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BIOC12H3 (56)
Lecture 10

Lec10 Questions.docx

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University of Toronto Scarborough
Biological Sciences
Shelley A.Brunt

Lec10 Questions Slide 4 a. the specificity pocket near the active site serine is very different for each enzyme i. emphasis on this / what does this mean? 1. the sequence of amino acids before and after serine determine the specificity Slide 6 a. mechanism can be applied to other hydrolases i. i.e. cleavage of amide or ester bonds via a similar process ii. what process? what mechanism? 1. similar mechanism to the superoxide dismutase mechanisms discussed in lec09 (slide 30) Slide 7 i. the conformation of the three residues stabilized by a h bond between 1. the carbonyl oxygen of the carboxylate side chain of asp-102 and 2. the peptide bond nitrogen of his-57 3. no mention of serine? Slide 9 a. ser-195 becomes a strong nucleophile that will attack the peptide bond i. what peptide bond? 1. refer to slide 11 Slide 11 1. Mechanism a. step 1 i. formation of ES complex orients substrate 1. puts the substrate (with scissle bond) next to core triad b. step 2 i. attack of nucleophilic oxygen from ser-195 ii. results in tetrahedral intermediate iii. stabilization of intermediate by formation of oxyanion hole 1. with gly-193 and ser-195 c. step 3 i. his-57 donates a proton to facilitate cleavage of amine group from substrate ii. carbonyl group from substrate forms covalent bond with ser-195 (enzyme) iii. amine product is removed d. step 4 i. water enters and donates a proton to his-57 ii. provides OH group to attack carbonyl group of ES covalent complex 1. forming second tetrahedral intermediate 2. stabilization occurs again by oxyanion hole iii. results in hydrolysis of the acyl enzyme intermediate iv. his-57 is now an imidazolium ion again and donates a proton resulting in the collapse of the second intermediate 1. his-57 donates proton to ser-195 facilitating the collapse of second intermediate e. step 5 i. formation of second product with COOH terminus (carboxy terminus) f. step 6 i. release of product Slide 22 a. Generate a nucleophile that attacks the peptide carbonyl group i. instead of serine, these major peptide cleaving enzymes facilitate the mechanism from substrate to product Slide 28 1. What is the difference between coenzyme and cosubstrate and prosthetic group? a. cosubstrate i. regenerated by another enzyme b. prosthetic group i. regenerates at the end of reaction Slide 29 i. The magnesium shields negatively charged phosphate groups of ATP 1. Making them more susceptible to nucleophilic attack
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