M 4 Now, assume that a hypothetical two-subunit hemoglobin has an n of 2. The ratio of the concentrations of the T and R stateswith no ligands bound, or L, is 1000. The dissociation constant for a ligand binding to a single site in the R state, KR, is 1 torr.The ratio of the dissociation constants KR and KT, or c, is 0.01.Using the concerted model, which oxygen-binding curve best represents the hypothetical two-subunit hemoglobin?1.01.00.80.80.60.6Если ва0.40.40.20.20I I J0I050 100 150 20050 100 150 200po₂ (torr)po₂ (torr)1.01.00.8KU50 100 150 2000.60.40.2 -00po₂ (torr)0.80.60.4D0.2050J100 150 200po₂ (torr)

Our hypothetical Hemoglobin (Hb) consists of 2 subunits . 'n' denotes the number of binding sites in…

Answered: Now, assume that a hypothetical…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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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.
A protein-ligand binding reaction is run. At equilibrium, half the protein is ligand bound, the unboundligand concentration is 0.657 nM. Calculate the koff value for this reaction. Assume the kon value is typical ofprotein-ligand interactions.
An antibody binds to another protein with anequilibrium constant, K, of 5 × 109 M–1. When it binds toa second, related protein, it forms three fewer hydrogenbonds, reducing its binding affinity by 11.9 kJ/mole. Whatis the K for its binding to the second protein? (Free-energychange is related to the equilibrium constant by the equa-tion ΔG° = –2.3 RT log K, where R is 8.3 × 10–3 kJ/(mole K)and T is 310 K.)
Consider the dissociation reaction for a protein-ligand complex: P•L P + L A. Sketch a binding curve (fractional saturation θ vs. ligand concentration [L]) for this protein-ligand complex (ligand A). Show where on that curve you could obtain the dissociation equilibrium constant Kd for the reaction. B. Now sketch on the same axes a θ vs. [L] plot for a different ligand (B) that binds more weakly than the first ligand. C. Does the weaker binding ligand have a higher, or lower, Kd than the tighter binding ligand? D. Sketch a binding curve for a cooperatively bound ligand with K0.5 higher than that of Kd for A or B. (Note: for cooperative binding, each protein molecule would have to have more than 1 binding site for the ligand; K0.5 is the experimentally determined ligand concentration that gives θ = 0.5.)
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?
If instead of using 3.5 µM myoglobin (receptor) you used half of this (that is, 1.75 µM myoglobin), what would be that value of the Kd, that you calculated ( how would it change)? Please explain so I can solve on my own :) (How does changing concentration of the receptor in a ligand-receptor binding experiment affect the dissociation constant?)
The hexapeptide Ala-Met-Leu-Lys-Phe-Asp is digested in the same tube with both Cyanogen Bromide and Trypsin at the same time at pH=7. Draw the structure of the product(s) that would bind to a cation exchange column. (Relevant pKa values are 2.2, 3.9, 9.5 and 10.5. Assume pKa values for any newly generated a-amino and a-carboxyl groups are 9.5 and 2.2 respectively)
Which of the following situations would produce a Hill plot with nH < 1.0? Explain your reasoning in each case.(a) The protein has multiple subunits, each with a single ligand-binding site. Binding of ligand to one site decreases the binding affinity of other sites for the ligand.(b) The protein is a single polypeptide with two ligand-binding sites, each having a different affinity for the ligand.(c) The protein is a single polypeptide with a single ligand-binding site. As purified, the protein preparation is heterogeneous, containing some protein molecules that are partially denatured and thus have a lower binding affinity for the ligand.
An experiment was carried out to measure the reaction rate of hydrolysis of acetylcholme (substrate) with serum enzymes (Eadie, 1949). In the experiment, two experiments were conducted, namely experiment 1 without using a prostigmine inhibitor and experiment 2 using a prostigmine inhibitor at 1.5 x 10^-7 mol/l. the data obtained are: a. Is prostigmine competitive or noncompetitive inhibitor? b. determine the value of km and rmax for the two experiments, compare
In a molecular disease of hemoglobin, Hemoglobin Rainier, Tyr 145β is replaced by Cys, which forms a disulfide bond with another Cysresidue in the same subunit. This prevents the formation of ion pairs that normally stabilize the T state. How does hemoglobin Rainier differ from normal hemoglobin with respect to the Hill coefficient
An enzyme has the following values: vmax's; 0.028 M s-' and 0.021 M s-' (I), and km's; 0.00198 M and 0.00197 M (I), when the total concentration of enzyme is 10-º M. The (I) values were determined with 1 microM inhibitor. Select the value closest to the k, for this enzyme. (hint 1 microM = 10-6 M).
affinity of a protein-protein or protein-ligand interaction can be described by the Dissociation Constant, Kd (written below). Consider a protein P and its inhibitor, I. I inhibits P's activity when bound to it: koff _ [A][B] Dissociation Constant: Ka = koN [AB] Question When [I] is 10-7 M, 99% of P's activity is inhibited. What is the Kd of this Protein- Inhibitor interaction?

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