Bioenergetics and Biochemical Reaction Types PDF
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This document provides an overview of bioenergetics and biochemical reaction types. It reviews the laws of thermodynamics and their application to biological systems, focusing on chemical reactions in living cells. The text explores concepts like free energy, enthalpy, and entropy, and their roles in energy transformations.
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13 Bioenergetics and Biochemical Reaction Types 13.1 Bioenergetics and Thermodynamics 506 candle, and that, from this point of view, animals that respire are true combustible bodies that burn 13.2 Chemical Lo...
13 Bioenergetics and Biochemical Reaction Types 13.1 Bioenergetics and Thermodynamics 506 candle, and that, from this point of view, animals that respire are true combustible bodies that burn 13.2 Chemical Logic and Common Biochemical Reactions 511 and consume themselves.... One may say that this 13.3 Phosphoryl Group Transfers and ATP 517 analogy between combustion and respiration has not escaped the notice of the poets, or rather the 13.4 Biological Oxidation-Reduction Reactions 528 philosophers of antiquity, and which they had expounded and interpreted. This fire stolen from heaven, this torch of Prometheus, does not only L iving cells and organisms must perform work to stay alive, to grow, and to reproduce. The ability to har- represent an ingenious and poetic idea, it is a faith- ness energy and to channel it into biological work is ful picture of the operations of nature, at least for a fundamental property of all living organisms; it must animals that breathe; one may therefore say, with have been acquired very early in cellular evolution. the ancients, that the torch of life lights itself at the Modern organisms carry out a remarkable variety of moment the infant breathes for the first time, and it energy transductions, conversions of one form of energy does not extinguish itself except at death.* to another. They use the chemical energy in fuels to In the twentieth century, we began to understand bring about the synthesis of complex, highly ordered much of the chemistry underlying that “torch of life.” macromolecules from simple precursors. They also con- Biological energy transductions obey the same chemical vert the chemical energy of fuels into concentration and physical laws that govern all other natural processes. gradients and electrical gradients, into motion and heat, It is therefore essential for a student of biochemistry to and, in a few organisms such as fireflies and deep-sea understand these laws and how they apply to the flow fish, into light. Photosynthetic organisms transduce of energy in the biosphere. light energy into all these other forms of energy. In this chapter we first review the laws of thermody- The chemical mechanisms that underlie biological namics and the quantitative relationships among free energy transductions have fascinated and challenged energy, enthalpy, and entropy. We then review the com- biologists for centuries. The mon types of biochemical reactions that occur in living French chemist Antoine Lavo- cells, reactions that harness, store, transfer, and release isier recognized that animals the energy taken up by organisms from their surround- somehow transform chemical ings. Our focus then shifts to reactions that have special fuels (foods) into heat and roles in biological energy exchanges, particularly those that this process of respiration involving ATP. We finish by considering the importance of is essential to life. He observed oxidation-reduction reactions in living cells, the energet- that ics of biological electron transfers, and the electron carri-... in general, respiration is ers commonly employed as cofactors in these processes. nothing but a slow combustion of carbon and hydrogen, which *From a memoir by Armand Seguin and Antoine Lavoisier, dated Antoine Lavoisier, is entirely similar to that which 1789, quoted in Lavoisier, A. (1862) Oeuvres de Lavoisier, 1743–1794 occurs in a lighted lamp or Imprimerie Impériale, Paris. 505 506 Bioenergetics and Biochemical Reaction Types it may be an organism, a cell, or two reacting compounds. 13.1 Bioenergetics and Thermodynamics The reacting system and its surroundings together con- Bioenergetics is the quantitative study of energy stitute the universe. In the laboratory, some chemical or transductions—changes of one form of energy into physical processes can be carried out in isolated or another—that occur in living cells, and of the nature closed systems, in which no material or energy is and function of the chemical processes underlying these exchanged with the surroundings. Living cells and transductions. Although many of the principles of ther- organisms, however, are open systems, exchanging both modynamics have been introduced in earlier chapters material and energy with their surroundings; living sys- and may be familiar to you, a review of the quantitative tems are never at equilibrium with their surroundings, aspects of these principles is useful here. and the constant transactions between system and sur- roundings explain how organisms can create order Biological Energy Transformations Obey within themselves while operating within the second law of thermodynamics. the Laws of Thermodynamics In Chapter 1 (p. 23) we defined three thermody- Many quantitative observations made by physicists and namic quantities that describe the energy changes chemists on the interconversion of different forms of occurring in a chemical reaction: energy led, in the nineteenth century, to the formulation of two fundamental laws of thermodynamics. The first Gibbs free energy, G, expresses the amount of an law is the principle of the conservation of energy: for energy capable of doing work during a reaction at any physical or chemical change, the total amount of constant temperature and pressure. When a reac- energy in the universe remains constant; energy tion proceeds with the release of free energy (that may change form or it may be transported from one is, when the system changes so as to possess less region to another, but it cannot be created or free energy), the free-energy change, DG, has a destroyed. The second law of thermodynamics, which negative value and the reaction is said to be exer- can be stated in several forms, says that the universe gonic. In endergonic reactions, the system gains always tends toward increasing disorder: in all natural free energy and DG is positive. processes, the entropy of the universe increases. Enthalpy, H, is the heat content of the reacting system. It reflects the number and kinds of chemi- cal bonds in the reactants and products. When a chemical reaction releases heat, it is said to be exo- thermic; the heat content of the products is less than that of the reactants and DH has, by conven- tion, a negative value. Reacting systems that take up heat from their surroundings are endothermic and have positive values of DH. 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 reac- tion is said to proceed with a gain in entropy. The units of DG and DH are joules/mole or calories/mole (recall that 1 cal 5 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 Living organisms consist of collections of molecules in free energy, enthalpy, and entropy are related to each much more highly organized than the surrounding other quantitatively by the equation materials from which they are constructed, and organ- ¢G 5 ¢H 2 T ¢S (13–1) isms maintain and produce order, seemingly immune to the second law of thermodynamics. But living organisms in which DG is the change in Gibbs free energy of the do not violate the second law; they operate strictly reacting system, DH is the change in enthalpy of the sys- within it. To discuss the application of the second law to tem, T is the absolute temperature, and DS is the biological systems, we must first define those systems change in entropy of the system. By convention, DS has and their surroundings. a positive sign when entropy increases and DH, as noted The reacting system is the collection of matter that above, has a negative sign when heat is released by the is undergoing a particular chemical or physical process; system to its surroundings. Either of these conditions, 13.1 Bioenergetics and Thermodynamics 507 concentration of reactants and products, the rates of TABLE 13–1 Some Physical Constants and Units the forward and reverse reactions are exactly equal and Used in Thermodynamics no further net change occurs in the system. The con- Boltzmann constant, k 5 1.381 3 10223 J/K centrations of reactants and products at equilibrium Avogadro’s number, N 5 6.022 3 1023 mol21 define the equilibrium constant, Keq (p. 25). In the gen- Faraday constant, 5 96,480 J/V? mol eral reaction aA 1 bB ∆ cC 1 dD, where a, b, c, Gas constant, R 5 8.315 J/mol?K and d are the number of molecules of A, B, C, and D (5 1.987 cal/mol? K) participating, the equilibrium constant is given by Units of DG and DH are J/mol (or cal/mol) [C]c[D]d !eq 5 (13–2) Units of ¢S are J/mol? K (or cal/mol? K) [A]a[B]b 1 cal 5 4.184 J where [A], [B], [C], and [D] are the molar concentrations Units of absolute temperature, T, are Kelvin, K of the reaction components at the point of equilibrium. 25 8C 5 298 K When a reacting system is not at equilibrium, the At 25 8C, RT 5 2.478 kJ/mol tendency to move toward equilibrium represents a (5 0.592 kcal/mol) driving force, the magnitude of which can be expressed as the free-energy change for the reaction, DG. Under standard conditions (298 K 5 25 8C), when reactants and products are initially present at 1 M concentrations which are typical of energetically favorable processes, or, for gases, at partial pressures of 101.3 kilopascals tend to make DG negative. In fact, DG of a spontane- (kPa), or 1 atm, the force driving the system toward ously reacting system is always negative. equilibrium is defined as the standard free-energy The second law of thermodynamics states that the change, DG8. By this definition, the standard state for entropy of the universe increases during all chemical reactions that involve hydrogen ions is [H1] 5 1 M, or and physical processes, but it does not require that the pH 0. Most biochemical reactions, however, occur in entropy increase take place in the reacting system well-buffered aqueous solutions near pH 7; both the pH itself. The order produced within cells as they grow and and the concentration of water (55.5 M) are essentially divide is more than compensated for by the disorder constant. they create in their surroundings in the course of growth and division (see Box 1–3, case 2). In short, liv- KEY CONVENTION: For convenience of calculations, bio- ing organisms preserve their internal order by taking chemists define a standard state different from that from the surroundings free energy in the form of nutri- used in chemistry and physics: in the biochemical ents or sunlight, and returning to their surroundings an standard state, [H1] is 1027 M (pH 7) and [H2O] is 55.5 M. equal amount of energy as heat and entropy. For reactions that involve Mg21 (which include most of those with ATP as a reactant), [Mg21] in solution is com- Cells Require Sources of Free Energy monly taken to be constant at 1 mM. Cells are isothermal systems—they function at essentially constant temperature (and also function at constant pres- Physical constants based on this biochemical stan- sure). Heat flow is not a source of energy for cells, dard state are called standard transformed con- because heat can do work only as it passes to a zone or stants and are written with a prime (such as DG98 and object at a lower temperature. The energy that cells can K9eq) to distinguish them from the untransformed con- and must use is free energy, described by the Gibbs free- stants used by chemists and physicists. (Note that most energy function G, which allows prediction of the direc- other textbooks use the symbol DG89 rather than DG98. tion of chemical reactions, their exact equilibrium posi- Our use of DG98, recommended by an international com- tion, and the amount of work they can (in theory) perform mittee of chemists and biochemists, is intended to at constant temperature and pressure. Heterotrophic emphasize that the transformed free energy, DG9, is the cells acquire free energy from nutrient molecules, and criterion for equilibrium.) For simplicity, we will hereaf- photosynthetic cells acquire it from absorbed solar radia- ter refer to these transformed constants as standard tion. Both kinds of cells transform this free energy into free-energy changes. ATP and other energy-rich compounds capable of provid- ing energy for biological work at constant temperature. KEY CONVENTION: In another simplifying convention used by biochemists, when H2O, H1, and/or Mg21 are reac- tants or products, their concentrations are not included Standard Free-Energy Change Is Directly Related in equations such as Equation 13–2 but are instead to the Equilibrium Constant incorporated into the constants K¿eq and DG98. The composition of a reacting system (a mixture of chemical reactants and products) tends to continue Just as K¿eq is a physical constant characteristic for changing until equilibrium is reached. At the equilibrium each reaction, so too is DG98 a constant. As we noted in 508 Bioenergetics and Biochemical Reaction Types Chapter 6, there is a simple relationship between K¿eq and DG98: TABLE 13–3 Relationships among K9eq, DG98, and the Direction of Chemical Reactions ¢G¿8 5 2R! ln K¿eq (13–3) Starting with all The standard free-energy change of a chemical components at 1 M, reaction is simply an alternative mathematical way When K9eq is... DG98 is... the reaction... of expressing its equilibrium constant. Table 13–2 shows the relationship between DG98 and K¿eq. If the.1.0 negative proceeds forward equilibrium constant for a given chemical reaction is 1.0 zero is at equilibrium 1.0, the standard free-energy change of that reaction ,1.0 positive proceeds in reverse is 0.0 (the natural logarithm of 1.0 is zero). If K¿eq of a reaction is greater than 1.0, its DG98 is negative. If K¿eq is less than 1.0, DG98 is positive. Because the relation- ship between DG98 and K¿eq is exponential, relatively small changes in DG98 correspond to large changes WORKED EXAMPLE 13–1 Calculation of DG98 in K¿eq. Calculate the standard free-energy change of the reac- It may be helpful to think of the standard free- tion catalyzed by the enzyme phosphoglucomutase energy change in another way. ¢G¿8 is the difference Glucose 1-phosphate ∆ glucose 6-phosphate between the free-energy content of the products and the free-energy content of the reactants, under stan- given that, starting with 20 mM glucose 1-phosphate and dard conditions. When DG98 is negative, the products no glucose 6-phosphate, the final equilibrium mixture at contain less free energy than the reactants and the 25 8C and pH 7.0 contains 1.0 mM glucose 1-phosphate reaction will proceed spontaneously under standard and 19 mM glucose 6-phosphate. Does the reaction in conditions; all chemical reactions tend to go in the the direction of glucose 6-phosphate formation proceed direction that results in a decrease in the free energy of with a loss or a gain of free energy? the system. A positive value of DG98 means that the products of the reaction contain more free energy than Solution: First we calculate the equilibrium constant: the reactants, and this reaction will tend to go in the [glucose 6-phosphate 4 19 mM 5 19 [glucose 1-phosphate 4 reverse direction if we start with 1.0 M concentrations of K¿eq 5 5 1.0 mM all components (standard conditions). Table 13–3 sum- marizes these points. We can now calculate the standard free-energy change: ¢G¿8 5 2RT ln K¿eq 5 2(8.315 J/mol?K)(298 K)(ln 19) 5 27.3 kJ/mol TABLE 13–2 Relationship between Equilibrium Because the standard free-energy change is negative, Constants and Standard Free-Energy the conversion of glucose 1-phosphate to glucose Changes of Chemical Reactions 6-phosphate proceeds with a loss (release) of free energy. (For the reverse reaction, DG98 has the same magnitude DG98 but the opposite sign.) K9eq (kJ/mol) (kcal/mol)* 3 10 217.1 24.1 Table 13–4 gives the standard free-energy changes 102 211.4 22.7 for some representative chemical reactions. Note that 101 25.7 21.4 hydrolysis of simple esters, amides, peptides, and glyco- 1 0.0 0.0 sides, as well as rearrangements and eliminations, pro- 1021 5.7 1.4 ceed with relatively small standard free-energy changes, whereas hydrolysis of acid anhydrides is accompanied 1022 11.4 2.7 by relatively large decreases in standard free energy. 1023 17.1 4.1 The complete oxidation of organic compounds such as 1024 22.8 5.5 glucose or palmitate to CO2 and H2O, which in cells 1025 28.5 6.8 requires many steps, results in very large decreases in standard free energy. However, standard free-energy 1026 34.2 8.2 changes such as those in Table 13–4 indicate how much *Although joules and kilojoules are the standard units of energy and are used throughout free energy is available from a reaction under standard this text, biochemists and nutritionists sometimes express DG98 values in kilocalories per conditions. To describe the energy released under the mole. We have therefore included values in both kilojoules and kilocalories in this table and in Tables 13–4 and 13–6. To convert kilojoules to kilocalories, divide the number of conditions existing in cells, an expression for the actual kilojoules by 4.184. free-energy change is essential. 13.1 Bioenergetics and Thermodynamics 509 TABLE 13–4 Standard Free-Energy Changes of Some Chemical Reactions DG98 Reaction type (kJ/mol) (kcal/mol) Hydrolysis reactions Acid anhydrides Acetic anhydride 1 H2O 88n 2 acetate 291.1 221.8 ATP 1 H2O 88n ADP 1 Pi 230.5 27.3 ATP 1 H2O 88n AMP 1 PPi 245.6 210.9 PPi 1 H2O 88n 2Pi 219.2 24.6 UDP-glucose 1 H2O 88n UMP 1 glucose 1-phosphate 243.0 210.3 Esters Ethyl acetate 1 H2O 88n ethanol 1 acetate 219.6 24.7 Glucose 6-phosphate 1 H2O 88n glucose 1 Pi 213.8 23.3 Amides and peptides Glutamine 1 H2O 88n glutamate 1 NH 14 214.2 23.4 Glycylglycine 1 H2O 88n 2 glycine 29.2 22.2 Glycosides Maltose 1 H2O 88n 2 glucose 215.5 23.7 Lactose 1 H2O 88n glucose 1 galactose 215.9 23.8 Rearrangements Glucose 1-phosphate 88n glucose 6-phosphate 27.3 21.7 Fructose 6-phosphate 88n glucose 6-phosphate 21.7 20.4 Elimination of water Malate 88n fumarate 1 H2O 3.1 0.8 Oxidations with molecular oxygen Glucose 1 6O2 88n 6CO2 1 6H2O 22,840 2686 Palmitate 1 23O2 88n 16CO2 1 16H2O 29,770 22,338 Actual Free-Energy Changes Depend on Reactant will necessarily match the standard conditions as defined above. Moreover, the DG of any reaction proceeding and Product Concentrations spontaneously toward its equilibrium is always negative, We must be careful to distinguish between two different becomes less negative as the reaction proceeds, and is quantities: the actual free-energy change, DG, and the zero at the point of equilibrium, indicating that no more standard free-energy change, DG98. Each chemical reac- work can be done by the reaction. tion has a characteristic standard free-energy change, DG and DG98 for any reaction aA 1 bB ∆ cC 1 dD which may be positive, negative, or zero, depending on are related by the equation the equilibrium constant of the reaction. The standard free-energy change tells us in which direction and how [C]c[D]d far a given reaction must go to reach equilibrium when ¢G 5 ¢G¿8 1 RT ln (13–4) [A]a[B]b the initial concentration of each component is 1.0 M, the pH is 7.0, the temperature is 25 8C, and the pressure in which the terms in red are those actually prevailing is 101.3 kPa (1 atm). Thus DG98 is a constant: it has a in the system under observation. The concentration characteristic, unchanging value for a given reaction. terms in this equation express the effects commonly But the actual free-energy change, DG, is a function of called mass action, and the term [C]c[D]d/[A]a[B]b is called reactant and product concentrations and of the tem- the mass-action ratio, Q. Thus Equation 13–4 can be perature prevailing during the reaction, none of which expressed as DG 5 DG98 1 RT ln Q. As an example, let 510 Bioenergetics and Biochemical Reaction Types us suppose that the reaction A 1 B ∆ C 1 D is tak- supplying additional heat but by lowering the activation ing place under the standard conditions of temperature energy through use of an enzyme. An enzyme provides (25 8C) and pressure (101.3 kPa) but that the concen- an alternative reaction pathway with a lower activation trations of A, B, C, and D are not equal and none of the energy than the uncatalyzed reaction, so that at room components is present at the standard concentration of temperature a large fraction of the substrate molecules 1.0 M. To determine the actual free-energy change, DG, have enough thermal energy to overcome the activation under these nonstandard conditions of concentration barrier, and the reaction rate increases dramatically. as the reaction proceeds from left to right, we simply The free-energy change for a reaction is indepen- enter the actual concentrations of A, B, C, and D in dent of the pathway by which the reaction occurs; it Equation 13–4; the values of R, T, and DG98 are the depends only on the nature and concentration of the standard values. DG is negative and approaches zero as initial reactants and the final products. Enzymes can- the reaction proceeds, because the actual concentrations not, therefore, change equilibrium constants; but of A and B decrease and the concentrations of C and D they can and do increase the rate at which a reaction increase. Notice that when a reaction is at equilibrium— proceeds in the direction dictated by thermodynamics when there is no force driving the reaction in either (see Section 6.2). direction and ¢G is zero—Equation 13–4 reduces to [C]eq[D]eq 0 5 ¢G 5 ¢G¿8 1 RT ln Standard Free-Energy Changes Are Additive [A]eq[B]eq In the case of two sequential chemical reactions, or A ∆ B and B ∆ C, each reaction has its own equilibrium constant and each has its characteristic ¢G¿8 5 2RT ln K¿eq standard free-energy change, ¢G¿18 and ¢G¿28. As the which is the equation relating the standard free-energy two reactions are sequential, B cancels out to give the change and equilibrium constant (Eqn 13–3). overall reaction A ∆ C, which has its own equilibrium The criterion for spontaneity of a reaction is the constant and thus its own standard free-energy value of DG, not DG98. A reaction with a positive DG98 can change, ¢G¿8 total. The DG98 values of sequential chemi- go in the forward direction if DG is negative. This is pos- cal reactions are additive. For the overall reaction sible if the term RT ln ([products]/[reactants]) in Equa- A ∆ C, ¢G¿8 total is the sum of the individual standard tion 13–4 is negative and has a larger absolute value than free-energy changes, ¢G¿18 and ¢G¿28, of the two reac- DG98. For example, the immediate removal of the prod- tions: ¢G¿8 total 5 ¢G¿18 1 ¢G¿28. ucts of a reaction can keep the ratio [products]/[reactants] (1) A 88n B ¢G¿18 well below 1, such that the term RT ln ([products]/ (2) B 88n C ¢G¿28 [reactants]) has a large, negative value. DG98 and DG are expressions of the maximum amount of free energy that Sum: A 88n C ¢G¿18 1 ¢G¿8 2 a given reaction can theoretically deliver—an amount of This principle of bioenergetics explains how a thermo- energy that could be realized only if a perfectly efficient dynamically unfavorable (endergonic) reaction can be device were available to trap or harness it. Given that no driven in the forward direction by coupling it to a such device is possible (some energy is always lost to highly exergonic reaction through a common interme- entropy during any process), the amount of work done diate. For example, the synthesis of glucose 6-phos- by the reaction at constant temperature and pressure is phate is the first step in the utilization of glucose by always less than the theoretical amount. many organisms: Another important point is that some thermody- namically favorable reactions (that is, reactions for Glucose 1 Pi 88n glucose 6-phosphate 1 H2O which DG98 is large and negative) do not occur at mea- ¢G¿8 5 13.8 kJ/mol surable rates. For example, combustion of firewood to The positive value of DG98 predicts that under standard CO2 and H2O is very favorable thermodynamically, but conditions the reaction will tend not to proceed spon- firewood remains stable for years because the activation taneously in the direction written. Another cellular energy (see Figs 6–2 and 6–3) for the combustion reac- reaction, the hydrolysis of ATP to ADP and Pi, is very tion is higher than the energy available at room tem- exergonic: perature. If the necessary activation energy is provided (with a lighted match, for example), combustion will ATP 1 H2O 88n ADP 1 Pi!!¢G¿8 5 230.5 kJ/mol begin, converting the wood to the more stable products These two reactions share the common intermediates CO2 and H2O and releasing energy as heat and light. The Pi and H2O and may be expressed as sequential heat released by this exothermic reaction provides the reactions: activation energy for combustion of neighboring regions of the firewood; the process is self-perpetuating. (1) Glucose 1 Pi 88n glucose 6-phosphate 1 H2O In living cells, reactions that would be extremely (2) ATP 1 H2O 88n ADP 1 Pi slow if uncatalyzed are caused to proceed not by Sum: ATP 1 glucose 88n ADP 1 glucose 6-phosphate 13.2 Chemical Logic and Common Biochemical Reactions 511 The overall standard free-energy change is obtained by ! Bioenergetics is the quantitative study of energy adding the DG98 values for individual reactions: relationships and energy conversions in biological systems. Biological energy transformations obey ¢G¿8 5 13.8 kJ/mol 1 (230.5 kJ/mol) 5 216.7 kJ/mol the laws of thermodynamics. The overall reaction is exergonic. In this case, energy ! All chemical reactions are influenced by two stored in ATP is used to drive the synthesis of glucose forces: the tendency to achieve the most stable 6-phosphate, even though its formation from glucose bonding state (for which enthalpy, H, is a useful and inorganic phosphate (Pi) is endergonic. The path- expression) and the tendency to achieve the way of glucose 6-phosphate formation from glucose by highest degree of randomness, expressed as phosphoryl transfer from ATP is different from reac- entropy, S. The net driving force in a reaction is tions (1) and (2) above, but the net result is the same DG, the free-energy change, which represents the as the sum of the two reactions. In thermodynamic cal- net effect of these two factors: ¢G 5 ¢H 2 T ¢S. culations, all that matters is the state of the system at ! The standard transformed free-energy change, the beginning of the process and its state at the end; the ¢G¿8, is a physical constant that is characteristic route between the initial and final states is immaterial. for a given reaction and can be calculated from the We have said that DG98 is a way of expressing the equilibrium constant for the reaction: equilibrium constant for a reaction. For reaction (1) ¢G¿8 5 2RT ln K¿eq. above, ! The actual free-energy change, DG, is a [glucose 6-phosphate ] variable that depends on DG98 and on the ! e¿ q 1 5 5 3.9 3 1023 M21 [glucose ] [Pi ] concentrations of reactants and products: Notice that H2O is not included in this expression, as its DG 5 DG98 1 RT ln ([products]/[reactants]). concentration (55.5 M) is assumed to remain unchanged ! When DG is large and negative, the reaction tends by the reaction. The equilibrium constant for the hy- to go in the forward direction; when DG is large drolysis of ATP is and positive, the reaction tends to go in the reverse direction; and when DG 5 0, the system is [ADP] [Pi ] ! e¿ q 2 5 5 2.0 3 105 M at equilibrium. [ATP] ! The free-energy change for a reaction is The equilibrium constant for the two coupled reactions is independent of the pathway by which the reaction [glucose 6-phosphate ] [ADP] [Pi ] occurs. Free-energy changes are additive; the net ! e¿ q 3 5 chemical reaction that results from successive [glucose ] [Pi ] [ATP] reactions sharing a common intermediate has an 5 ( ! e¿ q1 ) (K¿eq2 ) 5 (3.9 3 1023 M21 ) (2.0 3 105 M ) overall free-energy change that is the sum of the 5 7.8 3 102 DG values for the individual reactions. This calculation illustrates an important point about equilibrium constants: although the DG98 values for two reactions that sum to a third, overall reaction are addi- 13.2 Chemical Logic and Common tive, the K¿eq for the overall reaction is the product of the individual K¿eq values for the two reactions. Equilib- Biochemical Reactions rium constants are multiplicative. By coupling ATP The biological energy transductions we are concerned hydrolysis to glucose 6-phosphate synthesis, the K¿eq for with in this book are chemical reactions. Cellular chem- formation of glucose 6-phosphate from glucose has istry does not encompass every kind of reaction learned been raised by a factor of about 2 3 105. in a typical organic chemistry course. Which reactions This common-intermediate strategy is employed by take place in biological systems and which do not is all living cells in the synthesis of metabolic intermediates determined by (1) their relevance to that particular and cellular components. Obviously, the strategy works metabolic system and (2) their rates. Both consider- only if compounds such as ATP are continuously avail- ations play major roles in shaping the metabolic path- able. In the following chapters we consider several of the ways we consider throughout the rest of the book. A most important cellular pathways for producing ATP. relevant reaction is one that makes use of an available substrate and converts it to a useful product. However, even a potentially relevant reaction may not occur. SUMMARY 13.1 Bioenergetics and Thermodynamics Some chemical transformations are too slow (have acti- ! Living cells constantly perform work. They require vation energies that are too high) to contribute to living energy for maintaining their highly organized systems even with the aid of powerful enzyme catalysts. structures, synthesizing cellular components, The reactions that do occur in cells represent a toolbox generating electric currents, and many other that evolution has used to construct metabolic pathways processes. that circumvent the “impossible” reactions. Learning to 512 Bioenergetics and Biochemical Reaction Types recognize the plausible reactions can be a great aid in Nucleophiles Electrophiles developing a command of biochemistry. :R Even so, the number of metabolic transformations O–: C taking place in a typical cell can seem overwhelming. Negatively charged Most cells have the capacity to carry out thousands of oxygen (as in an O specific, enzyme-catalyzed reactions: for example, unprotonated hydroxyl Carbon atom of a group or an ionized carbonyl group (the transformation of a simple nutrient such as glucose into more electronegative carboxylic acid) amino acids, nucleotides, or lipids; extraction of energy oxygen of the carbonyl from fuels by oxidation; and polymerization of mono- group pulls electrons S– : away from the carbon) meric subunits into macromolecules. Negatively charged To study these reactions, some organization is essen- sulfhydryl :R + tial. There are patterns within the chemistry of life; you do C N not need to learn every individual reaction to comprehend C–: H the molecular logic of biochemistry. Most of the reactions Carbanion Protonated imine group in living cells fall into one of five general categories: (activated for nucleophilic (1) reactions that make or break carbon–carbon bonds; : N attack at the carbon by protonation of the imine) (2) internal rearrangements, isomerizations, and elimina- Uncharged tions; (3) free-radical reactions; (4) group transfers; and amine group O– :R (5) oxidation-reductions. We discuss each of these in –O P O more detail below and refer to some examples of each O– type in later chapters. Note that the five reaction types HN N: Phosphorus of are not mutually exclusive; for example, an isomerization a phosphate group Imidazole reaction may involve a free-radical intermediate. :R Before proceeding, however, we should review two H O–: H+ basic chemical principles. First, a covalent bond con- Hydroxide ion Proton sists of a shared pair of electrons, and the bond can be broken in two general ways (Fig. 13–1). In homolytic FIGURE 13–2 Common nucleophiles and electrophiles in biochemical cleavage, each atom leaves the bond as a radical, reactions. Chemical reaction mechanisms, which trace the formation carrying one unpaired electron. In heterolytic cleavage, and breakage of covalent bonds, are communicated with dots and curved arrows, a convention known informally as “electron pushing.” A covalent bond consists of a shared pair of electrons. Nonbonded elec- Homolytic.. trons important to the reaction mechanism are designated by dots (:). C H C ! H cleavage Curved arrows ( ) represent the movement of electron pairs. For Carbon H atom movement of a single electron (as in a free radical reaction), a single- radical headed (fishhook-type) arrow is used ( ). Most reaction steps involve an unshared electron pair... C C C ! C which is more common, one atom retains both bonding Carbon radicals electrons. The species most often generated when COC and COH bonds are cleaved are illustrated in Figure Heterolytic 13–1. Carbanions, carbocations, and hydride ions are C H C :– ! H+ cleavage highly unstable; this instability shapes the chemistry of Carbanion Proton these ions, as we shall see. The second basic principle is that many biochemical reactions involve interactions between nucleophiles C H C+ ! H:– (functional groups rich in and capable of donating elec- trons) and electrophiles (electron-deficient functional Carbocation Hydride groups that seek electrons). Nucleophiles combine with and give up electrons to electrophiles. Common biological nucleophiles and electrophiles are shown in Figure 13–2. C C C :– ! +C Note that a carbon atom can act as either a nucleophile or an electrophile, depending on which bonds and func- Carbanion Carbocation tional groups surround it. FIGURE 13–1 Two mechanisms for cleavage of a COC or COH bond. In a homolytic cleavage, each atom keeps one of the bonding electrons, Reactions That Make or Break Carbon–Carbon Bonds Hetero- resulting in the formation of carbon radicals (carbons having unpaired lytic cleavage of a COC bond yields a carbanion and a electrons) or uncharged hydrogen atoms. In a heterolytic cleavage, one carbocation (Fig. 13–1). Conversely, the formation of a of the atoms retains both bonding electrons. This can result in the for- COC bond involves the combination of a nucleophilic mation of carbanions, carbocations, protons, or hydride ions. carbanion and an electrophilic carbocation. Carbanions 13.2 Chemical Logic and Common Biochemical Reactions 513 and carbocations are generally so unstable that their O R2 R3 O R2 R3 H! formation as reaction intermediates can be energetically R1 C C ! C O R1 C C C OH inaccessible even with enzyme catalysts. For the purpose H R4 H R4 of cellular biochemistry they are impossible reactions— Aldol condensation unless chemical assistance is provided in the form of functional groups containing electronegative atoms O H R1 O H R1 (O and N) that can alter the electronic structure of adja- H! HS — R2 cent carbon atoms so as to stabilize and facilitate the CoA-S C C ! C O CoA-S C C C O formation of carbanion and carbocation intermediates. H S — R2 H Carbonyl groups are particularly important in the Claisen ester condensation chemical transformations of metabolic pathways. The carbon of a carbonyl group has a partial positive O H O H O H! charge due to the electron-withdrawing property of the R C C C R C C H ! CO2 carbonyl oxygen, and thus is an electrophilic carbon O! (Fig. 13–3a). A carbonyl group can thus facilitate the H H formation of a carbanion on an adjoining carbon by delo- Decarboxylation of a b-keto acid calizing the carbanion’s negative charge (Fig. 13–3b). FIGURE 13–4 Some common reactions that form and break COC An imine group (see Fig. 1–16) can serve a similar func- bonds in biological systems. For both the aldol condensation and the tion (Fig. 13–3c). The capacity of carbonyl and imine Claisen condensation, a carbanion serves as nucleophile and the carbon groups to delocalize electrons can be further enhanced of a carbonyl group serves as electrophile. The carbanion is stabilized in by a general acid catalyst or by a metal ion such as Mg21 each case by another carbonyl at the adjoining carbon. In the decarbox- (Fig. 13–3d). ylation reaction, a carbanion is formed on the carbon shaded blue as the The importance of a carbonyl group is evident in CO2 leaves. The reaction would not occur at an appreciable rate without three major classes of reactions in which COC bonds the stabilizing effect of the carbonyl adjacent to the carbanion carbon. are formed or broken (Fig. 13–4): aldol condensations, Wherever a carbanion is shown, a stabilizing resonance with the adjacent Claisen ester condensations, and decarboxylations. In carbonyl, as shown in Figure 13–3b, is assumed. An imine (Fig. 13–3c) or each type of reaction, a carbanion intermediate is sta- other electron-withdrawing group (including certain enzymatic cofactors bilized by a carbonyl group, and in many cases another such as pyridoxal) can replace the carbonyl group in the stabilization of carbonyl provides the electrophile with which the carbanions. nucleophilic carbanion reacts. An aldol condensation is a common route to the citric acid cycle (see Fig. 16–9). Decarboxylation also formation of a COC bond; the aldolase reaction, which commonly involves the formation of a carbanion stabi- converts a six-carbon compound to two three-carbon lized by a carbonyl group; the acetoacetate decarboxyl- compounds in glycolysis, is an aldol condensation in ase reaction that occurs in the formation of ketone bodies reverse (see Fig. 14–6). In a Claisen condensation, during fatty acid catabolism provides an example (see the carbanion is stabilized by the carbonyl of an adjacent Fig. 17–19). Entire metabolic pathways are organized thioester; an example is the synthesis of citrate in the around the introduction of a carbonyl group in a particu- lar location so that a nearby carbon–carbon bond can be formed or cleaved. In some reactions, an imine or a spe- O!! O O! cialized cofactor such as pyridoxal phosphate plays the (a) C!! (b) C C! mn C C electron-withdrawing role of the carbonyl group. The carbocation intermediate occurring in some ! NH2 NH2 reactions that form or cleave COC bonds is generated by the elimination of a very good leaving group, such as pyro- (c) C C C! mn C C C phosphate (see Group Transfer Reactions below). An example is the prenyltransferase reaction (Fig. 13–5), an Me2! HA early step in the pathway of cholesterol biosynthesis. ø ø O O (d) C C Internal Rearrangements, Isomerizations, and Eliminations FIGURE 13–3 Chemical properties of carbonyl groups. (a) The carbon Another common type of cellular reaction is an intramo- atom of a carbonyl group is an electrophile by virtue of the electron- lecular rearrangement in which redistribution of electrons withdrawing capacity of the electronegative oxygen atom, which results in alterations of many different types without a results in a structure in which the carbon has a partial positive charge. change in the overall oxidation state of the molecule. For (b) Within a molecule, delocalization of electrons into a carbonyl group example, different groups in a molecule may undergo stabilizes a carbanion on an adjacent carbon, facilitating its formation. oxidation-reduction, with no net change in oxidation (c) Imines function much like carbonyl groups in facilitating electron state of the molecule; groups at a double bond may withdrawal. (d) Carbonyl groups do not always function alone; their undergo a cis-trans rearrangement; or the positions of capacity as electron sinks often is augmented by interaction with either double bonds may be transposed. An example of an isom- a metal ion (Me21, such as Mg21) or a general acid (HA). erization entailing oxidation-reduction is the formation of 514 Bioenergetics and Biochemical Reaction Types CH3 fructose 6-phosphate from glucose 6-phosphate in gly- O O H2 C C colysis (Fig. 13–6); this reaction is discussed in detail in J G G Chapter 14): C-1 is reduced (aldehyde to alcohol) and G ! O P O P O C CH3 ! ! H C-2 is oxidized (alcohol to ketone). Figure 13–6b shows O O the details of the electron movements in this type of Dimethylallyl pyrophosphate isomerization. A cis-trans rearrangement is illustrated by the prolyl cis-trans isomerase reaction in the folding of Isopentenyl PPi certain proteins (see Fig. 4–8). A simple transposition of pyrophosphate a CPC bond occurs during metabolism of oleic acid, a common fatty acid (see Fig. 17–10). Some spectacular CH3 examples of double-bond repositioning occur in the bio- CH3 ! H2 synthesis of cholesterol (see Fig. 21–33). C C J G G O O H2 An example of an elimination reaction that does not C G C C CH3 G affect overall oxidation state is the loss of water from an G J ! H O P O P O C G CH2 alcohol, resulting in the introduction of a CPC bond: G O! O! H H Isopentenyl pyrophosphate Dimethylallylic carbocation H H H2O R H R C C R1 C C H! H2O H R1 H OH O O Similar reactions can result from eliminations in amines. ! O P O P O Free-Radical Reactions Once thought to be rare, the homo- ! ! O O lytic cleavage of covalent bonds to generate free radicals Geranyl pyrophosphate has now been found in a wide range of biochemical FIGURE 13–5 Carbocations in carbon–carbon bond formation. In one of processes. These include: isomerizations that make use the early steps in cholesterol biosynthesis, the enzyme prenyltransferase of adenosylcobalamin (vitamin B12) or S-adenosyl- catalyzes condensation of isopentenyl pyrophosphate and dimethylallyl methionine, which are initiated with a 59-deoxyadenosyl pyrophosphate to form geranyl pyrophosphate (see Fig. 21–36). The radical (see the methylmalonyl-CoA mutase reaction in reaction is initiated by elimination of pyrophosphate from the dimethyl- Box 17–2); certain radical-initiated decarboxylation allyl pyrophosphate to generate a carbocation, stabilized by resonance reactions (Fig. 13–7); some reductase reactions, such as with the adjacent CPC bond. that catalyzed by ribonucleotide reductase (see Fig. 22–41); (a) H OH H H H O! H OH H H H O! H 1C 2 C C C C C O P O! H 1C 2 C C C C C O P O! phosphohexose O OH H OH OH H O isomerase OH O H OH OH H O Glucose 6-phosphate Fructose 6-phosphate (b) B1 : 1 B1 abstracts a B1 B1: proton. H 5 An electron pair is displaced H from the C C bond to form H 2 This allows the C C a C H bond with formation of a C C the proton donated C C C C double bond. by B1. O O OH O O OH H H 3 Electrons from 4 B2 abstracts a H carbonyl form an proton, allowing B2: H O H bond with the formation of B2 the hydrogen ion aC O bond. B2 donated by B2. Enediol intermediate FIGURE 13–6 Isomerization and elimination reactions. (a) The conver- follow the path of oxidation from left to right. B1 and B2 are ionizable sion of glucose 6-phosphate to fructose 6-phosphate, a reaction of groups on the enzyme; they are capable of donating and accepting pro- sugar metabolism catalyzed by phosphohexose isomerase. (b) This tons (acting as general acids or general bases) as the reaction proceeds. reaction proceeds through an enediol intermediate. Light red screens 13.2 Chemical Logic and Common Biochemical Reactions 515 ! ! OOC OOC X ! H e! H3C R !XH ! H3C R H3C R NH NH CO2 NH R R R Coproporphyrinogen III Coproporphyrinogenyl Protoporphyrinogen IX III radical FIGURE 13–7 A free radical–initiated decarboxylation reaction. The bio- decarboxylation via the free-radical mechanism shown here. The acceptor synthesis of heme (see Fig. 22–26) in Escherichia coli includes a decarbox- of the released electron is not known. For simplicity, only the relevant ylation step in which propionyl side chains on the coproporphyrinogen III portions of the large coproporphyrinogen III and protoporphyrinogen intermediate are converted to the vinyl side chains of protoporphyrinogen IX. molecules are shown; the entire structures are given in Figure 22–26. When the bacteria are grown anaerobically the enzyme oxygen-independent When E. coli are grown in the presence of oxygen, this reaction is an coproporphyrinogen III oxidase, also called HemN protein, promotes oxidative decarboxylation and is catalyzed by a different enzyme. and some rearrangement reactions, such as that cata- (a) lyzed by DNA photolyase (see Fig. 25–26). O! O !O P O !O P O! Group Transfer Reactions The transfer of acyl, glycosyl, and O! O! 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 car- O! O! bon of an acyl group to form a tetrahedral intermediate: !O P O! O P O! O O! O O! O (b) C R C X C 3! O O R X Y R Y :Y : X! O P O Tetrahedral O P intermediate O O O The chymotrypsin reaction is one example of acyl group transfer (see Fig. 6–22). Glycosyl group transfers (c) O O O involve nucleophilic substitution at C-1 of a sugar ring, Adenine Ribose O P O P O P O! HO R which is the central atom of an acetal. In principle, the ! ! ! Glucose O O O substitution could proceed by an SN1 or SN2 pathway, as ATP described in Figure 6–28 for the enzyme lysozyme. Phosphoryl group transfers play a special role in O O O metabolic pathways, and these transfer reactions are ! ! Adenine Ribose O P O P O ! O P O R discussed in detail in Section 13.3. A general theme in metabolism is the attachment of a good leaving group to ! ! ! O O O a metabolic intermediate to “activate” the intermediate ADP Glucose 6-phosphate, a phosphate ester for subsequent reaction. Among the better leaving (d) groups in nucleophilic substitution reactions are inor- O O ganic orthophosphate (the ionized form of H3PO4 at 22 Z P W Z!R OH neutral pH, a mixture of H2PO2 4 and HPO4 , commonly W ! ADP abbreviated Pi) and inorganic pyrophosphate (P2O42 7 , O abbreviated PPi); esters and anhydrides of phosphoric FIGURE 13–8 Phosphoryl group transfers: some of the participants. acid are effectively activated for reaction. Nucleophilic (a) In one (inadequate) representation of Pi, three oxygens are single- substitution is made more favorable by the attachment bonded to phosphorus, and the fourth is double-bonded, allowing the of a phosphoryl group to an otherwise poor leaving four different resonance structures shown here. (b) The resonance group such as OOH. Nucleophilic substitutions in structures of Pi can be represented more accurately by showing all four which the phosphoryl group (OPO22 3 ) serves as a leav- phosphorus–oxygen bonds with some double-bond character; the hybrid ing group occur in hundreds of metabolic reactions. orbitals so represented are arranged in a tetrahedron with P at its center. Phosphorus can form five covalent bonds. The (c) When a nucleophile Z (in this case, the OOH on C-6 of glucose) conventional representation of Pi (Fig. 13–8a), with attacks ATP, it displaces ADP (W). In this SN2 reaction, a pentacovalent three POO bonds and one PPO bond, is a convenient intermediate (d) forms transiently. 516 Bioenergetics and Biochemical Reaction Types but inaccurate picture. In Pi, four equivalent phospho- OH 2H! ! 2e! O O O rus–oxygen bonds share some double-bond character, CH3 CH C CH3 C C and the anion has a tetrahedral structure (Fig. 13–8b). O! O! Because oxygen is more electronegative than phos- 2H! ! 2e! phorus, the sharing of electrons is unequal: the cen- Lactate lactate Pyruvate dehydrogenase tral phosphorus bears a partial positive charge and can therefore act as an electrophile. In a great many FIGURE 13–10 An oxidation-reduction reaction. Shown here is the oxi- metabolic reactions, a phosphoryl group (OPO22 3 ) is dation of lactate to pyruvate. In this dehydrogenation, two electrons and transferred from ATP to an alcohol, forming a phos- two hydrogen ions (the equivalent of two hydrogen atoms) are removed phate ester (Fig. 13–8c), or to a carboxylic acid, form- from C-2 of lactate, an alcohol, to form pyruvate, a ketone. In cells the ing a mixed anhydride. When a nucleophile attacks reaction is catalyzed by lactate dehydrogenase and the electrons are the electrophilic phosphorus atom in ATP, a relatively transferred to the cofactor nicotinamide adenine dinucleotide (NAD). stable pentacovalent structure forms as a reaction This reaction is fully reversible; pyruvate can be reduced by electrons intermediate (Fig. 13–8d). With departure of the leav- transferred from the cofactor. ing group (ADP), the transfer of a phosphoryl group is complete. The large family of enzymes that catalyze phosphoryl group transfers with ATP as donor are called kinases (Greek kinein, “to move”). Hexoki- compound loses two electrons and two hydrogen nase, for example, “moves” a phosphoryl group from ions (that is, two hydrogen atoms); these reactions ATP to glucose. are commonly called dehydrogenations and the Phosphoryl groups are not the only groups that enzymes that catalyze them are called dehydrogenases activate molecules for reaction. Thioalcohols (thiols), (Fig. 13–10). In some, but not all, biological oxida- in which the oxygen atom of an alcohol is replaced tions, a carbon atom becomes covalently bonded to an with a sulfur atom, are also good leaving groups. Thi- oxygen atom. The enzymes that catalyze these oxida- ols activate carboxylic acids by forming thioesters tions are generally called oxidases or, if the oxygen (thiol esters). In later chapters we discuss several atom is derived directly from molecular oxygen (O2) reactions, including those catalyzed by the fatty acyl oxygenases. synthases in lipid synthesis (see Fig. 21–2), in which Every oxidation must be accompanied by a reduc- nucleophilic substitution at the carbonyl carbon of a tion, in which an electron acceptor acquires the elec- thioester results in transfer of the acyl group to another trons removed by oxidation. Oxidation reactions gener- moiety. ally release energy (think of camp fires: the compounds in wood are oxidized by oxygen molecules in the air). Oxidation-Reduction Reactions Carbon atoms can exist in Most living cells obtain the energy needed for cellular five oxidation states, depending on the elements with work by oxidizing metabolic fuels such as carbohydrates which they share electrons (Fig. 13–9), and transi- or fat (photosynthetic organisms can also trap and use tions between these states are of crucial importance in the energy of sunlight). The catabolic (energy-yielding) metabolism (oxidation-reduction reactions are the pathways described in Chapters 14 through 19 are oxi- topic of Section 13.4). In many biological oxidations, a dative 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 exer- gonic, providing the energy that drives ATP synthesis— the central goal of catabolism. CH2 CH3 Alkane Many of the reactions within these five classes are CH2 CH2OH Alcohol facilitated by cofactors, in the form of coenzymes and O metals (vitamin B12, S-adenosylmethionine, folate, nico- CH2 C Aldehyde (ketone) tinamide, and iron are some examples). Cofactors bind H(R) to enzymes—in some cases reversibly, in other cases almost irreversibly—and confer on them the capacity to O promote a particular kind of chemistry (p. 190). Most CH2 C Carboxylic acid OH cofactors participate in a narrow range of closely related reactions. In the following chapters, we will introduce O C O Carbon dioxide and discuss each important cofactor at the point where FIGURE 13–9 The oxidation levels of carbon in biomolecules. Each we first encounter it. The cofactors provide another way compound is formed by oxidation of the red carbon in the compound to organize the study of biochemical processes, since shown immediately above. Carbon dioxide is the most highly oxidized the reactions facilitated by a given cofactor generally form of carbon found in living systems. are mechanistically related. 13.3 Phosphoryl Group Transfers and ATP 517 Biochemical and Chemical Equations Are Not Identical intermediates are common and are stabilized by adjacent carbonyl groups or, less often, by imines Biochemists write metabolic equations in a simplified or certain cofactors. way, and this is particularly evident for reactions involving ATP. Phosphorylated compounds can exist in ! A redistribution of electrons can produce several ionization states and, as we have noted, the dif- internal rearrangements, isomerizations, and ferent species can bind Mg21. For example, at pH 7 and eliminations. Such reactions include 2 mM Mg21, ATP exists in the forms ATP42 , HATP32 , intramolecular oxidation-reduction, change in H2ATP22 , MgHATP2, and Mg2ATP. In thinking about cis-trans arrangement at a double bond, and the biological role of ATP, however, we are not always transposition of double bonds. interested in all this detail, and so we consider ATP as an ! Homolytic cleavage of covalent bonds to generate entity made up of a sum of species, and we write its free radicals occurs in some pathways, such as in hydrolysis as the biochemical equation certain isomerization, decarboxylation, reductase, and rearrangement reactions. ATP 1 H2O 88n ADP 1 Pi ! Phosphoryl transfer reactions are an especially where ATP, ADP, and Pi are sums of species. The cor- important type of group transfer in cells, required responding standard transformed equilibrium constant, for the activation of molecules for reactions that K¿eq 5 [ADP4 [Pi 4/[ATP4, depends on the pH and the would otherwise be highly unfavorable. concentration of free Mg21. Note that H1 and Mg21 do ! Oxidation-reduction reactions involve the loss not appear in the biochemical equation because they or gain of electrons: one reactant gains are held constant. Thus a biochemical equation does not electrons and is reduced, while the other loses necessarily balance H, Mg, or charge, although it does electrons and is oxidized. Oxidation reactions balance all other elements involved in the reaction generally release energy and are important in (C, N, O, and P in the equation above). catabolism. We can write a chemical equation that does balance for all elements and for charge. For example, when ATP is hydrolyzed at a pH above 8.5 in the absence of Mg21, the chemical reaction is represented by 13.3 Phosphoryl Group Transfers and ATP 42 32 ATP 1 H2O 88n ADP 1 HPO22 4 1H 1 Having developed some fundamental principles of energy changes in chemical systems and reviewed the The corresponding equilibrium constant, K¿eq 5 [ADP32 ] common classes of reactions, we can now examine [HPO224 ][H ]/[ATP 1 42 ], depends only on temperature, the energy cycle in cells and the special role of ATP pressure, and ionic strength. as the energy currency that links catabolism and Both ways of writing a metabolic reaction have anabolism (see Fig. 1–29). Heterotrophic cells obtain value in biochemistry. Chemical equations are needed free energy in a chemical form by the catabolism of when we want to account for all atoms and charges in nutrient molecules, and they use that energy to make a reaction, as when we are considering the mechanism ATP from ADP and Pi. ATP then donates some of its of a chemical reaction. Biochemical equations are chemical energy to endergonic processes such as the used to determine in which direction a reaction will synthesis of metabolic intermediates and macromol- proceed spontaneously, given a specified pH and ecules from smaller precursors, the transport of sub- [Mg21], or to calculate the equilibrium constant of stances across membranes against concentration such a reaction. gradients, and mechanical motion. This donation of Throughout this book we use biochemical equa- energy from ATP generally involves the covalent par- tions, unless the focus is on chemical mechanism, and ticipation of ATP in the reaction that is to be driven, we use values of DG98 and K¿eq as determined at pH 7 with the eventual result that ATP is converted to and 1 mM Mg21. ADP and Pi or, in some reactions, to AMP and 2 Pi. We discuss here the chemical basis for the large free- energy changes that accompany hydrolysis of ATP SUMMARY 13.2 Chemical Logic and Common and other high-energy phosphate compounds, and we show that most cases of energy donation by ATP Biochemical Reactions involve group transfer, not simple hydrolysis of ATP. ! Living systems make use of a large number of To illustrate the range of energy transductions in chemical reactions that can be classified into five which ATP provides the energy, we consider the syn- general types. thesis of information-rich macromolecules, the trans- ! Carbonyl groups play a special role in reactions port of solutes across membranes, and motion produced that form or cleave COC bonds. Carbanion by muscle contraction. 518 Bioenergetics and Biochemical Reaction Types O O O FIGURE 13–11 Chemical basis for the large free-energy change associ- B B B " ated with ATP hydrolysis. 1 The charge separation that results from OO PO O OP OO OP OO O Rib O Adenine A A A hydrolysis relieves electrostatic repulsion among the four negative H O O" O" O" ATP4! charges on ATP. 2 The product inorganic phosphate (Pi) is stabilized by H formation of a resonance hybrid, in which each of the four phosphorus– oxygen bonds has the same degree of double-bond character and the O 1 hydrogen ion is not permanently associated with any one of the oxygens. hydrolysis, B (Some degree of resonance stabilization also occurs in phosphates " with relief O OP OOH of charge involved in ester or anhydride linkages, but fewer resonance forms are A repulsion Pi O" possible than for Pi.) A third factor (not shown) that favors ATP hydroly- sis is the greater degree of solvation (hydration) of the products Pi and resonance 2 stabilization ADP relative to ATP, which further stabilizes the products relative to the reactants. $" 3" O A $ "OOP OO $ " H# A O $" O O B B HO OP OO OP OO O Rib O Adenine terminal phosphoric acid anhydride (phosphoanhy- A A dride) bond in ATP separates one of the three nega- O" O" ADP2!