15 29 Sept 2010 - The first step is binding The second step...

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The first step is binding The second step is the chemical reaction – i.e. create the transition state Once bound in the proper orientation, side chains and cofactors are involved in catalysis Acid-base catalysis – addition or removal of protons Covalent catalysis – a covalent bond to the protein is part of the transition Metal ion catalysis – water activation and redox Active sites stabilize charge associated with transition
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Water is not a good source of protons for acid-base catalysis Weak acids (carboxyl groups) are good proton donors Weak bases (amines) are good proton acceptors Side chains of amino acids situated within the active site become the acid-base donor-acceptors Isolation from solvent modifies the pKa
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E + S ES E + P *1* k 1 k -1 k 2 With enzymes, several steps can have comparable rates therefore an accumulative rate limit occurs Combine these into one rate – product release is rate limiting in the general case Simplify the equilibrium – focus on the formation of ES E + S ES EP E + P Enzymes Kinetics
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Under most physiological conditions, [S] >> [E].
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