The major difference between a protein molecule in its native state and in itsdenatured state lies in the number of conformations available. To a first ap-proximation, the native, folded state can be thought to have one conforma-tion. The unfolded state can be estimated to have three possible orientationsabout cach bond between residues.(a) For a protein of 100 residues, estimate the entropy change per mole upondenaturation.(b) What must be the enthalpy change accompanying denaturation to allowthe protein to be half-denatured at 50 °C?(c) Will the fraction denatured increase or decrease with increasingtemperature?

The Native state of a protein is the functional three-dimensional form of a protein. The Native…

Answered: The major difference between a protein…

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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The major difference between a protein molecule in its native state and inits denatured state lies in the number of conformations available. To a firstapproximation, the native, folded state can be thought to have one conformation. The unfolded state can be estimated to have three possible orientations about each bond between residues.(a) For a protein of 100 residues, estimate the entropy change per moleupon denaturation.(b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C?(c) Will the fraction denatured increase or decrease with increasingtemperature?
Peptides and small proteins fold spontaneously in aqueous solution at room temperature. Thus, for a small protein in water, we can say ΔG FOLD < 0. Denoting the unfolded protein as Unf and the folded protein as Fld, we can write the following equation:Unf(aq)--DELTA G FOLD----> Fld(aq)Considering the transition from the unfolded state (in which there are many possible conformations) to the folded state (only one conformation), there is clearly a decrease in the entropy of the protein. However, protein folding is (correctly) described as an entropically driven process.a) Resolve this apparent paradox by identifying the enthalpy (ΔH) and entropy (−TΔS)components involved in protein…
Which intermolecular forces are important in acetic acid, CH3 –(C=0)-oh? A particular amino acid contains a- CHNH3+ group. Is this amino acid more likely to be found on the inside or the outside of the folded protein? Briefly explain. The addition of ethanol, CH3CHOH, t an aqueous solution lowers the surface tension of the solution. Predict whether adding ethanol to an aqueous protein solution will tend to stabilize or unfold the protein. Briefly explain.
The dissociation constant, Kd for a complex between protein A and protein B is 4.1 μM. If the two proteins are mixed together at initial concentrations of [A]= 0.025 μM and [B] = 4.7 μM, calculate (a) the equilibrium concentrations of A, B, and AB (the dimer formed by A and B) (b) the percentage of A bound to B
Assume that some protein molecule, in its folded native state, has onefavored conformation. But when it is denatured, it becomes a “random coil,” with many possible conformations.(a) If we only consider the change in entropy for the protein, what mustbe the sign of ΔS for the change: native → denatured? (Note: As suggestedin the next problem, this does not include solvent effects, which also make significant contributions to ΔS.)(b) How will the contribution of ΔS for native → denatured affect thefavorability of the process? What apparent requirement does this imposeon ΔH if proteins are to be stable structures?
Consider a protein with two surface-exposed histidine residues: HisA is a “typical” histidine residue with a pKa = 6.2 HisB is involved in a stabilizing interaction (His-NH+ ..... -O2C-Glu) with a neighboring glutamic acid residue. For HisB, the Gibbs free energy of deprotonation at pH = 7.0 and T = 293K is ΔG'o = +15 kj mol-1. If you had a solution, at pH = 7.0 and T = 293K, containing this protein: a) What fraction of HisA residues are protonated? b) What fraction of HisB residues are protonated? c) What is the pKa of HisB?
Consider a small protein containing 101 amino acid residues. The proteinbackbone will have 200 bonds about which rotation can occur. Assume thatthree orientations are possible about each of these bonds.(a) Based on these assumptions, about how many random-coil conformationswill be possible for this protein?(b) The estimate obtained in (a) is surely too large. Give one reason why.
Consider a protein in which a negatively charged glutamic acid side chain (pKa = 4.2) makes a salt bridge (ion–ion interaction) with a positively charged histidine side chain (pKa = 6.5). (a) Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5? (b) Justify your answer with calculations of partial charges on these amino acid side chains.
Consider a protein in which a negatively charged glutamic acid side chain(pKa = 4.2) makes a salt bridge (ion–ion interaction) with a positively charged histidine side chain (pKa = 6.5).(a) Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5?(b) Justify your answer with calculations of partial charges on these aminoacid side chains.
. Assume that some protein molecule, in its folded native state, has one favored conformation. But, when it is denatured, it becomes a "random coil," with many possible conformations. (a) What must be the sign of AS for the change: native → denatured? (b) How will the contribution of AS for native → denatured affect the favorability of the process? What apparent requirement does this impose on AH if proteins are to be stable structures?
A cytosolic protein has an important alpha amino group. The pKa of this group is approximately 8 when exposed to water outside of a protein. 1. What would happen to the pKa if this group was instead buried in the hydrophobic interior of the protein? Explain. 2. Let’s say in the hydrophobic interior of the protein, the group forms an ionic bond with a carboxylate group of the side chain of a charged Asparagine residue. How would the pKa of this alpha amino group compare with the pKa of the alpha amino group in the hydrophobic interior of the protein without a nearby Asparagine residue to form this ionic bond? Explain.
Calculate and compare the approximate MW of a protein with 682 amino acid residues in a single polypeptide chain and ahomotrimeric protein with 227 amino acid residues in each subunit.

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