7.What is an allosteric effect? What is are homotropic and heterotropic allostery? Name one exampleof homotropic allostery.8.The graph below describes the binding curve of three difference proteins to the same ligand (L).(a) Define what ¤, [L] and Kå signify on this graph.(b) Which protein has the highest affinity for the ligand?(c) Do these proteins bind the ligand cooperatively? Why or why not?(d) For the binding reaction described in the green curve, at which concentration of L would 50% ofthe binding sites be occupied? Why?Ꮎ0.5K=1 nMK=10 nM0.0+ŏ K₁K=100 nM20406080[L] (nM)

Q. 8. ANSWER. (a) θ (Theta): This represents the fraction of protein molecules that bind to the…

Answered: 7.What is an allosteric effect? What is…

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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12 mM of protein A is combined with 6 mM of ligand X in water. After the protein-ligand complex binding reaches equilibrium, you measure that the free ligand concentration is 3 mM and the concentration of protein-ligand complex is 3 mM. What is the Kd for protein A? Although they would be in mM, do not include units in your answer, only the number as a whole integer.
Calculate the concentration of the ligand required to fill 25% of the binding site. X+A ⇌ XA , ka = 1.5 ×10-6 Y+A ⇌ YA , ka = 4.7 × 10-4 (i.e, q = 0.25) for both proteins.
Two proteins, A and B, bind to the same ligand, L, with the binding curvesshown below. What is the dissociation constant, Kd , for each protein? Which protein (A or B) has a greater affinity for ligand L?
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.
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.)
6) Proteins can be modified by phosphorylation, which adds a phosphate group to the hydroxyl group of serine, threonine, or tyrosine residues. The R-group for phosphoserine is shown at right. A) The image below is an Isoelectric focusing strip that shows the unphosphorylated protein-of-interest (in blue). To which side of the unphosphorylated protein would you expect to see the phosphorylated protein? (Draw an arrow to indicate direction). Briefly justify your answer. un-phosphorylatable: Low pH Justify: B) To study the effects of phosphorylation, researchers often mutate a Ser/Thr to appear as though it is always phosphorylated or never phosphorylated at a particular site. What amino acid substitution should you use to preserve similar dimensions as Ser (or Thr) but make the side chain appear to be: constitutively (always) phosphorylated: Justify: Ser or Thr → O O=P-O O I CH₂ Ser or Thr➜ Phosphoserine High pH
Three different ligands, Ligand Q, Ligand T, and Ligand W, bind to the same protein but with different affinity: The association constant (Ka) for the binding of Ligand Q to the protein is 0.033 nM-1. The fractional saturation (Y) of the protein is 0.20 when the concentration of Ligand T is 1.25 nM. The fractional saturation (Y) of the protein is 0.80 when the concentration of Ligand W is 72 nM. Given this information, Calculate Kd for the binding of each ligand to this protein. Which ligand binds with greatest affinity? Which ligand binds with the lowest affinity?
6. For a 1:1 ligand-receptor binding interaction that is modeled by X + Y XY : (A) Show how the fraction of ligand-receptor binding (fo) is represented by the [X] [X]+ K, equation of f, (i.e., derive this expression for this reaction beginning eg with the relationship for K = f([X].[X],[XY]) under equilibrium conditions). (B) shown to the right for this reaction, what is the estimated value of Keg? Give your answer in units of M. For the data plot 0.9 0.8 0.7 0.6 문 0.5 0.4 0.3 0.2 0.1 0.0000 0.0050 0.0100 0.0150 0.0200 0.0250 0.0300 0.0350 0.0400 [X) (mM)
Crystal structures exist for three neurokinin-1 (NK1) ligand complexes with the following pdb codes (6hll, 6hlo, 6hlp) For each of the three crystal structures identify four amino acids in the NK1 binding site that contact the ligand indicating both the residue type in three letter code and the residue number. One of the chose amino acids should form a hydrogen binding interaction to the ligand, state which functional group the amino acid utilises in each case
A binding protein binds to a ligand L with a Kd of 400 nM. How much ligand is present when Y is (a) 0.25, (b) 0.6, (c) 0.95?
Protein A has a binding site for ligand X with a Kd of 10 −6 M. Protein B has a binding site for ligand X with a Kd of 10 −9 M. Which protein has a higher affinity for ligand X? Explain your reasoning. Convert the Kd to Ka for both proteins.
A quantitative amino acid analysis reveals that bovine serum albumin (BSA) contains 0.58% tryptophan (Mr 204) by weight.(a) Calculate the minimum molecular weight of BSA (i.e., assume there is only one Trp residue per protein molecule).(b) Size-exclusion chromatography of BSA gives a molecular weight estimate of 70,000. How many Trp residues are present in a molecule of serum albumin?

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