G). For example, a diver on top of a platform is less stable (more likely to fall) than when floating in the water; a drop of concentrated dye is less stable (more likely to disperse) than when the dye is spread randomly through the liquid; and a glucose molecule is less stable (more likely to break down) than the simpler molecules into which it can be split (Figure 8.5). Unless something prevents it, each of these systems will move toward greater stability: The diver falls, the solution becomes uniformly colored, and the glucose molecule is broken down. Another term that describes a state of maximum stability is equilibrium, which you learned about in Chapter 2 in connection with chemical reactions. There is an important relationship between free energy and equilibrium, including chemical equilibrium. Recall that most chemical reactions are reversible and proceed to a point at which the forward and \nbackward reactions occur at the same rate. The reaction is then said to be at chemical equilibrium, and there is no further net change in the relative concentration of products and reactants. As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products decreases. Free energy increases when a reaction is somehow pushed away from equilibrium, perhaps by removing some of the products (and thus changing their concentration relative to that of the reactants). For a system at equilibrium, G is at its lowest possible value in that system. We can think of the equilibrium state as a free-energy valley. Any change from the equilibrium position will have a positive deltaG and will not be spontaneous. For this reason, systems never spontaneously move away from equilibrium. Because a system at equilibrium cannot spontaneously change, it can do no work. A process is spontaneous and can perform work only when it is moving toward equilibrium." ]

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[ "We can now apply the free-energy concept more specifically to the chemistry of life's processes." ]

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[ "Figure 8.6 Free energy changes (deltaG) in exergonic and endergonic reactions. Based on their free-energy changes, chemical reactions can be classified as either exergonic (\"energy outward\") or endergonic (\"energy inward\"). An exergonic reaction proceeds with a net release of free energy (Figure 8.6a). Because the chemical mixture loses free energy (G decreases), deltaG is negative for an exergonic reaction. Using deltaG as a standard for spontaneity, exergonic reactions are those that occur spontaneously. (Remember, the word spontaneous implies that it is energetically favorable, not that it will occur rapidly. ) The magnitude of deltaG for an exergonic reaction represents the maximum amount of work the reaction can perform. The word maximum qualifies this statement, because some of the free energy is released as heat and cannot do work. Therefore, deltaG represents a theoretical upper limit of available energy. The greater the decrease in free energy, the greater the amount of work \nthat can be done. We can use the overall reaction for cellular respiration as an example: C6H12O6 + 6 O2 ->' 6 CO2 + 6 H2O deltaG = -'686 kcal/mol (-'2,870 kJ/mol) For each mole (180 g) of glucose broken down by respiration under what are called \"standard conditions\" (1 M of each reactant and product, 25 degree C, pH 7), 686 kcal (2,870 kJ) of energy are made available for work. Because energy must be conserved, the chemical products of respiration store 686 kcal less free energy per mole than the reactants. The products are, in a sense, the spent exhaust of a process that tapped the free energy stored in the bonds of the sugar molecules." ]

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[ "A living system's free energy is energy that can do work under cellular conditions. The change in free energy (deltaG) during a biological process is related directly to enthalpy change (deltaH) and to the change in entropy (deltaS): deltaG = deltaH - TdeltaS. Organisms live at the expense of free energy. During a spontaneous change, free energy decreases and the stability of a system increases. At maximum stability, the system is at equilibrium and can do no work." ]

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[ "During a catabolic reaction, some bonds are broken and others formed, releasing energy and resulting in lower-energy breakdown products. This transformation also occurs, for example, in the engine of a car when the hydrocarbons of gasoline react explosively with oxygen, releasing the energy that pushes the pistons and producing exhaust. Although less explosive, a similar reaction of food molecules with oxygen provides chemical energy in biological systems, producing carbon dioxide and water as waste products. Biochemical pathways, carried out in the context of cellular structures, enable cells to release chemical energy from food molecules and use the energy to power life processes." ]

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[ "In an open system, energy and matter can be transferred between the system and its surroundings. Organisms are open systems. They absorb energy: for instance, light energy or chemical energy in the form of organic molecules: and release heat and metabolic waste products, such as carbon dioxide, to the surroundings." ]

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[ "Living cells require transfusions of energy from outside sources to perform their many tasks: for example, assembling polymers, pumping substances across membranes, moving, and reproducing. The chimpanzee in Figure 9.1 obtains energy for its cells by eating plants; some animals feed on other organisms that eat plants. The energy stored in the organic molecules of food ultimately comes from the sun. Energy flows into an ecosystem as sunlight and exits as heat; in contrast, the chemical elements essential to life are recycled (Figure 9.2). Photosynthesis generates oxygen and organic molecules used by the mitochondria of eukaryotes (including plants and algae) as fuel for cellular respiration. Respiration breaks this fuel down, generating ATP. The waste products of this type of respiration, carbon dioxide and water, are the raw materials for photosynthesis." ]

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[ "Metabolism as a whole manages the material and energy resources of the cell. Some metabolic pathways release energy by breaking down complex molecules to simpler compounds. These degradative processes are called catabolic pathways, or breakdown pathways. A major pathway of catabolism is cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water." ]

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[ "Living systems increase the entropy of their surroundings, as predicted by thermodynamic law. It is true that cells create ordered structures from less organized starting materials. For example, simpler molecules are ordered into the more complex structure of an amino acid, and amino acids are ordered into polypeptide chains. At the organismal level as well, complex and beautifully ordered structures result from biological processes that use simpler starting materials (Figure 8.4). However, an organism also takes in organized forms of matter and energy from the surroundings and replaces them with less ordered forms. For example, an animal obtains starch, proteins, and other complex molecules from the food it eats. As catabolic pathways break these molecules down, the animal releases carbon dioxide and water: small molecules that possess less chemical energy than the food did. The depletion of chemical energy is accounted for by heat generated during metabolism. On a larger scale, \nenergy flows into most ecosystems in the form of light and exits in the form of heat (see Figure 1.6)." ]

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[ "If deltaG = -'686 kcal/mol for respiration, which converts glucose and oxygen to carbon dioxide and water, then the reverse process: the conversion of carbon dioxide and water to glucose and oxygen: must be strongly endergonic, with deltaG = +686 kcal/mol." ]

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[ "Although very different in mechanism, aerobic respiration is in principle similar to the combustion of gasoline in an automobile engine after oxygen is mixed with the fuel (hydrocarbons). Food provides the fuel for respiration, and the exhaust is carbon dioxide and water. The overall process can be summarized as follows: Organic Carbon compounds + Oxygen S dioxide + Water + Energy Although carbohydrates, fats, and proteins can all be processed and consumed as fuel, it is helpful to learn the steps of cellular respiration by tracking the degradation of the sugar glucose (C6H12O6): C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + Energy (ATP + heat)" ]

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[ "As diagrammed in Figure 9.6, glycolysis and pyruvate oxidation followed by the citric acid cycle are the catabolic pathways that break down glucose and other organic fuels. Glycolysis, which occurs in the cytosol, begins the degradation process by breaking glucose into two molecules of a compound called pyruvate. In eukaryotes, pyruvate enters the mitochondrion and is oxidized to a compound called acetyl CoA, which enters the citric acid cycle. There, the breakdown of glucose to carbon dioxide is completed. (In prokaryotes, these processes take place in the cytosol. ) Thus, the carbon dioxide produced by respiration represents fragments of oxidized organic molecules." ]

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[ "For each molecule of glucose degraded to carbon dioxide and water by respiration, the cell makes up to about 32 molecules of ATP, each with 7.3 kcal/mol of free energy. Respiration cashes in the large denomination of energy banked in a single molecule of glucose (686 kcal/mol) for the small change of many molecules of ATP, which is more practical for the cell to spend on its work." ]

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[ "During respiration, most energy flows in this sequence: glucose→ NADH→ electron transport chain→ proton-motive force→ ATP. We can do some bookkeeping to calculate the ATP profit when cellular respiration oxidizes a molecule of glucose to six molecules of carbon dioxide. The three main departments of this metabolic enterprise are glycolysis, the citric acid cycle, and the electron transport chain, which drives oxidative phosphorylation." ]

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[ "A living system's free energy is energy that can do work under cellular conditions. The change in free energy (deltaG) during a biological process is related directly to enthalpy change (deltaH) and to the change in entropy (deltaS): deltaG = deltaH - TdeltaS. Organisms live at the expense of free energy. During a spontaneous change, free energy decreases and the stability of a system increases. At maximum stability, the system is at equilibrium and can do no work. In an exergonic (spontaneous) chemical reaction, the products have less free energy than the reactants (-'deltaG). Endergonic (nonspontaneous) reactions require an input of energy (+deltaG). The addition of starting materials and the removal of end products prevent metabolism from reaching equilibrium." ]

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[ "All cells have voltages across their plasma membranes. Voltage is electrical potential energy: a separation of opposite charges. The cytoplasmic side of the membrane is negative in charge relative to the extracellular side because of an unequal distribution of anions and cations on the two sides. The voltage across a membrane, called a membrane potential, ranges from about -'50 to -'200 millivolts (mV). (The minus sign indicates that the inside of the cell is negative relative to the outside. ) The membrane potential acts like a battery, an energy source that affects the traffic of all charged substances across the membrane. Because the inside of the cell is negative compared with the outside, the membrane potential favors the passive transport of cations into the cell and anions out of the cell. Thus, two forces drive the diffusion of ions across a membrane: a chemical force (the ion's concentration gradient) and an electrical force (the effect of the membrane potential on the ion's \nmovement). This combination of forces acting on an ion is called the electrochemical gradient." ]

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[ "Cell-cell recognition, a cell's ability to distinguish one type of neighboring cell from another, is crucial to the functioning of an organism. It is important, for example, in the sorting of cells into tissues and organs in an animal embryo. It is also the basis for the rejection of foreign cells by the immune system, an important line of defense in vertebrate animals (see Chapter 43). Cells recognize other cells by binding to molecules, often containing carbohydrates, on the extracellular surface of the plasma membrane (see Figure 7.10d). Membrane carbohydrates are usually short, branched chains of fewer than 15 sugar units. Some are covalently bonded to lipids, forming molecules called glycolipids. (Recall that glyco refers to the presence of carbohydrate. ) However, most are covalently bonded to proteins, which are thereby glycoproteins (see Figure 7.5). The carbohydrates on the extracellular side of the plasma membrane vary from species to species, among individuals of the same \nspecies, and even from one cell type to another in a single individual. The diversity of the molecules and their location on the cell's surface enable membrane carbohydrates to function as markers that distinguish one cell from another. For example, the four human blood types designated A, B, AB, and O reflect variation in the carbohydrate part of glycoproteins on the surface of red blood cells." ]

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[ "An atom's electrons vary in the amount of energy they possess. Energy is defined as the capacity to cause change: for instance, by doing work. Potential energy is the energy that matter possesses because of its location or structure. For example, water in a reservoir on a hill has potential energy because of its altitude. When the gates of the reservoir's dam are opened and the water runs downhill, the energy can be used to do work, such as turning generators. Because energy has been expended, the water has less energy at the bottom of the hill than it did in the reservoir. Matter has a natural tendency to move to the lowest possible state of potential energy; in this example, the water runs downhill. To restore the potential energy of a reservoir, work must be done to elevate the water against gravity. Figure 2.8 Energy levels of an atom's electrons. Electrons exist only at fixed levels of potential energy called electron shells. The electrons of an atom have potential energy because \nof how they are arranged in relation to the nucleus. The negatively charged electrons are attracted to the positively charged nucleus. It takes work to move a given electron farther away from the nucleus, so the more distant an electron is from the nucleus, the greater its potential energy. Unlike the continuous flow of water downhill, changes in the potential energy of electrons can occur only in steps of fixed amounts. An electron having a certain amount of energy is something like a ball on a staircase (Figure 2.8a). The ball can have different amounts of potential energy, depending on which step it is on, but it cannot spend much time between the steps. Similarly, an electron's potential energy is determined by its energy level. An electron cannot exist between energy levels. An electron's energy level is correlated with its average distance from the nucleus. Electrons are found in different electron shells, each with a characteristic average distance and energy level. In diagrams, shells can be \nrepresented by concentric circles (Figure 2.8b). The first shell is closest to the nucleus, and electrons in this shell have the lowest potential energy. Electrons in the second shell have more energy, and electrons in the third shell even more energy. An electron can change the shell it occupies, but only by absorbing or losing an amount of energy equal to the difference in potential energy between its position in the old shell and that in the new shell. When an electron absorbs energy, it moves to a shell farther out from the nucleus. For example, light energy can excite an electron to a higher energy level. (Indeed, this is the first step taken when plants harness the energy of sunlight for photosynthesis, the process that produces food from carbon dioxide and water. ) When an electron loses energy, it \"falls back\" to a shell closer to the nucleus, and the lost energy is usually released to the environment as heat. For example, sunlight excites electrons in the surface of a car to higher energy levels. \nWhen the electrons fall back to their original levels, the car's surface heats up. This thermal energy can be transferred to the air or to your hand if you touch the car." ]

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[ "Molecules have a type of energy called thermal energy (heat), due to their constant motion. One result of this motion is diffusion, the movement of molecules of any substance so that they spread out evenly into the available space. Each molecule moves randomly, yet diffusion of a population of molecules may be directional. To understand this process, let's imagine a synthetic membrane separating pure water from a solution of a dye in water. Study Figure 7.13a carefully to appreciate how diffusion would result in both solutions having equal concentrations of the dye molecules. Once that point is reached, there will be a dynamic equilibrium, with as many dye molecules crossing the membrane each second in one direction as in the other. We can now state a simple rule of diffusion: In the absence of other forces, a substance will diffuse from where it is more concentrated to where it is less concentrated. Put another way, any substance will diffuse down its concentration gradient, the \nregion along which the density of a chemical substance increases or decreases (in this case, decreases). No work must be done to make this happen; diffusion is a spontaneous process, needing no input of energy. Note that each substance diffuses down its own concentration gradient, unaffected by the concentration gradients of other substances (Figure 7.13b)." ]

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[ "Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change. Unstable systems (top) are rich in free energy, G. They have a tendency to change spontaneously to a more stable state (bottom), and it is possible to harness this \"downhill\" change to perform work. We can think of free energy as a measure of a system's instability: its tendency to change to a more stable state. Unstable systems (higher G) tend to change in such a way that they become more stable (lower G). For example, a diver on top of a platform is less stable (more likely to fall) than when floating in the water; a drop of concentrated dye is less stable (more likely to disperse) than when the dye is spread randomly through the liquid; and a glucose molecule is less stable (more likely to break down) than the simpler molecules into which it can be split (Figure 8.5). Unless something prevents it, each of these systems will move toward greater stability: The diver falls, the solution \nbecomes uniformly colored, and the glucose molecule is broken down." ]

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[ "Cell-cell recognition, a cell's ability to distinguish one type of neighboring cell from another, is crucial to the functioning of an organism. It is important, for example, in the sorting of cells into tissues and organs in an animal embryo. It is also the basis for the rejection of foreign cells by the immune system, an important line of defense in vertebrate animals (see Chapter 43). Cells recognize other cells by binding to molecules, often containing carbohydrates, on the extracellular surface of the plasma membrane (see Figure 7.10d)." ]

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[ "Moreover, animal cells may communicate via direct contact between membrane-bound cell-surface molecules in a process called cell-cell recognition (Figure 11.4b). This sort of local signaling is important in embryonic development and the immune response." ]

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[ "A membrane remains fluid as temperature decreases until finally the phospholipids settle into a closely packed arrangement and the membrane solidifies, much as bacon grease forms lard when it cools. The temperature at which a membrane solidifies depends on the types of lipids it is made of. The membrane remains fluid to a lower temperature if it is rich in phospholipids with unsaturated hydrocarbon tails (see Figures 5.11 and 5.12). Because of kinks in the tails where double bonds are located, unsaturated hydrocarbon tails cannot pack together as closely as saturated hydrocarbon tails, and this makes the membrane more fluid (Figure 7.8a)." ]

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[ "A cell without rigid walls can tolerate neither excessive uptake nor excessive loss of water. This problem of water balance is automatically solved if such a cell lives in isotonic surroundings. Seawater is isotonic to many marine invertebrates. The cells of most terrestrial (land-dwelling) animals are bathed in an extracellular fluid that is isotonic to the cells." ]

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[ "We include glycolysis, however, because most respiring cells deriving energy from glucose use glycolysis to produce the starting material for the citric acid cycle. Figure 9.6 An overview of cellular respiration. During glycolysis, each glucose molecule is broken down into two molecules of the compound pyruvate. In eukaryotic cells, as shown here, the pyruvate enters the mitochondrion. There it is oxidized to acetyl CoA, which is further oxidized to CO2 in the citric acid cycle. NADH and a similar electron carrier, a coenzyme called FADH2, transfer electrons derived from glucose to electron transport chains, which are built into the inner mitochondrial membrane. (In prokaryotes, the electron transport chains are located in the plasma membrane. ) During oxidative phosphorylation, electron transport chains convert the chemical energy to a form used for ATP synthesis in the process called chemiosmosis. As diagrammed in Figure 9.6, glycolysis and pyruvate oxidation followed by the citric \nacid cycle are the catabolic pathways that break down glucose and other organic fuels. Glycolysis, which occurs in the cytosol, begins the degradation process by breaking glucose into two molecules of a compound called pyruvate. In eukaryotes, pyruvate enters the mitochondrion and is oxidized to a compound called acetyl CoA, which enters the citric acid cycle. There, the breakdown of glucose to carbon dioxide is completed. (In prokaryotes, these processes take place in the cytosol. ) Thus, the carbon dioxide produced by respiration represents fragments of oxidized organic molecules." ]

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[ "Oxidation of Pyruvate to Acetyl CoA The Citric Acid Cycle Glycolysis releases less than a quarter of the chemical energy in glucose that can be released by cells; most of the energy remains stockpiled in the two molecules of pyruvate. If molecular oxygen is present, the pyruvate enters a mitochondrion (in eukaryotic cells), where the oxidation of glucose is completed. (In prokaryotic cells, this process occurs in the cytosol. )" ]

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[ "Figure 9.10 Oxidation of pyruvate to acetyl CoA, the step before the citric acid cycle. Pyruvate is a charged molecule, so in eukaryotic cells it must enter the mitochondrion via active transport, with the help of a transport protein. Next, a complex of several enzymes (the pyruvate dehydrogenase complex) catalyzes the three numbered steps, which are described in the text. The acetyl group of acetyl CoA will enter the citric acid cycle. The CO2 molecule will diffuse out of the cell. By convention, coenzyme A is abbreviated S-CoA when it is attached to a molecule, emphasizing the sulfur atom (S). Upon entering the mitochondrion via active transport, pyruvate is first converted to a compound called acetyl coenzyme A, or acetyl CoA (Figure 9.10). This step, linking glycolysis and the citric acid cycle, is carried out by a multienzyme complex that catalyzes three reactions: ➊ Pyruvate's carboxyl group (: COO-'), which is already fully oxidized and thus has little chemical energy,\n is removed and given off as a molecule of CO2. (This is the first step in which CO2 is released during respiration. ) ➋ The remaining two-carbon fragment is oxidized, forming acetate (CH3COO-', the ionized form of acetic acid). The extracted electrons are transferred to NAD+, storing energy in the form of NADH. ➌ Finally, coenzyme A (CoA), a sulfur-containing compound derived from a B vitamin, is attached via its sulfur atom to the acetate, forming acetyl CoA, which has a high potential energy; in other words, the reaction of acetyl CoA to yield lower-energy products is highly exergonic. This molecule will now feed its acetyl group into the citric acid cycle for further oxidation." ]

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[ "Figure 9.12 A closer look at the citric acid cycle. In the chemical structures, red type traces the fate of the two carbon atoms that enter the cycle via acetyl CoA (step 1), and blue type indicates the two carbons that exit the cycle as CO2 in steps 3 and 4. (The red labeling goes only through step 5 because the succinate molecule is symmetrical; the two ends cannot be distinguished from each other. ) Notice that the carbon atoms that enter the cycle from acetyl CoA do not leave the cycle in the same turn. They remain in the cycle, occupying a different location in the molecules on their next turn, after another acetyl group is added." ]

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[ "Now let's look at the citric acid cycle in more detail. The cycle has eight steps, each catalyzed by a specific enzyme. You can see in Figure 9.12 that for each turn of the citric acid cycle, two carbons (red) enter in the relatively reduced form of an acetyl group (step 1), and two different carbons (blue) leave in the completely oxidized form of CO2 molecules (steps 3 and 4). The acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate, forming citrate (step 1). (Citrate is the ionized form of citric acid, for which the cycle is named. ) The next seven steps decompose the citrate back to oxaloacetate. It is this regeneration of oxaloacetate that makes this process a cycle." ]

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[ "Other organisms, including yeasts and many bacteria, can make enough ATP to survive using either fermentation or respiration. Such species are called facultative anaerobes. On the cellular level, our muscle cells behave as facultative anaerobes. In such cells, pyruvate is a fork in the metabolic road that leads to two alternative catabolic routes (Figure 9.18). Under aerobic conditions, pyruvate can be converted to acetyl CoA, and oxidation continues in the citric acid cycle via aerobic respiration. Under anaerobic conditions, lactic acid fermentation occurs: Pyruvate is diverted from the citric acid cycle, serving instead as an electron acceptor to recycle NAD+. To make the same amount of ATP, a facultative anaerobe has to consume" ]

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[ "Catabolism can also harvest energy stored in fats obtained either from food or from storage cells in the body. After fats are digested to glycerol and fatty acids, the glycerol is converted to glyceraldehyde 3-phosphate, an intermediate of glycolysis. Most of the energy of a fat is stored in the fatty acids. A metabolic sequence called beta oxidation breaks the fatty acids down to two-carbon fragments, which enter the citric acid cycle as acetyl CoA. NADH and FADH2 are also generated during beta oxidation; they can enter the electron transport chain, leading to further ATP production. Fats make excellent fuel, in large part due to their chemical structure and the high energy level of their electrons (equally shared between carbon and hydrogen) compared to those of carbohydrates. A gram of fat oxidized by respiration produces more than twice as much ATP as a gram of carbohydrate. Unfortunately, this also means that a person trying to lose weight must work hard to use up fat stored in \nthe body because so many calories are stockpiled in each gram of fat." ]

[]

[ "Compounds formed as intermediates of glycolysis and the citric acid cycle can be diverted into anabolic pathways as precursors from which the cell can synthesize the molecules it requires. For example, humans can make about half of the 20 amino acids in proteins by modifying compounds siphoned away from the citric acid cycle; the rest are \"essential amino acids\" that must be obtained in the diet. Also, glucose can be made from pyruvate, and fatty acids can be synthesized from acetyl CoA. Of course, these anabolic, or biosynthetic, pathways do not generate ATP, but instead consume it." ]

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[ "9.3 After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules (pp. 170-172) In eukaryotic cells, pyruvate enters the mitochondrion and is oxidized to acetyl CoA, which is further oxidized in the citric acid cycle." ]

[]

[ "The fatty acids of fats undergo beta oxidation to two-carbon fragments and then enter the citric acid cycle as acetyl CoA." ]

[]

[ "Despite the help of transport proteins, facilitated diffusion is considered passive transport because the solute is moving down its concentration gradient, a process that requires no energy. Facilitated diffusion speeds transport of a solute by providing efficient passage through the membrane, but it does not alter the direction of transport." ]

[]

[ "Let's look more closely at how water and certain hydrophilic solutes cross a membrane. As mentioned earlier, many polar molecules and ions impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane. This phenomenon is called facilitated diffusion. Cell biologists are still trying to learn exactly how various transport proteins facilitate diffusion. Most transport proteins are very specific: They transport some substances but not others. Figure 7.17 Two types of transport proteins that carry out facilitated diffusion. In both cases, the protein can transport the solute in either direction, but the net movement is down the concentration gradient of the solute. As described earlier, the two types of transport proteins are channel proteins and carrier proteins. Channel proteins simply provide corridors that allow specific molecules or ions to cross the membrane (Figure 7.17a). The hydrophilic passageways provided by these \nproteins can allow water molecules or small ions to diffuse very quickly from one side of the membrane to the other. Aquaporins, the water channel proteins, facilitate the massive amounts of diffusion that occur in plant cells and in animal cells such as red blood cells (see Figure 7.15). Certain kidney cells also have a high number of aquaporins, allowing them to reclaim water from urine before it is excreted. If the kidneys did not perform this function, you would excrete about 180 L of urine per day: and have to drink an equal volume of water! Channel proteins that transport ions are called ion channels. Many ion channels function as gated channels, which open or close in response to a stimulus. For some gated channels, the stimulus is electrical. The ion channel shown in Figure 7.1, for example, opens in response to an electrical stimulus, allowing potassium ions to leave the cell. Other gated channels open or close when a specific substance other than the one to be transported binds to the channel. Both \ntypes of gated channels are important in the functioning of the nervous system, as you'll learn in Chapter 48. Carrier proteins, such as the glucose transporter mentioned earlier, seem to undergo a subtle change in shape that somehow translocates the solute-binding site across the membrane (Figure 7.17b). Such a change in shape may be triggered by the binding and release of the transported molecule. Like ion channels, carrier proteins involved in facilitated diffusion result in the net movement of a substance down its concentration gradient. No energy input is thus required: This is passive transport." ]

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[ "The distinction between passive transport and active transport is reviewed in Figure 7.19." ]

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[ "All cells have voltages across their plasma membranes. Voltage is electrical potential energy: a separation of opposite charges. The cytoplasmic side of the membrane is negative in charge relative to the extracellular side because of an unequal distribution of anions and cations on the two sides. The voltage across a membrane, called a membrane potential, ranges from about -'50 to -'200 millivolts (mV). (The minus sign indicates that the inside of the cell is negative relative to the outside. ) The membrane potential acts like a battery, an energy source that affects the traffic of all charged substances across the membrane. Because the inside of the cell is negative compared with the outside, the membrane potential favors the passive transport of cations into the cell and anions out of the cell. Thus, two forces drive the diffusion of ions across a membrane: a chemical force (the ion's concentration gradient) and an electrical force (the effect of the membrane potential on the ion's \nmovement). This combination of forces acting on an ion is called the electrochemical gradient. In the case of ions, then, we must refine our concept of passive transport: An ion diffuses not simply down its concentration gradient but, more exactly, down its electrochemical gradient. For example, the concentration of Na+ inside a resting nerve cell is much lower than outside it. When the cell is stimulated, gated channels open that facilitate Na+ diffusion. Sodium ions then \"fall\" down their electrochemical gradient, driven by the concentration gradient of Na+ and by the attraction of these cations to the negative side (inside) of the membrane. In this example, both electrical and chemical contributions to the electrochemical gradient act in the same direction across the membrane, but this is not always so." ]

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[ "In a type of passive transport called facilitated diffusion, a transport protein speeds the movement of water or a solute across a membrane down its concentration gradient. Ion channels, some of which are gated channels, facilitate the diffusion of ions across a membrane." ]

[]

[ "Many different kinds of polar compounds are dissolved (along with ions) in the water of such biological fluids as blood, the sap of plants, and the liquid within all cells. Water is the solvent of life." ]

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[ "Any substance that has an affinity for water is said to be hydrophilic (from the Greek hydro, water, and philios, loving)." ]

[]

[ "Water is an unusually versatile solvent because its polar molecules are attracted to charged and polar substances capable of forming hydrogen bonds. Hydrophilic substances have an affinity for water; hydrophobic substances do not." ]

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[ "The phospholipid bilayer shown here is the main fabric of biological membranes. Note that the hydrophilic heads of the phospholipids are in contact with water in this structure, whereas the hydrophobic tails are in contact with each other and remote from water. The two ends of phospholipids show different behavior toward water. The hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate group and its attachments form a hydrophilic head that has an affinity for water. When phospholipids are added to water, they self-assemble into double-layered structures called \"bilayers,\" shielding their hydrophobic portions from water (Figure 5.13). At the surface of a cell, phospholipids are arranged in a similar bilayer. The hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solutions inside and outside of the cell. The hydrophobic tails point toward the interior of the bilayer, away from the water. The phospholipid \nbilayer forms a boundary between the cell and its external environment; in fact, cells could not exist without phospholipids." ]

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[ "A sphere of water molecules, called a hydration shell, surrounds each solute ion. Suppose, for example, that a spoonful of table salt, the ionic compound sodium chloride (NaCl), is placed in water (Figure 3.7). At the surface of each grain, or crystal, of salt, the sodium and chloride ions are exposed to the solvent. These ions and the water molecules have a mutual affinity owing to the attraction between opposite charges. The oxygen regions of the water molecules are negatively charged and are attracted to sodium cations. The hydrogen regions are positively charged and are attracted to chloride anions. As a result, water molecules surround the individual sodium and chloride ions, separating and shielding them from one another. The sphere of water molecules around each dissolved ion is called a hydration shell. Working inward from the surface of each salt crystal, water eventually dissolves all the ions. The result is a solution of two solutes, sodium cations and chloride anions, \nhomogeneously mixed with water, the solvent." ]

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[ "Another source of electrons for the transport chain is FADH2, the other reduced product of the citric acid cycle. Notice in Figure 9.13 that FADH2 adds its electrons to the electron transport chain from within complex II, at a lower energy level than NADH does. Consequently, although NADH and FADH2 each donate an equivalent number of electrons (2) for oxygen reduction, the electron transport chain provides about one-third less energy for ATP synthesis when the electron donor is FADH2 rather than NADH." ]

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[ "As complexes I, III, and IV accept and then donate electrons, they pump protons from the mitochondrial matrix into the intermembrane space. (In prokaryotes, protons are pumped outside the plasma membrane. ) Note that FADH2 deposits its electrons via complex II and so results in fewer protons being pumped into the intermembrane space than occurs with NADH. Chemical energy originally harvested from food is transformed into a proton-motive force, a gradient of H+ across the membrane. ➋ During chemiosmosis, the protons flow back down their gradient via ATP synthase, which is built into the membrane nearby. The ATP synthase harnesses the proton-motive force to phosphorylate ADP, forming ATP. Together, electron transport and chemiosmosis make up oxidative phosphorylation." ]

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[ "We know that 1 NADH results in 10 H+ being transported out across the inner mitochondrial membrane, but the exact number of H+ that must reenter the mitochondrial matrix via ATP synthase to generate 1 ATP has long been debated. Based on experimental data, however, most biochemists now agree that the most accurate number is 4 H+. Therefore, a single molecule of NADH generates enough proton-motive force for the synthesis of 2.5 ATP. The citric acid cycle also supplies electrons to the electron transport chain via FADH2, but since its electrons enter later in the chain, each molecule of this electron carrier is responsible for transport of only enough H+ for the synthesis of 1.5 ATP." ]

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[ "In general, organic molecules that have an abundance of hydrogen are excellent fuels because their bonds are a source of \"hilltop\" electrons, whose energy may be released as these electrons \"fall\" down an energy gradient when they are transferred to oxygen." ]

[]

[ "Fats make excellent fuel, in large part due to their chemical structure and the high energy level of their electrons (equally shared between carbon and hydrogen) compared to those of carbohydrates." ]

[]

[ "What exactly happens when chlorophyll and other pigments absorb light? The colors corresponding to the absorbed wavelengths disappear from the spectrum of the transmitted and reflected light, but energy cannot disappear. When a molecule absorbs a photon of light, one of the molecule's electrons is elevated to an orbital where it has more potential energy. When the electron is in its normal orbital, the pigment molecule is said to be in its ground state. Absorption of a photon boosts an electron to an orbital of higher energy, and the pigment molecule is then said to be in an excited state. The only photons absorbed are those whose energy is exactly equal to the energy difference between the ground state and an excited state, and this energy difference varies from one kind of molecule to another. Thus, a particular compound absorbs only photons corresponding to specific wavelengths, which is why each pigment has a unique absorption spectrum." ]

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[ "Although allosteric regulation is probably quite widespread, relatively few of the many known metabolic enzymes have been shown to be regulated in this way. Allosteric regulatory molecules are hard to characterize, in part because they tend to bind the enzyme at low affinity and are therefore hard to isolate. Recently, however, pharmaceutical companies have turned their attention to allosteric regulators. These molecules are attractive drug candidates for enzyme regulation because they exhibit higher specificity for particular enzymes than do inhibitors that bind to the active site. (An active site may be similar to the active site in another, related enzyme, whereas allosteric regulatory sites appear to be quite distinct between enzymes. )" ]

[]

[ "A unique leaf anatomy is correlated with the mechanism of C4 photosynthesis (Figure 10.20; compare with Figure 10.4). In C4 plants, there are two distinct types of photosynthetic cells: bundle-sheath cells and mesophyll cells. Bundle-sheath cells are arranged into tightly packed sheaths around the veins of the leaf. Between the bundle sheath and the leaf surface are the more loosely arranged mesophyll cells. The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells. However, the Calvin cycle is preceded by incorporation of CO2 into organic compounds in the mesophyll cells. See the numbered steps in Figure 10.20, which are also described here: The first step is carried out by an enzyme present only in mesophyll cells called PEP carboxylase. This enzyme adds CO2 to phosphoenolpyruvate (PEP), forming the four-carbon product oxaloacetate. PEP carboxylase has a much higher affinity for CO2 than does rubisco and no affinity for O2. Therefore, PEP carboxylase can fix carbon \nefficiently when rubisco cannot: that is, when it is hot and dry and stomata are partially closed, causing CO2 concentration in the leaf to fall and O2 concentration to rise." ]

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[ "Figure 7.8 Factors that affect membrane fluidity. The steroid cholesterol, which is wedged between phospholipid molecules in the plasma membranes of animal cells, has different effects on membrane fluidity at different temperatures (Figure 7.8b). At relatively high temperatures: at 37 degree C, the body temperature of humans, for example: cholesterol makes the membrane less fluid by restraining phospholipid movement. However, because cholesterol also hinders the close packing of phospholipids, it lowers the temperature required for the membrane to solidify. Thus, cholesterol can be thought of as a \"fluidity buffer\" for the membrane, resisting changes in membrane fluidity that can be caused by changes in temperature." ]

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[ "The unsaturated hydrocarbon tails of some phospholipids keep membranes fluid at lower temperatures, while cholesterol helps membranes resist changes in fluidity caused by temperature changes." ]

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[ "Cell-cell recognition, a cell's ability to distinguish one type of neighboring cell from another, is crucial to the functioning of an organism. It is important, for example, in the sorting of cells into tissues and organs in an animal embryo. It is also the basis for the rejection of foreign cells by the immune system, an important line of defense in vertebrate animals (see Chapter 43). Cells recognize other cells by binding to molecules, often containing carbohydrates, on the extracellular surface of the plasma membrane (see Figure 7.10d). Membrane carbohydrates are usually short, branched chains of fewer than 15 sugar units. Some are covalently bonded to lipids, forming molecules called glycolipids. (Recall that glyco refers to the presence of carbohydrate. )" ]

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[ "Short chains of sugars linked to proteins (in glycoproteins) and lipids (in glycolipids) on the exterior side of the plasma membrane interact with surface molecules of other cells." ]

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[ "Recall from Chapter 5 that the three-dimensional structures of proteins are sensitive to their environment. As a consequence, each enzyme works better under some conditions than under other conditions, because these optimal conditions favor the most active shape for the enzyme molecule. Figure 8.16 Environmental factors affecting enzyme activity. Each enzyme has an optimal (a) temperature and (b) pH that favor the most active shape of the protein molecule. Temperature and pH are environmental factors important in the activity of an enzyme. Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when the molecules move rapidly. Above that temperature, however, the speed of the enzymatic reaction drops sharply. The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein \nmolecule eventually denatures. Each enzyme has an optimal temperature at which its reaction rate is greatest. Without denaturing the enzyme, this temperature allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules. Most human enzymes have optimal temperatures of about 35-40 degree C (close to human body temperature). The thermophilic bacteria that live in hot springs contain enzymes with optimal temperatures of 70 degree C or higher (Figure 8.16a on the next page)." ]

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[ "Membranes must be fluid to work properly; they are usually about as fluid as salad oil. When a membrane solidifies, its permeability changes, and enzymatic proteins in the membrane may become inactive if their activity requires them to be able to move within the membrane. However, membranes that are too fluid cannot support protein function either. Therefore, extreme environments pose a challenge for life, resulting in evolutionary adaptations that include differences in membrane lipid composition." ]

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[ "EVOLUTION Variations in the cell membrane lipid compositions of many species appear to be evolutionary adaptations that maintain the appropriate membrane fluidity under specific environmental conditions. For instance, fishes that live in extreme cold have membranes with a high proportion of unsaturated hydrocarbon tails, enabling their membranes to remain fluid (see Figure 7.8a). At the other extreme, some bacteria and archaea thrive at temperatures greater than 90 degree C (194 degree F) in thermal hot springs and geysers. Their membranes include unusual lipids that may prevent excessive fluidity at such high temperatures. The ability to change the lipid composition of cell membranes in response to changing temperatures has evolved in organisms that live where temperatures vary. In many plants that tolerate extreme cold, such as winter wheat, the percentage of unsaturated phospholipids increases in autumn, an adjustment that keeps the membranes from solidifying during winter. Certain \nbacteria and archaea can also change the proportion of unsaturated phospholipids in their cell membranes, depending on the temperature at which they are growing. Overall, natural selection has apparently favored organisms whose mix of membrane lipids ensures an appropriate level of membrane fluidity for their environment." ]

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[ "EVOLUTION Variations in the cell membrane lipid compositions of many species appear to be evolutionary adaptations that maintain the appropriate membrane fluidity under specific environmental conditions. For instance, fishes that live in extreme cold have membranes with a high proportion of unsaturated hydrocarbon tails, enabling their membranes to remain fluid (see Figure 7.8a). At the other extreme, some bacteria and archaea thrive at temperatures greater than 90 degree C (194 degree F) in thermal hot springs and geysers. Their membranes include unusual lipids that may prevent excessive fluidity at such high temperatures." ]

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[ "Figure 27.16 Extreme thermophiles. Orange and yellow colonies of thermophilic prokaryotes grow in the hot water of a Nevada geyser. Extreme thermophiles (from the Greek thermos, hot) thrive in very hot environments (Figure 27.16). For example, archaea in the genus Sulfolobus live in sulfur-rich volcanic springs as hot as 90 degree C. At temperatures this high, the cells of most organisms die because, for example, their DNA does not remain in a double helix and many of their proteins denature. Sulfolobus and other extreme thermophiles avoid this fate because their DNA and proteins have adaptations that make them stable at high temperatures. One extreme thermophile that lives near deep-sea hot springs called hydrothermal vents is informally known as \"strain 121,\" since it can reproduce even at 121 degree C. Another extreme thermophile, Pyrococcus furiosus, is used in biotechnology as a source of DNA polymerase for the PCR technique (see Chapter 20)." ]

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[ "One important use of proton gradients in the cell is for ATP synthesis during cellular respiration, as you will see in Chapter 9. Another is a type of membrane traffic called cotransport." ]

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[ "Figure 7.21 Cotransport: active transport driven by a concentration gradient. A carrier protein, such as this sucrose-H+ cotransporter in a plant cell, is able to use the diffusion of H+ down its electrochemical gradient into the cell to drive the uptake of sucrose. The H+ gradient is maintained by an ATP-driven proton pump that concentrates H+ outside the cell, thus storing potential energy that can be used for active transport, in this case of sucrose. Thus, ATP indirectly provides the energy necessary for cotransport. (The cell wall is not shown. ) A single ATP-powered pump that transports a specific solute can indirectly drive the active transport of several other solutes in a mechanism called cotransport. A substance that has been pumped across a membrane can do work as it moves back across the membrane by diffusion, analogous to water that has been pumped uphill and performs work as it flows back down. Another transport protein, a cotransporter separate from the pump, can couple \nthe \"downhill\" diffusion of this substance to the \"uphill\" transport of a second substance against its own concentration (or electrochemical) gradient. For example, a plant cell uses the gradient of H+ generated by its proton pumps to drive the active transport of amino acids, sugars, and several other nutrients into the cell. One transport protein couples the return of H+ to the transport of sucrose into the cell (Figure 7.21). This protein can translocate sucrose into the cell against a concentration gradient, but only if the sucrose molecule travels in the company of a hydrogen ion. The hydrogen ion uses the transport protein as an avenue to diffuse down the electrochemical gradient maintained by the proton pump. Plants use sucrose-H+ cotransport to load sucrose produced by photosynthesis into cells in the veins of leaves. The vascular tissue of the plant can then distribute the sugar to nonphotosynthetic organs, such as roots." ]

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[ "Figure 36.7 Solute transport across plant cell plasma membranes. Hydrogen ions (H+), rather than sodium ions (Na+), play the primary role in basic transport processes in plant cells. For example, in plant cells the membrane potential (the voltage across the membrane) is established mainly through the pumping of H+ by proton pumps (Figure 36.7a), rather than the pumping of Na+ by sodium-potassium pumps. Also, H+ is most often cotransported in plants, whereas Na+ is typically cotransported in animals. During cotransport, plant cells use the energy in the H+ gradient and membrane potential to drive the active transport of many different solutes. For instance, cotransport with H+ is responsible for absorption of neutral solutes, such as the sugar sucrose, by phloem cells and other plant cells. An H+/sucrose cotransporter couples movement of sucrose against its concentration gradient with movement of H+ down its electrochemical gradient (Figure 36.7b). Cotransport with H+ also facilitates \nmovement of ions, as in the uptake of nitrate (NO3-') by root cells (Figure 36.7c)." ]

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[ "36.5 Sugars are transported from sources to sinks via the phloem (pp. 779-781) Mature leaves are the main sugar sources, although storage organs can be seasonal sources. Growing organs such as roots, stems, and fruits are the main sugar sinks. Phloem loading depends on the active transport of sucrose. Sucrose is cotransported with H+, which diffuses down a gradient generated by proton pumps. Loading of sugar at the source and unloading at the sink maintain a pressure difference that keeps sap flowing through a sieve tube." ]

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[ "The reaction catalyzed by each enzyme is very specific; an enzyme can recognize its specific substrate even among closely related compounds. For instance, sucrase will act only on sucrose and will not bind to other disaccharides, such as maltose. What accounts for this molecular recognition? Recall that most enzymes are proteins, and proteins are macromolecules with unique three-dimensional configurations. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence. Figure 8.14 Induced fit between an enzyme and its substrate. Only a restricted region of the enzyme molecule actually binds to the substrate. This region, called the active site, is typically a pocket or groove on the surface of the enzyme where catalysis occurs (Figure 8.14a). Usually, the active site is formed by only a few of the enzyme's amino acids, with the rest of the protein molecule providing a framework that determines the configuration of the active site. The specificity \nof an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substrate. An enzyme is not a stiff structure locked into a given shape. In fact, recent work by biochemists has shown clearly that enzymes (and other proteins as well) seem to \"dance\" between subtly different shapes in a dynamic equilibrium, with slight differences in free energy for each \"pose. \" The shape that best fits the substrate isn't necessarily the one with the lowest energy, but during the very short time the enzyme takes on this shape, its active site can bind to the substrate. It has been known for more than 50 years that the active site itself is also not a rigid receptacle for the substrate. As the substrate enters the active site, the enzyme changes shape slightly due to interactions between the substrate's chemical groups and chemical groups on the side chains of the amino acids that form the active site. This shape change makes the active site fit even more snugly around the substrate (\nFigure 8.14b). This induced fit is like a clasping handshake. Induced fit brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction." ]

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[ "The plasma membrane is the edge of life, the boundary that separates the living cell from its surroundings. A remarkable film only about 8 nm thick: it would take over 8,000 plasma membranes to equal the thickness of this page: the plasma membrane controls traffic into and out of the cell it surrounds. Like all biological membranes, the plasma membrane exhibits selective permeability; that is, it allows some substances to cross it more easily than others. One of the earliest episodes in the evolution of life may have been the formation of a membrane that enclosed a solution different from the surrounding solution while still permitting the uptake of nutrients and elimination of waste products. The ability of the cell to discriminate in its chemical exchanges with its environment is fundamental to life, and it is the plasma membrane and its component molecules that make this selectivity possible. Figure 7.1 How do cell membrane proteins help regulate chemical traffic? In this chapter, \nyou will learn how cellular membranes control the passage of substances. The image in Figure 7.1 shows the elegant structure of a eukaryotic plasma membrane protein that plays a crucial role in nerve cell signaling. This protein provides a channel for a stream of potassium ions (K+) to exit a nerve cell at a precise moment after nerve stimulation, restoring the cell's ability to fire again. (The orange ball in the center represents one potassium ion moving through the channel. ) In this way, the plasma membrane and its proteins not only act as an outer boundary but also enable the cell to carry out its functions. The same applies to the many varieties of internal membranes that partition the eukaryotic cell: The molecular makeup of each membrane allows compartmentalized specialization in cells. To understand how membranes work, we'll begin by examining their architecture." ]

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[ "The biological membrane is an exquisite example of a supramolecular structure: many molecules ordered into a higher level of organization: with emergent properties beyond those of the individual molecules. The remainder of this chapter focuses on one of the most important of those properties: the ability to regulate transport across cellular boundaries, a function essential to the cell's existence. We will see once again that form fits function: The fluid mosaic model helps explain how membranes regulate the cell's molecular traffic. A steady traffic of small molecules and ions moves across the plasma membrane in both directions. Consider the chemical exchanges between a muscle cell and the extracellular fluid that bathes it. Sugars, amino acids, and other nutrients enter the cell, and metabolic waste products leave it. The cell takes in O2 for use in cellular respiration and expels CO2. Also, the cell regulates its concentrations of inorganic ions, such as Na+, K+, Ca2+, and Cl-', by \nshuttling them one way or the other across the plasma membrane. In spite of heavy traffic through them, cell membranes are selectively permeable, and substances do not cross the barrier indiscriminately. The cell is able to take up some small molecules and ions and exclude others. Also, substances that move through the membrane do so at different rates." ]

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[ "Nonpolar molecules, such as hydrocarbons, carbon dioxide, and oxygen, are hydrophobic and can therefore dissolve in the lipid bilayer of the membrane and cross it easily, without the aid of membrane proteins. However, the hydrophobic interior of the membrane impedes the direct passage of ions and polar molecules, which are hydrophilic, through the membrane. Polar molecules such as glucose and other sugars pass only slowly through a lipid bilayer, and even water, an extremely small polar molecule, does not cross very rapidly. A charged atom or molecule and its surrounding shell of water (see Figure 3.7) find the hydrophobic interior of the membrane even more difficult to penetrate. Furthermore, the lipid bilayer is only one aspect of the gatekeeper system responsible for the selective permeability of a cell. Proteins built into the membrane play key roles in regulating transport." ]

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[ "Cell membranes are permeable to specific ions and a variety of polar molecules. These hydrophilic substances can avoid contact with the lipid bilayer by passing through transport proteins that span the membrane. Some transport proteins, called channel proteins, function by having a hydrophilic channel that certain molecules or atomic ions use as a tunnel through the membrane (see Figure 7.10a, left). For example, the passage of water molecules through the membrane in certain cells is greatly facilitated by channel proteins known as aquaporins. Each aquaporin allows entry of up to 3 billion (3 * 109) water molecules per second, passing single file through its central channel, which fits ten at a time. Without aquaporins, only a tiny fraction of these water molecules would pass through the same area of the cell membrane in a second, so the channel protein brings about a tremendous increase in rate. Other transport proteins, called carrier proteins, hold onto their passengers and change \nshape in a way that shuttles them across the membrane (see Figure 7.10a, right). A transport protein is specific for the substance it translocates (moves), allowing only a certain substance (or a small group of related substances) to cross the membrane. For example, a specific carrier protein in the plasma membrane of red blood cells transports glucose across the membrane 50,000 times faster than glucose can pass through on its own. This \"glucose transporter\" is so selective that it even rejects fructose, a structural isomer of glucose. Thus, the selective permeability of a membrane depends on both the discriminating barrier of the lipid bilayer and the specific transport proteins built into the membrane." ]

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[ "7.2 Membrane structure results in selective permeability (pp. 131-132) A cell must exchange molecules and ions with its surroundings, a process controlled by the selective permeability of the plasma membrane. Hydrophobic substances are soluble in lipid and pass through membranes rapidly, whereas polar molecules and ions generally require specific transport proteins to cross the membrane." ]

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[ "In most plants, initial fixation of carbon occurs via rubisco, the Calvin cycle enzyme that adds CO2 to ribulose bisphosphate. Such plants are called C3 plants because the first organic product of carbon fixation is a three-carbon compound, 3-phosphoglycerate (see Figure 10.19). Rice, wheat, and soybeans are C3 plants that are important in agriculture. When their stomata partially close on hot, dry days, C3 plants produce less sugar because the declining level of CO2 in the leaf starves the Calvin cycle. In addition, rubisco can bind O2 in place of CO2. As CO2 becomes scarce within the air spaces of the leaf, rubisco adds O2 to the Calvin cycle instead of CO2. The product splits, and a two-carbon compound leaves the chloroplast. Peroxisomes and mitochondria rearrange and split this compound, releasing CO2. The process is called photorespiration because it occurs in the light (photo) and consumes O2 while producing CO2 (respiration). However, unlike normal cellular respiration, \nphotorespiration generates no ATP; in fact, photorespiration consumes ATP. And unlike photosynthesis, photorespiration produces no sugar. In fact, photorespiration decreases photosynthetic output by siphoning organic material from the Calvin cycle and releasing CO2 that would otherwise be fixed." ]

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[ "Whether there are other benefits of photorespiration is still unknown. In many types of plants: including a significant number of crop plants: photorespiration drains away as much as 50% of the carbon fixed by the Calvin cycle. As heterotrophs that depend on carbon fixation in chloroplasts for our food, we naturally view photorespiration as wasteful. Indeed, if photorespiration could be reduced in certain plant species without otherwise affecting photosynthetic productivity, crop yields and food supplies might increase." ]

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[ "In photorespiration, O2 substitutes for CO2 in the active site of rubisco. This process consumes organic fuel and releases CO2 without producing ATP or carbohydrate." ]

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[ "To pump a solute across a membrane against its gradient requires work; the cell must expend energy. Therefore, this type of membrane traffic is called active transport." ]

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[ "7.4 Active transport uses energy to move solutes against their gradients (pp. 135-138) Specific membrane proteins use energy, usually in the form of ATP, to do the work of active transport." ]

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[ "7.3 Passive transport is diffusion of a substance across a membrane with no energy investment 7.4 Active transport uses energy to move solutes against their gradients" ]

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[ "7.4 Active transport uses energy to move solutes against their gradients" ]

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[ "The Need for Energy in Active Transport" ]

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[ "Crossing over begins very early in prophase I as homologous chromosomes pair loosely along their lengths. Each gene on one homolog is aligned precisely with the corresponding gene on the other homolog. In a single crossover event, the DNA of two nonsister chromatids: one maternal and one paternal chromatid of a homologous pair: is broken by specific proteins at precisely corresponding points, and the two segments beyond the crossover point are each joined to the other chromatid. Thus, a paternal chromatid is joined to a piece of maternal chromatid beyond the crossover point, and vice versa. In this way, crossing over produces chromosomes with new combinations of maternal and paternal alleles (see Figure 13.11)." ]

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[ "During meiosis, homologous chromosomes, one inherited from each parent, trade some of their alleles by crossing over. These homologous chromosomes and the alleles they carry are then distributed at random into gametes." ]

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[ "The important point for now is that crossing over, by combining DNA inherited from two parents into a single chromosome, is an important source of genetic variation in sexual life cycles." ]

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[ "Crossing over involves breakage and rejoining of the DNA of nonsister chromatids in a homologous pair, resulting in recombinant chromatids that will become recombinant chromosomes." ]

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[ "Subsequent experiments demonstrated that this process, now called crossing over, accounts for the recombination of linked genes. In crossing over, which occurs while replicated homologous chromosomes are paired during prophase of meiosis I, a set of proteins orchestrates an exchange of corresponding segments of one maternal and one paternal chromatid (see Figure 13.11). In effect, end portions of two nonsister chromatids trade places each time a crossover occurs." ]

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[ "X-linked genes in humans follow the same pattern of inheritance that Morgan observed for the eye-color locus he studied in Drosophila (see Figure 15.4). Fathers pass X-linked alleles to all of their daughters but to none of their sons. In contrast, mothers can pass X-linked alleles to both sons and daughters, as shown in Figure 15.7. If an X-linked trait is due to a recessive allele, a female will express the phenotype only if she is homozygous for that allele. Because males have only one locus, the terms homozygous and heterozygous lack meaning for describing their X-linked genes; the term hemizygous is used in such cases. Any male receiving the recessive allele from his mother will express the trait. For this reason, far more males than females have X-linked recessive disorders. However, even though the chance of a female inheriting a double dose of the mutant allele is much less than the probability of a male inheriting a single dose, there are females with X-linked disorders." ]

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[ "Figure 15.5 Human sex chromosomes. Whether we are male or female is one of our more obvious phenotypic characters. Although the anatomical and physiological differences between women and men are numerous, the chromosomal basis for determining sex is rather simple. In humans and other mammals, there are two varieties of sex chromosomes, designated X and Y. The Y chromosome is much smaller than the X chromosome (Figure 15.5). A person who inherits two X chromosomes, one from each parent, usually develops as a female. A male develops from a zygote containing one X chromosome and one Y chromosome (Figure 15.6a)." ]

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[ "Animals, however, must carry their energy stores with them, so there is an advantage to having a more compact reservoir of fuel: fat. Humans and other mammals stock their long-term food reserves in adipose cells (see Figure 4.6a), which swell and shrink as fat is deposited and withdrawn from storage." ]

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[ "In humans, the first sites used for energy storage are liver and muscle cells. In these cells, excess energy from the diet is stored in glycogen, a polymer made up of many glucose units (see Figure 5.6b). Once glycogen depots are full, any additional excess energy is usually stored in fat in adipose cells. When fewer calories are taken in than are expended: perhaps because of sustained heavy exercise or lack of food: the human body generally expends liver glycogen first and then draws on muscle glycogen and fat. Fats are especially rich in energy; oxidizing a gram of fat liberates about twice the energy liberated from a gram of carbohydrate or protein. For this reason, adipose tissue provides the most space-efficient way for the body to store large amounts of energy. Most healthy people have enough stored fat to sustain them through several weeks without food." ]

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[ "40.4 Energy requirements are related to animal size, activity, and environment (pp. 868-872) Animals obtain chemical energy from food, storing it for short-term use in ATP." ]

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[ "Experimental deforestation of a watershed dramatically increased the flow of water and minerals leaving the watershed (Figure 55.16b and c). Over three years, water runoff from the newly deforested watershed was 30-40% greater than in a control watershed, apparently because there were no plants to absorb and transpire water from the soil. The concentration of Ca2+ in the creek increased 4-fold, and the concentration of K+ increased by a factor of 15. Most remarkable was the loss of nitrate, whose concentration in the creek increased 60-fold, reaching levels considered unsafe for drinking water (Figure 55.16c). The Hubbard Brook deforestation study showed that the amount of nutrients leaving an intact forest ecosystem is controlled mainly by the plants. Retaining nutrients in ecosystems helps to maintain the productivity of the systems and, in some cases, to avoid problems cause by excess nutrient runoff (see Figure 55.8)." ]

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[ "In addition, as we saw in the case of Hubbard Brook (see Figure 55.16), without plants to take up nitrates from the soil, the nitrates are likely to be leached from the ecosystem." ]