enzyme active siteSer-CH₂-C195Asp102substrate15. A substrate binds to enzyme active site.a) List the roles of serine, histidine and aspartic acidb) Show how the first tetrahedral intermediate would be formed.c) Show acyl-enzyme intermediate.d) What is the pka for Histidine? How is this pka relate to physiological pH(7.4)? Do you anticipate any enzymatic reaction will occur if histidine isreplaced with cysteine? Why?

The enzyme has serine, histidine and aspartate in the active site. Serine proteases are protein…

Answered: 15. A substrate binds to enzyme active…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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Will rate ASAP Which of the following amino acid residues would not provide a side chain for acid-base catalysis at physiological pH? (Assume pK values of each amino acid are equal to the pK value for the free amino acid in solution.) I. leucine II. lysine III. aspartic acid IV. histidine A) I, II, III B) I, II C) I D) II E) I, III
One sample of the globular protein peroxidase is hydrolyzed by heating with 6 M HC1. A second sample is denatured by treatment with acetone. a) How does the peroxidase structure change during hydrolysis? Will this change the biological activity of peroxidase? b) How does the peroxidase structure change during denatur-ation? Will this change the biological activity of perox-idase? c) Are either of these processes likely to be reversible?
if the reaction pH drops significantly (pH=2 for example), how would reaction catalyzed be serine proteases be affected? why? (assumin that the rest of the protein structure remain intact)
Draw the first tetrahedral intermediate of the chymotrypsin mechanism (a single structure, no arrows required). Circle the oxyanion hole. How does the oxyanion hole of chymotrypsin compare to that of carboxypeptidase?
16. This figure from Foundations should look familiar. Which protein is shown here? A) Aglycosidase B) A G-protein C) Chymotrypsin D) Hexokinase E) Trypsin catalytic triad Ser 195 His 57 H Gly 193 N-H R Ņ Ca CB Asp 102 R' 17. What kind of enzymatic mechanism is shown in this figure from Foundations? A) Specific acid-base catalysis with His57 as the base B) Specific acid-base catalysis with Ser195 as the base C) General acid-base catalysis with Ser195 as the base D) General acid-base catalysis with His57 as the base E) Metal ion catalysis N-H
(i) Describe the mechanism of chymotrypsin in cleaving a peptide bond, highlighting the roles of the catalytice triad for the two phases of the catalytic reactions. Explain the significance of the oxyanion hole for the catalysis. (ii) All serine proteases contain the catalytic triad and these amino acids are positioned in the exact same conformation. Since this is true, why do trypsin and chymotrypsin have such different substrate specificity? What features of the enzyme allow for this situation?
4. a) Structures A, B and C are derivatives of penicillin Н NHH +x A i) ii) iii) CO₂H HH Ex B CO₂H R Describe briefly how the activity of B and C compares with A. b) The biosynthesis of penicillin involves two amino acids с Name the two amino acids. What is the name of the enzyme inhibited by the penicillin? What does penicillin mimic in bacteria cell wall synthesis?
Polyvinyl acetate undergoes a non-chain scission degradation reaction. (i) Illustrate the mechanism for this process, and the structures of all resulting products. (ii) Would this particular degradation reaction be the faster at a pH of 7 or a pH of 13? Justify your choice.
. The following diagram shows the biosynthesis of B12 coenzymes, starting with the vitamin. DMB is dimethylbenzimidazole. (a) What one additional substrate or cofactor is required by enzyme B? (b) Genetic deficiency in animals of enzyme C would result in exces- sive urinary excretion of what compound?
6-One method to determine proximity of two locations in a protein molecule or protein complex is FRET. This technique uses fluorescence transfer between two fluorophores where the ability of the transfer to occur is correlated to distance between the two residues. A) On the following graph using colored pencils, pens, or markers draw the emission spectra from the donor and the absorbance spectra of the acceptor (this should be a general schematic, does not need to be a FRET pair). Include a key for your graph B) As a rescarch student in my group you want to study the proximity of two residues in clamp region of a protein. Draw a schematic of your protein and label the two locations of your fluorophores. In 2-4 sentences (or figures) explain how your FRET fluorophores would give determine if these two residues were close to one another.
б. Draw all possible products of a single hydrolysis being completed on the following polypeptide: Ala-Ser-Met-Ser
Given the following reaction, identify the class and subclass of the enzyme involved. H. CH2OH H-C-OH C=0 но-с-н но-с-н H-C-OH H-C-OH H-C-OH H-C-OH CH2OPO,2 CH2OPO,2- Class: [ Select] [ Select ] Ligase Hydrolase Lyase Subcla Transferase Isomerase Oxidoreductase

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