What is the catalytic triad of chymotrypsin? Describe the mechanism of chymotrypsin in cleaving a peptide bond, highlighting the roles of the catalytic triad and the significance of the oxyanion hole.
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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?What are the amino acids of the catalytic triad of chymotrypsin? State the mode of catalysis shown by each of the amino acids that you have named. (a) (b) Predict what will happen if aspartic acid of the triad is replaced by asparagine. (c) Briefly explain the role of the oxyanion hole for the catalysis of chymotrypsin.With the aid of the simple generic diagram, identify and explain how the type of chemical bonding stabilizes a secondary structure present in 3GRS (glutathione reductase).
- What is the difference between an enol phosphate and a normal phosphate ester that gives PEP such a high phosphoryl group transfer potential?How would chymotrypsin's catalytic triad be affected by extremely low and extremely high pH values (assuming the rest of the protein remains intact)?An inhibitor that specifically labels chymotrypsin at histidine 57 is N-tosylamido-l-phenylethyl chloromethylketone. How would you modify the structure of this inhibitor tolabel the active site of trypsin?
- Draw the first tetrahedral intermediate of the chymotrypsin mechanism (a single structure, no arrows required). Circle the oxyanion hole. How does the oxyanion hole of chymotrypsin compare to that of carboxypeptidase?An inhibitor that specifically labels chymotrypsin at histidine 57 is Ntosylamido-l-phenylethyl chloromethyl ketone. How would you modify the structure of this inhibitor to label the active site of trypsin?In many biochemical reactions which involves the formation of an enolate intermediate, the carbonyl oxygen of the substrate is coordinated to a divalent metal ion (usually zinc or magnesium) in the active site. Explain with structural drawings, how this ion-dipole interactions affect the acidity of the a-protons?
- 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.describe a detailed experimental procedure for the chemical synthesis of proteins with the α-ketoacid hydroxylamine (KAHA ligation), using (S)-5-oxaproline (Opr) as a key building block.On the basis of the information provided in Figure 9.17, complete the mechanisms for peptide-bond cleavage by (a) a cysteine protease, (b) an aspartyl protease, and (c) a metalloprotease.