The following data describe the catalysis of cleavage of peptide bonds in small peptides by a protease: Substrate k (1/s) K₁, (mM) k/Kµ (mM/s). A a. A b. B BCDEF C. C d. D e. E f. F с 10 1 10 0.1 100 0.02 8,000 0.05 10,000 0.5 Use this information to answer the next three questions. 0.1 1 4. Which substrate binds to the enzyme with the highest affinity? 0.01 1 100 5,000 160,000 20,000
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- The following data describe the catalysis of cleavage of peptide bonds insmall peptides by the enzyme elastase. The arrow indicates the peptide bond cleaved in each case.(a) If a mixture of these three substrates was presented to elastase withthe concentration of each peptide equal to 0.5 mM, which would bedigested most rapidly? Which most slowly? (Assume enzyme is presentin excess.)(b) On the basis of these data, suggest what features of amino acid sequence dictate the specificity of proteolytic cleavage by elastase.(c) Elastase is closely related to chymotrypsin. Suggest two kinds of aminoacid residues you might expect to find in or near the active site.Consider the binding reaction L + R → LR, where L is a ligand and R is its receptor. When 1 × 10−3 M of L is added to a solution containing 5 × 10−2 M of R, 90 percent of the L binds to form LR. What is the Keq of this reaction? How will the Keq be affected by the addition of a protein that facilitates (catalyzes) this binding reaction? What is the dissociation equilibrium constant Kd?What is the fractional occupancy of a protein binding site when the ligand concentration (L) =1mM and the ligand equilibrium binding constant at the binding site K10= 10microM. 0.01 B.0.1 C.0.91 D.0.99 none of the listed values
- The following data describe the catalysis of cleavage of peptide bonds in small peptides by the enzyme UTSAse (the arrow indicates the peptide bond cleaved in each case). Substrate Km(mM) kcat(s-1) PAPA↓G 4.0 26 PAPA↓A 1.5 37 PAPA↓F 0.64 18 what features of amino acid sequence dictate the specificity of the proteolytic cleavage? Large hydrophilic R-groups Large hydrophobic R-groups Neutral R-groups Small hydrophilic R-groups Large hydrophobic R-groups Negatively charged R-groups Positively charged R-groupsA biochemist wants to separate two peptides by ion-exchange chromatography. At the pH of the mobile phase to be used on the column,one peptide (A) has a net charge of −3 due to the presence of more Glu andAsp residues than Arg, Lys, and His residues. Peptide B has a net charge of+1. Which peptide would elute first from a cation-exchange resin? Whichwould elute first from an anion-exchange resin?In a mixed heteropolymer experiment, messages were createdwith either 4/5C:1/5A or 4/5A:1/5C. These messages yielded proteinswith the amino acid compositions shown in the followingtable. Using these data, predict the most specific coding compositionfor each amino acid.4/5C:1/5A 4/5A:1/5CPro 63.0% Pro 3.5%His 13.0% His 3.0%Thr 16.0% Thr 16.6%Glu 3.0% Glu 13.0%Asp 3.0% Asp 13.0%Lys 0.5% Lys 50.0% 98.5% 99.1%
- Under what conditions can we assume that KM indicates the binding affinity between substrate and enzyme?What is the first thing that must occur in order for the catalysis of the peptide bond to begin. What is a specificity pocket? What are the preferences of chymotrypsin due to its specificity pocket?In a paragraph form, provide the experimental procedures in removal of the carbon dioxide present in the mechanism of reaction of protein that contain native serine residues by the reaction of oxazetidine-containing peptides and α-ketoacid
- The enzyme phospholipase A2 has an optimal pH of 5.5. If a biochemist wants to set up an in vitro assay to screen inhibitors of this enzyme, which buffer system would be BEST?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?Determine 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.