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. Asp C-Nocleg Ap H₂ ↓ Gly Ser Binding of bac yeyo dation by Ha Fo amino produt Aup LOHB HAR Formation of covalent (ES complex Ger¹0s
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- Using the ActiveModel for aldose reductase, describe the structure of the TIM barrel motif and the structure and location of the active site.Bovine chymotrypsin is a serine protease. The enzyme is structurally stable over the pH range of 4.0 – 10.0. It exhibits optimum protease activity in the pH range of 7.5 – 9.0, but its protease activity is strongly inhibited at pH < 6.0. Based on your knowledge of serine protease mechanisms, how would you explain this effect of pH on chymotrypsin’s mechanism of catalysis?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)RuBP carboxylase is by no means an ideal enzyme. Describe some of the problems with its active site and its substrate specificity. If we compare the amino acid sequences of this enzyme from many different species, they are almost identical. What is the significance of this uniformity?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?
- UDP-glucuronosyltransferase enzymes bind the organic compound UDP-glucuronic acid (UDP-GA) in order to catalyse the transfer of a glucuronic acid group from UDP-GA to a drug molecule, releasing UDP from the active site as a product. UDP is then regenerated by the activity of another enzyme. What terms could be used to describe UDP-GA?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.Shown below is a proposed mechanism for the cleavage of sialic acid by the viral enzyme neuraminidase. The kcat for the wild-type enzyme at pH =6.15, 37 °C is 26.8 s-1.(a) Describe the roles of the following amino acids in the catalytic mechanism: Glu117, Tyr409, and Asp149. List all of the following that apply:general acid/base catalysis (GABC), covalent catalysis, electrostaticstabilization of transition state.(b) Based on the information shown in the scheme, would you expect mutation of Glu 117 to Ala to have a greater effect on KM or kcat?(c) For the R374N mutant at pH = 6.15, 37 °C, kcat is 0.020 s-1, and KMis relatively unaffected. Based on this result, it seems that R374 is morecritical for catalysis than for substrate binding. Explain how R374 stabilizesthe reaction transition state more than the substrate (i.e., what feature of this reaction would explain tighter binding to the transition state vs. substrate?).
- 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.…1.1)the following data duscribe an enzyme-catalyzed reaction(hydrolysis of cabobenzoxyglycyl-L-tryptophan) Plot these results using a lineweaver-Burk method, and determine values for Km and Vmax. substrate concenrate(mM) Velocity(mM.sec-1) 2,5 0.024 5 0.036 10 0.053 15 0.060 20 0.061 25 0.062 1.2) If the Km of an enzyme for it's substrate remains constant as the concentration of the inhibitor icreaces, what can be said about the mode of inhibition and why? 1.3) calculate the turnover number for an enzyme, assuming Vmax is 0.5M.sec-1 and the concentration of the enzyme used is 0.002M . why is it usefull to know this? 1.4) discuss the mechanism of the bohr effect that occurs during the interactions of Hb with oxygen under physiological conditions in the lungs and tissues. make use of relavant graphs and diagrams to explain your answer.We talked about the types (mechanisms) of catalysis, including acid-base catalysis, covalent bond formation, metal ion stabilization, and nucleophile attacks of reactants/intermediates following substrate binding. Using the SN2 mechanism for Peptidoglycan cleavage by Lysozyme, indicate the type of catalysis that each of these groups are taking part in. Provide your answers in the thread. Note: this is not part of the assignments for Friday. i. Glu35 ii. Asp52 iii. H2O