lecture9_9_30_08 - Chapter 9 Stryer Lecture 9 Catalytic...

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Lecture 9 Chapter 9: Stryer Overview: Catalytic strategies & mechanisms : • serine proteases • carbonic anhydrase • restriction enzymes • NMP kinases Catalytic strategies What are the sources of catalytic power and specificity? What are the roles of the protein side chains? From Ch. 8: binding energy – the free energy released in the formation of a large number of weak interactions between the enzyme and its substrate . It serves two purposes: 1) establish substrate specificity, 2) increase catalytic efficiency. Interactions between the enzyme and substrate in its transition state are most important. Why? Lower the activation energy. Induced fit – changes in the enzyme and substrate to facilitate catalysis. What are the types of strategies that enzymes use? • covalent catalysis • general acid-base catalysis • catalysis by approximation • metal-ion catalysis Acid-base catalysis General acid catalysis - a process in which partial or complete proton transfer from a Brønsted acid lowers the free energy of a reactions transition state. General base catalysis - a process in which partial or complete proton abstraction by a Brønsted acid lowers the free energy of a reactions transition state. Compare this mechanism with an acid-catalyzed cleavage. Covalent catalysis Covalent catalysis - rate acceleration achieved through the transient formation of a covalent enzyme-substrate complex Good side chains for covalent catalysis must combine high nucleophilicity and the ability to act as a good leaving group Groups that are known to act in covalent catalysis -His, Cys, Asp, Glu, Ser and Lys -also some cofactors (pyridoxal phosphate, thiamine pyrophosphate, biotin, etc.) Example - Serine Proteases - acyl-enzyme intermediate
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Metal-ion catalysis Nearly 1/3 of all enzymes require a metal ion cofactor for activity!! Common roles of metal-ion cofactors: • Bind and orient substrates Mediate oxidation-reduction reactions (1 or 2 e - depending on ion) Stabilize anionic intermediates (charge shielding) Activate water to make it a better nucleophile His Zn His His O H H -H + His Zn His His O - H substrate 2+ 2+ Catalysis by approximation Many reactions include two distinct substrates. In these cases, the reaction rate may be considerably enhanced by bringing the two substrate together along a single binding surface on an enzyme.
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