(a) Fill in the blank regarding the mechanism of chymotrypsin below.(1) Polypeptide substrate binds non covalently in the enzyme active site. The catalyticTriad includes a reactiveNucleophile that attacks the electrophilic amide Catom.(2) The resulting tetrahedral- Is stabilized by H-bonding interactions with thehole.(Note: this is the same word repeated)(3) Collapse of the tetrahedral intermediate and H * Transfer from-Lead to theCleavage of the C-N bond. The N-terminal peptide is bound through acyl linkage to serine.(4) AMolecule then binds to the active site and attacks the acyl ester car-bonyl.(5) The resulting tetrahedralTions with theSame word repeated).(6) The second peptide fragment is released, and the enzyme returns to its initial state.Intermediate is stabilized via enthalpic interac-hole. (Note: this is the same answer as (2), and is again the(b) Trypsin and chymotrypsin are two closely related proteases; however, trypsin cleaves afterpositively charged residues (i.e.ArgandLys) while chymotrypsin cleaves after aromaticresidues (i.e.Phe.TyrandTrp). Suggest how this specificity is achieved?

Serine proteases are protein cleaving enzymes that have Serine, Histidine and Aspartate (the…

Answered: (a) Fill in the blank regarding the…

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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(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?
Beginning with the 1st tetrahedral intermediate, show the complete steps in chymotrypsin mechanism that occurs to form the 2nd chymotrypsin intermediate in the chymotrypsin active site. The substrate for chymotrypsin to be used is Ala-Tyr-Gly. Further, name the amino acid(s) that would be released as a result of the reactions you'd illustrated above.
Draw a stepwise mechanism for the following reaction. The fourmemberedring in the starting material and product is called a β-lactam.This functional group confers biological activity on penicillin and many related antibiotics. (Hint: The mechanism begins with β elimination and involves only two steps.)
Which of the following statements is true about the chymotrypsin reaction? 1. The catalytic triad at the active site is formed by three residues: His, Gly, and Ser 2. When the substrate is p-Nitrophenylacetate, the rate-limiting step is the release of p-Nitrophenolate. 3. During the reaction, LBHB forms when the proton is donated to His from Ser or water. 4. The chymotrypsin reaction involves “only” specific acid-base catalysis 5. The “oxyanion hole” is formed by the amide nitrogens of Ser and Glu
1. In a catabolic pathway, metabolite X gets converted into metabolite Y, metabolite X 0 J mol-¹ and AG' is <0 J mol-¹ for this reaction. a) At standard states, is this reaction favorable? b) Is the reaction favorable or unfavorable at cellular condition? c) Is this an endergonic or exergonic reaction in the cell? d) Would you describe this as a thermodynamically downhill or uphill reaction in the cell?
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.
Which of the following is a true statement regarding sphingolipid synthesis? (A) The first step in sphingolipid synthesis is the condensation of palmitoyl CoA with aspartate to form b-ketosphinganine.(B) This process requires the reduction of a ketone that uses NADH as the reducing agent.(C) A fatty acid is attached to dihydrosphingosine to form dihydroceramide. (D) FAD is using as an oxidizing agent to remove a double bond from dihydroceramide.(E) The formation of sphingomyelin requires the attachment of a glucose or galactose molecule to ceramide.
Diazepam is converted in vivo to an active metabolite Oxazepam. Explain metabolic transfomation of diazepam to oxazepam. (Provide names of enzymes involved in this transformation. Drawings of structures ofintemediate metabolites is NOT required)
(a) What are the Vmax and Km (including units) for Tigerzyme? b) What are the Vmax and Km (including units) for Tigerzyme in the presenceof the inhibitor Tar Heel? (c) What are the Vmax and Km (including units) for Tigerzyme in the presenceof the inhibitor Blue Devil?
Which of the following statements about isozymes is correct? (Select all that apply.) (a) Isozymes allow reactions to be optimized under different conditions. (b) The main reason for isozymes is so that a given reaction is never completely inhibited. (c) Isozymes have completely different active sites. (d) Bind the same substrates but form different products. (e) Isozymes display different physical properties, such as kinetic parameters.
Consider the mechanism of enolase, as indicated below. Which of the following correctly describes the roles of the Mg2+ as illustrated in the figure? (This is a multi- select question). Mg2+ Mg2 Enolase PO3- OH -C-C-H H OH HO H-N-H Lys 345 Glu211 2-Phosphoglycerate bound to enzyme Mg2+ Mg2 PO3- OH C-C-H OH HO H H-N*-H Lys 345 O Glu211 Enolic intermediate HOH PO3- H Phosphoenolpyruvate The metal ion (Mg2+) is helping to stabilize the extra negative charge that developed on the carboxyl group in the enolic intermediate. The metal ion (Mg2+) is serving as a general base, removing a proton in order to improve the quality of the nucleophile. The metal ion (Mg2+) is assisting in the oxidation of the carboxyl carbon through metal ion catalysis. The metal ion (Mg2+) is helping to orient the substrate properly in the active site. The metal ion (Mg2+) is accepting a proton in order to improve the quality of the leaving group.
Carboxylic acids, such as the one shown below, can be difficult to reduce Provide the name of a reductant A. Explain why this reductant is able to react with the carboxylic acid whereas others cannot (Hint: Draw and discuss the potential reactive intermediates/transition states).

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