PART BIOENERGETICS AND METABOLISM 13 Principles of Bioenergetics 480 Although metabolism embraces hundreds of differ 14 Glycolysis, Gluconeogenesis, and the Pentose ent enzyme-catalyzed reactions, our major concern in Phosphate Pathway 521 Part II is the central metabolic pathways, which are few 15 Principles of Metabolic Regulation, Ilustrated with in number and remarkably similar in all forms of life the Metabolism of Glucose and Glycogen 560 ing organisms can be divided into two large groups according to the chemical form in which they obtain 16 The Citric Acid Cycle 601 carbon from the environment Autotrophs(such as 17 Fatty Acid Catabolism 631 photosynthetic bacteria and vascular plants)can use 18 Amino Acid Oxidation and the production carbon dioxide from the atmosphere as their sole source of carbon, from which they construct all their carbon of Urea 666 containing biomolecules(see Fig. 1-5). Some auto 19 Oxidative Phosphorylation and trophic organisms, such as cyanobacteria, can also Photophosphorylation 700 atmospheric nitrogen to generate all their nitrogenous 20 Carbohydrate Biosynthesis in Plants components. Heterotrophs cannot use atmospheric and Bacteria 761 carbon dioxide and must obtain carbon from their en vironment in the form of relatively complex organic mol 21 Lipid Biosynthesis 79 ecules such as glucose Multicellular animals and most 22 Biosynthesis of Amino Acids, Nucleotides, and microorganisms are heterotrophic. Autotrophic cells Related molecules 843 and organisms are relatively self-sufficient, whereas het 23 Integration and Hormonal Regulation of Mammalian erotrophic cells and organisms, with their requirements Metabolism 891 for carbon in more complex forms, must subsist on the products of other organisms Many autotrophic organisms are photosynthetic and obtain their energy from sunlight, whereas het erotrophic organisms obtain their energy from the etabolism is a highly coordinated cellular activity degradation of organic nutrients produced by auto in which many multienzyme systems(metabolic trophs. In our biosphere, autotrophs and heterotrophs pathways)cooperate to(1)obtain chemical energy by live together in a vast, interdependent cycle in which capturing solar energy or degrading energy-rich nutrients autotrophic organisms use atmospheric carbon dioxide from the environment;(2)convert nutrient molecules to build their organic biomolecules, some of them gen the cells own characteristic molecules, including en from water in the precursors of macromolecules;(3) polymerize mono- in turn use the organic products of autotrophs as nu meric precursors into macromolecules: proteins, nucleic trients and return carbon dioxide to the atmosphere acids, and polysaccharides; and (4)synthesize and Some of the oxidation reactions that produce carbon degrade biomolecules required for specialized cellular dioxide also he oxygen, converting it to water. functions, such as membrane lipids, intracellular mes. Thus carbon, oxygen, and water are constantly cycled sengers, and pigments between the heterotrophic and autotrophic worlds, with
Metabolism is a highly coordinated cellular activity in which many multienzyme systems (metabolic pathways) cooperate to (1) obtain chemical energy by capturing solar energy or degrading energy-rich nutrients from the environment; (2) convert nutrient molecules into the cell’s own characteristic molecules, including precursors of macromolecules; (3) polymerize monomeric precursors into macromolecules: proteins, nucleic acids, and polysaccharides; and (4) synthesize and degrade biomolecules required for specialized cellular functions, such as membrane lipids, intracellular messengers, and pigments. Although metabolism embraces hundreds of different enzyme-catalyzed reactions, our major concern in Part II is the central metabolic pathways, which are few in number and remarkably similar in all forms of life. Living organisms can be divided into two large groups according to the chemical form in which they obtain carbon from the environment. Autotrophs (such as photosynthetic bacteria and vascular plants) can use carbon dioxide from the atmosphere as their sole source of carbon, from which they construct all their carboncontaining biomolecules (see Fig. 1–5). Some autotrophic organisms, such as cyanobacteria, can also use atmospheric nitrogen to generate all their nitrogenous components. Heterotrophs cannot use atmospheric carbon dioxide and must obtain carbon from their environment in the form of relatively complex organic molecules such as glucose. Multicellular animals and most microorganisms are heterotrophic. Autotrophic cells and organisms are relatively self-sufficient, whereas heterotrophic cells and organisms, with their requirements for carbon in more complex forms, must subsist on the products of other organisms. Many autotrophic organisms are photosynthetic and obtain their energy from sunlight, whereas heterotrophic organisms obtain their energy from the degradation of organic nutrients produced by autotrophs. In our biosphere, autotrophs and heterotrophs live together in a vast, interdependent cycle in which autotrophic organisms use atmospheric carbon dioxide to build their organic biomolecules, some of them generating oxygen from water in the process. Heterotrophs in turn use the organic products of autotrophs as nutrients and return carbon dioxide to the atmosphere. Some of the oxidation reactions that produce carbon dioxide also consume oxygen, converting it to water. Thus carbon, oxygen, and water are constantly cycled between the heterotrophic and autotrophic worlds, with PART BIOENERGETICS AND METABOLISM II 13 Principles of Bioenergetics 480 14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway 521 15 Principles of Metabolic Regulation, Illustrated with the Metabolism of Glucose and Glycogen 560 16 The Citric Acid Cycle 601 17 Fatty Acid Catabolism 631 18 Amino Acid Oxidation and the Production of Urea 666 19 Oxidative Phosphorylation and Photophosphorylation 700 20 Carbohydrate Biosynthesis in Plants and Bacteria 761 21 Lipid Biosynthesis 797 22 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules 843 23 Integration and Hormonal Regulation of Mammalian Metabolism 891 481
Part l bic solar energy as the driving force for this global process Atmospheric All living organisms also require a source of nitro- gen,which is necessary for the synthesis of amino acids nucleotides, and other compounds. Plants can generall Ise either ammonia or nitrate as their sole source of ni- trogen, but vertebrates must obtain nitrogen in the form ids or other organic compounds. Only organisms-the cyanobacteria and many species of soil cteria that live symbiotica the roots of so plants-are capable of converting (fixing)atmos- Ammonia pheric nitrogen(N2) into ammonia. Other bacteria(the nitrifying bacteria) oxidize ammonia to nitrites and ni- trates; yet others convert nitrate to N2. Thus, in addi Animals tion to the global carbon and oxygen cycle, a nitrogen bacteria cycle operates in the biosphere, turning over huge amounts of nitrogen(Fig. 2). The cycling of carbon, oxy- gen,and nitrogen, which ultimately involves all species depends on a proper balance between the activities of Amino Nitrates the producers (autotrophs) and consumers(het erotrophs) in our biosphere These cycles of matter are driven by an enormous flow of energy into and through the biosphere, begin- Plants ning with the capture of solar energy by photosynthetic organisms and use of this energy to generate energy rich carbohydrates and other organic nutrients; these FIGURE 2 Cycling of nitrogen in the biosphere. Gaseous nitrogen nutrients are then used as energy sources by het- (N2) makes up 80% of the earths atmosphere erotrophic organisms. In metabolic processes, and in all energy transformations, there is a loss of useful energy (free energy) and an inevitable increase in the amount through the biosphere: organisms cannot regenerate of unusable energy(heat and entropy). In contrast useful energy from energy dissipated as heat and to the cycling of matter, therefore, energy flows one way entropy. Carbon, oxygen, and nitrogen recycle continu- ously, but energy is constantly transformed into unus. Metabolism, the sum of all the chemical transfo ations taking place in a cell or organism, occurs through a series of enzyme-catalyzed reactions that co stitute metabo lic pathways. Each of the consecutive steps in a metabolic pathway brings about a specific, small chemical change, usually the removal, transfer, ion of a particular atom or functional group precursor is converted into a product through a series of metabolic intermediates called metabolites. The term intermediary metabolism is often applied to the combined activities of all the metabolic pathways that interconvert precursors, metabolites, and products of Photosynthetic Heterotrophs low molecular weight(generally, M<1,000 autotrophs Catabolism is the degradative phase of metabolism in which organic nutrient molecules(carbohydrates fats, and proteins) are converted into smaller, simpler end products(such as lactic acid, CO2, NH3). Catabolic pathways release energy, of which is conserved in FIGURE 1 Cycling of carbon dioxide and oxygen between the auto. the formation of ATP and reduced electron carriers trophic (photosynthetic)and heterotrophic domains in the biosphere. (NADH, NADPH, and FADH2); the rest is lost as heat The flow of mass through this cycle is enormous about 4 x 10 In anabolism, also called biosynthesis, small, simple ric tons of carbon are tumed over in the biosphere annually. precursors are built up into larger and more co
solar energy as the driving force for this global process (Fig. 1). All living organisms also require a source of nitrogen, which is necessary for the synthesis of amino acids, nucleotides, and other compounds. Plants can generally use either ammonia or nitrate as their sole source of nitrogen, but vertebrates must obtain nitrogen in the form of amino acids or other organic compounds. Only a few organisms—the cyanobacteria and many species of soil bacteria that live symbiotically on the roots of some plants—are capable of converting (“fixing”) atmospheric nitrogen (N2) into ammonia. Other bacteria (the nitrifying bacteria) oxidize ammonia to nitrites and nitrates; yet others convert nitrate to N2. Thus, in addition to the global carbon and oxygen cycle, a nitrogen cycle operates in the biosphere, turning over huge amounts of nitrogen (Fig. 2). The cycling of carbon, oxygen, and nitrogen, which ultimately involves all species, depends on a proper balance between the activities of the producers (autotrophs) and consumers (heterotrophs) in our biosphere. These cycles of matter are driven by an enormous flow of energy into and through the biosphere, beginning with the capture of solar energy by photosynthetic organisms and use of this energy to generate energyrich carbohydrates and other organic nutrients; these nutrients are then used as energy sources by heterotrophic organisms. In metabolic processes, and in all energy transformations, there is a loss of useful energy (free energy) and an inevitable increase in the amount of unusable energy (heat and entropy). In contrast to the cycling of matter, therefore, energy flows one way through the biosphere; organisms cannot regenerate useful energy from energy dissipated as heat and entropy. Carbon, oxygen, and nitrogen recycle continuously, but energy is constantly transformed into unusable forms such as heat. Metabolism, the sum of all the chemical transformations taking place in a cell or organism, occurs through a series of enzyme-catalyzed reactions that constitute metabolic pathways. Each of the consecutive steps in a metabolic pathway brings about a specific, small chemical change, usually the removal, transfer, or addition of a particular atom or functional group. The precursor is converted into a product through a series of metabolic intermediates called metabolites. The term intermediary metabolism is often applied to the combined activities of all the metabolic pathways that interconvert precursors, metabolites, and products of low molecular weight (generally, Mr 1,000). Catabolism is the degradative phase of metabolism in which organic nutrient molecules (carbohydrates, fats, and proteins) are converted into smaller, simpler end products (such as lactic acid, CO2, NH3). Catabolic pathways release energy, some of which is conserved in the formation of ATP and reduced electron carriers (NADH, NADPH, and FADH2); the rest is lost as heat. In anabolism, also called biosynthesis, small, simple precursors are built up into larger and more complex 482 Part II Bioenergetics and Metabolism Heterotrophs O2 H2O Photosynthetic autotrophs Organic products CO2 FIGURE 1 Cycling of carbon dioxide and oxygen between the autotrophic (photosynthetic) and heterotrophic domains in the biosphere. The flow of mass through this cycle is enormous; about 4 1011 metric tons of carbon are turned over in the biosphere annually. Plants Nitrates, nitrites Nitrifying bacteria Denitrifying bacteria Animals Amino acids Ammonia Nitrogenfixing bacteria Atmospheric N2 FIGURE 2 Cycling of nitrogen in the biosphere. Gaseous nitrogen (N2) makes up 80% of the earth’s atmosphere.
Part l Bioenergetics and Metabolism molecules, including lipids, polysaccharides, proteins, simultaneous synthesis and degradation of fatty acids and nucleic acids. Anabolic reactions require an input would be wasteful, however, and this is prevented by of energy, generally in the form of the phosphoryl group reciprocally regulating the anabolic and catabolic reac. transfer potential of ATP and the reducing power of tion sequences: when one sequence is active, the other NADH, NADPH, and FADH2(Fig 3) is suppressed. Such regulation could not occur if ana- Some metabolic pathways are linear, and some are bolic and catabolic pathways were catalyzed by exactly branched, yielding multiple useful end products from a the same set of enzymes, operating in one direction for single precursor or converting several starting materi- anabolism, the opposite direction for catabolism: inhi- als into a single product. In general, catabolic pathways bition of an enzyme involved in catabolism would also are convergent and anabolic pathways divergent(Fig. inhibit the reaction sequence in the anabolic direction. 4). Some pathways are cyclic: one starting component Catabolic and anabolic pathways that connect the same of the pathway is regenerated in a series of reactions two end points (glucose - pyruvate and pyruvate that converts another starting component into a prod- >glucose, for example) may employ many of the uct. We shall see examples of each type of pathway in same enzymes, but invariably at least one of the steps the following chapters. is catalyzed by different enzymes in the catabolic and Most cells have the enzymes to carry out both the anabolic directions, and these enzymes are the sites of degradation and the synthesis of the important cate- separate regulation. Moreover, for both anabolic and gories of biomolecules-fatty acids, for example. The catabolic pathways to be essentially irreversible, the re- actions unique to each direction must include at least one that is thermodynamically very favorable-in other words, a reaction for which the reverse reaction is very Cell unfavorable. As a further contribution to the separate macromolecules nutrients regulation of catabolic and anabolic reaction sequences, paired catabolic and anabolic pathways commonly take place in different cellular compartments: for example, Nucleic acids Proteins fatty acid catabolism in mitochondria, fatty acid syn- thesis in the cytosol. The concentrations of intermedi ates, enzymes, and regulators can be maintained at different levels in these different compartments. Be- cause metabolic pathways are subject to kinetic con- ADP +hPo2- trol by substrate concentration, separate pools of anabolic and catabolic intermediates also contribute to the control of metabolic rates. Devices that separate processes will be of particular nterest in our discussions of metabolism Catabolism NADH Metabolic pathways are regulated at several levels. NADPH from within the cell and from outside the most imme- FADH diate regulation is by the availability of substrate; when is near or below Km (as is commonly the case), the rate Chemical of the reaction depends strongly upon substrate con- centration(see Fig. 6-11). A second type of rapid con- trol from within is allosteric regulation(p. 225) by metabolic intermediate or coenzyme-an amino acid or Precursor Energy ATP, for example-that signals the cells internal meta bolic state. When the cell contains an amount of, say end products aspartate sufficient for its immediate needs, or when the cellular level of atp indicates that further fuel con- Nitrogenous bases sumption is unnecessary at the moment, these signals allosterically inhibit the activity of one or more enzymes in the relevant pathway In multicellular organisms the 3 Energy relationships between catabolic and anabolic metabolic activities of different tissues are regulated and ays Catabolic pathways deliver chemical energy in the form integrated by growth factors and hormones that act from of ATP, NADH, NADPH, and FADH2. These energy carriers are used outside the cell. In some cases this regulation occurs in anabolic pathways to convert small precursor molecules into cell virtually instantaneously(sometimes in less than a mil lisecond)through changes in the levels of intracellular
molecules, including lipids, polysaccharides, proteins, and nucleic acids. Anabolic reactions require an input of energy, generally in the form of the phosphoryl group transfer potential of ATP and the reducing power of NADH, NADPH, and FADH2 (Fig. 3). Some metabolic pathways are linear, and some are branched, yielding multiple useful end products from a single precursor or converting several starting materials into a single product. In general, catabolic pathways are convergent and anabolic pathways divergent (Fig. 4). Some pathways are cyclic: one starting component of the pathway is regenerated in a series of reactions that converts another starting component into a product. We shall see examples of each type of pathway in the following chapters. Most cells have the enzymes to carry out both the degradation and the synthesis of the important categories of biomolecules—fatty acids, for example. The simultaneous synthesis and degradation of fatty acids would be wasteful, however, and this is prevented by reciprocally regulating the anabolic and catabolic reaction sequences: when one sequence is active, the other is suppressed. Such regulation could not occur if anabolic and catabolic pathways were catalyzed by exactly the same set of enzymes, operating in one direction for anabolism, the opposite direction for catabolism: inhibition of an enzyme involved in catabolism would also inhibit the reaction sequence in the anabolic direction. Catabolic and anabolic pathways that connect the same two end points (glucose n n pyruvate and pyruvate n n glucose, for example) may employ many of the same enzymes, but invariably at least one of the steps is catalyzed by different enzymes in the catabolic and anabolic directions, and these enzymes are the sites of separate regulation. Moreover, for both anabolic and catabolic pathways to be essentially irreversible, the reactions unique to each direction must include at least one that is thermodynamically very favorable—in other words, a reaction for which the reverse reaction is very unfavorable. As a further contribution to the separate regulation of catabolic and anabolic reaction sequences, paired catabolic and anabolic pathways commonly take place in different cellular compartments: for example, fatty acid catabolism in mitochondria, fatty acid synthesis in the cytosol. The concentrations of intermediates, enzymes, and regulators can be maintained at different levels in these different compartments. Because metabolic pathways are subject to kinetic control by substrate concentration, separate pools of anabolic and catabolic intermediates also contribute to the control of metabolic rates. Devices that separate anabolic and catabolic processes will be of particular interest in our discussions of metabolism. Metabolic pathways are regulated at several levels, from within the cell and from outside. The most immediate regulation is by the availability of substrate; when the intracellular concentration of an enzyme’s substrate is near or below Km (as is commonly the case), the rate of the reaction depends strongly upon substrate concentration (see Fig. 6–11). A second type of rapid control from within is allosteric regulation (p. 225) by a metabolic intermediate or coenzyme—an amino acid or ATP, for example—that signals the cell’s internal metabolic state. When the cell contains an amount of, say, aspartate sufficient for its immediate needs, or when the cellular level of ATP indicates that further fuel consumption is unnecessary at the moment, these signals allosterically inhibit the activity of one or more enzymes in the relevant pathway. In multicellular organisms the metabolic activities of different tissues are regulated and integrated by growth factors and hormones that act from outside the cell. In some cases this regulation occurs virtually instantaneously (sometimes in less than a millisecond) through changes in the levels of intracellular Part II Bioenergetics and Metabolism 483 Precursor molecules Amino acids Sugars Fatty acids Nitrogenous bases Energycontaining nutrients Carbohydrates Fats Proteins Anabolism ATP NADH NADPH FADH2 Catabolism Chemical energy ADP HPO2 NAD NADP FAD 4 Cell macromolecules Proteins Polysaccharides Lipids Nucleic acids Energydepleted end products CO2 H2O NH3 FIGURE 3 Energy relationships between catabolic and anabolic pathways. Catabolic pathways deliver chemical energy in the form of ATP, NADH, NADPH, and FADH2. These energy carriers are used in anabolic pathways to convert small precursor molecules into cell macromolecules.
84 Part l Bioenergetics and Metabolism Steroid pigments hormones Phospholipids pyrophosphate → Cholesterol bl. Mevalonate Vitamin K Alanine Phenyl- anine Acetoacetyl-CoAEicosanoids acrose Isoleucine Fatty acids Triacylglycerols a)Converging catabolism Citrate CDP-diacylglycerol>Phospholipid Oxaloacetate (b)Diverging anabolism CO2 (c)Cyclic pathway FIGURE 4 Three types of nonlinear metabolic pathways. (a)Con- the breakdown product of a variety of fuels(a), serves as the precur verging, catabolic; (b) diverging, anabolic; and (c)cyclic, in which sor for an array of products(b), and is consumed in the catabolic path one of the starting materials (oxaloacetate in this case) is regenerated way known as the citric acid cycle(c) and reenters the pathway. Acetate, a key metabolic intermediate, is messengers that modify the activity of existing enzyme Before reviewing the five main reaction classes of molecules by allosteric mechanisms or by covalent mod- biochemistry, lets consider two basic chemical princi- ification such as phosphorylation. In other cases, the ex- ples. First, a covalent bond consists of a shared pair of tracellular signal changes the cellular concentration of electrons, and the bond can be broken in two general an enzyme by altering the rate of its synthesis or degra- ways(Fig. 5). In homolytic cleavage, each atom leaves dation, so the effect is seen only after minutes or hours. the bond as a radical, carrying one of the two electrons The number of metabolic transformations taking (now unpaired)that held the bonded atoms together place in a typical cell I overwhelming to a be- In the more common, heterolytic cleavage, one atom re- ginning student. Most cells have the capacity to carry tains both bonding electrons. The species generated out thousands of specific, enzyme-catalyzed reactions: when C-C and C-H bonds are cleaved are illustrated for example, transformation of a simple nutrient such in Figure 5. Carbanions, carbocations, and hydride ions as glucose into amino acids, nucleotides, or lipids; ex- are highly unstable; this instability shapes the chemistry traction of energy from fuels by oxidation; or polymer- of these ions, as described further below. ization of monomeric subunits into macromolecules The second chemical principle of interest here is that Fortunately for the student of biochemistry, there are many biochemical reactions involve interactions between patterns within this multitude of reactions you do not nucleophiles(functional groups rich in electrons and need to learn all these reactions to comprehend the capable of donating them) and electrophiles(electron molecular logic of biochemistry. Most of the reactions deficient functional groups that seek electrons). Nucle in living cells fall into one of five general categories: ophiles combine with, and give up electrons to, elec (1)oxidation-reductions;(2) reactions that make or trophies. Common nucleophiles and electrophiles are break carbon-carbon bonds; (3)internal rearrangements, listed in Figure 6-21. Note that a carbon atom can act isomerizations, and eliminations;(4) group transfers; as either a nucleophile or an electrophile, depending on and(5) free radical reactions. Reactions within each which bonds and functional groups surround it. general category usually proceed by a limited set of We now consider the five main reaction classes you mechanisms and often employ characteristic cofactors. will encounter in upcoming chapters
messengers that modify the activity of existing enzyme molecules by allosteric mechanisms or by covalent modification such as phosphorylation. In other cases, the extracellular signal changes the cellular concentration of an enzyme by altering the rate of its synthesis or degradation, so the effect is seen only after minutes or hours. The number of metabolic transformations taking place in a typical cell can seem overwhelming to a beginning student. Most cells have the capacity to carry out thousands of specific, enzyme-catalyzed reactions: for example, transformation of a simple nutrient such as glucose into amino acids, nucleotides, or lipids; extraction of energy from fuels by oxidation; or polymerization of monomeric subunits into macromolecules. Fortunately for the student of biochemistry, there are patterns within this multitude of reactions; you do not need to learn all these reactions to comprehend the molecular logic of biochemistry. Most of the reactions in living cells fall into one of five general categories: (1) oxidation-reductions; (2) reactions that make or break carbon–carbon bonds; (3) internal rearrangements, isomerizations, and eliminations; (4) group transfers; and (5) free radical reactions. Reactions within each general category usually proceed by a limited set of mechanisms and often employ characteristic cofactors. Before reviewing the five main reaction classes of biochemistry, let’s consider two basic chemical principles. First, a covalent bond consists of a shared pair of electrons, and the bond can be broken in two general ways (Fig. 5). In homolytic cleavage, each atom leaves the bond as a radical, carrying one of the two electrons (now unpaired) that held the bonded atoms together. In the more common, heterolytic cleavage, one atom retains both bonding electrons. The species generated when COC and COH bonds are cleaved are illustrated in Figure 5. Carbanions, carbocations, and hydride ions are highly unstable; this instability shapes the chemistry of these ions, as described further below. The second chemical principle of interest here is that many biochemical reactions involve interactions between nucleophiles (functional groups rich in electrons and capable of donating them) and electrophiles (electrondeficient functional groups that seek electrons). Nucleophiles combine with, and give up electrons to, electrophiles. Common nucleophiles and electrophiles are listed in Figure 6–21. Note that a carbon atom can act as either a nucleophile or an electrophile, depending on which bonds and functional groups surround it. We now consider the five main reaction classes you will encounter in upcoming chapters. 484 Part II Bioenergetics and Metabolism Rubber Bile acids Steroid hormones (a) Converging catabolism Oxaloacetate (b) Diverging anabolism CO2 CO2 (c) Cyclic pathway Acetate (acetyl-CoA) Citrate Glycogen Glucose Pyruvate Phospholipids Alanine Fatty acids Leucine Phenylalanine Isoleucine Starch Sucrose Serine Eicosanoids Phospholipids Carotenoid pigments Vitamin K Triacylglycerols Cholesteryl esters Triacylglycerols Mevalonate Isopentenylpyrophosphate Fatty acids Acetoacetyl-CoA CDP-diacylglycerol Cholesterol FIGURE 4 Three types of nonlinear metabolic pathways. (a) Converging, catabolic; (b) diverging, anabolic; and (c) cyclic, in which one of the starting materials (oxaloacetate in this case) is regenerated and reenters the pathway. Acetate, a key metabolic intermediate, is the breakdown product of a variety of fuels (a), serves as the precursor for an array of products (b), and is consumed in the catabolic pathway known as the citric acid cycle (c)
Part Bioenergetics and Metabolism 485 Haneaytie-(H=C+H alyze these oxidations are generally called oxidases r,if the oxygen atom is derived directly from molecu Carbon h atom lar oxygen(02), oxygenases radical Every oxidation must be accompanied by a reduc tion, in which an electron acceptor acquires the electrons 一C-C--C+"C removed by oxidation. Oxidation reactions generally release energy(think of camp fires: the compounds in Carbon radicals wood are oxidized by oxygen molecules in the air). Most living cells obtain the energy needed for cellular work by oxidizing metabolic fuels such as carbohydrates or fat; photosynthetic organisms can also trap and use the en ergy of sunlight. The catabolic(energy-yielding) path- Carbanion Proton ways described in Chapters 14 through 19 are oxidative reaction sequences that result in the transfer of electrons from fuel molecules, through a series of electron carri- ers, to oxygen. The high affinity of O2 for electrons makes the overall electron-transfer process highly exergonic. Carbocation Hydride providing the energy that drives ATP synthesis-the central goal of catabolism. 2. Reactions that make or break carbon-carbon bonds het- Carbanion Carbocation erolytic cleavage of a C-C bond yields a carbanion and a carbocation(Fig. 5). Conversely, the formation of a FIGURE 5 Two mechanisms for cleavage of a C-C or C-H bond. C-C bond involves the combination of a nucleophilic In homolytic cleavages, each atom keeps one of the bonding elt carbanion and an electrophilic carbocation. Groups with trons, resulting in the formation of carbon radicals (carbons having electronegative atoms play key roles in these reactions unpaired electrons)or uncharged hydrogen atoms. In heterolytic cleav- Carbonyl groups are particularly important in the chem- ages, one of the atoms retains both bonding electrons. This can result ical transformations of metabolic pathways. As noted in the formation of carbanions, carbocations, protons, or hydride ions. above, the carbon of a carbonyl group has a partial pos- itive charge due to the electron-withdrawing nature of 1. Oxidation-reduction reactions Carbon atoms encoun- the adjacent bonded oxygen, and thus is an electrophilic tered in biochemistry can exist in five oxidation states, carbon. The presence of a carbonyl group depending on the elements with which carbon shares facilitate the formation of a carbanion on an adjoining electrons( Fig. 6). In many biological oxidations, a com- carbon, because the carbonyl group can delocalize elec- pound loses two electrons and two hydrogen ions(that trons through resonance(Fig. 8a, b). The importance is, two hydrogen atoms); these reactions are commonly of a carbonyl group is evident in three major classes of called dehydrogenations and the enzymes that catalyze reactions in which C-C bonds are formed or broken them are called dehydrogenases(Fig. 7). In some, but(Fig 8c): aldol condensations(such as the aldolase not all, biological oxidations, a carbon atom becomes co- reaction; see Fig. 14-5), Claisen condensations(as valently bonded to an oxygen atom. The enzymes that in the citrate synthase reaction; see Fig. 16-9), and 2H++2e- -CH2-CH Alkane -CH2-CH2OH Alcohol CH3-CH一C、 一cH3-C-C 2H++2e- dehyde(ketone) Lactate lactate An oxidation-reduction reaction shown here is the ox -CH2-C Carboxylic acid of lactate to pyruvate. In this dehydrogenation, two electrons and two hydrogen ions(the equivalent of two hydrogen atoms) are re- O=C=0 Carbon dioxide moved from C-2 of lactate, an alcohol, to form pyruvate, a ketone. In cells the reaction is catalyzed by lactate dehydrogenase and the elec FIGURE 6 The oxidation states of carbon in biomolecules. Each com. trons are transferred to a cofactor called nicotinamide adenine dinu. pound is formed by oxidation of the red carbon in the compound cleotide. This reaction is fully reversible: pyruvate can be reduced by isted above it. Carbon dioxide is the most highly oxidized form of electrons from the cofactor. In Chapter 13 we discuss the factors that carbon found in living systems determine the direction of a reaction
1. Oxidation-reduction reactions Carbon atoms encountered in biochemistry can exist in five oxidation states, depending on the elements with which carbon shares electrons (Fig. 6). In many biological oxidations, a compound loses two electrons and two hydrogen ions (that is, two hydrogen atoms); these reactions are commonly called dehydrogenations and the enzymes that catalyze them are called dehydrogenases (Fig. 7). In some, but not all, biological oxidations, a carbon atom becomes covalently bonded to an oxygen atom. The enzymes that catalyze these oxidations are generally called oxidases or, if the oxygen atom is derived directly from molecular oxygen (O2), oxygenases. Every oxidation must be accompanied by a reduction, in which an electron acceptor acquires the electrons removed by oxidation. Oxidation reactions generally release energy (think of camp fires: the compounds in wood are oxidized by oxygen molecules in the air). Most living cells obtain the energy needed for cellular work by oxidizing metabolic fuels such as carbohydrates or fat; photosynthetic organisms can also trap and use the energy of sunlight. The catabolic (energy-yielding) pathways described in Chapters 14 through 19 are oxidative reaction sequences that result in the transfer of electrons from fuel molecules, through a series of electron carriers, to oxygen. The high affinity of O2 for electrons makes the overall electron-transfer process highly exergonic, providing the energy that drives ATP synthesis—the central goal of catabolism. 2. Reactions that make or break carbon–carbon bonds Heterolytic cleavage of a COC bond yields a carbanion and a carbocation (Fig. 5). Conversely, the formation of a COC bond involves the combination of a nucleophilic carbanion and an electrophilic carbocation. Groups with electronegative atoms play key roles in these reactions. Carbonyl groups are particularly important in the chemical transformations of metabolic pathways. As noted above, the carbon of a carbonyl group has a partial positive charge due to the electron-withdrawing nature of the adjacent bonded oxygen, and thus is an electrophilic carbon. The presence of a carbonyl group can also facilitate the formation of a carbanion on an adjoining carbon, because the carbonyl group can delocalize electrons through resonance (Fig. 8a, b). The importance of a carbonyl group is evident in three major classes of reactions in which COC bonds are formed or broken (Fig 8c): aldol condensations (such as the aldolase reaction; see Fig. 14–5), Claisen condensations (as in the citrate synthase reaction; see Fig. 16–9), and Part II Bioenergetics and Metabolism 485 C C Carbon radicals C C C H Carbanion Proton Heterolytic C H cleavage C H Carbon radical C H Homolytic cleavage C H Carbocation Hydride C C C Carbanion Carbocation C C H atom H FIGURE 5 Two mechanisms for cleavage of a COC or COH bond. In homolytic cleavages, each atom keeps one of the bonding electrons, resulting in the formation of carbon radicals (carbons having unpaired electrons) or uncharged hydrogen atoms. In heterolytic cleavages, one of the atoms retains both bonding electrons. This can result in the formation of carbanions, carbocations, protons, or hydride ions. CH2 CH3 Alkane CH2 CH2 Alcohol Aldehyde (ketone) Carboxylic acid Carbon dioxide CH2OH O H(R) C CH2 O O O OH C C FIGURE 6 The oxidation states of carbon in biomolecules. Each compound is formed by oxidation of the red carbon in the compound listed above it. Carbon dioxide is the most highly oxidized form of carbon found in living systems. FIGURE 7 An oxidation-reduction reaction. Shown here is the oxidation of lactate to pyruvate. In this dehydrogenation, two electrons and two hydrogen ions (the equivalent of two hydrogen atoms) are removed from C-2 of lactate, an alcohol, to form pyruvate, a ketone. In cells the reaction is catalyzed by lactate dehydrogenase and the electrons are transferred to a cofactor called nicotinamide adenine dinucleotide. This reaction is fully reversible; pyruvate can be reduced by electrons from the cofactor. In Chapter 13 we discuss the factors that determine the direction of a reaction. CH3 Lactate Pyruvate lactate dehydrogenase CH CH3 OH C C C O O O 2H 2e 2H 2e O O
Part l Bioenergetics and Metabolism decarboxylations(as in the acetoacetate decarboxylase electrons results in isomerization, transposition of dou- eaction; see Fig 17-18). Entire metabolic pathways are ble bonds, or cis-trans rearrangements of double bonds organized around the introduction of a carbonyl group An example of isomerization is the formation of fruc in a particular location so that a nearby carbon-carbon tose 6-phosphate from glucose 6-phosphate during bond can be formed or cleaved. In some reactions, this sugar metabolism(Fig ga; this reaction is discussed in sle is played by an imine group or a specialized cofac. detail in Chapter 14). Carbon-l is reduced(from alde- tor such as pyridoxal phosphate, rather than by a car- hyde to alcohol) and C-2 is oxidized(from alcohol to bonyl group ketone). Figure 9b shows the details of the electron movements that result in isomerization 3. Internal rearrangements, isomerizations, and eliminations A simple transposition of a C=C bond occurs dur- Another common type of cellular reaction is an in- ing metabolism of the common fatty acid oleic acid(see tramolecular rearrangement, in which redistribution of Fig 17-9), and you will encounter some spectacular ex amples of double-bond repositioning in the synthesis of cholesterol(see Fig 21-35) Elimination of water introduces a c=c bond be. tween two carbons that previously were saturated (as in the enolase reaction; see Fig 6-23). Similar reactions can result in the elimination of alcohols and amines Po (b-C-C H OH o R2 Roh R2 4. Group transfer reactions The transfer of acyl, glycosyl, and phosphoryl groups from one nucleophile to another is common in living cells. Acyl group transfer generally involves the addition of a nucleophile to the carbonyl OH R1H O H RI carbon of an acyl group to form a tetrahedral interme- CoAS-C-C:→C=0 CoA-S Claisen ester condensation R-C-X 一R-C-C-H+co Y Tetrahedral Decarboxylation of a B-keto acid The chymotrypsin reaction is one example of acyl group transfer(see Fig. 6-21). Glycosyl group transfers in- 8 Carbon-carbon bond formation reactions. (a)The carbon volve nucleophilic substitution at C-1 of a sugar ring. carbonyl group is an electrophile by virtue of the electron- which is the central atom of an acetal. In principle, the awing capacity of the electronegative oxygen atom, which results substitution could proceed by an SNl or SN2 path, in a resonance hybrid structure in which the carbon has a partial pos- described for the enzyme lysozyme(see Fig. 6-25) itive charge.(b)Within a molecule, delocalization of electrons into a Phosphoryl group transfers play a special role in carbonyl group facilitates the transient formation of a carbanion on an metabolic pathways. A general theme in metabolism is adjacent carbon (c)Some of the major reactions involved in the for mation and breakage of C-c bonds in biological systems. For both the the attachment of a god Idol condensation and the claisen condensation a carbanion serves intermediate to "activate"the intermediate for subse- as nucleophile and the carbon of a carbonyl group serves as elec. quent reaction. Among the better leaving groups in rophile. The carbanion is stabilized in each case by another carbony nucleophilic substitution reactions are inorganic or at the carbon adjoining the carbanion carbon. In the decarboxylation thophosphate(the ionized form of H PO, at neutral pH, leaves. The reaction would not occur at an appreciable rate but for Pi) and inorganic pyrophosphate(P207, abbreviated the stabilizing effect of the carbonyl adjacent to the carbanion car. PP); esters and anhydrides of phosphoric acid are bon. Wherever a carbanion is shown, a stabilizing resonance with the effectively activated for reaction. Nucleophilic substi- adjacent carbonyl, as shown in(a), is assumed. The formation of the tution is made more favorable by the attachment of a carbanion is highly disfavored unless the stabilizing carbonyl group, phosphoryl group to an otherwise poor leaving group or a group of similar function such such as-OH. Nucleophilic substitutions in which th
decarboxylations (as in the acetoacetate decarboxylase reaction; see Fig. 17–18). Entire metabolic pathways are organized around the introduction of a carbonyl group in a particular location so that a nearby carbon–carbon bond can be formed or cleaved. In some reactions, this role is played by an imine group or a specialized cofactor such as pyridoxal phosphate, rather than by a carbonyl group. 3. Internal rearrangements, isomerizations, and eliminations Another common type of cellular reaction is an intramolecular rearrangement, in which redistribution of electrons results in isomerization, transposition of double bonds, or cis-trans rearrangements of double bonds. An example of isomerization is the formation of fructose 6-phosphate from glucose 6-phosphate during sugar metabolism (Fig 9a; this reaction is discussed in detail in Chapter 14). Carbon-1 is reduced (from aldehyde to alcohol) and C-2 is oxidized (from alcohol to ketone). Figure 9b shows the details of the electron movements that result in isomerization. A simple transposition of a CUC bond occurs during metabolism of the common fatty acid oleic acid (see Fig. 17–9), and you will encounter some spectacular examples of double-bond repositioning in the synthesis of cholesterol (see Fig. 21–35). Elimination of water introduces a CUC bond between two carbons that previously were saturated (as in the enolase reaction; see Fig. 6–23). Similar reactions can result in the elimination of alcohols and amines. 4. Group transfer reactions The transfer of acyl, glycosyl, and phosphoryl groups from one nucleophile to another is common in living cells. Acyl group transfer generally involves the addition of a nucleophile to the carbonyl carbon of an acyl group to form a tetrahedral intermediate. The chymotrypsin reaction is one example of acyl group transfer (see Fig. 6–21). Glycosyl group transfers involve nucleophilic substitution at C-1 of a sugar ring, which is the central atom of an acetal. In principle, the substitution could proceed by an SN1 or SN2 path, as described for the enzyme lysozyme (see Fig. 6–25). Phosphoryl group transfers play a special role in metabolic pathways. A general theme in metabolism is the attachment of a good leaving group to a metabolic intermediate to “activate” the intermediate for subsequent reaction. Among the better leaving groups in nucleophilic substitution reactions are inorganic orthophosphate (the ionized form of H3PO4 at neutral pH, a mixture of H2PO4 and HPO4 2, commonly abbreviated Pi ) and inorganic pyrophosphate (P2O7 4, abbreviated PPi ); esters and anhydrides of phosphoric acid are effectively activated for reaction. Nucleophilic substitution is made more favorable by the attachment of a phosphoryl group to an otherwise poor leaving group such as OOH. Nucleophilic substitutions in which the R C Tetrahedral intermediate O Y X R C O Y X R C O Y X R C C H H OH R1 H2O H H C H2O H R C R1 486 Part II Bioenergetics and Metabolism C C C C C (a) (b) (c) O O O R1 C Aldol condensation C O R2 H C R3 R4 O H R1 C C O R2 H C R3 R4 OH CoA-S C Claisen ester condensation C O H H C R1 R2 O H CoA-S C C O H H C R1 R2 OH R C Decarboxylation of a -keto acid C O H H C O O H R C C O H H H CO2 FIGURE 8 Carbon–carbon bond formation reactions. (a) The carbon atom of a carbonyl group is an electrophile by virtue of the electronwithdrawing capacity of the electronegative oxygen atom, which results in a resonance hybrid structure in which the carbon has a partial positive charge. (b) Within a molecule, delocalization of electrons into a carbonyl group facilitates the transient formation of a carbanion on an adjacent carbon. (c) Some of the major reactions involved in the formation and breakage of COC bonds in biological systems. For both the aldol condensation and the Claisen condensation, a carbanion serves as nucleophile and the carbon of a carbonyl group serves as electrophile. The carbanion is stabilized in each case by another carbonyl at the carbon adjoining the carbanion carbon. In the decarboxylation reaction, a carbanion is formed on the carbon shaded blue as the CO2 leaves. The reaction would not occur at an appreciable rate but for the stabilizing effect of the carbonyl adjacent to the carbanion carbon. Wherever a carbanion is shown, a stabilizing resonance with the adjacent carbonyl, as shown in (a), is assumed. The formation of the carbanion is highly disfavored unless the stabilizing carbonyl group, or a group of similar function such as an imine, is present.
Part l Bioenergetics and Metabolism H OHH HH OHH H-C-2C--C-C-C-C-0-P-o H--C-C-C-C-C-C-0-P- O H OHOHH OH O H OHoHH O Glucose 6-pho Fructose 6-phosphate H H② This allows t a c-hbo formation of a C=C o by B B, abstracts a proton, allawi H the hydrogen ion aC=O bond. donated by b FIGURE 9 Isomerization and elimination reactions.(a) The conver- rows represent the movement of bonding electrons from nucleophile sion of glucose 6-phosphate to fructose 6-phosphate, a reaction of(pink] to electrophile(blue). B, and B2 are basic groups on the sugar metabolism catalyzed by phosphohexose isomerase(b)This re. enzyme: they are capable of donating and accepting hydrogen ions action proceeds through an enediol intermediate. The curved blue ar.(protons)as the reaction progresses. phosphoryl group (P03")serves as a leaving group charge and can therefore act as an electrophile. Ina very occur in hundreds of metabolic reactions large number of metabolic reactions, a phosphoryl group Phosphorus can form five covalent bonds. The con-(P03)is transferred from atP to an alcohol(form- ventional representation of Pi( Fig. 10a), with three ing a phosphate ester)(Fig. 10c)or to a carboxylic acid P-O bonds and one P=0 bond, is not an accurate pic- (forming a mixed anhydride). When a nucleophile at ture.In P. four equivalent phosphorus-oxygen bonds tacks the electrophilic phosphorus atom in ATP, a rela share some double-bond character, and the anion has a tively stable pentacovalent structure is formed as a re tetrahedral structure( Fig. 10b). As oxygen is more elec- action intermediate (Fig. 10d). With departure of the tronegative than phosphorus, the sharing of electrons is leaving group (ADP), the transfer of a phosphoryl group unequal: the central phosphorus bears a partial positive complete. The large family of enzymes that catalyze o-P=0 O-P-0 Adenine HRiboseF0-P-0-P-0-P-0 HO-R ATP 0→P-0 O=P-0- Adenine H Ribose 0-P-0-P-0+-0-P-0-R Glucose 6-phosphate. Z---P--w Z=R-OH FIGURE 10 Altermative ways of showing the structure of inorganic all four phosphorus-oxygen bonds with some double-bond character; orthophosphate (a) In one(inadequate)representation, three oxygens the hybrid orbitals so represented are arranged in a tetrahedron with are single- bonded to phosphorus, and the fourth is double -bonded, P at its center. (c)When a nucleophile Z (in this case, the-OH on allowing the four different resonance structures shown. (b)The four C-o of glucose)attacks ATP, it displaces ADP (W). In this SN2 reac. resonance structures can be represented more accurately by showing tion, a pentacovalent intermediate(d) forms transiently
phosphoryl group (OPO3 2) serves as a leaving group occur in hundreds of metabolic reactions. Phosphorus can form five covalent bonds. The conventional representation of Pi (Fig. 10a), with three POO bonds and one PUO bond, is not an accurate picture. In Pi , four equivalent phosphorus–oxygen bonds share some double-bond character, and the anion has a tetrahedral structure (Fig. 10b). As oxygen is more electronegative than phosphorus, the sharing of electrons is unequal: the central phosphorus bears a partial positive charge and can therefore act as an electrophile. In a very large number of metabolic reactions, a phosphoryl group (OPO3 2) is transferred from ATP to an alcohol (forming a phosphate ester) (Fig. 10c) or to a carboxylic acid (forming a mixed anhydride). When a nucleophile attacks the electrophilic phosphorus atom in ATP, a relatively stable pentacovalent structure is formed as a reaction intermediate (Fig. 10d). With departure of the leaving group (ADP), the transfer of a phosphoryl group is complete. The large family of enzymes that catalyze Part II Bioenergetics and Metabolism 487 H 1 C 2 C B1 H O OH Glucose 6-phosphate B2 H C C H O OH C OH H C H OH C H OH C H H O P O O O H 1 C 2 C OH O Fructose 6-phosphate Enediol intermediate H C OH H C H OH C H OH C H H O P O O O (a) (b) phosphohexose isomerase 1 B1 abstracts a proton. 4 B2 abstracts a proton, allowing the formation of a C 2 This allows the formation of a C double bond. 3 Electrons from carbonyl form an 5 An electron leaves the C the hydrogen ion donated by B2. C C O bond. C bond to form a O H bond with C H bond with the proton donated by B1. B1 H H C H O O H C OH H C O B1 B2 B2 rows represent the movement of bonding electrons from nucleophile (pink) to electrophile (blue). B1 and B2 are basic groups on the enzyme; they are capable of donating and accepting hydrogen ions (protons) as the reaction progresses. FIGURE 9 Isomerization and elimination reactions. (a) The conversion of glucose 6-phosphate to fructose 6-phosphate, a reaction of sugar metabolism catalyzed by phosphohexose isomerase. (b) This reaction proceeds through an enediol intermediate. The curved blue arO P O O O O O O P O O O P O O O O O O P O O O 3 O P (a) (b) O P O O O O O O Z P W (d) (c) Adenine Ribose O O P O P O HO R O P O O O O O Glucose ATP Adenine Ribose O O P O O O P O O P R O O O O ADP Glucose 6-phosphate, a phosphate ester Z R OH W ADP FIGURE 10 Alternative ways of showing the structure of inorganic orthophosphate. (a) In one (inadequate) representation, three oxygens are single-bonded to phosphorus, and the fourth is double-bonded, allowing the four different resonance structures shown. (b) The four resonance structures can be represented more accurately by showing all four phosphorus–oxygen bonds with some double-bond character; the hybrid orbitals so represented are arranged in a tetrahedron with P at its center. (c) When a nucleophile Z (in this case, the OOH on C-6 of glucose) attacks ATP, it displaces ADP (W). In this SN2 reaction, a pentacovalent intermediate (d) forms transiently.
Part l Bioenergetics and Metabolism phosphoryl group transfers with ATP as donor are called chemiosmotic energy coupling, a universal mechanism kinases(Greek kinein. " to move"). Hexokinase, for ex- in which a transmembrane electrochemical potential ample, "moves"a phosphoryl group from ATP to glucose. produced either by substrate oxidation or by light ab- Phosphoryl groups are not the only activators of this sorption, drives the synthesis of ATP type. Thioalcohols(thiols), in which the oxygen atom Chapters 20 through 22 describe the major anabolic of an alcohol is replaced with a sulfur atom, are also pathways by which cells use the energy in atP to pro- good leaving groups. Thiols activate carboxylic acids by duce carbohydrates, lipids, amino acids, and nucleotides forming thioesters(thiol esters)with them. We will dis- from simpler precursors. In Chapter 23 we step back cuss a number of cases, including the reactions cat- from our detailed look at the metabolic pathways-as alyzed by the fatty acyl transferases in lipid synthesis they occur in all organisms, from Escherichia coli to (see Fig 21-2), in which nucleophilic substitution at the humans-and consider how they are regulated and in carbonyl carbon of a thioester results in transfer of the tegrated in mammals by hormonal mechanisms. acyl group to another moiety As we undertake our study of intermediary metab olism, a final word. Keep in mind that the myriad re- 5. Free radical reactions Once thought to be rare, the actions described in these pages take place in, and play homolytic cleavage of covalent bonds to generate free crucial roles in, living organisms. As you encounter each adicals has now been found in a range of biochemical reaction and each pathway ask, What does this chemi processes. Some examples are the reactions of methyl- cal transformation do for the organism? How does this malonyl-CoA mutase(see Box 17-2), ribonucleotide pathway interconnect with the other pathways operat- reductase(see Fig. 22-41), and DNa photolyase(see ing simultaneously in the same cell to produce the en Fig25-25) ergy and products required for cell maintenance and growth? How do the multilayered regulatory mecha- We begin Part II with a discussion of the basic en- nisms cooperate to balance metabolic and energy in- ergetic principles that govern all metabolism( Chapter puts and outputs, achieving the dynamic steady state 13). We then consider the major catabolic pathways by of life? Studied with this perspective, metabolism pro which cells obtain energy from the oxidation of various vides fascinating and revealing insights into life, with fuels( Chapters 14 through 19). Chapter 19 is the piv- countless applications in medicine, agriculture, and otal point of our discussion of metabolism; it concerns biotechnology
phosphoryl group transfers with ATP as donor are called kinases (Greek kinein, “to move”). Hexokinase, for example, “moves” a phosphoryl group from ATP to glucose. Phosphoryl groups are not the only activators of this type. Thioalcohols (thiols), in which the oxygen atom of an alcohol is replaced with a sulfur atom, are also good leaving groups. Thiols activate carboxylic acids by forming thioesters (thiol esters) with them. We will discuss a number of cases, including the reactions catalyzed by the fatty acyl transferases in lipid synthesis (see Fig. 21–2), in which nucleophilic substitution at the carbonyl carbon of a thioester results in transfer of the acyl group to another moiety. 5. Free radical reactions Once thought to be rare, the homolytic cleavage of covalent bonds to generate free radicals has now been found in a range of biochemical processes. Some examples are the reactions of methylmalonyl-CoA mutase (see Box 17–2), ribonucleotide reductase (see Fig. 22–41), and DNA photolyase (see Fig. 25–25). We begin Part II with a discussion of the basic energetic principles that govern all metabolism (Chapter 13). We then consider the major catabolic pathways by which cells obtain energy from the oxidation of various fuels (Chapters 14 through 19). Chapter 19 is the pivotal point of our discussion of metabolism; it concerns chemiosmotic energy coupling, a universal mechanism in which a transmembrane electrochemical potential, produced either by substrate oxidation or by light absorption, drives the synthesis of ATP. Chapters 20 through 22 describe the major anabolic pathways by which cells use the energy in ATP to produce carbohydrates, lipids, amino acids, and nucleotides from simpler precursors. In Chapter 23 we step back from our detailed look at the metabolic pathways—as they occur in all organisms, from Escherichia coli to humans—and consider how they are regulated and integrated in mammals by hormonal mechanisms. As we undertake our study of intermediary metabolism, a final word. Keep in mind that the myriad reactions described in these pages take place in, and play crucial roles in, living organisms. As you encounter each reaction and each pathway ask, What does this chemical transformation do for the organism? How does this pathway interconnect with the other pathways operating simultaneously in the same cell to produce the energy and products required for cell maintenance and growth? How do the multilayered regulatory mechanisms cooperate to balance metabolic and energy inputs and outputs, achieving the dynamic steady state of life? Studied with this perspective, metabolism provides fascinating and revealing insights into life, with countless applications in medicine, agriculture, and biotechnology. 488 Part II Bioenergetics and Metabolism
chapter PRINCIPLES OF BIOENERGETICS 13.1 Bioenergetics and Thermodynamics 490 heat and that this process of 13.2 Phosphoryl Group Transfers and AIP 496 respiration is essential to life He observed that 13.3 Biological Oxidation-Reduction Reactions 507 in general, respiration The total energy of the universe is constant; the total bustion of carbon and hy entropy is continually increasing drogen, which is entirely -Rudolf Clausius, The Mechanical Theory of Heat with Its similar to that which oc- m-Engine and to the Physic urs in a lighted lamp or Properties of Bodies, 1865(trans. 1867) candle, and that, from this int of view. animals that respire are true com- 1743-1794 The isomorphism of entropy and information establishes a bustible bodies that burn link between the two forms of power: the power to do and and consume themselves.. One may say that this the power to direct what is done analogy between combustion and respiration has francois Jacob, La logique du vivant: une histoire de Iheredite not escaped the notice of the poets, or rather (The Logic of Life: A History of Heredity), 1970 philosophers of antiquity, and which they had heaven, this torch of Prometheus, does not only rep sent an ingenious and poetic idea, it is a faithful picture of the operations of nature, at least for an ness energy and to channel it into biological work is a imals that breathe: one may therefore say, with the fundamental property of all living organisms; it must ancients, that the torch of life lights itself at the mo- have been acquired very early in cellular evolution. Mod ment the infant breathes for the first time. and it ern organisms carry out a remarkable variety of energy does not extinguish itself except at death. transductions, conversions of one form of energy to an- In this century, biochemical studies have revealed other. They use the chemical energy in fuels to bring much of the chemistry underlying that"torch of life about the synthesis of complex, highly ordered macro- Biological energy transductions obey the same physical molecules from simple precursors. They also convert the laws that govern all other natural processes. It is there. chemical energy of fuels into concentration gradients fore essential for a student of biochemistry to under- and electrical gradients, into motion and heat, and, in a stand these laws and how they apply to the flow of few organisms such as fireflies and some deep-sea fish, energy in the biosphere. In this chapter we first review to light. Photosynthetic organisms transduce light en. the laws of thermodynamics and the quantitative rela- ergy into all these other forms of energy The chemical mechanisms that underlie biologica tionships among free energy, enthalpy, and entropy. We hen describe the special role of ATP in biologi energy transductions have fascinated and challenged Mlogists for centuries. Antoine Lavoisier, before he lost his head in the French Revolution, recognized that an- avoisier,a( 1862)Oeuvres de lavoisier, imals somehow transform chemical fuels(foods) into Imperiale,Paris
chapter Living cells and organisms must perform work to stay alive, to grow, and to reproduce. The ability to harness energy and to channel it into biological work is a fundamental property of all living organisms; it must have been acquired very early in cellular evolution. Modern organisms carry out a remarkable variety of energy transductions, conversions of one form of energy to another. They use the chemical energy in fuels to bring about the synthesis of complex, highly ordered macromolecules from simple precursors. They also convert the chemical energy of fuels into concentration gradients and electrical gradients, into motion and heat, and, in a few organisms such as fireflies and some deep-sea fish, into light. Photosynthetic organisms transduce light energy into all these other forms of energy. The chemical mechanisms that underlie biological energy transductions have fascinated and challenged biologists for centuries. Antoine Lavoisier, before he lost his head in the French Revolution, recognized that animals somehow transform chemical fuels (foods) into heat and that this process of respiration is essential to life. He observed that ... in general, respiration is nothing but a slow combustion of carbon and hydrogen, which is entirely similar to that which occurs in a lighted lamp or candle, and that, from this point of view, animals that respire are true combustible bodies that burn and consume themselves . . . One may say that this analogy between combustion and respiration has not escaped the notice of the poets, or rather the philosophers of antiquity, and which they had expounded and interpreted. This fire stolen from heaven, this torch of Prometheus, does not only represent an ingenious and poetic idea, it is a faithful picture of the operations of nature, at least for animals that breathe; one may therefore say, with the ancients, that the torch of life lights itself at the moment the infant breathes for the first time, and it does not extinguish itself except at death.* In this century, biochemical studies have revealed much of the chemistry underlying that “torch of life.” Biological energy transductions obey the same physical laws that govern all other natural processes. It is therefore essential for a student of biochemistry to understand these laws and how they apply to the flow of energy in the biosphere. In this chapter we first review the laws of thermodynamics and the quantitative relationships among free energy, enthalpy, and entropy. We then describe the special role of ATP in biological PRINCIPLES OF BIOENERGETICS 13.1 Bioenergetics and Thermodynamics 490 13.2 Phosphoryl Group Transfers and ATP 496 13.3 Biological Oxidation-Reduction Reactions 507 The total energy of the universe is constant; the total entropy is continually increasing. —Rudolf Clausius, The Mechanical Theory of Heat with Its Applications to the Steam-Engine and to the Physical Properties of Bodies, 1865 (trans. 1867) The isomorphism of entropy and information establishes a link between the two forms of power: the power to do and the power to direct what is done. —François Jacob, La logique du vivant: une histoire de l’hérédité (The Logic of Life: A History of Heredity), 1970 13 489 *From a memoir by Armand Seguin and Antoine Lavoisier, dated 1789, quoted in Lavoisier, A. (1862) Oeuvres de Lavoisier, Imprimerie Impériale, Paris. Antoine Lavoisier, 1743–1794
490 Chapter 13 Principles of Bioenergetics energy exchanges. Finally, we consider the importance not violate the second law, they operate strictly within of oxidation-reduction reactions in living cells, the en- it. To discuss the application of the second law to bio rgetics of electron-transfer reactions, and the electron logical systems, we must first define those systems and carriers commonly employed as cofactors of the en- their surroundings zymes that catalyze these reactions The reacting system is the collection of matter that is undergoing a particular chemical or physical process: it may be an organism, a cell, or two reacting com- 13.1 Bioenergetics and Thermodynamics pounds. The reacting system and its surroundings to- gether constitute the universe. In the laboratory, some Bioenergetics is the quantitative study of the energy chemical or physical processes can be carried out in iso transductions that occur in living cells and of the nature lated or closed systems, in which no material or energy and function of the chemical processes underlying these is exchanged with the surroundings. Living cells and or- modynamics have been introduced in earlier chapters material and energy with their surroundings: living sys- and the constant transactions between system and sur- Biological Energy Transformations Obey the Laws roundings explain how organisms can create order within themselves while operating within the second law of Thermodynamics of thermodynamics Many quantitative observations made by physicists and In Chapter 1(p. 23)we defined three thermody chemists on the interconversion of different forms of namic quantities that describe the energy changes oc energy led, in the nineteenth century. to the formula- curring in a chemical reaction tion of two fundamental laws of thermodynamics. The first law is the principle of the conservation of energy. Gibbs free energy, G, expresses the amount of for any physical or chemical change, the tota energy capable of doing work during a reaction amount of energy in the universe remains constant, at constant temperature and pressure. When a energy may change form or it may be transported reaction proceeds with the release of free energy from one region to another, but it cannot be created (that is, when the system changes so as to or destroyed. The second law of thermodynamics, which possess less free energy), the free-energy change, can be stated in several forms, says that the universe AG, has a negative value and the reaction is said always tends toward increasing disorder: in all natu- exergonIc endergonic reactions, the ral processes, the entropy of the universe increases. system gains free energy and AG is positive Living organisms consist of collections of molecules Enthalpy, H, is the heat content of the reacting much more highly organized than the surrounding ma system. It reflects the number and kinds of terials from which they are constructed, and organisms chemical bonds in the reactants and products. maintain and produce order, seemingly oblivious to the When a chemical reaction releases heat, it is second law of thermodynamics. But living organisms do said to be exothermic. the heat content of the products is less than that of the reactants an AHhas, by convention, a negative value. Reacting systems that take up heat from their surroundings are endothermic and have positive values of AH. Entropy, S, is a quantitative expression for the randomness or disorder in a system(see Box 1-3) When the products of a reaction are less complex and more disordered than the reactants the reaction is said to proceed with a gain in entropy. The units of AG and aH are joules/mole or calories/mole (recall that 1 cal= 4.184 J); units of entropy ar joules/mole. Kelvin(J/mol K)(Table 13-1) Under the conditions existing in biological systen (including constant temperature and pressure changes in free energy, enthalpy, and entropy are re- "Now, in the second law of thermodynamics lated to each other quantitatively by the equation △G=△H-TAS (13-1)
energy exchanges. Finally, we consider the importance of oxidation-reduction reactions in living cells, the energetics of electron-transfer reactions, and the electron carriers commonly employed as cofactors of the enzymes that catalyze these reactions. 13.1 Bioenergetics and Thermodynamics Bioenergetics is the quantitative study of the energy transductions that occur in living cells and of the nature and function of the chemical processes underlying these transductions. Although many of the principles of thermodynamics have been introduced in earlier chapters and may be familiar to you, a review of the quantitative aspects of these principles is useful here. Biological Energy Transformations Obey the Laws of Thermodynamics Many quantitative observations made by physicists and chemists on the interconversion of different forms of energy led, in the nineteenth century, to the formulation of two fundamental laws of thermodynamics. The first law is the principle of the conservation of energy: for any physical or chemical change, the total amount of energy in the universe remains constant; energy may change form or it may be transported from one region to another, but it cannot be created or destroyed. The second law of thermodynamics, which can be stated in several forms, says that the universe always tends toward increasing disorder: in all natural processes, the entropy of the universe increases. Living organisms consist of collections of molecules much more highly organized than the surrounding materials from which they are constructed, and organisms maintain and produce order, seemingly oblivious to the second law of thermodynamics. But living organisms do not violate the second law; they operate strictly within it. To discuss the application of the second law to biological systems, we must first define those systems and their surroundings. The reacting system is the collection of matter that is undergoing a particular chemical or physical process; it may be an organism, a cell, or two reacting compounds. The reacting system and its surroundings together constitute the universe. In the laboratory, some chemical or physical processes can be carried out in isolated or closed systems, in which no material or energy is exchanged with the surroundings. Living cells and organisms, however, are open systems, exchanging both material and energy with their surroundings; living systems are never at equilibrium with their surroundings, and the constant transactions between system and surroundings explain how organisms can create order within themselves while operating within the second law of thermodynamics. In Chapter 1 (p. 23) we defined three thermodynamic quantities that describe the energy changes occurring in a chemical reaction: Gibbs free energy, G, expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure. When a reaction proceeds with the release of free energy (that is, when the system changes so as to possess less free energy), the free-energy change, G, has a negative value and the reaction is said to be exergonic. In endergonic reactions, the system gains free energy and G is positive. Enthalpy, H, is the heat content of the reacting system. It reflects the number and kinds of chemical bonds in the reactants and products. When a chemical reaction releases heat, it is said to be exothermic; the heat content of the products is less than that of the reactants and H has, by convention, a negative value. Reacting systems that take up heat from their surroundings are endothermic and have positive values of H. Entropy, S, is a quantitative expression for the randomness or disorder in a system (see Box 1–3). When the products of a reaction are less complex and more disordered than the reactants, the reaction is said to proceed with a gain in entropy. The units of G and H are joules/mole or calories/mole (recall that 1 cal 4.184 J); units of entropy are joules/mole Kelvin (J/mol K) (Table 13–1). Under the conditions existing in biological systems (including constant temperature and pressure), changes in free energy, enthalpy, and entropy are related to each other quantitatively by the equation G H T S (13–1) 490 Chapter 13 Principles of Bioenergetics