7.05 Spring 2004 March 12, Recitation #4

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1 7.05 Spring 2004 March 12, 2004 Recitation #4 ontact Information TA: Victor Sai Recitation: Friday, 34pm, ffice ours: Friday, 45pm, 2132 Unit 2 Schedule Recitation/Exam Date Lectures covered Recitation #4 Friday, March 12 10, 11 Recitation #5 Friday, March 19 12, 13, 14 Recitation #6 Tuesday, March 30, 5pm, , 16, 17, 18 Exam 2 Review Wednesday, March 31, 7pm, Exam 2 Friday, April 2, 9:3011am, Walker 1018 Recitation verview Topic Problems 1. Enzyme hemistry 1, 2, [6] 2. Enzyme atalysis 3, 4, 5 Problems 1. (2001 Exam 4 Question 2, 15 points) What would you predict would be the effect on the enzymatic activity of hymotrypsin if you were to modify the αamino group of Ile16 to form a carbamate? 2. (2002 Exam 2 Question 6, 20 points) Suppose that compound X binds at the active site of trypsin. 3 + ( 2 ) 4 2 P 2 ompound X (a) (15 pts) What three features of compound X do you expect to contribute to the affinity of this compound with the enzyme active site? Explain your rationale for choosing these features. Recitation 4 Page 1 of 4

2 7.05 Spring 2004 March 12, 2004 (b) onsider compound X bound to the active site of a mutant form of trypsin that lacks the serine residue of the. ompared to the k uncat of compound X hydrolysis, would you expect the rate constant for hydrolysis of compound X bound to the mutant enzyme to be enhanced, decreased, or remain about the same? Explain. 3. (a) Why are transition state analogs such good inhibitors? (b) What kind of inhibitor do you think transition state analogs are? Why? (c) Draw a reaction coordinate for both E + S ES E + P and E + I EI where I stands for the transition state analog. 4. Why is tight binding of an enzyme to its substrate not desirable for enzyme catalysis? Explain with a diagram. Recitation 4 Page 2 of 4

3 7.05 Spring 2004 March 12, (2002 Exam 2 Question 2, 20 points) The breakdown of ethanol in the liver is catalyzed by the enzyme alcohol dehydrogenase to form acetaldehyde, and the acetaldehyde is then broken down by acetaldehyde dehydrogenase into acetate in the simplified reaction shown below: Ethanol Acetaldehyde Acetate 3 2 alcohol dehydrogenase 3 acetaldehyde dehydrogenase 3 Accumulation of acetaldehyde leads to facial flushing and sensations of discomfort. Some people have the A form of acetaldehyde dehydrogenase and others have the B form, which is 100 times slower than the A form. (c) (10 pts) Draw a diagram of the reaction coordinate for the uncatalyzed reaction, and for the reaction catalyzed by the A form and for the B form of the enzyme. (d) (10 pts) If the activation energy for the uncatalyzed breakdown of acetaldehyde into acetate, G act, is 14 kcal/mol, and the reaction catalyzed by the A form proceeds 10 6 times more rapidly at 25º, what are the G act for the reaction catalyzed by the A form and by the B form? Recitation 4 Page 3 of 4

4 7.05 Spring 2004 March 12, 2004 Practice Problem 6. (2001 Exam 4 Question 3, 20 points) (a) onsider the hydrolysis of the dipeptide PheAla by αchymotrypsin. Draw plausible structures for the two transition states in the hydrolysis of the acylenzyme intermediate. (for the enzyme, you only need to draw the serine and histidine side chains). (b) What two features of the αchymotrypsin active site, other than the, help decrease the activation free energy of the transition states shown in (a)? Recitation 4 Page 4 of 4

5 hymotrypsin Mechanism of atalysis Victor Sai 7.05 Spring 2004 verall Energy Diagram TS #1 TS #2 TS #3 TS #4 Energy Substrate Tetrahedral Intermediate 1 Tetrahedral Intermediate 2 Acyl Intermediate + Product 1 Product 2 Reaction oordinate The Ser195, is57, Asp102 atalytic Triad of hymotrypsin + 3 ::::::: Ile 16 salt bridge is Asp Asp Substrate Specificity: only cleaves after Phe, Tyr, and Trp (aromatic residues) 2. Posttranslational Modifications: a. Precursor chymotrypsinogen (made in the pancreas) is folded but enzymatically inactive b. Trypsin cleaves between residues 15 and 16 to form πchymotrypsin (active) c. πchymotrypsin then cleaves another πchymotrypsin to form αchymotrypsin (active) 3. Features: a. The cleaved Isoleucine 16 turns inward and forms an ionic bond with aspartate 194, which stabilizes the active form of chymotrypsin. b. The two groups at the stabilize the negatively charged carbonyl oxygen during the transition state in catalysis. ne of these groups is not present in chymotrypsinogen, so the is incomplete in the zymogen. c. Residues 189 make up the substratespecific binding pocket for aromatic groups, which is not fully formed in the zymogen. Page 1 of 6

6 Substrate is 57 Asp R Asp 102 TS #1 is 57 Asp R Asp 102 istidine removes serine's proton to make it a more powerful nucleophile and prepare it for catalysis Aspartate orients the histidine and takes part in transition state stabilization Page 2 of 6

7 Tetrahedral Intermediate #1 is 57 Asp R Asp 102 TS #2 is 57 Asp R Asp 102 Page 3 of 6

8 Acyl Intermediate + Product 1 is 57 Asp R Asp 102 Product 1 Acyl Intermediate + 2 is 57 Asp Asp 102 Page 4 of 6

9 TS #3 is 57 Asp Asp 102 Tetrahedral Intermediate 2 is 57 Asp Asp 102 Page 5 of 6

10 TS #4 is 57 Asp Asp 102 Product 2 is 57 Asp Asp 102 Product 2 Page 6 of 6