A/B:3. Amino acid residues and peptide bonds(a) Draw the chemical structure of F, S and H joined by peptide bonds and alsoconnected to neighboring residues as found in a protein.(b) Include all charges as expected at physiological pH (pH = 7.5)() Rank these three amino acid residues by hydrophobicity, pKa, and by nucleophilicity(d) For the central amino acid residue, identify the phi and psi dihedral angles by drawinga curved arrow indicating rotation about the chemical bond.(e) What group(s) eclipse each other if Phi = 0 degrees? Words and Pictures.(f) While Phi = 0 is not well tolerated, Psi = 0 is not uncommon, a so-called “allowed"but not most-favored region of the Ramachandran plot. What group(s) eclipse eachother if Psi = 0 degrees and why is this less problematic than the situation created byPhi = 0. Words and PicturesH₂N*Pka: 9.13H₂CсC._hydrophobicity:1. phenylalanine (most)2. Serine3. Histidinelleast)دهHH.HINOHICH₂CHOpka:1. Serine (nighest)2. Histidinellowest)H-NH-H₂Cpka: 1.82|сNHне-Nnucleophili city1. Serine (most)CHPka: 6.002. Histidine3. phenylalanine (least)

It is hard and hence often found confusing to explain a 3-D concept like dihedral angles in the 2-D…

Answered: 3. Amino acid residues and 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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3. Which best describes the contribution of tertiary (3’) structure of to the native conformation of polypeptides and proteins: a) Structure that results from intrachain interactions of amino acid side chains b) Structure that results from interchain interactions of amino acid side chains c) Structure that results from base pairing d) Structure that results from the linear sequence of amino acids from beginning to end of molecule
32) You are working with an molecule with a pl of 6.00 and the pKa's of the ionizable groups on the molecule are 1.3, 4.1 and 7.9. You would like this amino acid to have a net negative charge. Which of the following pH values would result in a net negative charge? A) 1.3 B) 4.1 C) 4.43 D) 6.0 E) 7.9
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.…
1.Describe in detail how to detect the primary structure of protein. 2.Given a mixture of lysine,histidine and cysteine.The isoelectronic point of the amino acids are as follows: histidine:7.64 lysine:9.74 cysteine:5.02 Show how you will separate the mixture into the pure forms. State and describe any instrument that you will use to separate the components in the mixture.
1.Describe in detail how to determine the primary structure of protein. 2.You have been given a mixture of lysine, histidine and cysteine.The isoelectric point of the amino acids are as follows; histidine 7.64 lysine:9.74 cysteine:5.02 Show how you will separate the mixture into the pure forms. State and describe any instrument that you will use to separate the components in the mixture.
2. | Calculate the overall charge (pH 7) on the following three polypeptides and answer the questions below. Assume the following pKa values: N-terminal –NH3®, 7.0; all -COOH groups, 4.0; Arg, 12.5; Cys, 8.4; His, 6.0; Lys, 10.0; Tyr, 10.0. (A) Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys–Pro–Val–Gly–Lys–Lys–Arg-Arg-Pro-Val-Lys–Val-Tyr-Pro-Asp-Ala -Gly- Glu-Asp-GIn– Ser-Ala-Glu-Ala-Phe-Pro-Leu-Arg-Glu-Phe (B) Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Ala-Pro-Val-Gly-Glu-Glu–Cys-Asp-Pro-Val-Glu–Val–Tyr-Pro-Asp- Ala-Gly-Glu-Asp-Gln-Ser-Ala-Glu-Ala-Phe-Pro-Leu-Glu-Phe-Cys-Ser-Tyr-Ser-Met-Glu–His-Phe-Asp-Trp-Gly- Asp-Pro-Val-Gly-Pro-Asp-Ala-Gly-Asp-Gln-Pro-Val–Gly–Glu-Glu-Cys-Asp-Pro–Val-Glu–Val–Tyr-Pro-Asp-Ala (C) Gly-Ser-Val-Arg-Asp-Pro-Val-Lys-Glu-Val-Tyr-Pro-Asp- Lys–Ala-Gly-Arg-Glu-Ser-Arg-Ala (d) Which of the three peptides would migrate the closest to the anode in isoelectric focusing? (e) Which of the above peptides would elute last from a gel filtration column? (f) Which of the three…
32. Would you expect to find hydrophobic amino acids on the external surface or internally in proteins? Why?
20. The dissociation constant of protein Z for ligand Y is: 10 micromolar. What fraction of the ligand is bound at ligand concentration = 5 micromolar?
4. What type of tertiary structure interactions are most likely between the following amino acids? (Use a reference chart as necessary.) (b) methionine and methionine (a) glycine and valine (d) serine and lysine (c) cysteine and cysteine

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