2. (the active site in the Michaelis complex of a-chy-motrypsin and a polypeptide substrate. Describebriefly the catalytic or structural roles of the: To the right is a schematic diagram ofHis $7residues listed below:HOSer 195(а) Ser195AAn-C-ÇH-NH-ÇÇH-NH -AAnRHH.-N-195193GlySer(b) His57(c) NH groups of Gly193 and Ser195(d) The most favorable side chain R for binding(e) Identify the scissile bond with an arrow, i.e., the bond in the peptide substrate that is cleaved as aresult of the catalytic action of the enzyme. You can point to it on the diagram above.

Chymotrypsin is a protease that cleaves a peptide at the C-terminal of all aromatic amino acid.…

Answered: 2. ( To the right is a schematic…

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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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
(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?
(b) The values of kinetic parameters for a variety of synthetic ester and peptide substrates ofa- chymotrypsin are compared for the reaction scheme below where ES is the Michaelis complex, ES' E+S Substrate K₁ N-Ac-Trp–OC₂H5 N-Ac-Phe-OC2H5 N-Ac-Leu-OC2H5 N-Ac-Phe-CONH2 N-Ac-Tyr-p-nitro-anilide ES K₂ 3.5 13.0 3.2 1.7 K-₁ is the acylenzyme, P₁ is the first product to be released, P2 is the second product, k2 is the acylation rate constant, k3 is the deacylation rate constant, and kcat = k2 k3/( k2 + k³). In the table below, N- Ac = N-acetyl; -CONH₂ = carboxamide; -OC₂H5 = ethyl ester; p-nitroanilide = −NH-C6H4-NO2 simulating a peptide group. ES' K2 (S-¹) K3 (S-1) 0.84 2.2 0.19 P₁ K3 0.073 H → E+ P2 Kcat (S-1) 0.82 1.9 0.18 0.070 0.038 KM (MM) 0.08 1.3 4.2 24.0 0.35 1 Kcat/ KM (mM-¹ s¯¹) 10.3 1.5 0.04 0.003 0.11 The value of kcat for N-Ac-Phe-OC2H5 is two-fold greater than that for the L-tryptophanyl analog and more than 10-fold greater than the value of kcat for the ester substrate…
2. To the right is a schematic diagram of His $7 the active site in the Michaelis complex of a-chy- motrypsin and a polypeptide substrate. Describe briefly the catalytic or structural roles of the residues listed below: но — Ser 195 (а) Ser195 AA,-C-ÇH-NH-C-ÇH -NH -AAn R R H H. 193 Gly Ser195 (b) His57 (c) NH groups of Gly193 and Ser195 (d) The most favorable side chain R for binding (e) Identify the scissile bond with an arrow, i.e., the bond in the peptide substrate that is cleaved as a result of the catalytic action of the enzyme. You can point to it on the diagram above.
#1 Specify the role each of the following amino acids play within the crystal structure and/or active site for Be as specific as possible, with pictures (and mechanistic arrows) as necessary. His11 Arg140 Glu89 Trp68 #2 Provide a step-wise mechanism for the reaction Bisphosphoglycerate mutase catalyzes, using the amino acids responsible for aiding in catalysis. You do not need to add surrounding amino acids that aid in substrate specificity. (drawn out)
3. Subtilisin (Mol. weight 27,600) is a protease that can catalyze hydrolysis of certain amino acid esters and amides. For the synthetic substrate N-acetyl-L-tyrosine ethyl ester (Ac-Try-OEt), subtilisn exhibits Km and kcat values of 0.15 M and 550 s-¹, respectively. a) What is the Vmax when the subtilisin concentration is 0.4 mg/ml? b) Indole is a competitive inhibitor of subtilisin with a Ki of 0.05 M. What is the Vmax for Ac-Try-OEt hydrolysis by 0.4 mg/ml subtilisin in the presence of 6.25 mM indole? c) What is the Vo when 0.4 mg/ml subtilisin is incubated with 0.25 M Ac-Try-OEt and 1.0 M indole?
22) answer the following question.. Refer to the kinetic scheme for competitive inhibition and the structures shown below to E+S ES E +P -co- CO- 1 2 EI Compound 1 was determined to act as a competitive inhibitor through standard inhibition studies. Structural studies did not show any resemblance to the transition state. Compound 2 was also determined to act as a competitive inhibitor. Structural studies showed that it does resemble the transition-state. The K, constant is used to assess relative affinity of inhibitors for enzymes. That is, each compound has its own K, value. We can interpret K, the same way we do with Ka values. True or False: K, > Kµ2. Briefly explain your answer.
complete the following mechanism showing the cleavge of the peptide bond for the following cysteine protease reaction. you only need a catalytic dyad for cystein proteases because the pKa of cysteine is low enough (8) and close enough to the pH of 7.4 that is can easily be deprotonated by histidine.
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).
Draw the structure of the PTH derivative product you would obtain by Edman degradation of the following peptides: (a) I-L-P-F (b) D-T-S-G-A
Determine the Primary amino acid sequence of an Octapeptide Composition · Tyr , Arg，Pro, Lys ,Lys ,Met ,Trp，Phe N terminal 1 2 3 4 5 6 7 8 C terminal 1) Treatment with an Edman reagent gives a PTH-AA that shows a Yellow color with Ninhydrin. 2) Trypsin digestion of the Octapeptide gives tetepeptide, dipeptide， free Arg ，free Trp. 3）CNBr = pentapeptide and tripeptide. 4) chymotrysin - tetapeptide and two dipeptiele. The tetrapeptide contains an amino acid with an OH group in the side chain.
Chymotrypsin has the highest affinity for which of the following substrates: Table. The values of KM and kcat for some Enzymes and Substrates Enzyme Chymotrypsin Ки (М) 4.4 x 10-1 8.8 x 10-2 6.6 x 104 Kcat (S-1) 5.1 x 10-2 1.7 x 10-1 1.9 x 102 Substrate N-acetylglycine ethyl ester N-acetylvaline ethyl ester N-acetyltyrosine ethyl ester Catalase H2O2 2.5 x 10-2 1.0 x 107 Urease Urea 2.5 x 10-2 4.0 x 105 OA. N-acetylglycine ethyl ester OB. N-acetylvaline ethyl ester OC. N-acetyltyrosine ethyl ester D. Urea

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