2) A group of three researchers (who often tend to disagree with one another) isolated a new proteinand found that the gene sequence of this protein contained a Cys-X3-Cys-X2-Cys-X2-Cys motif (whereX is any amino acid).а)you agree? Briefly explain why (or why not).One of the researchers suggested that this must be an enzyme containing a Mn-cluster. Dob)center and this Zn site must have a structural (rather than catalytic) role. Do you agree (ordisagree) that this would indeed be a structural Zn site? Briefly explain.The second researcher instead claimed that this must be a protein containing a single Zn

Protein: It is a macromolecule that is made up of amino acids joined together with a Polypeptide…

Answered: 2) A group of three researchers (who…

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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Consider a short peptide that forms an alpha-helix within a larger protein structure. Suppose that one glutamate residue at some specific position in the helix were mutated to a leucine residue. The mutation could either make the helix more stable, or less stable. i) Describe two situations in which a Glu-to-Leu mutation could make the helix more stable. ii) Describe two situations in which the Glu-to-Leu mutation could make the helix less stable. Explain briefly the basis for the stabilizing and destabilizing effect in all cases.
In a mixed heteropolymer experiment, messages were createdwith either 4/5C:1/5A or 4/5A:1/5C. These messages yielded proteinswith the amino acid compositions shown in the followingtable. Using these data, predict the most specific coding compositionfor each amino acid.4/5C:1/5A 4/5A:1/5CPro 63.0% Pro 3.5%His 13.0% His 3.0%Thr 16.0% Thr 16.6%Glu 3.0% Glu 13.0%Asp 3.0% Asp 13.0%Lys 0.5% Lys 50.0% 98.5% 99.1%
. Disulfide bonds have been shown to stabilize proteins (i.e., make them less likely to unfold). Consider the cases shown schematically below for two variants of the same protein. In case #1 the disulfide forms between Cys residues that have been introduced near the protein N- and C-termini, and in case #2 the disulfide forms between Cys residues that have been introduced in the middle of the protein sequence. Which protein is likely to be more stable? (Note: Assume the disulfide bond is intact in both the unfolded and folded states). Explain your reasoning.
In most cases, mutations in the core of a protein that replace a smaller nonpolar side chain in the wild-type (e.g., Ala, Val) with a larger nonpolar side chain (e.g., Leu, Ile, Phe, Trp) in the mutant, result in significant destabilization and misfolding of the mutant. What feature of the protein core explains this observation? Why would such a mutation prevent a protein from folding properly?
Imagine a globular protein with a histidine that is involved in a salt bridge to an aspartic acid, in an internal (hydrophobic) region of the protein. What would happen to the pKa of that histidine R group if the protein was mutated, and the aspartic acid was replaced with an alanine? (i.e., would the pKa increase, decrease, or stay the same?). Assume that the location of the histidine stays the same. Explain your answer clearly
When performing his experiments on protein refolding, Christian Anfinsen obtained a quite different result when reduced ribonuclease was reoxidized while it was still in 8 M urea and the preparation was then dialyzed to remove the urea. Ribonuclease reoxidized in this way had only 1% of the enzymatic activity of the native protein. Why were the outcomes so different when reduced ribonuclease was reoxidized in the presence and absence of urea?
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 post doc was working on charaterizing a new enzyme and found that in a 357 amino acid enzyme, the amino acids 33,34,35 and amino acids 301,303,306 form one active site. Q1:As the PI, would you tell him 1) that this result doesn't make any sense or 2) that this is a interesting finding? Explain your answer Q2: if the amino acid residues 33,34,35 were Phe,Val, and Ala, would this be possible to occur?
In the fungus Neurospora, some mutants were obtainedthat lacked activity for a certain enzyme. The mutationswere found, by mapping, to be in either of two unlinkedgenes. Provide a possible explanation in reference to quaternary protein structure
At physiological pH (i.e. 7.4), polylysine assumes a random structure in solution. Given that the pKa for the e-amino group of lysine is 10.5, under what conditions would you expect polylysine to form an a-helix? Explain your reasoning. Under what conditions would you expect polyglutamate to form an a-helix, given that the pKa for the side-chain COOH group is 4.3?
If an Arg residue in a protein was replaced with either Lys or Glu amino acid, whichsubstitution would you expect to result in the greatest structural change and why?
Considering the chemical characteristics of the amino acids valine and glutamic acid (see Figure 5.14), propose a possible explanation for the dramatic effect on protein function that occurs when valine is substituted for glutamic acid.

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