chap. 6a enzymes introduction to enzymes how enzymes work enzyme kinetics as an approach to...
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Chap. 6A Enzymes Introduction to Enzymes How Enzymes Work Enzyme Kinetics as an Approach to Understanding Mechanism Examples of Enzymatic Reactions Regulatory EnzymesFig. 6-22. The chymotrypsin enzyme-substrate complex.
Intro. to EnzymesAll living organisms must be able to self-replicate and catalyze chemical reactions efficiently and selectively. Enzymes (from the Greek enzymos, leavened) are the chemical catalysts of biological systems. Enzymes have extraordinary catalytic power, often far greater than that of synthetic or inorganic catalysts. They have a high degree of specificity for their substrates and they accelerate chemical reactions tremendously. They function in aqueous solutions under very mild conditions of temperature and pH, unlike many catalysts used in organic chemistry. Enzymes are central to every biochemical process. They catalyze the hundreds of stepwise reactions of metabolism, conserve and transform chemical energy, and make biological macromolecules from simple precursors. In many diseases, the activity of one or more enzymes is abnormal. Many drugs act via binding to enzymes.
Chemical Features of Enzymes (I)With the exception of a small group of catalytically active RNA molecules (Chap. 26), all enzymes are proteins. Their catalytic activity depends on the integrity of their native protein conformation. Some enzymes require no chemical groups for activity other than their amino acid residues. Others require an additional chemical component called a cofactor. Cofactors can be inorganic ions (Table 6-1), or complex organic or metalloorganic molecules called coenzymes (Table 6-2, next slide).
Chemical Features of Enzymes (II)Coenzymes usually act as transient carriers of specific functional groups (Table 6-2). Most are derived from vitamins, which are organic nutrients that are required in small amounts in the diet. Some enzymes require both a coenzyme and one or more metal ions for activity. A coenzyme or metal ion that is very tightly or even covalently bound to an enzyme protein is called a prosthetic group. A complete, catalytically active enzyme together with its bound coenzyme and/or metal ion is called a holoenzyme. The protein part of such an enzyme is called the apoenzyme or apoprotein. Many enzymes are modified by phosphorylation or other processes. Modifications often are used to regulate enzyme activity.
Enzyme ClassificationMany enzymes have been named by adding the suffix -ase to the name of their substrate or to a word or phrase describing their activity. Biochemists by international agreement have adopted a system for naming and classifying enzymes based on the type of reaction catalyzed (Table 6-3). Each enzyme is assigned a four-part classification number and a systematic name, which identifies the reaction it catalyzes. For example the enzyme know commonly as hexokinase is formally ATP:glucose phosphotransferase. Its Enzyme Commission number is 18.104.22.168, in which the first number (2) denotes the class name (transferase); the second number (7), denotes the subclass (phosphotransferase); the third number (1), a phosphotransferase with a hydroxyl group as acceptor; and the fourth number (1), D-glucose as the phosphoryl group acceptor.
Enzyme Active SitesUnder biologically relevant conditions, uncatalyzed reactions tend to be slow because most biological molecules are quite stable in the neutral-pH, mild-temperature, aqueous environment inside cells. Enzymes greatly increase the rates of biological reactions by providing a specific environment within which a reaction can occur more rapidly. Enzyme-catalyzed reactions take place within the confines of a pocket on the enzyme called the active site. The reactant molecule is referred to as the substrate. The surface of the active site is lined with amino acid residues with substituent groups that bind to the substrate and catalyze its chemical transformation. Often, the active site encloses the substrate, sequestering it from solution. The active site of the enzyme chymotrypsin is highlighted in Fig. 6-1.
Enzymes Affect Rxn Rates, Not Equilibria (I)Any reaction, such as S P, can be described by a reaction coordinate diagram, in which the free energy change during the reaction is plotted as a function of the progress of the reaction (Fig. 6-2). The free energy change (G0) (and equilibrium position) of the reaction is determined by the difference in ground state free energies of S and P. The rate of the reaction is dependent on the height of the free energy barrier between S and P. At the top of this hump is the transition state. The transition state is not a chemical species with any significant stability, and should not be confused with a reaction intermediate. Rather it is a fleeting molecular moment in which events such as bond breakage, bond formation, and charge development have proceeded to the point at which decay to either substrate or product is equally likely. The difference between the energy levels of the ground state and the transition state is the activation energy, G. The rate of the reaction is inversely and exponentially proportional to the value of G.
Enzymes Affect Rxn Rates, Not Equilibria (II)Like other catalysts, enzymes enhance reaction rates by lowering activation energies (Fig. 6-3). They have no effect on the position of reaction equilibria. The example shown is for an enzyme which follows the simple enzymatic steps ofE + S ES EP E + P.(E-enzyme; S-substrate; P-product; ES-transient complex between the enzyme and substrate; EP-transient complex between the enzyme and product). In the presence of the enzyme, three peaks occur in the reaction coordinate diagram. Whichever peak is the highest signifies the rate-limiting step of the overall reaction. As discussed below, binding energy provided by the interaction of the enzyme with the transition state contributes strongly to lowering the activation energy of the reaction, and accelerating its rate.
Relationship Between Keq and G0To describe the free energy changes for reactions, chemists define a standard set of conditions (temperature 298K; partial pressure of each gas = 1 atm; concentration of each solute 1 M) and express the free energy change for a reacting system under these conditions as G0, the standard free energy change. Because biochemical systems commonly have H+ concentrations far below 1 M, biochemists define a biochemical standard free energy change, G0, the standard free energy change at pH 7.0.The equilibrium constant for a reaction (Keq) under standard biochemical conditions is mathematically linked to the standard free energy change for a reaction, G0, via the equationG0 = -2.303 RT log Keq.In this equation, R is the gas constant, 8.315 J/mol.K, and T is the absolute temperature, 298K (25C). The numerical values for G0 as a function of Keq are tabulated in Table 6-4. Note that a large negative value of G0 reflects a favorable equilibrium in which the ratio of products to reactants is much greater than 1/1.
Relationship Between G and Rxn RateThe rate of a chemical reaction is determined by the concentration of the reactant(s) and by a rate constant usually denoted by k. For the unimolecular reaction S P, the rate (or velocity) of the reaction, V--representing the amount of S that reacts per unit time--is expressed by a rate equation, V = k[S]. In this reaction, the rate depends only on the concentration of S. This is a first-order reaction. The factor k is a proportionality constant that reflects the probability of a reaction under a given set of conditions (pH, temperature, etc.). Here, k is a first-order rate constant and has the units of reciprocal time (s-1). If a reaction rate depends on the concentration of two different compounds, or if the reaction is between two molecules of the same compound, then the reaction is second-order and k is a second-order rate constant, with units of M-1s-1. The rate equation then becomes V = k[S1][S2]. From physical chemistry, it can be derived that the magnitude of a rate constant is inversely and exponentially related to the activation energy, G. Thus, a lower activation energy means a faster reaction rate.
Catalytic Power and Specificity of EnzymesEnzymes commonly bring about enhancements in reaction rates in the range of 5 to 17 orders of magnitude (Table 6-5). Enzymes are also very specific, readily discriminating between substrates with quite similar structures. The rate enhancements observed for enzymes come from two distinct but interwoven parts. First, catalytic functional groups on an enzyme react with a substrate and lower the activation energy barrier for the reactions by providing an alternative, lower-energy reaction path. Second, noncovalent binding interactions between the substrate and enzyme release a small amount of free energy with each interaction that helps lower the energy of the transition state. The energy derived from enzyme-substrate interaction is called the binding energy, GB.
Complementary Shapes of Enzymes and SubstratesThe active site of an enzyme has a surface contour that is complementary in shape to its substrate (and products). This is illustrated for the two substrates of the enzyme dihydrofolate reductase in Fig. 6-4. Structural complementarity is responsible for the high specificity of enzyme reactions. The idea that the enzyme and substrate are complementary to one another was first proposed by the organic chemist, Emil Fisher, in 1894. He stated that the two components fit together like a lock and key. This proposal has greatly influenced the development of biochemistry. However, it is slightly misleading in that precise complementarity between an enzyme and its substrate would be counterproductive to efficient catalysis. Later day biochemical researchers instead realized that th