**Peptide Bond Isomerization in Protein Folding**Peptide bonds involving the amino acid proline can exist in both "trans" and "cis" isomeric forms. The isomerization reaction between these forms can be a rate-limiting step in protein folding. In certain proteins, such as staphylococcal nuclease with a specific proline residue (Pro-117), the rates of transformation between these isomers are given by the following constants:- Forward reaction (\(k_\text{{trans→cis}}\)): \(3.1 \times 10^{-2}\, \text{s}^{-1}\)- Reverse reaction (\(k_\text{{cis→trans}}\)): \(2.5 \times 10^{-3}\, \text{s}^{-1}\)The diagram illustrates the chemical structures of the trans and cis isomers of proline, alongside the equilibrium between them.### Questions:**(a)** What is \(\Delta G^\circ\) for this reaction?**(b)** A prolyl isomerase enzyme increases the rate of the forward reaction to \(k_\text{{cat, trans→cis}} = 2.6\, \text{s}^{-1}\).- What is the new rate constant for the reverse reaction (\(k_\text{{cat, cis→trans}}\))?**(c)** This prolyl isomerase follows Michaelis-Menten kinetics with:- \(k_\text{{cat}} = 2.6\, \text{s}^{-1}\)- \(K_M = 1.9\, \mu\text{M}\)Given:- Enzyme concentration \(= 1\, \text{nM}\)Evaluate \(V_0\) for the following substrate concentrations:- \([S]_0 = 0.7\, \mu\text{M}\)- \([S]_0 = 30\, \mu\text{M}\)For each condition, identify what limits the reaction speed.

Michaelis-Menten model of enzyme kinetics is a very useful model which describe the relationship…

Answered: 2. As we've seen previously, peptide…

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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2. Consider the following quaternary cartoon structure below, where each colored shape represents a different subunit. i. ii. iii. How many N-termini are there in this complex? Suppose the blue square and orange triangle subunit are held together by a disulfide bond, sketch below what you would expect to see after the addition of BME. What kind of interactions may be responsible for holding the orange triangle and green circle subunits together? List at least three.
2. The diagram to the right shows the change in the structure of the C-terminal portion of each of the ẞ-subu- nits of human hemoglobin (HbA) in the oxyHb to deox- yHb or R-to-T transition. The hydrogen bonding interac- tion of the C-terminal ẞHis 146 residue with the side chain of Asp94, highlighted by the red ellipse, has been shown to be responsible for a major portion of the proton uptake associated with the Bohr effect. Treatment of HbA with the enzyme carboxypeptidase A (CPA) results in loss of the C-terminal ẞHis 146 and ẞTyr145 residues of the ẞ- subunits. (a) ( ) Draw a Hill plot [log(Y/[1-Y]) vs. log(pO2), Y = fraction of heme groups occupied by O2] to compare the values of the Hill coefficient nн and the O2-binding affinity at pH 7.4 of normal HbA before and after treat- ment of with CPA. (b) (' ) How will the plot for CPA-digested HbA change at pH 7.2? (c) 1 Hi5146 HN- ✓ Low PK B-chain. CH2 CH-NH-CO-CH-NH- CH₂ Tyr145 он HbO2 or R state Туг145 CH-CH2- OH co NH CH CH₂ His…
2. Chymotrypsin, trypsin, and elastase are members of a family of enzymes referred to as serine proteases. The enzyme papain (found in papaya) is also a protease but is a member of a family of enzymes referred to as cysteine proteases. The amino acid residues in the active site of papain critical for peptide bond hydrolysis are a protonated histidine and a deprotonated cysteine residue. The cysteine residue functions as the nucleophile similarly to the serine residue in serine proteases. (a) Using what you know about chymotrypsin's mechanism, draw a reaction mecha- nisn for the hydrolysis of a peptide bond by papain. Does the mechanism you have drawn employ acid-base catalysis, covalent catalysis, (b) or both? (c) The pKa values of the active site residues that control the pH profile of the activity of pa- pain are 4.2 and 8.2. The pH optimum for the reaction is 6.0. Through the many years of re- search carried out on cysteine proteases, it has been demonstrated that the pKa of 4.2…
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5. Refer to Model 2 for information relevant to this question. A sample of the peptide Lys-Glu-Ser has a net charge of zero between what two pH values? What is the pl of Lys-Glu-Ser? Model 2: The pl of a peptide is determined by examining the ionizable groups. The protonated and unprotonated forms of each ionizable group are in equilibrium. Consider the peptide Lys-Glu-Ser shown below at pH 7.2. The complete structure is on on the left and a stylized structure with just the ionizable groups is on the right. While the N-terminal is depicted as protonated, a sample of Lys-Glu-Ser is composed of a population of molecules and within that population some molecules contain a non-protonated N-terminal group at pH 7.2. may H3N* COO- H3N-CH-CIN-CH C N-CH C- H. pK 3.5 OH H. pK= 8.5 COO- CH2 CH2 CH2 NH, pK 10.0 pK 4.2 CH2 CH2 OH CH2 c=0
5. Heparin, a highly negatively charged glycosaminoglycan, is used clinically as an anticoagulant. It acts by binding several plasma proteins, including antithrombin II, an inhibitor of blood clotting. The 1:1 binding of heparin to antithrombin III seems to cause a conformational change in the protein that greatly increases its ability to inhibit clotting. What amino acid residues of antithrombin III are likely to interact with heparin?
1. Sickle cell anemia results from a substitution of a valine for a glutamic acid. What do you expect the effect might be if the mutation were to have placed a leucine at that site? An aspartic acid? 2. Of the following amino acids, glycine, isoleucine, and lysine, which would you expect to be the most soluble in an acidic aqueous solution? Which the least? 3. How many structural isomers could be formed from a molecule with the formula C5H12? C4H8?
4. You're working on a structure of a protein and its folding. You think that the interaction between Asp123 and Arg29 is important in determining the structure of the protein. a) What type of amino acid is Asp (acidic, basic, hydrophobic, or polar)? b) What type of amino acid is Arg (acidic, basic, hydrophobic, or polar)? c) What is the strongest interaction that can form between Asp123 and Arg29? You create a mutant Arg29> Lys d) What type of amino acid is Lys (acidic, basic, hydrophobic, or polar)? e) Would you expect this substitution mutation to cause major folding problems? Why or why not? You create mutant Arg29> Glu you discover that this mutant is unable to fold properly, so the protein is nonfunctional. f What type of amino acid is Glu (acidic, basic, hydrophobic, or polar)? g) How does this amino acid substitution cause the protein to fold incorrectly? You find another mutant that also as the same Arg29> Glu mutation. However, this mutant protein įs able to fold normally.…
10. A new protein of unknown structure has been purified. Gel filtration chromatography reveals that the physiological protein has a molecular weight of 240,000 Daltons. Chromatography in the presence of 6 M urea yields a single peak corresponding to a protein of 60,000 Daltons. Chromatography in the presence of 6 M urea and 10 mM mercaptoethanol yields peaks for proteins of 34,000 Daltons and 26,000 Daltons. What can we learn about protein's tertiary and quaternary structure from this data?
a. Suppose that you have the peptide Ala-Gly-Tyr-His-Leu and you treat it with FDNB and then 6M HCl. Draw the structures of all the products that you will have in solution (assume all reactions to go to completion).
9. Shown below is a binding pocket for a protein with a ligand bound. The ligand interacts with a serine and a valine side chain. ligand a. Briefly explain, in terms of Ka, the effect of a mutation that replaces the serine residue with a valine residue. b. Briefly explain, in terms of Kd, the effect of a mutation that alters the ligand (as seen below) binding to the original, unmutated, binding site. :0: ligand 2
6) Proline is not commonly found in the middle of a-helices because its ring structure prevents it from adopting the proper value and because it disrupts the hydrogen-bonding pattern of the helix. Looking at the structure of proline in the amino acid sequence below, suggest how this residue would disrupt the hydrogen-bonding pattern of an a-helix. 'N H R N N H *** R

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