The diagram below shows the substrate binding cleft for a protease, providing thesubstrate structure, and indicating the residues (using one-letter code) that line thefour specificity pockets.F452452The protease is known to cleave the amide linkage between W and E residues forsubstrates containing the WEFD sequence.Of the bonds indicated, which identifies the scissile bond?1M3NH₂N2O3FW Consider the metabolic pathway show below that converts substrate A to B with the enzyme A-ase,B to C with B-ase(I), and so forth.Acety/A-aseA-aseAcetate DeacetylaseDProteaseB-ase C-aseA-aseABC-What is the mechanism of regulation of B-ase?Positive allosteryReversible Covalent modificationIsoenzymesProteolytic ActivationFeedback Inhibition

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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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Consider the metabolic pathway show below that converts substrate A to B with the enzyme A-ase, B to C with B-ase(I), and so forth. Acety/A-ase Acetate - A-ase Deacetylase A-ase Protease & C-ase B-ase ABCD What is the mechanism of regulation of B-ase? Positive allostery Reversible Covalent modification Isoenzymes Proteolytic Activation Feedback Inhibition 1
One of the reasons for oxidizing the disulfide bonds in RNase A before removing the urea in the Anfinsen experiment was to demonstrate that ... Urea promotes disulfide bond exchange O Incorrectly-folded proteins lose their enzymatic activity. Urea prevents disulfide bond formation. Urea forms thio-esters with reduced cysteines at pH 8.2 Disulfide bonds are required for enzyme activity.
о 6. What is the catalytic triad and what particular protein family would you find this? What is the general role of the catalytic triad? Predict what would happen if Asp were mutated to Gly. ructure formation of alpha heli
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In many biochemical reactions which involves the formation of an enolate intermediate, the carbonyl oxygen of the substrate is coordinated to a divalent metal ion (usually zinc or magnesium) in the active site. Explain with structural drawings, how this ion-dipole interactions affect the acidity of the a-protons?
The diagram below shows the substrate binding cleft for a protease, providing the substrate structure, and indicating the residues (using one-letter code) that line the four specificity pockets. 1 M F H₂N K R IZ 2 3 P F S W оо E 4 The protease is known to cleave the amide linkage between W and E residues for substrates containing the WEFD sequence. Using 3-letter code with amino acids linked by a "dash" (ex. GLY-ALA), the N-terminal product is A and the C-terminal product is A
5. Shown below are the first steps in the mechanism of a cysteine protease, which catalyses amide bond hydrolysis in a similar manner as serine proteases. (a) Complete this mechanisms, and (b) sketch the approximate reaction coordinate diagram for this catalyzed reaction relative to the uncatalyzed proteolysis. HN N HN cysteine protease
If the allosteric coefficient for ATCase increases from 250 to 1300, the rate of the N-carbamoylaspartate formation: O stays the same and the sigmoidal curve of reaction rate as a function of substrate shifts up. O decreases and the sigmoidal curve of reaction rate as a function of substrate shifts to the left. O increases and the sigmoidal curve of reaction rate as a function of substrate shifts to the left. O stays the same and the sigmoidal curve of reaction rate as a function of substrate shifts to the right. O decreases and the sigmoidal curve of reaction rate as a function of substrate shifts to the right. Question 9 Which of the following CANNOT be targeted for phosphorylation to modulate the activity of an enzyme? O Ser Ala O None of the amino acids listed can be targeted for phosphorylation to modulate enzyme activity The Tyr
a particular enzyme catalyzes a single reactant S to a single product P, following michaelis-menten kinetics rp=(VmaxCs) / (Km + Cs) 1. A reaction with this enzyme is carried out at very low substrate concentrations. Draw and label a curve on the plot that describes the reaction kinetics under those conditions.
The catalytic triad consists of Asp, His, and Ser. What would be an alternative for histidine and how would we draw the interactions in a mechanism?
The biosynthetic pathway for the two amino acides E and H is shown schematically in the Figure below: A W E 2 Z H How would this pathway change if C was mutated and non-functional?
5. For a Michaelis-Menten enzyme, k1 = 5.2 ⅹ 108 M-1 s-1, k-1 = 3.1 ⅹ 104 s-1, and k2 = 3.4 ⅹ 105 s-1. a) Write out the reaction, showing k1, k-1, and k2. Calculate Ks and Km. Does substrate binding approach equilibrium or the steady state? Justify your answer. b) What is kcat for this reaction? Justify your answer. c) Calculate Vmax for the enzyme. The total enzyme concentration is 25 pmol L-1, and each enzyme has two active sites. d) What substrate concentration would be required for the reaction in (c) to reach half of Vmax. Justify your answer mathematically. e) A second Michaelis-Menten enzyme has k1 = 4.2 ⅹ 107 M-1 s-1, k-1 = 6.1 ⅹ 104 s-1, and k2 = 5.3 ⅹ 102 s-1. Which enzyme is most efficient? 6. A pharmaceutical company is trying to develop a

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