Snake venom contains many hydrolase enzymes, including several serine
proteases. One such protease (present in high concentrations in snake venom) mimics the
action of thrombin to activate fibrin. The venom protease cleaves peptide bonds with a
specificity for basic, positively charged amino acids. This enzyme is incubated with a substrate
peptide with the sequence SNPDCKVALYMTW. Draw a mechanism for the peptide hydrolysis
of this specific peptide catalyzed by this snake venom protease. Include the structure of the
active site amino acids of the enzyme and the substrate peptide group (including the full
structure of the 2 specific amino acids that contribute to the scissile peptide group in the
substrate) in your mechanism. Use the curved arrow convention to illustrate the flow of
electrons.
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- Propose a plausible enzyme mechanism for triose kinase, the enzyme that catalyzes the conversion of glyceraldehyde to glyceraldehyde-3-phosphate. You may use "B:" for a general base amino and "H-A" for a general acid amino acid if needed.arrow_forwardThe active site of an enzyme that uses a general acid-base catalytic mechanism contains a Glu and an Asp residue (both of which are essential for catalysis) with pKa values of 5.9 and 4.5, respectively. If the enzyme is found in the lysosome (pH = 5.2), which residue will act as the general acid and which will act as the general base during the initial steps of the reaction?arrow_forwardDiisopropylphosphofluoridate (DIPF) inactivates chymotrypsin by covalently modifying serine 195. Which statement is true of DIPF's inhibitory mechanism? DIPF randomly modifies all serine residues on the protein, and if enough is added, the serine in the active site will eventually be modified. DIPF approaches serine 195 more closely than other substrates. DIPF looks like the substrate for chymotrypsin and binds in the active site as a competitive inhibitor. Serine 195 is in an environment that gives it a higher than normal reactivity with respect to DIPF.arrow_forward
- Phosphoglycerate mutase transfers a phosphoryl group from C3 of 3-phosphoglycerate to C2 position to give 2-phosphoglycerate. Why is it important to have the phosphoryl group at position 2 rather than at C3? It was observed that the activity of some preparations of the enzyme could be increased if catalytic (very small) amount of 2, 3-bisphosphoglycerate was added to the enzyme. Give a possible explanation for this observation.arrow_forwardTrypsin contains a/an [aspartate/serine/histidine] in its specificity pocket to attract lysine and arginine side chains. It contains a potent nucleophilic [histidine/serine/aspartate] in its active site that is capable of attacking the electrophilic [carbon/nitrogen/oxygen] of the closest peptide bond. The [acyl-enzyme/specificity pocket/oxyanion] transition state is stabilized by the backbone amide hydrogens of glycine and serine. In this way, the enzyme is able to catalyze the [hydrolysis/ligation/metalysis/hydrogenation] of the peptide bond.arrow_forwardDraw the catalytic triad of a serine protease at the first tetrahedryl intermediate stage. Your drawing should include the amino acids that make up the triad, any part of the substrate that should be present, and any other molecules that are present in the active site.arrow_forward
- When performing his experiments on protein refolding, Christian Anfinsen obtained a quite different result when reduced ribonuclease was reoxidized while it was still in 8 M urea and the preparation was then dialyzed to remove the urea. Ribonuclease reoxidized in this way had only 1% of the enzymatic activity of the native protein. Why were the outcomes so different when reduced ribonuclease was reoxidized in the presence and absence of urea?arrow_forwardPLP is a cofactor for a number of enzymes involved in amino acid metabolism. Give an example of reaction in which PLP participates in cleavage of the a, b, and c bonds of an amino acid, as diagrammed in shown Fig.arrow_forwardConsider a hexapeptide of the sequence thr asn glu trp lys gln. After complete hydrolysis, which amino acid would elute first from a cation exchange column at pH 7? O Asn O GIn Thr Glu O Trp O Lysarrow_forward
- “Caspase” describes the catalytic activity of this enzyme. What amino acyl residue participates in the catalytic mechanism? What substrate motif does caspase-8 recognize?arrow_forwardSketch the following two tripeptide chains: Asp-Gly-Ser and Ile-Asn-Met at physiological pH . Please provide only typed answer solution no handwritten solution needed allowedarrow_forwardDetermine the amino acid sequence of Peptide A, which was obtained by hydrolyzing a larger peptide with trypsin, using the data below: Total hydrolysis of Peptide A produces (Ala2, Arg, Glu, Gly, Met, Pro2, Ser, Tyr). Sequential Edman degradation of Peptide A produces a derivative of Ala in the first cycle; a derivative of Serine in the second cycle; and a derivative of Proline in the third cycle. Cleavage of Peptide A with chymotrypsin yields two peptides: a tripeptide III containing Ala, Arg and Gly; and a heptapeptide IV containing Ala, Glu, Met, Pro2, Ser and Tyr. Edman treatment of tripeptide III generated a derivative of Alanine. Cleavage of Peptide A with cyanogen bromide (which cleaves peptides on the C-terminal side of Methionine) yields two pentapeptides labeled I and II. Total hydrolysis or peptide I indicate that it contains Ala, Arg, Gly, Pro and Tyr; pentapeptide II contains Ala, Glu, Met, Pro, and Ser.arrow_forward
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