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Lecture 10

BCH2011: Textbook summary - Lecture 10

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LECTURE 10 Most Enzymes Are Proteins: With the exception of a small group of catalytic RNA molecules, all enzymes are proteins. Their catalytic activity depends on the integrity of their native protein conformation. If an enzyme is denatured or dissociated into its subunits, catalytic activity is usually lost. If an enzyme is broken down into its component amino acids, its catalytic activity is always destroyed. Thus the primary, secondary, tertiary and quaternary structures of protein enzymes are essential to their catalytic activity. How Enzymes Work: The enzymatic catalysis of reactions is essential to living systems. Under biologically relevant conditions, uncatalysed reactions tend to be slow – most biological molecules are quite stable in the neutral pH, mild-temperature, aqueus environment inside cells. Many common chemical processes are unfavorable or unlikely in the cellular environment, such as the transient formation of unstable charged intermediates or the collision of two or more molecules in the precise orientation required for reaction. The distinguishing feature of an enzyme-catalysed reaction is that it takes place within the confines of a pocket on the enzyme called the active site. The molecule that is bound in the active site and acted upon by the enzyme is called the substrate. The surface of the active site is lined with amino acid residues with substituent groups that bind the substrate and catalyse its chemical transformation. Enzymes Affect Reaction Rates, Not Equilibria: A simple enzymatic reaction might be written: E + S  ES  EP  E + P Where E, S and P represent the enzyme, substrate and product; ES and EP are transient complexes of the enzyme with the substrate and with the product. The function of a catalyst is to increase the rate of a reaction. Catalysts do not affect reaction equilibria (A reaction is at equilibrium when there is no net change in the concentrations of reactants or products). Any reaction, such as S  P, can be described by a reaction coordinate diagram. Energy in biological systems is described in terms of free energy, G. In the coordinate diagram, the free energy of the system is plotted against the progress of the reaction (the reaction coordinate). The starting point for either the forward or the reverse reaction is called the ground state, the contribution to the free energy of the system by an average molecule (S or P) under a given set of conditions. The equilibrium between S and P reflects the difference in the free energies of their ground states. In the reaction coordinate diagram, the free energy of the ground state of P is lower than that of S, so the standard free energy change (ΔG’˚) for the reaction is negative (the reaction is exergonic) and at equilibrium there is more P than S (the equilibrium favors (P). The position and direction of equilibrium are not affected by any catalyst. Refer to lecture notes 9; ‘Enzymes increase reaction rate’ reaction coordinate graph. A favorable equilibrium does not mean that the S  P conversion will occur at a detectable rate. The rate of a reaction is dependent on an entirely different parameter. There is an energy barrier between S and P: the energy required for alignment of reacting groups, formation of transient unstable charges, bond rearrangements, and other transformations required for the reaction to proceed in either direction. To undergo this reaction, the molecules must overcome this barrier and therefore must be raised to a higher energy level. At the top of the energy hill is a point at which decay to the S or P state is equally probable. This is called the transition state. The transition state is not a chemical species with any significant stability and should not be confused with a reaction intermediate (such as ES or EP). It is simply a fleeting molecular movement in which events such as bond breakage, bond formation, and charge development have proceeded to the precise 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, . The rate of a reaction reflects this activation energy: a higher activation energy corresponds to a slower reaction. Reaction rates can be increased by raising temperature and/or pressure, thereby increasing the number of molecules with sufficient energy to overcome the energy barrier. Alternatively, the activation energy can be lowered by adding a catalyst. Catalysts enhance reaction rates by lowering activation energies. A Few Principles Explain the Catalytic Power and Specificity of Enzymes: Enzymes are extraordinary catalysts. They are also very specific, readily discriminating between substrates with quite similar structures. Chemical reactions of many types take place between substrates and enzymes’ functional groups (specific amino acid chains, metal ions, and coenzymes). Catalytic functional groups on an enzyme may form a transient covalent bond with a substrate and activate it for reaction, or a group may be transiently transferred from the substrate to the enzyme. In many cases, these reactions occur only in the enzyme active site. Covalent interactions between enzymes and substrates lower the activation energy (and thereby accelerate the reaction) by providing an alternative, lower-energy reaction path. Non-covalent interactions help stabilize protein structure and protein-protein interactions. These same interactions are critical to the formation of complexes between proteins and small molecules, including enzyme substrates. Much of the energy required to lower activation energies is derived from weak, non-covalent interactions between substrate and enzyme. What really sets enzymes apart from most other catalyst
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