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.F1 MThe protease is known to cleave the amide linkage between W and E residues forsubstrates containing the WEFD sequence.1OMatch the specificity pocket (identified by red number) to the residue that occupiesit.3RMatch the specificity pocket (identified by red number) to the residue that occupiesit.4W21. D2. E3. F4. R5. W6. Y

Proteases preferentially hydrolyze polypeptide substrate peptide bonds based on the amino acids…

Answered: Match the specificity pocket…

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter26: Synthesis And Degradation Of Nucleotides

Section: Chapter Questions

Problem 6P: Allosteric Regulation of Ribonucleotide Reductase by ATP and Deoxynucleotides Describe the...

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Shown below is a substrate for a Elastase. CH, HN NH NH, Draw the mechanism for this serine protease using the artificial substrate. Be sure to draw the catalytic triad, and show the role of the oxyanion hole. Draw the complete structure of every intermediate and product and PUSH ARROWS!
Using the catalytic mechanism of serine proteases, draw and label a reaction coordinate diagram/graph of the chymotrypsin-catalyzed hydrolysis of a peptide bond.
If the substrate for an enzyme catalyzed reaction contained a negative charge, which of the following amino acids would most likely be present in the active site to provide electrostatic destabilization of the ES complex? Leu Val O Asp O LYS QUESTION 15 What is the function of the histidine in the diagram of the mechanism at right with the substrate, a phenylalanine residue? (n) His Asp Nucleophilic affack by water stabilization of a metal ion covalent catalysis electrostatic attraction of the substrate O acid base catalysis 789 Mustly cloudy Click Save and Submit to save and submit. Click Save All Ansuwers to save all answers. here to search
An active site of a hypothetical serine protease with a peptide substrate bound is shown below: This serine protease has 3 specificity pockets (S1, S2, S1') as shown in the figure above. S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1' pocket is deep and hydrophobic. Based on this information you can conclude that R1 is most likely side chain of a. Asp b. Lys c. Lle d. Gly e. Phe
Shown below is a substrate for a Trypsin. Draw the mechanism for this serine protease using the artificial substrate. Be sure to draw the catalytic triad, and show the role of the oxyanion hole. Draw the complete structure of every intermediate and product and PUSH ARROWS!!!!! Do not abbreviate structures using R and R' H₂N _N_CH. сно CH₂ CH₂ CH₂ NH d=19H₂ NH₂ O CH- H₂C HN O CH
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Construct the mechanism of a serine-protease with a catalytic triad.
In serine protease catalytic triad mechanism, the first and second products that leaves the active site are Carboxylic acid and amide respectively Amide and carboxylic acid respectively Ester and amide respectively Carboxylic acid and ester respectively
10. Chymotrypsin is a serine protease enzyme. The Km for the reaction of chymotrypsin with N-acetylvaline ethyl ester is 8.8*102, and the Km for the reaction of chymotrypsin with N- acetyltyrosine ethyl ester is 6.6*10“ M. catalytic triad Ser 195 His 57 Gly 193 N-H OH R-N- Ca N-H O-C- Asp 102 N-acetyl valine N-acetyl tyrosine Chymotrypsin Active Site a. What is the nucleophile here and how is it activated? b. Which substrate has an apparent higher affinity for the enzyme. c. Propose a reason for the difference in affinity based on the shape of each of the substrates (see active site figure, cleaves on the C-side of aromatic residues).
1. Please fully explain (use illustrate where appropriate) the Modes of Enzyme Catalysis exemplified by the serine protease: Chymotrypsin. In your answer discuss employing the illustration whenever possible: the overall reaction mechanism, stability of the reaction transition state, proximity and orientation effects, acid-base catalysis, and covalent catalysis. (c) (0) Ap Asp Toe His Asp 10 C-N bond cleavage HN Ho Ser Ger Binding of substi 196 Ser Gly alto video LBHB NH Sere HAR Proton donation by H (h) Fel of amino product yest OHN Hig Ser Ap (0) Formation of covalent (ES) Alp Me complex Serios
(c) On the right is a diagram of the ac tive site of E. coli aspartate aminotrans- ferase illustrating the cofactor pyridoxal phosphate (labeled PLP) with the dicar- boxylic acid maleate (labeled MAL) bound in the active site. The structural formula of maleate is shown on the right. Am 194 MAL Arg292 Arg386 Ilx17 Lauf 'coo- H get H Coo- Maleate (c1) Draw the structure of L-aspartate and draw a border around the atoms in the amino acid that maleate simulates. (c2) Identify the active site residues that make hydrogen bonds and electrostatic interac- tions with the oxygen atoms of the carboxylate groups of maleate in the diagram above. Identify the carboxylate groups according to the numbering in the diagram of maleate above. Indicate the hydrogen donor groups of the active site residues. (C3) Compare and draw the structures of L-Arg and L-Lys. On the basis of the diagram why does replacement of an arginine for a lysine have an effect on substrate binding to AspAT? (c4) Of the mutant…
1/Vo 1/[S] with I without I with I with I 1/vo without I *-*- 1/vo without I 1/[S] 1/[S] 3. The above graphs are lineweaver-burk plots that demonstrate how inhibitors affect Michaelis Menten enzymes. For each graph identify the type of inhibition and explain how you determined that this enzyme is kinetically demonstrating this type of inhibition.

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Match the specificity pocket (identified by red number) to the residue that occupies it. 1 3 4 2 1. D 2. E 3. F 4. R 5. W 6. Y