While R256T and K364R are at different positions, both mutations are present in the active site. Researchers were unable to get kinetics data on R256T. What does this tell you about its ability to function properly? Why might K364R be tolerated better than R256T?
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- Several temperature-sensitive mutant strains of E. coli displaythe following characteristics. Predict what enzyme or function isbeing affected by each mutation. Okazaki fragments accumulate, and DNA synthesis is never completedCatalytic residues are often found in loops between helices or strands for increased mobility duringcatalysis. Is the catalytic Cys predicted to be located in a loop between helices/strands?Are the other two catalytic residues, His and Asn, also found in loops?The covalent catalytic mechanism of an enzyme depends on a single active site Cys residue with a pKa of 8.0. A mutation in a nearby residue alters the microenvironment such that the pKa of the Cys residue increases to 10.2 Would the mutation cause the reaction rate to increase or decrease? Explain.
- We learned that three different amino acid transformations of PLP-dependent enzymes canresult from different conformations of the PLP-amino acid imine adduct in the active site.Starting from the PLP adduct of (S)-serine, show mechanisms fora) Decarboxylation of serineb) Racemization of serinec) Conversion of serine to glycine and formaldehyde.An enzyme that follows the MWC (concerted) model for allostery has a T/R ratio of 300 in the absence of substrate. Suppose that a mutation were to reverse that ratio (T/R = 1/300 = 3.3 x 10–3 in the absence of any substrate). How would this mutation affect the relation between the rate of the reaction and substrate concentration, i.e., what would a Vo vs. [S] plot look like, and why?Structural similarity between the SARS-CoV-2 Mpro protease and chymotrypsin suggests that they would use the same catalytic mechanisms. What feature of the active site would you expect to find in Mpro that would be important in stabilizing the transition state? Describe how that feature would act to stabilize the transition state.
- The S3’ pocket on PfSUB1 (attached) contains the side chains of Lys465 and Tyr427. Researchers discovered that the Km for substrates with acidic residues in the P3’ position are much lower than those with nonpolar resides at the P3’ position in PfSUB1. Explain the Km data.Lysozyme residues Asp 101 and Arg 114 are required for effi cient catalysis, although they are located at some distance from the active site Glu 35 and Asp 52. Substituting Ala for either Asp 101 or Arg 114 does not signifi cantly alter the enzyme’s tertiary structure, but it signifi cantly reduces its catalytic activity. Explain.In chymotrypsin, a mutant was constructed with Ser 189, which is in the bottom of the substrate specificity pocket, changed to Asp. What effect would you predict for this Ser 198 → Asp 189 mutation? Explain your answer.
- Allosteric Regulation of Ribonucleotide Reductase by ATP and Deoxynucleotides Describe the underlying rationale for the regulatory effects exerted on ribonucleotide reductase by ATP, dATP, dTTP, and dGTP.What is the evidence that aspartate transcarbamoylase (ATCase) effects catalysis primarily by proximity? In the figure, what is the role of Lys 84' in the active site- interaction that appear to make with the substrate?If a small amount of ATP labeled with radioactive phosphorus in the terminal position, [γ-32P]ATP, is added to a yeast extract, about half of the 32P activity is found in Pi within a few minutes, but the concentration of ATP remains unchanged. Explain. If the same experiment is carried out using ATP labeled with 32P in the central position, [β-32P]ATP, the 32P does not appear inPi within such a short time. Why?