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 5P
In some reactions, in which a protein molecule is binding to specific site on DNA, a rate greater than that predicted by the diffusion limit is observed. Suggest an explanation. [Hint: The protein molecule can also bind weakly and nonspecifically to any DNA site.]
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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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- Some of the following four amino acids : alanine, arginine, histidine, aspartic acid would provide a side chain for acid-base catalysis at physiological pH (assume pK of each amino acid is equal to pK value for the free amino acid in solution). Explain for each amino acid how and why each would or would not provide the side chain residue to support acid-base catalysis at physiological pH.arrow_forwardif the reaction pH drops significantly (pH=2 for example), how would reaction catalyzed be serine proteases be affected? why? (assumin that the rest of the protein structure remain intact)arrow_forwardConsider 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?arrow_forward
- An engineered ligand binds its target with 5 nM affinity at high pH. However, protonation of a histidine residue in the binding site of the ligand renders it unable to bind. Plot the ligand:target complex concentration versus the initial ligand concentration (in protonated or unprotonated form) at pH 4, 5, 6, 7, or 8 (five lines on one plot). Use a total target concentration of 10 nM.arrow_forwardA different Fab fragment binds to lysozyme with a dissociation constant of Kd=10-6 M. A 1 nM (10-9 M) solution of lysozyme is treated with increasing concentrations of this Fab fragment. At what concentration of added Fab will half of the lysozyme be bound to this Fab?arrow_forwardGive the general Adiar equation for the binding of a ligand to a dimeric protein. Explain further what your understanding is of the terms "no-, positive-, and negative cooperativity” and graphically present the relationship between Ȳ and [S] for each of these cases. Also, give the relationship between the constants Kb1 and Kb2 in each case.arrow_forward
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- The process of a protein folding from an inactive unfolded structure to theactive folded structure can be represented by the following equation: unfolded protein ⇌ folded proteinThe values of ΔH° and ΔS° for the folding of the protein lysozyme are: ΔH ° = -280 kJ/ mol ΔS ° = -790 J/mol • K(a) Calculate the value of ΔG° for the folding of lysozyme at 25 °C.(b) At what temperature would you expect the unfolding of lysozyme tobecome favorable? (c) At what temperature would the ratio of unfolded protein to foldedprotein be 1:5?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_forwardDo letter 4 and draw a titration curve as directed in letter 4 c) for pka 4.7, labelling all the axes.arrow_forward
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