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biology_how_why_corpus

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[ "So far, we have focused on synapses where a neurotransmitter binds directly to an ion channel, causing the channel to open. However, there are also synapses in which the receptor for the neurotransmitter is not part of an ion channel. At these synapses, the neurotransmitter binds to a metabotropic receptor, so called because the resulting opening or closing of ion channels depends on one or more metabolic steps. Binding of a neurotransmitter to a metabotropic receptor activates a signal transduction pathway in the postsynaptic cell involving a second messenger (see Chapter 11). Compared with the postsynaptic potentials produced by ligand-gated channels, the effects of these second-messenger systems have a slower onset but last longer (minutes or even hours). Second messengers modulate the responsiveness of postsynaptic neurons to inputs in diverse ways, such as by altering the number of open potassium channels." ]

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[ "In vertebrates, there are two major classes of acetylcholine receptor. One type is a ligand-gated ion channel. We know the most about its function at the neuromuscular junction, the site where motor neurons synapse with skeletal muscle cells. When acetylcholine released by motor neurons binds this receptor, the ion channel opens, producing an EPSP. This excitatory activity is soon terminated by acetylcholinesterase, an enzyme in the synaptic cleft that hydrolyzes the neurotransmitter." ]

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[ "48.3 Action potentials are the signals conducted by axons (pp. 1050-1055) Neurons have gated ion channels that open or close in response to stimuli, leading to changes in the membrane potential. An increase in the magnitude of the membrane potential is a hyperpolarization; a decrease is a depolarization. Changes in membrane potential that vary continuously with the strength of a stimulus are known as graded potentials. An action potential is a brief, all-or-none depolarization of a neuron's plasma membrane. When a graded depolarization brings the membrane potential to the threshold, many voltage-gated ion channels open, triggering an inflow of Na+ that rapidly brings the membrane potential to a positive value. A negative membrane potential is restored by the inactivation of sodium channels and by the opening of many voltage-gated potassium channels, which increases K+ outflow. A refractory period follows, corresponding to the interval when the sodium channels are inactivated." ]

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[ "Although animals use a range of sensory receptors to detect widely varying stimuli, the effect in all cases is to open or close ion channels. Thus, for example, ion channels open or close when a substance outside the cell binds to a chemical receptor in the plasma membrane. The resulting flow of ions across the membrane changes the membrane potential." ]

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[ "Mechanoreceptors sense physical deformation caused by forms of mechanical energy such as pressure, touch, stretch, motion, and sound. Mechanoreceptors typically consist of ion channels that are linked to structures that extend outside the cell, such as \"hairs\" (cilia), as well as internal cell structures, such as the cytoskeleton. Bending or stretching of the external structure generates tension that alters the permeability of the ion channels. This change in ion permeability alters the membrane potential, resulting in a depolarization or hyperpolarization (see Chapter 48)." ]

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[ "Unlike the other identified taste receptors, the receptor for sour tastants belongs to the TRP family (see p. 1089). Formed from a pair of TRP proteins, the sour receptor is similar to the capsaicin receptor and other thermoreceptor proteins. In taste buds, the TRP proteins of the sour receptor assemble into a channel in the plasma membrane of the taste cell. Binding of an acid or other sour-tasting substance to the receptor triggers a change in the ion channel. Depolarization occurs, activating a sensory neuron." ]

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[ "The model of light as waves explains many of light's properties, but in certain respects light behaves as though it consists of discrete particles, called photons. Photons are not tangible objects, but they act like objects in that each of them has a fixed quantity of energy. The amount of energy is inversely related to the wavelength of the light: the shorter the wavelength, the greater the energy of each photon of that light. Thus, a photon of violet light packs nearly twice as much energy as a photon of red light." ]

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[ "Endocytosis Water and small solutes enter and leave the cell by diffusing through the lipid bilayer of the plasma membrane or by being pumped or moved across the membrane by transport proteins. However, large molecules, such as proteins and polysaccharides, as well as larger particles, generally cross the membrane in bulk by mechanisms that involve packaging in vesicles. Like active transport, these processes require energy." ]

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[ "As we described in Chapter 6, the cell secretes certain biological molecules by the fusion of vesicles with the plasma membrane; this process is called exocytosis. A transport vesicle that has budded from the Golgi apparatus moves along microtubules of the cytoskeleton to the plasma membrane. When the vesicle membrane and plasma membrane come into contact, specific proteins rearrange the lipid molecules of the two bilayers so that the two membranes fuse. The contents of the vesicle then spill to the outside of the cell, and the vesicle membrane becomes part of the plasma membrane (see Figure 7.12, step 4). Many secretory cells use exocytosis to export products. For example, the cells in the pancreas that make insulin secrete it into the extracellular fluid by exocytosis. In another example, neurons (nerve cells) use exocytosis to release neurotransmitters that signal other neurons or muscle cells. When plant cells are making walls, exocytosis delivers proteins and carbohydrates from \nGolgi vesicles to the outside of the cell." ]

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[ "In endocytosis, the cell takes in biological molecules and particulate matter by forming new vesicles from the plasma membrane. Although the proteins involved in the processes are different, the events of endocytosis look like the reverse of exocytosis. A small area of the plasma membrane sinks inward to form a pocket. As the pocket deepens, it pinches in, forming a vesicle containing material that had been outside the cell. Study Figure 7.22 carefully to understand the three types of endocytosis: phagocytosis (\"cellular eating\"), pinocytosis (\"cellular drinking\"), and receptor-mediated endocytosis." ]

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[ "7.5 Bulk transport across the plasma membrane occurs by exocytosis and endocytosis (p. 138) In exocytosis, transport vesicles migrate to the plasma membrane, fuse with it, and release their contents. In endocytosis, molecules enter cells within vesicles that pinch inward from the plasma membrane. The three types of endocytosis are phagocytosis, pinocytosis, and receptor-mediated endocytosis." ]

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[ "41.2 The main stages of food processing are ingestion, digestion, absorption, and elimination (pp. 880-883) Food processing in animals involves ingestion (eating), digestion (enzymatic breakdown of large molecules), absorption (uptake of nutrients by cells), and elimination (passage of undigested materials out of the body in feces). Animals differ in the ways they obtain and ingest food. Most animals are bulk feeders, eating large pieces of food. Compartmentalization is necessary to avoid self-digestion. In intracellular digestion, food particles are engulfed by endocytosis and digested within food vacuoles that have fused with lysosomes. In extracellular digestion, which is used by most animals, enzymatic hydrolysis occurs outside cells in a gastrovascular cavity or alimentary canal." ]

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[ "The electron transport chain makes no ATP directly. Instead, it eases the fall of electrons from food to oxygen, breaking a large free-energy drop into a series of smaller steps that release energy in manageable amounts. How does the mitochondrion (or the prokaryotic plasma membrane) couple this electron transport and energy release to ATP synthesis? The answer is a mechanism called chemiosmosis." ]

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[ "Populating the inner membrane of the mitochondrion or the prokaryotic plasma membrane are many copies of a protein complex called ATP synthase, the enzyme that actually makes ATP from ADP and inorganic phosphate. ATP synthase works like an ion pump running in reverse. Recall from Chapter 7 that ion pumps usually use ATP as an energy source to transport ions against their gradients. In fact, the proton pump shown in Figure 7.20 is an ATP synthase. As we mentioned in Chapter 8, enzymes can catalyze a reaction in either direction, depending on the deltaG for the reaction, which is affected by the local concentrations of reactants and products. Rather than hydrolyzing ATP to pump protons against their concentration gradient, under the conditions of cellular respiration ATP synthase uses the energy of an existing ion gradient to power ATP synthesis. The power source for the ATP synthase is a difference in the concentration of H+ on opposite sides of the inner mitochondrial membrane. (We can \nalso think of this gradient as a difference in pH, since pH is a measure of H+ concentration. ) This process, in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP, is called chemiosmosis (from the Greek osmos, push). We have previously used the word osmosis in discussing water transport, but here it refers to the flow of H+ across a membrane. Figure 9.14 ATP synthase, a molecular mill. The ATP synthase protein complex functions as a mill, powered by the flow of hydrogen ions. Multiple copies of this complex reside in mitochondrial and chloroplast membranes of eukaryotes and in the plasma membranes of prokaryotes. Each of the four parts of ATP synthase consists of a number of polypeptide subunits. From studying the structure of ATP synthase, scientists have learned how the flow of H+ through this large enzyme powers ATP generation. ATP synthase is a multisubunit complex with four main parts, each made up of multiple \npolypeptides. Protons move one by one into binding sites on one of the parts (the rotor), causing it to spin in a way that catalyzes ATP production from ADP and inorganic phosphate (Figure 9.14). The flow of protons thus behaves somewhat like a rushing stream that turns a waterwheel. ATP synthase is the smallest molecular rotary motor known in nature. Figure 9.15 Chemiosmosis couples the electron transport chain to ATP synthesis. ➊ NADH and FADH2 shuttle high-energy electrons extracted from food during glycolysis and the citric acid cycle into an electron transport chain built into the inner mitochondrial membrane. The gold arrows trace the transport of electrons, which finally pass to oxygen at the \"downhill\" end of the chain, forming water. As Figure 9.13 showed, most of the electron carriers of the chain are grouped into four complexes. Two mobile carriers, ubiquinone (Q) and cytochrome c (Cyt c), move rapidly, ferrying electrons between the large complexes. As complexes I, III, and IV accept \nand 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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[ "Figure 10.17 Comparison of chemiosmosis in mitochondria and chloroplasts. In both kinds of organelles, electron transport chains pump protons (H+) across a membrane from a region of low H+ concentration (light gray in this diagram) to one of high H+ concentration (dark gray). The protons then diffuse back across the membrane through ATP synthase, driving the synthesis of ATP. Although the spatial organization of chemiosmosis differs slightly between chloroplasts and mitochondria, it is easy to see similarities in the two (Figure 10.17). The inner membrane of the mitochondrion pumps protons from the mitochondrial matrix out to the intermembrane space, which then serves as a reservoir of hydrogen ions. The thylakoid membrane of the chloroplast pumps protons from the stroma into the thylakoid space (interior of the thylakoid), which functions as the H+ reservoir. If you imagine the cristae of mitochondria pinching off from the inner membrane, this may help you see how the thylakoid space \nand the intermembrane space are comparable spaces in the two organelles, while the mitochondrial matrix is analogous to the stroma of the chloroplast. In the mitochondrion, protons diffuse down their concentration gradient from the intermembrane space through ATP synthase to the matrix, driving ATP synthesis." ]

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[ "Cellular respiration does not oxidize glucose in a single explosive step either. Rather, glucose and other organic fuels are broken down in a series of steps, each one catalyzed by an enzyme. At key steps, electrons are stripped from the glucose. As is often the case in oxidation reactions, each electron travels with a proton: thus, as a hydrogen atom. The hydrogen atoms are not transferred directly to oxygen, but instead are usually passed first to an electron carrier, a coenzyme called NAD+ (nicotinamide adenine dinucleotide, a derivative of the vitamin niacin). NAD+ is well suited as an electron carrier because it can cycle easily between oxidized (NAD+) and reduced (NADH) states. As an electron acceptor, NAD+ functions as an oxidizing agent during respiration. Figure 9.4 NAD+ as an electron shuttle. The full name for NAD+, nicotinamide adenine dinucleotide, describes its structure: The molecule consists of two nucleotides joined together at their phosphate groups (shown in yellow). \n(Nicotinamide is a nitrogenous base, although not one that is present in DNA or RNA; see Figure 5.26. ) The enzymatic transfer of 2 electrons and 1 proton (H+) from an organic molecule in food to NAD+ reduces the NAD+ to NADH; the second proton (H+) is released. Most of the electrons removed from food are transferred initially to NAD+. How does NAD+ trap electrons from glucose and other organic molecules? Enzymes called dehydrogenases remove a pair of hydrogen atoms (2 electrons and 2 protons) from the substrate (glucose, in this example), thereby oxidizing it. The enzyme delivers the 2 electrons along with 1 proton to its coenzyme, NAD+ (Figure 9.4). The other proton is released as a hydrogen ion (H+) into the surrounding solution: By receiving 2 negatively charged electrons but only 1 positively charged proton, NAD+ has its charge neutralized when it is reduced to NADH. The name NADH shows the hydrogen that has been received in the reaction. NAD+ is the most versatile electron acceptor in cellular \nrespiration and functions in several of the redox steps during the breakdown of glucose. Electrons lose very little of their potential energy when they are transferred from glucose to NAD+. Each NADH molecule formed during respiration represents stored energy that can be tapped to make ATP when the electrons complete their \"fall\" down an energy gradient from NADH to oxygen." ]

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[ "Some of the steps of glycolysis and the citric acid cycle are redox reactions in which dehydrogenases transfer electrons from substrates to NAD+, forming NADH. In the third stage of respiration, the electron transport chain accepts electrons from the breakdown products of the first two stages (most often via NADH) and passes these electrons from one molecule to another." ]

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[ "Note that glycolysis is a source of ATP and NADH. Figure 9.8 The energy input and output of glycolysis. As summarized in Figure 9.8, glycolysis can be divided into two phases: energy investment and energy payoff. During the energy investment phase, the cell actually spends ATP. This investment is repaid with interest during the energy payoff phase, when ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from the oxidation of glucose. The net energy yield from glycolysis, per glucose molecule, is 2 ATP plus 2 NADH. The ten steps of the glycolytic pathway are shown in Figure 9.9. All of the carbon originally present in glucose is accounted for in the two molecules of pyruvate; no carbon is released as CO2 during glycolysis. Glycolysis occurs whether or not O2 is present. However, if O2 is present, the chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation." ]

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[ "The citric acid cycle is also called the tricarboxylic acid cycle or the Krebs cycle, the latter honoring Hans Krebs, the German-British scientist who was largely responsible for working out the pathway in the 1930s. The cycle functions as a metabolic furnace that oxidizes organic fuel derived from pyruvate. Figure 9.11 summarizes the inputs and outputs as pyruvate is broken down to three CO2 molecules, including the molecule of CO2 released during the conversion of pyruvate to acetyl CoA. The cycle generates 1 ATP per turn by substrate-level phosphorylation, but most of the chemical energy is transferred to NAD+ and a related electron carrier, the coenzyme FAD (flavin adenine dinucleotide, derived from riboflavin, a B vitamin), during the redox reactions. The reduced coenzymes, NADH and FADH2, shuttle their cargo of high-energy electrons into the electron transport chain." ]

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[ "Now let's tally the energy-rich molecules produced by the citric acid cycle. For each acetyl group entering the cycle, 3 NAD+ are reduced to NADH (steps 3, 4, and 8)." ]

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[ "Now let's take a closer look at the electron transport chain in Figure 9.13. We'll first describe the passage of electrons through complex I in some detail, as an illustration of the general principles involved in electron transport. Electrons removed from glucose by NAD+, during glycolysis and the citric acid cycle, are transferred from NADH to the first molecule of the electron transport chain in complex I. This molecule is a flavoprotein, so named because it has a prosthetic group called flavin mononucleotide (FMN)." ]

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[ "During aerobic respiration, glucose (C6H12O6) is oxidized to CO2, and O2 is reduced to H2O. Electrons lose potential energy during their transfer from glucose or other organic compounds to oxygen. Electrons are usually passed first to NAD+, reducing it to NADH, and then from NADH to an electron transport chain, which conducts them to O2 in energy-releasing steps." ]

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[ "8.1 An organism's metabolism transforms matter and energy, subject to the laws of thermodynamics" ]

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[ "The totality of an organism's chemical reactions is called metabolism (from the Greek metabole, change). Metabolism is an emergent property of life that arises from orderly interactions between molecules." ]

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[ "We can picture a cell's metabolism as an elaborate road map of the thousands of chemical reactions that occur in a cell, arranged as intersecting metabolic pathways. A metabolic pathway begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product. Each step of the pathway is catalyzed by a specific enzyme: Analogous to the red, yellow, and green stoplights that control the flow of automobile traffic, mechanisms that regulate enzymes balance metabolic supply and demand. 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. (Pathways can have more than one \nstarting molecule and/or product. ) Energy that was stored in the organic molecules becomes available to do the work of the cell, such as ciliary beating or membrane transport. Anabolic pathways, in contrast, consume energy to build complicated molecules from simpler ones; they are sometimes called biosynthetic pathways. Examples of anabolism are the synthesis of an amino acid from simpler molecules and the synthesis of a protein from amino acids. Catabolic and anabolic pathways are the \"downhill\" and \"uphill\" avenues of the metabolic landscape. Energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways. In this chapter, we will focus on mechanisms common to metabolic pathways. Because energy is fundamental to all metabolic processes, a basic knowledge of energy is necessary to understand how the living cell works. Although we will use some nonliving examples to study energy, the concepts demonstrated by these examples also \napply to bioenergetics, the study of how energy flows through living organisms." ]

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[ "Energy is the capacity to cause change. In everyday life, energy is important because some forms of energy can be used to do work: that is, to move matter against opposing forces, such as gravity and friction. Put another way, energy is the ability to rearrange a collection of matter." ]

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[ "Once we know the value of deltaG for a process, we can use it to predict whether the process will be spontaneous (that is, whether it is energetically favorable and will occur without an input of energy). More than a century of experiments has shown that only processes with a negative deltaG are spontaneous. For deltaG to be negative, either deltaH must be negative (the system gives up enthalpy and H decreases) or TdeltaS must be positive (the system gives up order and S increases), or both: When deltaH and TdeltaS are tallied, deltaG has a negative value (deltaG < 0) for all spontaneous processes. In other words, every spontaneous process decreases the system's free energy, and processes that have a positive or zero deltaG are never spontaneous. This information is immensely interesting to biologists, for it gives us the power to predict which kinds of change can happen without help. Such spontaneous changes can be harnessed to perform work. This principle is very important in \nthe study of metabolism, where a major goal is to determine which reactions can supply energy for cellular work." ]

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[ "8.1 An organism's metabolism transforms matter and energy, subject to the laws of thermodynamics (pp. 142-145) Metabolism is the collection of chemical reactions that occur in an organism." ]

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[ "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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[ "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." ]

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[ "Reactions in an isolated system eventually reach equilibrium and can then do no work, as illustrated by the isolated hydroelectric system in Figure 8.7a. The chemical reactions of metabolism are reversible, and they, too, would reach equilibrium if they occurred in the isolation of a test tube. Because systems at equilibrium are at a minimum of G and can do no work, a cell that has reached metabolic equilibrium is dead! The fact that metabolism as a whole is never at equilibrium is one of the defining features of life. Like most systems, a living cell is not in equilibrium. The constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium, and the cell continues to do work throughout its life. This principle is illustrated by the open (and more realistic) hydroelectric system in Figure 8.7b. However, unlike this simple single-step system, a catabolic pathway in a cell releases free energy in a series of reactions. An example is cellular \nrespiration, illustrated by analogy in Figure 8.7c. Some of the reversible reactions of respiration are constantly \"pulled\" in one direction: that is, they are kept out of equilibrium. The key to maintaining this lack of equilibrium is that the product of a reaction does not accumulate but instead becomes a reactant in the next step; finally, waste products are expelled from the cell. The overall sequence of reactions is kept going by the huge free-energy difference between glucose and oxygen at the top of the energy \"hill\" and carbon dioxide and water at the \"downhill\" end. As long as our cells have a steady supply of glucose or other fuels and oxygen and are able to expel waste products to the surroundings, their metabolic pathways never reach equilibrium and can continue to do the work of life." ]

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[ "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 of 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 \nlevel 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 represented 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 \"\nfalls 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. When 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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[ "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. Figure 10.12 Excitation of isolated \nchlorophyll by light. (a) Absorption of a photon causes a transition of the chlorophyll molecule from its ground state to its excited state. The photon boosts an electron to an orbital where it has more potential energy." ]

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[ "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. Figure 10.12 Excitation of isolated \nchlorophyll by light. (a) Absorption of a photon causes a transition of the chlorophyll molecule from its ground state to its excited state. The photon boosts an electron to an orbital where it has more potential energy." ]

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[ "A covalent bond is the sharing of a pair of valence electrons by two atoms. For example, let's consider what happens when two hydrogen atoms approach each other. Recall that hydrogen has 1 valence electron in the first shell, but the shell's capacity is 2 electrons. When the two hydrogen atoms come close enough for their 1s orbitals to overlap, they can share their electrons (Figure 2.11). Each hydrogen atom is now associated with 2 electrons in what amounts to a completed valence shell. Two or more atoms held together by covalent bonds constitute a molecule, in this case a hydrogen molecule. Figure 2.12 Covalent bonding in four molecules. The number of electrons required to complete an atom's valence shell generally determines how many covalent bonds that atom will form. This figure shows several ways of indicating covalent bonds. Figure 2.12a shows several ways of representing a hydrogen molecule. Its molecular formula, H2, simply indicates that the molecule consists of two atoms of \nhydrogen. Electron sharing can be depicted by an electron distribution diagram or by a Lewis dot structure, in which element symbols are surrounded by dots that represent the valence electrons (H:H). We can also use a structural formula, H-H, where the line represents a single bond, a pair of shared electrons. A space-filling model comes closest to representing the actual shape of the molecule. Oxygen has 6 electrons in its second electron shell and therefore needs 2 more electrons to complete its valence shell. Two oxygen atoms form a molecule by sharing two pairs of valence electrons (Figure 2.12b). The atoms are thus joined by a double bond (O\"O). Each atom that can share valence electrons has a bonding capacity corresponding to the number of covalent bonds the atom can form. When the bonds form, they give the atom a full complement of electrons in the valence shell. The bonding capacity of oxygen, for example, is 2. This bonding capacity is called the atom's valence and usually equals the number of \nunpaired electrons required to complete the atom's outermost (valence) shell. See if you can determine the valences of hydrogen, oxygen, nitrogen, and carbon by studying the electron distribution diagrams in Figure 2.9. You can see that the valence of hydrogen is 1; oxygen, 2; nitrogen, 3; and carbon, 4. However, the situation is more complicated for elements in the third row of the periodic table. Phosphorus, for example, can have a valence of 3, as we would predict from the presence of 3 unpaired electrons in its valence shell. In some molecules that are biologically important, however, phosphorus can form three single bonds and one double bond. Therefore, it can also have a valence of 5. The molecules H2 and O2 are pure elements rather than compounds because a compound is a combination of two or more different elements. Water, with the molecular formula H2O, is a compound. Two atoms of hydrogen are needed to satisfy the valence of one oxygen atom. Figure 2.12c shows the structure of a water molecule. \nWater is so important to life that Chapter 3 is devoted entirely to its structure and behavior. Methane, the main component of natural gas, is a compound with the molecular formula CH4. It takes four hydrogen atoms, each with a valence of 1, to complement one atom of carbon, with its valence of 4 (Figure 2.12d). We will look at many other compounds of carbon in Chapter 4. Figure 2.13 Polar covalent bonds in a water molecule. Atoms in a molecule attract shared electrons to varying degrees, depending on the element. The attraction of a particular atom for the electrons of a covalent bond is called its electronegativity. The more electronegative an atom is, the more strongly it pulls shared electrons toward itself. In a covalent bond between two atoms of the same element, the electrons are shared equally because the two atoms have the same electronegativity: the tug-of-war is at a standoff. Such a bond is called a nonpolar covalent bond. For example, the single bond of H2 is nonpolar, as is the double bond of \nO2. However, when one atom is bonded to a more electronegative atom, the electrons of the bond are not shared equally. This type of bond is called a polar covalent bond. Such bonds vary in their polarity, depending on the relative electronegativity of the two atoms. For example, the bonds between the oxygen and hydrogen atoms of a water molecule are quite polar (Figure 2.13). Oxygen is one of the most electronegative of all the elements, attracting shared electrons much more strongly than hydrogen does. In a covalent bond between oxygen and hydrogen, the electrons spend more time near the oxygen nucleus than they do near the hydrogen nucleus. Because electrons have a negative charge and are pulled toward oxygen in a water molecule, the oxygen atom has a partial negative charge (indicated by the Greek letter delta with a minus sign, delta-, or \"delta minus\"), and each hydrogen atom has a partial positive charge (, or \"delta plus\"). In contrast, the individual bonds of methane (CH4) are much less polar because \nthe electronegativities of carbon and hydrogen are similar." ]

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[ "Carbon has 6 electrons, with 2 in the first electron shell and 4 in the second shell; thus, it has 4 valence electrons in a shell that holds 8 electrons. A carbon atom usually completes its valence shell by sharing its 4 electrons with other atoms so that 8 electrons are present. Each pair of shared electrons constitutes a covalent bond (see Figure 2.12d). In organic molecules, carbon usually forms single or double covalent bonds. Each carbon atom acts as an intersection point from which a molecule can branch off in as many as four directions. This ability is one facet of carbon's versatility that makes large, complex molecules possible. Figure 4.3 The shapes of three simple organic molecules. When a carbon atom forms four single covalent bonds, the arrangement of its four hybrid orbitals causes the bonds to angle toward the corners of an imaginary tetrahedron (see Figure 2.17b). The bond angles in methane (CH4) are 109.5 degree (Figure 4.3a, and they are roughly the same in any group \nof atoms where carbon has four single bonds. For example, ethane (C2H6) is shaped like two overlapping tetrahedrons (Figure 4.3b). In molecules with more carbons, every grouping of a carbon bonded to four other atoms has a tetrahedral shape. But when two carbon atoms are joined by a double bond, as in ethene (C2H4), the atoms joined to those carbons are in the same plane as the carbons (Figure 4.3c). We find it convenient to write molecules as structural formulas, as if the molecules being represented are two-dimensional, but keep in mind that molecules are three-dimensional and that the shape of a molecule often determines its function. Figure 4.4 Valences of the major elements of organic molecules. Valence is the number of covalent bonds an atom can form. It is generally equal to the number of electrons required to complete the valence (outermost) shell (see Figure 2.9). All the electrons are shown for each atom in the electron distribution diagrams (top). Only the valence shell electrons are shown in the \nLewis dot structures (bottom). Note that carbon can form four bonds. The electron configuration of carbon gives it covalent compatibility with many different elements. Figure 4.4 shows the valences of carbon and its most frequent partners: hydrogen, oxygen, and nitrogen. These are the four major atomic components of organic molecules. These valences are the basis for the rules of covalent bonding in organic chemistry: the building code for the architecture of organic molecules." ]

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[ "Taking these observations into account, S. J. Singer and G. Nicolson proposed in 1972 that membrane proteins reside in the phospholipid bilayer with their hydrophilic regions protruding (Figure 7.3). This molecular arrangement would maximize contact of hydrophilic regions of proteins and phospholipids with water in the cytosol and extracellular fluid, while providing their hydrophobic parts with a nonaqueous environment. In this fluid mosaic model, the membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids." ]

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[ "Now we come to the mosaic aspect of the fluid mosaic model. Somewhat like a tile mosaic, a membrane is a collage of different proteins, often clustered together in groups, embedded in the fluid matrix of the lipid bilayer (see Figure 7.5). More than 50 kinds of proteins have been found so far in the plasma membrane of red blood cells, for example. Phospholipids form the main fabric of the membrane, but proteins determine most of the membrane's functions. Different types of cells contain different sets of membrane proteins, and the various membranes within a cell each have a unique collection of proteins. Figure 7.9 The structure of a transmembrane protein. Bacteriorhodopsin (a bacterial transport protein) has a distinct orientation in the membrane, with its N-terminus outside the cell and its C-terminus inside. This ribbon model highlights the ?-helical secondary structure of the hydrophobic parts, which lie mostly within the hydrophobic interior of the membrane. The protein includes \nseven transmembrane helices. The nonhelical hydrophilic segments are in contact with the aqueous solutions on the extracellular and cytoplasmic sides of the membrane. Notice in Figure 7.5 that there are two major populations of membrane proteins: integral proteins and peripheral proteins. Integral proteins penetrate the hydrophobic interior of the lipid bilayer. The majority are transmembrane proteins, which span the membrane; other integral proteins extend only partway into the hydrophobic interior. The hydrophobic regions of an integral protein consist of one or more stretches of nonpolar amino acids (see Figure 5.16), usually coiled into ? helices (Figure 7.9). The hydrophilic parts of the molecule are exposed to the aqueous solutions on either side of the membrane. Some proteins also have a hydrophilic channel through their center that allows passage of hydrophilic substances (see Figure 7.1)." ]

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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." ]

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[ "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 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 \nbreaking 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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[ "9.2 Glycolysis harvests chemical energy by oxidizing glucose to pyruvate" ]

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[ "The word glycolysis means \"sugar splitting,\" and that is exactly what happens during this pathway. Glucose, a six-carbon sugar, is split into two three-carbon sugars. These smaller sugars are then oxidized and their remaining atoms rearranged to form two molecules of pyruvate. (Pyruvate is the ionized form of pyruvic acid. )" ]

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[ "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." ]

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[ "Fermentation consists of glycolysis plus reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate. The NAD+ can then be reused to oxidize sugar by glycolysis, which nets two molecules of ATP by substrate-level phosphorylation. There are many types of fermentation, differing in the end products formed from pyruvate. Two common types are alcohol fermentation and lactic acid fermentation. Figure 9.17 Fermentation. In the absence of oxygen, many cells use fermentation to produce ATP by substrate-level phosphorylation. Pyruvate, the end product of glycolysis, serves as an electron acceptor for oxidizing NADH back to NAD+, which can then be reused in glycolysis. Two of the common end products formed from fermentation are (a) ethanol and (b) lactate, the ionized form of lactic acid. In alcohol fermentation (Figure 9.17a), pyruvate is converted to ethanol (ethyl alcohol) in two steps. The first step releases carbon dioxide from the pyruvate, \nwhich is converted to the two-carbon compound acetaldehyde. In the second step, acetaldehyde is reduced by NADH to ethanol. This regenerates the supply of NAD+ needed for the continuation of glycolysis. Many bacteria carry out alcohol fermentation under anaerobic conditions. Yeast (a fungus) also carries out alcohol fermentation. For thousands of years, humans have used yeast in brewing, winemaking, and baking. The CO2 bubbles generated by baker's yeast during alcohol fermentation allow bread to rise. During lactic acid fermentation (Figure 9.17b), pyruvate is reduced directly by NADH to form lactate as an end product, with no release of CO2. (Lactate is the ionized form of lactic acid. )" ]

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[ "Figure 9.18 Pyruvate as a key juncture in catabolism. Glycolysis is common to fermentation and cellular respiration. The end product of glycolysis, pyruvate, represents a fork in the catabolic pathways of glucose oxidation. In a facultative anaerobe or a muscle cell, which are capable of both aerobic cellular respiration and fermentation, pyruvate is committed to one of those two pathways, usually depending on whether or not oxygen is present. Some organisms, called obligate anaerobes, carry out only fermentation or anaerobic respiration. In fact, these organisms cannot survive in the presence of oxygen, some forms of which can actually be toxic if protective systems are not present in the cell. A few cell types, such as cells of the vertebrate brain, can carry out only aerobic oxidation of pyruvate, not fermentation. Other organisms, including yeasts and many bacteria, can make enough ATP to survive using either fermentation or respiration. Such species are called facultative \nanaerobes. 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 sugar at a much faster rate when fermenting than when respiring." ]

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[ "Figure 2.14 Electron transfer and ionic bonding. The attraction between oppositely charged atoms, or ions, is an ionic bond. An ionic bond can form between any two oppositely charged ions, even if they have not been formed by transfer of an electron from one to the other. In some cases, two atoms are so unequal in their attraction for valence electrons that the more electronegative atom strips an electron completely away from its partner. This is what happens when an atom of sodium (11Na) encounters an atom of chlorine (17Cl) (Figure 2.14). A sodium atom has a total of 11 electrons, with its single valence electron in the third electron shell. A chlorine atom has a total of 17 electrons, with 7 electrons in its valence shell. When these two atoms meet, the lone valence electron of sodium is transferred to the chlorine atom, and both atoms end up with their valence shells complete. (Because sodium no longer has an electron in the third shell, the second shell is now the valence shell. ) \nThe electron transfer between the two atoms moves one unit of negative charge from sodium to chlorine. Sodium, now with 11 protons but only 10 electrons, has a net electrical charge of 1+. A charged atom (or molecule) is called an ion. When the charge is positive, the ion is specifically called a cation; the sodium atom has become a cation. Conversely, the chlorine atom, having gained an extra electron, now has 17 protons and 18 electrons, giving it a net electrical charge of 1-. It has become a chloride ion: an anion, or negatively charged ion. Because of their opposite charges, cations and anions attract each other; this attraction is called an ionic bond." ]

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[ "Molecules consist of two or more covalently bonded atoms. The attraction of an atom for the electrons of a covalent bond is its electronegativity. If both atoms are the same, they have the same electronegativity and share a nonpolar covalent bond. Electrons of a polar covalent bond are pulled closer to the more electronegative atom. An ion forms when an atom or molecule gains or loses an electron and becomes charged. An ionic bond is the attraction between two oppositely charged ions." ]

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[ "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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[ "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." ]

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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. Carrier proteins can undergo changes in shape that translocate bound solutes across the membrane." ]

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[ "The carbohydrates on the extracellular side of the plasma membrane vary from species to species, among individuals of the same species, 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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[ "The division of cells to form new cells is the foundation for all reproduction and for the growth and repair of multicellular organisms. Inside the dividing cell in Figure 1.9, you can see structures called chromosomes, which are stained with a blue-glowing dye. The chromosomes have almost all of the cell's genetic material, its DNA (short for deoxyribonucleic acid). DNA is the substance of genes, the units of inheritance that transmit information from parents to offspring. Your blood group (A, B, AB, or O), for example, is the result of certain genes that you inherited from your parents." ]

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[ "Figure 14.11 Multiple alleles for the ABO blood groups. The four blood groups result from different combinations of three alleles. Only two alleles exist for the pea characters that Mendel studied, but most genes exist in more than two allelic forms. The ABO blood groups in humans, for instance, are determined by three alleles of a single gene: IA, IB, and i. A person's blood group (phenotype) may be one of four types: A, B, AB, or O. These letters refer to two carbohydrates: A and B: that may be found on the surface of red blood cells. A person's blood cells may have carbohydrate A (type A blood), carbohydrate B (type B), both (type AB), or neither (type O), as shown schematically in Figure 14.11. Matching compatible blood groups is critical for safe blood transfusions (see Chapter 43)." ]

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[ "To avoid a blood transfusion being recognized as foreign by the recipient's immune system, the ABO blood groups of the donor and recipient must be taken into account. As discussed in Chapter 14, red blood cells are designated as type A if they have the type A carbohydrate on their surface. Similarly, the type B carbohydrate is found on type B red blood cells; both A and B carbohydrates are found on type AB red blood cells; and neither carbohydrate is found on type O red blood cells (see Figure 14.11)." ]

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[ "One catabolic process, fermentation, is a partial degradation of sugars or other organic fuel that occurs without the use of oxygen. However, the most prevalent and efficient catabolic pathway is aerobic respiration, in which oxygen is consumed as a reactant along with the organic fuel (aerobic is from the Greek aer, air, and bios, life). The cells of most eukaryotic and many prokaryotic organisms can carry out aerobic respiration. Some prokaryotes use substances other than oxygen as reactants in a similar process that harvests chemical energy without oxygen; this process is called anaerobic respiration (the prefix an- means \"without\")." ]

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[ "Comparing Fermentation with Anaerobic and Aerobic Respiration The Evolutionary Significance of Glycolysis Because most of the ATP generated by cellular respiration is due to the work of oxidative phosphorylation, our estimate of ATP yield from aerobic respiration is contingent on an adequate supply of oxygen to the cell. Without the electronegative oxygen to pull electrons down the transport chain, oxidative phosphorylation eventually ceases. However, there are two general mechanisms by which certain cells can oxidize organic fuel and generate ATP without the use of oxygen: anaerobic respiration and fermentation. The distinction between these two is that an electron transport chain is used in anaerobic respiration but not in fermentation. (The electron transport chain is also called the respiratory chain because of its role in both types of cellular respiration. ) We have already mentioned anaerobic respiration, which takes place in certain prokaryotic organisms that live in \nenvironments without oxygen. These organisms have an electron transport chain but do not use oxygen as a final electron acceptor at the end of the chain. Oxygen performs this function very well because it is extremely electronegative, but other, less electronegative substances can also serve as final electron acceptors. Some \"sulfate-reducing\" marine bacteria, for instance, use the sulfate ion (SO42-') at the end of their respiratory chain. Operation of the chain builds up a proton-motive force used to produce ATP, but H2S (hydrogen sulfide) is produced as a by-product rather than water. The rotten-egg odor you may have smelled while walking through a salt marsh or a mudflat signals the presence of sulfate-reducing bacteria. Fermentation is a way of harvesting chemical energy without using either oxygen or any electron transport chain: in other words, without cellular respiration. How can food be oxidized without cellular respiration? Remember, oxidation simply refers to the loss of electrons to an electron \nacceptor, so it does not need to involve oxygen. Glycolysis oxidizes glucose to two molecules of pyruvate. The oxidizing agent of glycolysis is NAD+, and neither oxygen nor any electron transfer chain is involved. Overall, glycolysis is exergonic, and some of the energy made available is used to produce 2 ATP (net) by substrate-level phosphorylation. If oxygen is present, then additional ATP is made by oxidative phosphorylation when NADH passes electrons removed from glucose to the electron transport chain. But glycolysis generates 2 ATP whether oxygen is present or not: that is, whether conditions are aerobic or anaerobic. As an alternative to respiratory oxidation of organic nutrients, fermentation is an extension of glycolysis that allows continuous generation of ATP by the substrate-level phosphorylation of glycolysis. For this to occur, there must be a sufficient supply of NAD+ to accept electrons during the oxidation step of glycolysis. Without some mechanism to recycle NAD+ from NADH, glycolysis would \nsoon deplete the cell's pool of NAD+ by reducing it all to NADH and would shut itself down for lack of an oxidizing agent. Under aerobic conditions, NAD+ is recycled from NADH by the transfer of electrons to the electron transport chain. An anaerobic alternative is to transfer electrons from NADH to pyruvate, the end product of glycolysis." ]

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[ "Fermentation consists of glycolysis plus reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate. The NAD+ can then be reused to oxidize sugar by glycolysis, which nets two molecules of ATP by substrate-level phosphorylation." ]

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[ "A key difference among the three pathways is the contrasting mechanisms for oxidizing NADH back to NAD+, which is required to sustain glycolysis. In fermentation, the final electron acceptor is an organic molecule such as pyruvate (lactic acid fermentation) or acetaldehyde (alcohol fermentation). In cellular respiration, by contrast, electrons carried by NADH are transferred to an electron transport chain, where they move stepwise down a series of redox reactions to a final electron acceptor. In aerobic respiration, the final electron acceptor is oxygen; in anaerobic respiration, the final acceptor is another molecule that is electronegative (although invariably less so than oxygen). Passage of electrons from NADH to the electron transport chain not only regenerates the NAD+ required for glycolysis but pays an ATP bonus when the stepwise electron transport from this NADH to oxygen drives oxidative phosphorylation. An even bigger ATP payoff comes from the oxidation of pyruvate in the \nmitochondrion, which is unique to respiration. Without an electron transport chain, the energy still stored in pyruvate is unavailable to most cells. Thus, cellular respiration harvests much more energy from each sugar molecule than fermentation can. In fact, aerobic respiration yields up to 16 times as much ATP per glucose molecule as does fermentation: up to 32 molecules of ATP for respiration, compared with 2 molecules of ATP produced by substrate-level phosphorylation in fermentation." ]

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[ "9.5 Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen (pp. 177-179) Glycolysis nets 2 ATP by substrate-level phosphorylation, whether oxygen is present or not. Under anaerobic conditions, either anaerobic respiration or fermentation can take place. In anaerobic respiration, an electron transport chain is present with a final electron acceptor other than oxygen. In fermentation, the electrons from NADH are passed to pyruvate or a derivative of pyruvate, regenerating the NAD+ required to oxidize more glucose. Two common types of fermentation are alcohol fermentation and lactic acid fermentation. Fermentation and anaerobic or aerobic respiration all use glycolysis to oxidize glucose, but they differ in their final electron acceptor and whether an electron transport chain is used (respiration) or not (fermentation). Respiration yields more ATP; aerobic respiration, with O2 as the final electron acceptor, yields about 16 times as much ATP as does \nfermentation. Glycolysis occurs in nearly all organisms and is thought to have evolved in ancient prokaryotes before there was O2 in the atmosphere." ]

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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. Differences in membrane lipid composition, as well as the ability to change lipid composition, are evolutionary adaptations that ensure membrane fluidity." ]

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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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[ "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)." ]

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[ "In this chapter, you 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 7.18 The sodium-potassium pump: a specific case of active transport. This transport system pumps ions against steep concentration gradients: Sodium ion concentration ([Na+]) is high outside the cell and low inside, while potassium ion concentration ([K+]) is low outside the cell and high inside. The pump oscillates between two shapes in a cycle that moves 3 Na+ out of the cell for every 2 K+ pumped into the cell. The two shapes have different affinities for Na+ and K+. ATP powers the shape change by transferring a phosphate group to the transport protein (phosphorylating the protein). Active transport enables a cell to maintain internal concentrations of small solutes that differ from concentrations in its environment. For example, compared with its surroundings, an animal cell has a much higher concentration of potassium ions (K+) and a much lower concentration of sodium ions (Na+)." ]

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[ "An example is the sodium-potassium pump. Notice in Figure 7.18 that the pump does not translocate Na+ and K+ one for one, but pumps three sodium ions out of the cell for every two potassium ions it pumps into the cell. With each \"crank\" of the pump, there is a net transfer of one positive charge from the cytoplasm to the extracellular fluid, a process that stores energy as voltage. A transport protein that generates voltage across a membrane is called an electrogenic pump. The sodium-potassium pump appears to be the major electrogenic pump of animal cells." ]

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[ "ABA plays a major role in drought signaling. When a plant begins to wilt, ABA accumulates in the leaves and causes stomata to close rapidly, reducing transpiration and preventing further water loss. By affecting second messengers such as calcium, ABA causes potassium channels in the plasma membrane of guard cells to open, leading to a massive loss of potassium ions from the cells. The accompanying osmotic loss of water reduces guard cell turgor and leads to closing of the stomatal pores (see Figure 36.15)." ]

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[ "Potassium ions (K+) and sodium ions (Na+) play an essential role in the formation of the resting potential. Each type of ion has a concentration gradient across the plasma membrane of a neuron (Table 48.1). In the case of mammalian neurons, the concentration of K+ is highest inside the cell, while the concentration of Na+ is highest outside. These Na+ and K+ gradients are maintained by sodium-potassium pumps in the plasma membrane. As discussed in Chapter 7, these ion pumps use the energy of ATP hydrolysis to actively transport Na+ out of the cell and K+ into the cell (Figure 48.7). There are also concentration gradients for chloride ions (Cl-') and other anions, as shown in Table 48.1, but we will ignore these for the moment. Table 48.1 Ion Concentrations Inside and Outside of Mammalian Neurons Ion Intracellular Concentration (mM) Extracellular Concentration (mM) Potassium (K+) 140 5 Sodium (Na+) 15 150 Chloride (Cl-') 10 120 Large anions (A-') inside cell, such as proteins 100 (not \napplicable) Figure 48.7 The basis of the membrane potential. The sodium-potassium pump generates and maintains the ionic gradients of Na+ and K+ shown in Table 48.1. The pump uses ATP to actively transport Na+ out of the cell and K+ into the cell. Although there is a substantial concentration gradient of sodium across the membrane, very little net diffusion of Na+ occurs because there are very few open sodium channels. In contrast, the large number of open potassium channels allow a significant net outflow of K+. Because the membrane is only weakly permeable to chloride and other anions, this outflow of K+ results in a net negative charge inside the cell. A sodium-potassium pump transports three sodium ions out of the cell for every two potassium ions that it transports in. Although this pumping generates a net export of positive charge, the resulting voltage difference is only a few millivolts. Why, then, is there a voltage difference of 60-80 mV in a resting neuron? The answer lies in ion movement through \nion channels, pores formed by clusters of specialized proteins that span the membrane. Ion channels allow ions to diffuse back and forth across the membrane. As ions diffuse through channels, they carry with them units of electrical charge. Any resulting net movement of positive or negative charge will generate a membrane potential, or voltage across the membrane. The concentration gradients of K+ and Na+ across the plasma membrane represent a chemical form of potential energy. The ion channels that convert this chemical potential energy to electrical potential energy can do so because they have selective permeability, allowing only certain ions to pass. For example, a potassium channel allows K+ to diffuse freely across the membrane, but not other ions, such as Na+. Diffusion of K+ through open potassium channels is critical for formation of the resting potential. The K+ concentration is 140 mM inside the cell, but only 5 mM outside. The chemical concentration gradient thus favors a net outflow of K+. \nFurthermore, a resting neuron has many open potassium channels, but very few open sodium channels (see Figure 48.7). Because Na+ and other ions can't readily cross the membrane, K+ outflow leads to a net negative charge inside the cell. This buildup of negative charge within the neuron is the major source of the membrane potential. What stops the buildup of negative charge? The excess negative charges inside the cell exert an attractive force that opposes the flow of additional positively charged potassium ions out of the cell. The separation of charge (voltage) thus results in an electrical gradient that counterbalances the chemical concentration gradient of K+." ]

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[ "Figure 48.8 Modeling a mammalian neuron. Each container is divided into two chambers by an artificial membrane. Ion channels allow free diffusion for particular ions, resulting in the net ion flow represented by arrows. (a) The presence of open potassium channels makes the membrane selectively permeable to K+, and the inner chamber contains a 28-fold higher concentration of K+ than the outer chamber; at equilibrium, the inside of the membrane is -'90 mV relative to the outside. (b) The membrane is selectively permeable to Na+, and the inner chamber contains a tenfold lower concentration of Na+ than the outer chamber; at equilibrium, the inside of the membrane is +62 mV relative to the outside." ]

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[ "To explore how the membrane potential changes, let's consider what happens when gated potassium channels that are closed in a resting neuron are stimulated to open. Opening these potassium channels increases the membrane's permeability to K+. Net diffusion of K+ out of the neuron increases, shifting the membrane potential toward EK (-'90 mV at 37 degree C). This increase in the magnitude of the membrane potential, called a hyperpolarization, makes the inside of the membrane more negative (Figure 48.10a). In a resting neuron, hyperpolarization results from any stimulus that increases the outflow of positive ions or the inflow of negative ions. Although opening potassium channels in a resting neuron causes hyperpolarization, opening some other types of ion channels has an opposite effect, making the inside of the membrane less negative (Figure 48.10b)." ]

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[ "The characteristic shape of the graph of an action potential (see Figure 48.10c) reflects the large change in membrane potential resulting from ion movement through voltage-gated sodium and potassium channels. Membrane depolarization opens both types of channels, but they respond independently and sequentially. Sodium channels open first, initiating the action potential. As the action potential proceeds, the sodium channels become inactivated: A loop of the channel protein moves, blocking ion flow through the opening. Sodium channels remain inactivated until after the membrane returns to the resting potential and the channels close. Potassium channels open more slowly than sodium channels, but remain open and functional until the end of the action potential. Figure 48.11 The role of voltage-gated ion channels in the generation of an action potential. The circled numbers on the graph in the center and the colors of the action potential phases correspond to the five diagrams showing \nvoltage-gated sodium and potassium channels in a neuron's plasma membrane. (Ungated ion channels are not illustrated. ) To understand further how voltage-gated channels shape the action potential, we'll consider the process as a series of stages (Figure 48.11). ➊ When the membrane of the axon is at the resting potential, most voltage-gated sodium channels are closed. Some potassium channels are open, but most voltage-gated potassium channels are closed. ➋ When a stimulus depolarizes the membrane, some gated sodium channels open, allowing more Na+ to diffuse into the cell. The Na+ inflow causes further depolarization, which opens still more gated sodium channels, allowing even more Na+ to diffuse into the cell. ➌ Once the threshold is crossed, the positive-feedback cycle rapidly brings the membrane potential close to ENa. This stage of the action potential is called the rising phase. ➍ Two events prevent the membrane potential from actually reaching ENa: Voltage-\ngated sodium channels inactivate soon after opening, halting Na+ inflow; and most voltage-gated potassium channels open, causing a rapid outflow of K+. Both events quickly bring the membrane potential back toward EK. This stage is called the falling phase. ➎ In the final phase of an action potential, called the undershoot, the membrane's permeability to K+ is higher than at rest, so the membrane potential is closer to EK than it is at the resting potential. The gated potassium channels eventually close, and the membrane potential returns to the resting potential." ]

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[ "48.3 Action potentials are the signals conducted by axons (pp. 1050-1055) Neurons have gated ion channels that open or close in response to stimuli, leading to changes in the membrane potential. An increase in the magnitude of the membrane potential is a hyperpolarization; a decrease is a depolarization. Changes in membrane potential that vary continuously with the strength of a stimulus are known as graded potentials. An action potential is a brief, all-or-none depolarization of a neuron's plasma membrane. When a graded depolarization brings the membrane potential to the threshold, many voltage-gated ion channels open, triggering an inflow of Na+ that rapidly brings the membrane potential to a positive value. A negative membrane potential is restored by the inactivation of sodium channels and by the opening of many voltage-gated potassium channels, which increases K+ outflow." ]

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[ "In the end, the effect is the same: Water diffuses across the membrane from the region of lower solute concentration (higher free water concentration) to that of higher solute concentration (lower free water concentration) until the solute concentrations on both sides of the membrane are equal. The diffusion of free water across a selectively permeable membrane, whether artificial or cellular, is called osmosis. The movement of water across cell membranes and the balance of water between the cell and its environment are crucial to organisms. Let's now apply to living cells what we have learned about osmosis in artificial systems." ]

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[ "To explain the behavior of a cell in a solution, we must consider both solute concentration and membrane permeability. Both factors are taken into account in the concept of tonicity, the ability of a surrounding solution to cause a cell to gain or lose water. The tonicity of a solution depends in part on its concentration of solutes that cannot cross the membrane (nonpenetrating solutes) relative to that inside the cell. If there is a higher concentration of nonpenetrating solutes in the surrounding solution, water will tend to leave the cell, and vice versa. Figure 7.15 The water balance of living cells. How living cells react to changes in the solute concentration of their environment depends on whether or not they have cell walls. (a) Animal cells, such as this red blood cell, do not have cell walls. (b) Plant cells do. (Arrows indicate net water movement after the cells were first placed in these solutions. ) If a cell without a wall, such as an animal cell, is immersed in an \nenvironment that is isotonic to the cell (iso means \"same\"), there will be no net movement of water across the plasma membrane. Water diffuses across the membrane, but at the same rate in both directions. In an isotonic environment, the volume of an animal cell is stable (Figure 7.15a, on the next page). Now let's transfer the cell to a solution that is hypertonic to the cell (hyper means \"more,\" in this case referring to nonpenetrating solutes). The cell will lose water, shrivel, and probably die. This is one way an increase in the salinity (saltiness) of a lake can kill animals there; if the lake water becomes hypertonic to the animals' cells, the cells might shrivel and die. However, taking up too much water can be just as hazardous to an animal cell as losing water. If we place the cell in a solution that is hypotonic to the cell (hypo means \"less\"), water will enter the cell faster than it leaves, and the cell will swell and lyse (burst) like an overfilled water balloon." ]

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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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[ "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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[ "Cotransport: Coupled Transport by a Membrane Protein 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. Some transport proteins, however, can move solutes against their concentration gradients, across the plasma membrane from the side where they are less concentrated (whether inside or outside) to the side where they are more concentrated." ]

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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. The transport proteins that move solutes against their concentration gradients are all carrier proteins rather than channel proteins. This makes sense because when channel proteins are open, they merely allow solutes to diffuse down their concentration gradients rather than picking them up and transporting them against their gradients. Figure 7.18 The sodium-potassium pump: a specific case of active transport. This transport system pumps ions against steep concentration gradients: Sodium ion concentration ([Na+]) is high outside the cell and low inside, while potassium ion concentration ([K+]) is low outside the cell and high inside. The pump oscillates between two shapes in a cycle that moves 3 Na+ out of the cell for every 2 K+ pumped into the cell. The two shapes have different affinities for Na+ and K+. ATP powers \nthe shape change by transferring a phosphate group to the transport protein (phosphorylating the protein). Active transport enables a cell to maintain internal concentrations of small solutes that differ from concentrations in its environment. For example, compared with its surroundings, an animal cell has a much higher concentration of potassium ions (K+) and a much lower concentration of sodium ions (Na+). The plasma membrane helps maintain these steep gradients by pumping Na+ out of the cell and K+ into the cell." ]

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[ "Figure 7.20 A proton pump. Proton pumps are electrogenic pumps that store energy by generating voltage (charge separation) across membranes. A proton pump translocates positive charge in the form of hydrogen ions. The voltage and H+ concentration gradient represent a dual energy source that can drive other processes, such as the uptake of nutrients. Most proton pumps are powered by ATP. Some membrane proteins that actively transport ions contribute to the membrane potential. An example is the sodium-potassium pump. Notice in Figure 7.18 that the pump does not translocate Na+ and K+ one for one, but pumps three sodium ions out of the cell for every two potassium ions it pumps into the cell. With each \"crank\" of the pump, there is a net transfer of one positive charge from the cytoplasm to the extracellular fluid, a process that stores energy as voltage. A transport protein that generates voltage across a membrane is called an electrogenic pump. The sodium-potassium pump appears to be \nthe major electrogenic pump of animal cells. The main electrogenic pump of plants, fungi, and bacteria is a proton pump, which actively transports protons (hydrogen ions, H+) out of the cell. The pumping of H+ transfers positive charge from the cytoplasm to the extracellular solution (Figure 7.20). By generating voltage across membranes, electrogenic pumps help store energy that can be tapped for cellular work. 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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[ "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 the \"downhill\" diffusion of this substance to the \"uphill\" transport of a \nsecond 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." ]

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[ "Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. Chemical potential energy stored in ATP drives most cellular work. An organism at work uses ATP continuously, but ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP (Figure 8.11)." ]

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[ "Organic compounds possess potential energy as a result of the arrangement of electrons in the bonds between their atoms. Compounds that can participate in exergonic reactions can act as fuels. With the help of enzymes, a cell systematically degrades complex organic molecules that are rich in potential energy to simpler waste products that have less energy. Some of the energy taken out of chemical storage can be used to do work; the rest is dissipated as heat." ]

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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." ]

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[ "Catabolic pathways funnel electrons from many kinds of organic molecules into cellular respiration. Many carbohydrates can enter glycolysis, most often after conversion to glucose. Amino acids of proteins must be deaminated before being oxidized. The fatty acids of fats undergo beta oxidation to two-carbon fragments and then enter the citric acid cycle as acetyl CoA." ]

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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 7.14 Osmosis. Two sugar solutions of different concentrations are separated by a membrane that the solvent (water) can pass through but the solute (sugar) cannot. Water molecules move randomly and may cross in either direction, but overall, water diffuses from the solution with less concentrated solute to that with more concentrated solute. This diffusion of water, or osmosis, equalizes the sugar concentrations on both sides." ]

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[ "The \"Phosphate\" column in Figure 4.9 shows a simple example of an organic phosphate molecule. A more complicated organic phosphate, adenosine triphosphate, or ATP, is worth mentioning here because its function in the cell is so important. ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups: Where three phosphates are present in series, as in ATP, one phosphate may be split off as a result of a reaction with water. This inorganic phosphate ion, HOPO32-', is often abbreviated Pi in this book. Having lost one phosphate, ATP becomes adenosine diphosphate, or ADP. Although ATP is sometimes said to store energy, it is more accurate to think of it as storing the potential to react with water. This reaction releases energy that can be used by the cell." ]

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[ "A few chemical groups are key to the functioning of biological molecules (pp. 63-66) Chemical groups attached to the carbon skeletons of organic molecules participate in chemical reactions (functional groups) or contribute to function by affecting molecular shape (see Figure 4.9). ATP (adenosine triphosphate) consists of adenosine attached to three phosphate groups. ATP can react with water, forming inorganic phosphate and ADP (adenosine diphosphate). This reaction releases energy that can be used by the cell (see the equation at the top of the next page)." ]

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[ "The bonds between the phosphate groups of ATP can be broken by hydrolysis. When the terminal phosphate bond is broken by addition of a water molecule, a molecule of inorganic phosphate (HOPO32-, abbreviated Ⓟi throughout this book) leaves the ATP, which becomes adenosine diphosphate, or ADP (Figure 8.8b). The reaction is exergonic and releases 7.3 kcal of energy per mole of ATP hydrolyzed: ATP + H2O → ADP + Ⓟi ΔG = -'7.3 kcal/mol (-'30.5 kJ/mol) This is the free-energy change measured under standard conditions. In the cell, conditions do not conform to standard conditions, primarily because reactant and product concentrations differ from 1 M. For example, when ATP hydrolysis occurs under cellular conditions, the actual deltaG is about -'13 kcal/mol, 78% greater than the energy released by ATP hydrolysis under standard conditions. Because their hydrolysis releases energy, the phosphate bonds of ATP are sometimes referred to as high-energy phosphate \nbonds, but the term is misleading. The phosphate bonds of ATP are not unusually strong bonds, as \"high-energy\" may imply; rather, the reactants (ATP and water) themselves have high energy relative to the energy of the products (ADP and Ⓟi). The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves. ATP is useful to the cell because the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver. But why does this hydrolysis release so much energy? If we reexamine the ATP molecule in Figure 8.8a, we can see that all three phosphate groups are negatively charged. These like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule. The triphosphate tail of ATP is the chemical equivalent of a compressed spring." ]

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[ "Figure 8.11 The ATP cycle. Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. Chemical potential energy stored in ATP drives most cellular work. An organism at work uses ATP continuously, but ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP (Figure 8.11). The free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in the cell. This shuttling of inorganic phosphate and energy is called the ATP cycle, and it couples the cell's energy-yielding (exergonic) processes to the energy-consuming (endergonic) ones. The ATP cycle proceeds at an astonishing pace. For example, a working muscle cell recycles its entire pool of ATP in less than a minute. That turnover represents 10 million molecules of ATP consumed and regenerated per second per cell. If ATP could not be regenerated by the phosphorylation of ADP, humans would use up nearly their body weight in ATP \neach day. Because both directions of a reversible process cannot be downhill, the regeneration of ATP from ADP and Ⓟi is necessarily endergonic: ADP + Ⓟi → ATP + H2O ΔG = +7.3 kcal/mol (+30.5 kJ/mol) (standard conditions) Since ATP formation from ADP and Ⓟi is not spontaneous, free energy must be spent to make it occur. Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the endergonic process of making ATP. Plants also use light energy to produce ATP. Thus, the ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways." ]

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[ "8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions (pp. 149-151) ATP is the cell's energy shuttle. Hydrolysis of its terminal phosphate yields ADP and phosphate and releases free energy. Through energy coupling, the exergonic process of ATP hydrolysis drives endergonic reactions by transfer of a phosphate group to specific reactants, forming a phosphorylated intermediate that is more reactive. ATP hydrolysis (sometimes with protein phosphorylation) also causes changes in the shape and binding affinities of transport and motor proteins. Catabolic pathways drive regeneration of ATP from ADP + Pi." ]

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[ "Scientists have tried for centuries to piece together the process by which plants make food. Although some of the steps are still not completely understood, the overall photosynthetic equation has been known since the 1800s: In the presence of light, the green parts of plants produce organic compounds and oxygen from carbon dioxide and water. Using molecular formulas, we can summarize the complex series of chemical reactions in photosynthesis with this chemical equation: 6 CO2 + 12 H2O + Light energy → C6H12O6 + 6 O2 + 6 H2O We use glucose (C6H12O6) here to simplify the relationship between photosynthesis and respiration, but the direct product of photosynthesis is actually a three-carbon sugar that can be used to make glucose. Water appears on both sides of the equation because 12 molecules are consumed and 6 molecules are newly formed during photosynthesis. We can simplify the equation by indicating only the net consumption of water: 6 CO2 + 6 H2O + Light energy → \nC6H12O6 + 6 O2 Writing the equation in this form, we can see that the overall chemical change during photosynthesis is the reverse of the one that occurs during cellular respiration. Both of these metabolic processes occur in plant cells. However, as you will soon learn, chloroplasts do not synthesize sugars by simply reversing the steps of respiration." ]

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[ "How does the inner mitochondrial membrane or the prokaryotic plasma membrane generate and maintain the H+ gradient that drives ATP synthesis by the ATP synthase protein complex? Establishing the H+ gradient is a major function of the electron transport chain, which is shown in its mitochondrial location in Figure 9.15. The chain is an energy converter that uses the exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane, from the mitochondrial matrix into the intermembrane space. The H+ has a tendency to move back across the membrane, diffusing down its gradient. And the ATP synthases are the only sites that provide a route through the membrane for H+. As we described previously, the passage of H+ through ATP synthase uses the exergonic flow of H+ to drive the phosphorylation of ADP. Thus, the energy stored in an H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis, an example of chemiosmosis. At this point, \nyou may be wondering how the electron transport chain pumps hydrogen ions. Researchers have found that certain members of the electron transport chain accept and release protons (H+) along with electrons. (The aqueous solutions inside and surrounding the cell are a ready source of H+. ) At certain steps along the chain, electron transfers cause H+ to be taken up and released into the surrounding solution. In eukaryotic cells, the electron carriers are spatially arranged in the inner mitochondrial membrane in such a way that H+ is accepted from the mitochondrial matrix and deposited in the intermembrane space (see Figure 9.15). The H+ gradient that results is referred to as a proton-motive force, emphasizing the capacity of the gradient to perform work. The force drives H+ back across the membrane through the H+ channels provided by ATP synthases. In general terms, chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work." ]

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[ "There are three reasons we cannot state an exact number of ATP molecules generated by the breakdown of one molecule of glucose. First, phosphorylation and the redox reactions are not directly coupled to each other, so the ratio of the number of NADH molecules to the number of ATP molecules is not a whole number. 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 \nATP." ]

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[ "At certain steps along the electron transport chain, electron transfer causes protein complexes to move H+ from the mitochondrial matrix (in eukaryotes) to the intermembrane space, storing energy as a proton-motive force (H+ gradient). As H+ diffuses back into the matrix through ATP synthase, its passage drives the phosphorylation of ADP, a process called chemiosmosis." ]

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[ "Chloroplasts and mitochondria generate ATP by the same basic mechanism: chemiosmosis. An electron transport chain assembled in a membrane pumps protons across the membrane as electrons are passed through a series of carriers that are progressively more electronegative. In this way, electron transport chains transform redox energy to a proton-motive force, potential energy stored in the form of an H+ gradient across a membrane." ]

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[ "The harvesting of energy from glucose by cellular respiration is a cumulative function of three metabolic stages: Biochemists usually reserve the term cellular respiration for stages 2 and 3. 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 \nchains 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 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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[ "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 9.11 An overview of pyruvate oxidation and the citric acid cycle. The inputs and outputs per pyruvate molecule are shown. To calculate on a per-glucose basis, multiply by 2, because each glucose molecule is split during glycolysis into two pyruvate molecules. The citric acid cycle is also called the tricarboxylic acid cycle or the Krebs cycle, the latter honoring Hans Krebs, the German-British scientist who was largely responsible for working out the pathway in the 1930s. The cycle functions as a metabolic furnace that oxidizes organic fuel derived from pyruvate. Figure 9.11 summarizes the inputs and outputs as pyruvate is broken down to three CO2 molecules, including the molecule of CO2 released during the conversion of pyruvate to acetyl CoA. The cycle generates 1 ATP per turn by substrate-level phosphorylation, but most of the chemical energy is transferred to NAD+ and a related electron carrier, the coenzyme FAD (flavin adenine dinucleotide, derived from riboflavin, a B \nvitamin), during the redox reactions. The reduced coenzymes, NADH and FADH2, shuttle their cargo of high-energy electrons into the electron transport chain. 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. As a consequence, the oxaloacetate that is regenerated at step 8 is composed of different carbon atoms each time around. In eukaryotic cells, all the citric acid cycle enzymes are located in the mitochondrial matrix except \nfor the enzyme that catalyzes step 6, which resides in the inner mitochondrial membrane. Carboxylic acids are represented in their ionized forms, as : COO-', because the ionized forms prevail at the pH within the mitochondrion. For example, citrate is the ionized form of citric acid. 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)." ]