Biochemistry: Concepts and Connections (2nd Edition)
2nd Edition
ISBN: 9780134641621
Author: Dean R. Appling, Spencer J. Anthony-Cahill, Christopher K. Mathews
Publisher: PEARSON
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Textbook Question
Chapter 8, Problem 3P
An enzyme contains an active site aspartic acid with a pKa = 5.0, which acts as a general acid catalyst. On the accompanying template, draw the curve of enzyme activity (reaction rate) versus pH for the enzyme (assume that the protein is stably folded between pH 2-12 and that the active site Asp is the only ionizable residue involved in catalysis). Briefly explain the shape of your curve.
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An enzyme contains an active site aspartic acid with a pKa = 5.0, whichacts as a general acid catalyst. On the accompanying template, draw thecurve of enzyme activity (reaction rate) versus pH for the enzyme (assumethat the protein is stably folded between pH 2–12 and that the active siteAsp is the only ionizable residue involved in catalysis). Briefly explain theshape of your curve.
The pKa for histidine is pKa = 6.1 while that for cysteine is pKa = 8.0 2. Assume that both histidine and cysteine are catalytic groups for a particular enzyme. Assume also that the side chain of cysteine must be in the deprotonated form. Estimate the pH at which the catalytic activity of this enzyme is the maximum and sketch a pH-activity graph.
Chapter 8 Solutions
Biochemistry: Concepts and Connections (2nd Edition)
Ch. 8 - Prob. 1PCh. 8 - The enzyme urease catalyzes the hydrolysis of urea...Ch. 8 - An enzyme contains an active site aspartic acid...Ch. 8 - The folding and unfolding rate constants for a...Ch. 8 - In some reactions, in which a protein molecule is...Ch. 8 - Would you expect an “enzyme” designed to bind to...Ch. 8 - The initial rate for an enzyme-catalyzed reaction...Ch. 8 - a. If the total enzyme concentration in Problem 7...Ch. 8 - Prob. 9PCh. 8 - Prob. 10P
Ch. 8 - The following data describe the catalysis of...Ch. 8 - At 37 oC, the serine protease subtilisin has kcat...Ch. 8 - The accompanying figure shows three...Ch. 8 - The steady-state kinetics of an enzyme are studied...Ch. 8 - The same enzyme as in Problem 14 is studied in the...Ch. 8 - Enalapril is an anti-hypertension “pro-drug"...Ch. 8 - Initial rate data for an enzyme that obeys...Ch. 8 - Prob. 18PCh. 8 - Suggest the effects of each of the following...Ch. 8 - The inhibitory effect of an uncompetitive...Ch. 8 - Prob. 21PCh. 8 - Prob. 22PCh. 8 - Prob. 23PCh. 8 - In kinetics experiments, the hydrolysis of the...
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- Histidine is frequently used as a general acid or base in enzyme catalysis. Considering the pKa value of the side chain, suggest a reason why is this so?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_forwardRuBP 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?arrow_forward
- Using the appropriate graph and table above, explain what the N426S mutation appears to be doing to the enzyme’s function. Discuss the kinetic parameter changes and their meaning in this context, not the structure of the enzyme, which was not given to you.arrow_forwardA Lineweaver-Burk plot generates a line with the following formula: y = 0.3x + 0.4. What is the Km of this enzyme?arrow_forwardShown 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?).arrow_forward
- You are interested in purifying an enzyme X and decide to use an affinity chromatography followed by an enzymatic assay. You obtain the following data: Total volume of [protein] the sample (ml) (mg/mL) (U) |Total activity Sample name Specific activity |(U/mg) |Affinity | chromatography 2 0.12 5000 20833 You have obtained a 10X fold purification and a yield of 10% at the Affinity step. What was the protein concentration of your crude lysate sample, if its volume was 15 mL? Detail your answer by showing the calculations, and do not forget the UNITS!arrow_forwardAsp residue (both of which are essential for catalysis) with pK, 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? Explain your reasoning. (arrow_forwardThis question should be answered with two or three sentences using relevant biochemical vocabulary.arrow_forward
- The active site of lysozyme contains two amino acid residues essential for catalysis: Glu35 and Asp52. The pKa values of the carboxyl side chains of these residues are 5.9 and 4.5, respectively. What is the ionization state(protonated or deprotonated) of each residue at pH 5.2, the pH optimum of lysozyme? How can the ionization states of these residues explain the pH-activity profile of lysozyme shown below?arrow_forwardExperimental results describing a protein's amino acid composition are useful for estimating the molecular weight (MW) of the entire protein. A quantitative amino acid analysis reveals that bovine cytochrome c contains 1% tryptophan (M, 204) by weight. Calculate the approximate molecular weight of bovine cytochrome c if there is 1 tryptophan residue. Please enter your answer with three significant figures. approximate bovine cytochrome c MW: number of threonine residues: 19.4 20.4 x10³ Bovine chymotrypsinogen has a molecular weight of 25.6 kDa. Amino acid analysis shows that this enzyme is 9% threonine (M, 119). Calculate how many threonine residues are present in a molecule of bovine chymotrypsinogen. Round your answer to the nearest whole number. Incorrect Incorrect Daarrow_forwardThe enzymatic activity of lysozyme is optimal at pH 5.2 and decreases above and below this pH value. Lysozyme contains two amino acid residues in the active site essential for catalysis: Glu35 and Asp52. The pK value for the carboxyl side chains of these two residues are 5.9 and 4.5 respectively. What is the ionization state of each residue at the pH optimum of lysozyme? How can the ionization states of these 2 amino acid residues explain the pH-activity profile of lysozyme?arrow_forward
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