The major difference between a protein molecule in its native stateand in its denatured state lies in the number of conformations avail-able. To a first approximation, the native, folded state can be thoughtto have one conformation. The unfolded state can be estimated tohave three possible orientations about each bond between residues.(a) For a protein of 100 residues, estimate the entropy change permole upon denaturation.(b) What must be the enthalpy change accompanying denaturationto allow the protein to be half-denatured at 50 °C?(c) Will the fraction denatured increase or decrease with increasingtemperature?

Proteins are macromolecules formed by amino acids. A total of 20 different amino acids exist in…

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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Similar questions

The vast majority of structures deposited in the Protein Databank (>95%) have been determined using NMR Hard keratins (such as in the skin) are less resistant to stretch because the larger number of disulfide bonds resist deformative forces. Structures produced by X-ray diffraction are as good as the solutions from which they are derived they are false and I know that but explain why they are false
Imagine the main chain of a protein bends back on itself, so that two amino acid residues R₁ and R₂ come close to each other. Here's what R₁ looks like: -CH- CH₂ CH₂ CH₂ CH₂ 1 NH3 Could R₁ form a salt bridge with R₂ at physiological pH, if R₂ were the right kind of residue? O yes O no If you said R₁ could form a sal bridge with R₂, what would R₂ have to be? 0 If there's only one possibility, write its 3-letter code. If there is more than one possibility, write the 3-letter code of any of them. X ? BEET 号图 Ar
Among these amino acid combinations listed above, only the combination of Lys and Glu have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein. Explain by drawing (a) why Lys and Glu side chain interaction stabilizes the tertiary structure of a protein (b) why the pairs of Glu and Asp & Arg and Pro cannot provide the stability to the protein structure.
(iii) Draw a structural diagram of a hydrogen bond between β-D-glucose and the side chain of any polar residue in a protein. (iv) Name the type of bond that can occur between the axial hydrogens of glucose and the indole ring of tryptophan. Draw a structural diagram of this bond. (v) Comment on the polar / apolar nature of the bond in part (iv) and explain why this type of interaction is prevalent in protein-sugar complexes. Answer (iii) to (v) please.
Estimate the length, in nm, of the four identical beta-strands drawn in blue in panel (B) of the image below, if they consists of only the amino residues of the two alpha-helices highlighted in purple in panel (A) of the image below. Assume that the amino acid residues of the two alpha-helices combined were folded in four beta-strands of identical length.
Patients suffering from sickle cell anemia have a mutation in the gene that codes for one of the hemoglobin chains, in which a single glutamate is replaced by a valine. Propose an explanation for why this substitution has such a striking effect on protein structure and function with explanation. Suggest two other amino acids that would be less likely to cause such serious impairment of hemoglobin function if each was substituted for glutamate. Briefly explain your answer.
Theoretical and experimental data show that in many cases the ionic and hydrogen-bonding interactions to ΔH for protein folding are close to zero. Provide an explanation for this result.
Consider the phenolic hydroxyl group of a particular Tyr residue in a protein. Suppose the hydroxyl group in the unfolded protein in aqueous solution, where the group is exposed to H2O, has a pKa of 10.0. If that group is found in a hydrophobic environment in the interior of the protein when the protein is folded into its native tertiary structure, would you expect the pKa of the phenolic hydroxyl to be higher or lower in the folded protein interior than in H2O? Explain your reasoning.
A protein has a dissociation equilibrium constant equal to 4.0um. What is the concentration of free ligand when the fraction of bound sites is 0.7
Suppose you have a solution of a protein, which contains a specific Tyr residue that has an actual (measured) pKa of 8.8. The protein binds a ligand by several noncovalent interactions, one of which is a hydrogen bond in which the Tyr phenolic hydroxyl group must serve as a hydrogen bond donor. Calculate the percentage of the protein molecules in which that tyrosyl residue's phenolic hydroxyl group could serve as a hydrogen bond donor at pH 8.5
An organic chemist is generally happy with 95% yields. If you synthesized a polypeptide and realized a 95% yield with each amino acid residue added, what would be your overall yield after adding 10 residues (to the first amino acid)? After adding 50 residues? After 100 residues? Would these low yields be biochemically “satisfactory”? How are low yields avoided, biochemically?
An enzyme contains an active site aspartic acid with a pKa = 5.0, whichacts as a general acid catalyst. On the accompanying template, draw thecurve of enzyme activity (reaction rate) versus pH for the enzyme (assumethat the protein is stably folded between pH 2–12 and that the active siteAsp is the only ionizable residue involved in catalysis). Briefly explain theshape of your curve.

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