Consider a small protein containing 101 amino acid residues. Theprotein will have 200 bonds about which rotation can occur. Assumethat three orientations are possible about each of these bonds.(a) Based on these assumptions, about how many random-coil con-formations will be possible for this protein?(b) The estimate obtained in (a) is surely too large. Give one reason why.

Random coil conformations is the conformation in which the monomeric forms of amino acids are…

Answered: Consider a small protein containing 101…

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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Which of the following statements are False? (i) Parallel b-sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and antiparallel B-sheets are usually arranged with all their hydrophobic residues on one side of the sheet. (ii) Planarity of the peptide bond means that no rotation occurs about the N-Ca bond while rotation is allowed about the C(O)-N and Ca-C(O) bonds. (iii) Silk fibers consist of fibroin proteins consisting of alternating A and G or S residues. (iv) If an aspartic acid residue were present in the interior of a globular protein, it would most likely be deprotonated and thus negatively charged.
(b) The structure of a drug called tirbanibulin which is used to treat a pre-cancerous skin condition called actinic keratosis is shown below. (i) (ii) (iii) (iv) ہے مههممنن State Lipinski's Rule of Five (ROF) and Veber's addition to the ROF. Briefly state why the ROF is used in medicinal chemistry?. Given that the molecular mass of tirbanibulin is 431.536 g.mol-¹ and its log P is 3.2, apply the ROF and Veber's additional rule to this drug and show clearly how you arrived at your answer. Comment on the outcome of your analysis of the structure in part (iii).
Under physiological conditions, the protein hemerythrin exists as anoctamer of eight chains of the kind.(a) Name two symmetries possible for this molecule.(b) Which do you think is more likely? Explain.(c) For the more likely symmetry, what kinds of interactions (isologous,heterologous, or both) would you expect? Why?
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.
Assume you were given a mixture consisting of one molecule each of all possible sequences of a smallish protein of molecular weight 4800 daltons. If the average molecular weight of an amino acid is, say, 120 daltons, how much would the sample weigh? How big a container would you need to hold it?
What would you predict about the ratio of hydrophilic to hydro- phobic amino acid residues in a series of monomeric globular proteins that range in size from a molecular weight of 10,000 g/mole to a molecular weight of 100,000 g/mole? Note that the volume of a sphere is 4/3nr³, while the sur- face area of the outside of a sphere is 4nr². How would your prediction change if the monomeric proteins were fibrous instead of globular?
You are working at a major pharmaceutical company, and you have purified an engineered enzyme, and you need to determine the protein stability (kJ/mol). Accordingly, you have collected equilibrium unfolding data using the chemical denaturant urea at 20°C, pH 7.5 and I atmosphere using fluorescence spectroscopy. a) Determine the protein stability (AG [kJ/mol]) via nonlinear least squares (using the available data). b) Write the partial differential equation (i.e., general functional form, variable, constants). c) Describe what would happen to the isotherm if the temperature was increased to 25 °C. Urea [M] 0 0.25 0.5 0.75 1 1.25 1.5 2 2.25 2.5 2.75 3 3.25 3.5 3.75 4 4.25 4.5 4.75 5 FL 340nm 316 315.5 315 314.5 314 315 300 275 225 125 75 60 55 54 53 52.5 52.25 52 51.75 51.5 dG = Vdp-SdT+μA dnд + μB dng dGp = μA dnA+ μg dng A = Folded State B = Unfolded State
One technique that is used when attempting to solve the crystal structure of a large protein is not to solve the structure of the whole protein itself. Instead, the protein is broken down into smaller components and the structure of the smaller components is what is solved. Of course, when performing this technique, it must be ensured that the process of breaking down the protein into smaller components does not drastically change the structure of the smaller components. With this in mind, where would be the best locations to cut a protein? At the beginning and end of secondary structures. At beginning and end of protein domains. O At the beginning and end of motifs. At the beginning and end of protein subunits.
A protein hypothetically consists of two polypeptide chains with the given sequences in the picture. Based on the said sequences, a. Do you think it is possible that interchain disulfide bonds is present in the protein? Explain. b. Do you think it is possible that intrachain disulfide bonds is present in the protein? Explain.
A researcher isolates a new protein and finds that it contains 0.755% serine by weight upon amino acid analysis. The molecular mass of serine is 105 g.mol-¹. What is the minimum molecular mass for the protein assuming only one Ser residue per protein molecule? mmin = The researcher estimates the molecular mass of the protein using gel electrophoresis. From this estimated molecular mass, the researcher concludes the protein contains 3 Ser residues. What is the estimated molecular mass of the protein as shown by gel electrophoresis? g.mol-¹ mest = g.mol-1
The major difference between a protein molecule in its native state and in its denatured state lies in the number of conformations avail- able. To a first approximation, 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 mole upon 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 increasing temperature?

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