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Lecture 11

BCH2011: Textbook summary - Lecture 11

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LECTURE 11 Specific Catalytic Groups Contribute to Catalysis: In most enzymes, the binding energy used to form the ES complex is just one of the several contributors to the overall catalytic mechanism. Once a substrate is bound to an enzyme, properly positioned catalytic functional groups aid in the cleavage and formation of bonds by a variety of mechanisms, including general acid-base catalysis, covalent catalysis, and metal ion catalysis. These are distinct from mechanisms based on binding energy, because they generally involve transient covalent interaction with a substrate or group transfer to or from a substrate. General Acid-Base Catalysis: A proton transfer is the single most common reaction in biochemistry. One or, often, many proton transfers occur in the course of most reactions that take place in cells. Many biochemical reactions involve the formation of unsatable charged intermediates that tend to break down rapidly to their constituent reactant species, thus impeding the reaction. Charged intermediates can often be stabilized by the transfer of protons to or from the substrate or intermediate to form a species that breaks down more readily to products. Catalysis of the type that uses only the H+ (H3O+) or OH- ions present in water is referred to as specific acid-base catalysis. If protons are transferred between the intermediate and water faster than the intermediate breaks down to reactants, the intermediate is effectively stabilized every time it forms. No additional catalysis mediated by other proton acceptors or donors will occur. In many cases, however, water is not enough. The term general acid-base catalysis refers to proton transfers mediated by weak acids and bases other than water. For non- enzymatic reactions in aqueous solutions, added weak acids and bases provide an observed rate acceleration only when the unstable reaction intermediate breaks down to reactants faster than protons can be transferred to or from water alone. In the active site of an enzyme, where water may not be available as a proton donor or acceptor, general acid-base catalysis becomes crucial. A number of amino acid side chains can and do take on the role of proton donors and acceptors. Metal Ion Catalysis: Metals, whether tightly bound to the enzyme or taken up from solution along with the substrate, can participate in catalysis in several ways. Ionic interactions between an enzyme-bound metal and a substrate can help orient
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