Unit4 - Unit 4 1 UNIT 4 PART A: ENZYME MECHANISMS PART B:...

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Unit 4 1 U NIT 4 P ART A: E NZYME M ECHANISMS P ART B: P ROTEIN E VOLUTION P ART C: C ONTROL OF E NZYMATIC A CTIVITY NOTE: The unit 4 and 5 tests are combined! Please be sure to prepare both units before you try to tackle the quiz! P ART A: E NZYME M ECHANISMS Assignment: Nelson & Cox, pp. 196 - 202, 212 - 225. In Unit 3 we learned that enzymes form an ES complex when appropriate substrates make weak noncovalent interactions with amino acid side chains. This gives the complex its specificity. Once the ES complex has formed, weak noncovalent interactions are optimized to stabilize the transition state and allow the reaction to proceed. In this section we will learn how specific catalytic groups contribute to catalysis using three enzymes (chymotrypsin, hexokinase, and enolase) to illustrate the points.
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Unit 4 2 Objectives: 1. Binding energy contributes to reaction specificity and catalysis. a. Discuss the following forces that are involved in the binding of substrates to enzymes. For each, point out whether the interacting groups must be precisely aligned to get significant binding and whether the distance between interacting groups is critical for binding. 1) electrostatic interactions 2) hydrogen bonds (Fig. 2-5, p. 50) 3) van der Waals forces 4) hydrophobic interactions b. Discuss the importance of binding energy, Δ G B , in enzyme catalyzed reactions. c. Discuss each of the following in terms of binding energy (p. 199). 1) entropy reduction 2) desolvation 3) induced fit 2. Specific catalytic groups contribute to catalysis a. Use Fig. 6-10 (p. 202) to describe general acid-base catalysis. What is the general purpose of acid/base catalysis? Use Fig. 6-9 (p. 201) to identify the amino acid side chains that can function as acid-base catalysts. b. Use Fig. 6-10 (p. 202) to describe covalent catalysis. What is the purpose of covalent catalysis? c. Many enzymes require metal ions for activity. Describe two functions of these metal ions (p. 201).
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Unit 4 3 3. Enzyme activity is affected by pH a. List two reasons why enzyme activity is affected by pH (p. 212). b. In a folded protein, nearby amino acid side chains can influence the pK of a specific side chain. Discuss the effect of a positive microenvironment on the pK of aspartic acid. Will this positive microenvironment have the same affect on the pK of histidine? Discuss the effect of a negative microenvironment on each of these side chain types. (Note: The book does not give the answer to the above objective. The general idea, though, is that the presence of a positive charge decreases the local proton concentration and so other groups in the vicinity respond to a pH that is higher than the "bulk" value). 4.
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Unit4 - Unit 4 1 UNIT 4 PART A: ENZYME MECHANISMS PART B:...

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