1. Please fully explain (use illustrate where appropriate) the Modes of Enzyme Catalysisexemplified by the serine protease: Chymotrypsin. In your answer discuss employingthe illustration whenever possible: the overall reaction mechanism, stability of thereaction transition state, proximity and orientation effects, acid-base catalysis, andcovalent catalysis.(c)(0)ApAsp ToeHisAsp 10C-N bond cleavageHNHoSerGerBinding ofsubsti196SerGlyalto videoLBHBNHSereHARProtondonationby H(h)Fel ofamino productyestOHNHigSerAp(0)Formation ofcovalent (ES)Alp MecomplexSerios

The active site of chymotrypsin consist of a combination of 3 specific amino acid residues that work…

Answered: 1. Please fully explain (use illustrate…

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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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.
#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)
An example of an enzyme-catalyzed reaction proceeding via a transition-state stabilization mechanism is the hydrolysis of peptides by chymotrypsin while, Lysozyme is often cited as an example of an enzyme which operates by strain mechanism. Discuss both mechanisms in the context of each enzyme.
3CLpro is a cysteine protease, which are among the most common proteases in biochemistry, however they are a structurally diverse family of enzymes especially in the organization of the active site amino acids. A group of scientists have reported a potential drug molecule based on a binding study using circular dichroism. They report that the molecule binds to the active site. Can the experiment support the claims, why or why not? Which techniques might be used to support this claim?
Only a few amino acid residues are actually involved in catalysis in enzymes, yet enzymes are constructed of at least 100 amino acids, and often many more. Suggest some functions for the noncatalytic amino acids.
Lysosyme catalyzes the hydrolysis of the carbohydrate linkage in part of the bacterial cell wall (peptidoglycan layer). 1. Propose a mechanism using general acid/base catalysis 2. Propose a mechanism using covalent catalysis. (An intermediate has been observed that indicates a glycosidic bond to the aspartate).
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.
Mechanisms of catalysis : 2.1 Acid-base catalysis summary + example 2.2 Electrostatic catalysis summary + example 2.3 Covalent catalysis summary + example 2.4 Enzymen catalysis summary 2.5 Mechanism of chymotrypsin summary. These mechanisms involve several of the above-mentioned catalyses. In these summaries, do not just draw a diagram of the proposed mechanisms. It is more important to understand which reaction steps involve what kind of catalysis and how these help to reduce the activation energy needed for the reaction (e.g. a step in the reaction mechanism could be electrostatic catalysis to stabilise the transitions state) 2.6 Mechanism of lysozyme summary. These mechanisms involve several of the above-mentioned catalyses. In these summaries, do not just draw a diagram of the proposed mechanisms. It is more important to understand which reaction steps involve what kind of catalysis and how these help to reduce the activation energy needed for the reaction (e.g.…
The accompanying figure shows three Lineweaver–Burk plots for enzymereactions that have been carried out in the presence, or absence, of aninhibitor. Indicate what type of inhibition is predicted based on eachLineweaver–Burk plot. For each plot indicate which line corresponds to thereaction without inhibitor and which line corresponds to the reaction withinhibitor present.
Gout is a medical condition usually caused by a deficiency of the salvage enzyme hypoxanthine-guanine phosphoribosyltransferase. Uric acid accumulates in the joints and causes pain, inflammation, and in advanced disease gouty tophi. Allopurinol, an inhibitor of the enzyme xanthine oxidase, is used to treat chronic gout. Explain briefly the biochemical basis for this treatment.
A synthetic substrate, the para-nitrophenylacetate (PNPA), is used to monitor enzyme activity of protein P. The product of the hydrolysis reaction absorbs at 410 nm with a molar extinction coefficient of 4 000 M-¹.cm-¹. 1- Write the reaction catalyzed by the protease P using the pNPA substrate. 2- The enzyme extract is too concentrated and a 1/300 dilution is needed for enzyme tests. Considering that you would need at least 600 µL of diluted enzyme extract for activity tests, indicate which volume of buffer and enzyme extract you must use for the dilution.
1. For enzyme catalyzed reaction: ki S + E=X (fast) k2 X -2> P + E (slow) derive the rate law and answer the following: a) What is meant by Michaelis-Menten constant km? (b) Prove that order of reaction in substrate changes from unity to zero at higher [S]. (c) What is the rate and value of km, if k2 >> k1. (d) Draw the potential energy diagram for enzyme catalyzed reaction.

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