Biochemistry: Concepts and Connections
1st Edition
ISBN: 9780321839923
Author: Dean R. Appling, Spencer J. Anthony-Cahill, Christopher K. Mathews
Publisher: PEARSON
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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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A different Fab fragment binds to lysozyme with a dissociation constant of Ka 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?
[F] =
ab
M
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.
if 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)
Chapter 8 Solutions
Biochemistry: Concepts and Connections
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. 21P
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Need a deep-dive on the concept behind this application? Look no further. Learn more about this topic, biochemistry and related others by exploring similar questions and additional content below.Similar questions
- 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?arrow_forwardAn 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_forward
- Give 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_forwardAn Fab fragment binds to lysozyme with a dissociation constant of Ka = 10-11 M. A 1 nM (10-9 M) solution of lysozyme is treated with increasing concentrations of the Fab fragment. At what concentration of added Fab will half of the lysozyme be bound to the Fab? [Fab] 9.9 Incorrect nMarrow_forwardBacteriorhodopsin is an integral membrane protein containing 248 amino acids. X- ray analysis of this protein reveals that it consists of seven parallel a-helical segments, each of which traverses the bacterial cell membrane. Calculate the minimum number of amino acid residues necessary for a single a-helical segment to completely traverse the bacterial cell membrane (assume the membrane has a thickness of 4.1 nm). (a) (b) Estimate the fraction of the bacteriorhodopsin protein that is involved in membrane-spanning helices.arrow_forward
- 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
- 8) A Leu > Ala mutation at a site buried in the core of the enzyme lysozyme ends up being destabilizing. Explain why in terms of AH", AS" (for both the protein and solvent), and AG".arrow_forwardA bacterial lactose transporter, which is highly specific for lactose, contains a Cys residue that is essential to its transport activity. Covalent reaction of N-ethylmaleimide (NEM) with this Cys residue irreversibly inactivates the transporter. A high concentration of lactose in the medium prevents inactivation by NEM, presumably by sterically protecting the Cys residue, which is in or near the lactose-binding site. You know nothing else about the transporter protein. Suggest an experiment that might allow you to determine the Mr of this Cys-containing transporter polypeptide.arrow_forwardWhich of the following statements are descriptions of metal ion catalysis or examples of metal ion catalysis? Choose all correct answers a Zn²+ cofactor may properly orient the substrate in the active site through ionic interactions. a covalent bond forms between enzyme and substrate lowers the energy or stabilizes the transition state or intermediate catalyst retains its original form after reaction occurs catalysts may participate in oxidation-reduction reactions by changes in the oxidation statearrow_forward
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