Concept explainers
Answers to all problems are at the end οf this book. Detailed solutions are available in the Student Solutions Manual. Study Guide, and Problems Book.
Understanding the Implications of Transition State Stabilization
As noted in Section 14.4. a true transition state can bind to an enzyme active site with a KT as Low as 7 X 10-26 M. This is a remarkable number, with interesting consequences. Consider a hypothetical solution of an enzyme in equilibrium with a ligand that binds with a KD of 10-27 M. If the concentration of free enzyme. [EL]. is equal to the concentration of the enzyme-ligand complex. [EL], what would [L]. the concentration of free ligand, be? Calculate the volume of solution that would hold one molecule of free ligand at this concentration.
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Biochemistry
- Answers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Graphical Analysis of Negative Gooperativity in KNF Allosteric Enzyme Kinetics The KNF model for allosteric transitions includes the possibility of negative cooperativity Draw Lineweaver-Burk and Hanes-Woolf plots for the case of negative cooperatively m substrate binding. (As a point of reference, include a line showing the classic Michaelis-Menten response of v to [S].)arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. How Varying the Amount of Enzyme or the Addition of Inhibitors Affects v Versus [S] Plots Using Figure 13.7 as a model, draw curves that would be obtained in v versus [S] plots when a. twice as much enzyme is used. b. half as much enzyme is used. c. a competitive inhibitor is added. d. a pure noncompetitive inhibitor is added. e. an uncompetitive inhibitor is added. For each example, indicate how Vmax and Km change.arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Determining the Branch Points and Reducing Ends of Amylopectin A 0.2-g sample of amylopectin was analyzed to determine the fraction of the total glucose residues, that are branch points in the structure. The sample was exhaustively methylated and then digested, yielding 50-mol of 2,3-dimethylgluetose and 0.4 mol of 1,2,3,6- letramethylglucose. What fraction of the total residues are branch points? I low many reducing ends does this sample of amylopectin have?arrow_forward
- Answers to all problems are at the end οΓthis book. Detailed solutions are available in the Student Solutions Manual. Study Guide, and Problems Book. Using Site-Direcled Muta.nts to Understand an Enzyme Mechanism In this chapter, the exponent in which Craik and Rutter replaced Asp102 with Asn in trypsin (reducing activity 10,000 -fold) was discussed. On the basis of your knowledge of the catalytic triad structure in trypsin, suggest a structure for the “uncatalytic triad of Asn-His-Ser in this mutant enzyme. Explain why the structure you have proposed explains the reduced activity of the mutant trypsin. See the original journal articles (Sprang, et al., 1987. Science 237:905-913) to Craik, et al., 1987. Scieence 237:909-913) to see Craik and Rutter's answer to this question.arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Quantitative Relationships Between Rate Constants to Calculate Km, Kinetic Efficiency (kcat/Km) and Vmax - I Measurement of the rate constants for a simple enzymatic reaction obeying Michaelis-Menten kinetics gave the following results: k1=2108M1sec1k1=1103sec1k2=5103sec1a. What is Ks, the dissociation constant for the enzyme-substrate complex? b. What is Km, the Michaelis constant for this enzyme? c. What is kcat (the turnover number) for this enzyme? d. What is the catalytic efficiency (kcat/Km) for this enzyme? e. Does this enzyme approach kinetic perfection? (That is, does kcat/Km approach the diffusion-controlled rate of enzyme association with substrate?) f. If a kinetic measurement was made using 2 nanomoles of enzyme per mL and saturating amounts of substrate, what would Vmax equal? g. Again, using 2 nanomoles of enzyme per mL of reaction mixture, what concentration of substrate would give v = 0.75 Vmax? h. If a kinetic measurement was made using 4 nanomoles of enzyme per mL and saturating amounts of substrate, what would Vmax equal? What would Km equal under these conditions?arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Assessing the Formation and Composition of Limit Dextrins Prolonged exposure of amylopectin to starch phosphorylase yields a substance called a limit dextrin. Describe the chemical composition of limit dextrins. and draw a mechanism for the enzyme-catalyzed rcactioa that can begin the breakdown of a limit dextrin.arrow_forward
- Answers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Calculating and Keq for Coupled Reactions For the process A B. Keq (AB) is 0.02 at 370C. For the process B C. Keq (BC)=1000 at 370C. Determine Keq (AC), the equilibrium constant for the overall process A C, from Keq((AB) and (BC). Determine standard-state free energy changes for all three processes, and use G. (AC) to determine Keq (AC). Make sure that ibis value agrees with that determined m part a of this problem.arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Quantitative Relationships Between Rale Constants to Calculate Km, Kinetic Efficiency (kcat/Km) and Vmax - II Triose phosphate isomerase catalyzes the conversion of glyceraldehyde-3-phosphate to dihydroxy-acetone phosphate. Glyceraldehyde3PdihydroxyacetonePThe Km of this enzyme tor its substrate glyceraldehyde-3-phosphate is 1.8 10-5 M. When [glyceraldehydes-3-phosphate] = 30 M, the rate of the reaction, v, was 82.5 mol mL-1 sec-1. a. What is Vmax for this enzyme? b. Assuming 3 nanomoles per mL of enzyme was used in this experiment ([Etotal]) = 3 nanomol/mL), what is kcat for this enzyme? c. What is the catalytic efficiency (kcat/Km) for triose phosphate isomerase? d. Does the value of kcat/Km reveal whether triose phosphate isomerase approaches catalytic perfection? e. What determines the ultimate speed limit of an enzyme-catalyzed reaction? That is, what is it that imposes the physical limit on kinetic perfection?arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. (Research Problem) The Nature and Roles of Linear Motifs in Proteins In addition to domains and modules, there are other significant sequence patterns in proteins—known as linear motifs—that are associated with a particular function. Consult the biochemical literature to answer the following questions: 1. What are linear motifs? 2. How are they different from domains?. 3. What are their functions? 4. How can they be characterized? 5. There are several papers that are good starting points for this problem. Neduva, V., and Russell, R., 2005. Linear motifs: evolutionary interaction switches. FEBS Letters 579:3342-3345. Gibson, T., 2009. Cell regulation: determined to signal discrete cooperation. Trends in Biochemical Sciences 34:471-482. Diella, K. Haslam, N., Chica., C. et aL, 2009. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Frontiers of Bioscience 13:6580-6603.arrow_forward
- Answers to all problems are at the end οΓthis book. Detailed solutions are available in the Student Solutions Manual. Study Guide, and Problems Book. Consult the following reference (Samanta U. and Bahnson. B. J., 2008. Crystal structure of human plasma platelet-activating factor acetylhydrolase. Journal of Biological Chemistry 283:31617-3U624). consider the active-site structure of this enzyme in the Light of material in this chapter, and write a detailed mechanism for the PAF acetylhydrolase.arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Exploring the Michaelis-Menten Equation - II If Vmax=100mol/mLsecand Km=2mM, what is the velocity of the reaction when [S] = 20 mM?arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. General Controls Over Enzyme Activity List six general ways in which enzyme activity is controlled.arrow_forward
- BiochemistryBiochemistryISBN:9781305577206Author:Reginald H. Garrett, Charles M. GrishamPublisher:Cengage Learning