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enzyme catalysis

enzyme catalysis - #$/01"2'34$450262...

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>"0 39.#";$2 Mechanisms used by enzymes to enhance reaction rates include: Electrostatic catalysis, Desolvation (one type of electrostatic catalysis), Preferential binding of the transition state, Induced Ft Proximity & orientation, General acid/base catalysis, Covalent (nucleophilic) catalysis, Metal ion catalysis The chemical mechanism of serine proteases like chymotrypsin illustrates: Proximity and orientation Transition state stabilization Covalent catalysis, involving a “catalytic triad” of Asp, His and Ser in the active site General acid-base catalysis Electrostatic catalysis Different types of methods can be used to characterize the mechanism (X- ray, mutagenesis, irreversible inhibitors …) Knowing enzyme mechanism is helpful to design drugs – example HIV protease
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Terminology: proteolysis, serine protease , general acid, general base, catalytic triad, tetrahedral intermediate, acyl-enzyme intermediate, nucleophile, oxyanion hole Discuss (briefy explain): General concepts in catalysis related to protein-ligand binding General catalytic mechanisms used by enzymes to increase the rates oF chemical reactions. What is the role oF ion in metal-ion catalysis ? Which type oF Functional group can act as a general-base, general acid, nucleophile Given an enzyme mechanism, be able to identiFy which residue most likely acts as a general acid, general base or covalent catalyst How can pH aFFect enzyme activity? Why ? What is the optimum pH oF an enzyme ? Given a graph showing enzyme activity as a Function oF pH – be able to interpret the data, i.e what is the optimum pH, what residues could be involved in catalysis (see lysozyme pH pro±le) Given a amino acid pKa and a pH, predict whether it is likely to act as acid or base catalyst How can mutations (micro-environment) aFFect enzyme activity ? Name enzymes that use metal ion catalysis, general acid-base catalysis, covalent catalysis, catalysis by approximation or combination oF those
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Explain why peptide bonds are kinetically stable in the absence of a catalyst, given that equilibrium lies far in the direction of hydrolysis. What type of methods can be used to characterize the mechanism of an enzyme ? Describe the main features of the chemical mechanism of hydrolysis of peptide bonds by chymotrypsin, including the following: What is the "job" of the catalyst (the protease), i.e., what group needs to be made more susceptible to nucleophilic attack? Describe substrate binding, including the role and chemical nature of the "speciFcity pocket" in chymotrypsin, and which peptide bond in the substrate (relative to the speciFcity group) will be cleaved.
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This note was uploaded on 05/06/2010 for the course BIOC 460 taught by Professor Ziegler during the Spring '07 term at Arizona.

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enzyme catalysis - #$/01"2'34$450262...

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