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)(c) 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 Pictures

Amino acids are biomolecules that have a hydrogen atom, an amino group and a carboxyl group linked…

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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In a subunit of a protein, arginine and aspartic acid have an ionic interaction between their side chains. Part a) If arginine is changed to glutamic acid, would the ionic interaction's stability increase, decrease, or not change and what effect would it have on the protein structure? Explain why. Part b) If arginine is changed to lysine, would the ionic interaction's stability increase, decrease, or not change and what effect would it have on the protein structure? Explain why. Part c) If arginine is changed to isoleucine, would the ionic interaction's stability increase, decrease, or not change and what effect would it have on the protein structure? Explain why.
Consider a protein in which a negatively charged glutamic acid side chain (pKa = 4.2) makes a salt bridge (ion–ion interaction) with a positively charged histidine side chain (pKa = 6.5). (a) Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5? (b) Justify your answer with calculations of partial charges on these amino acid side chains.
1. Draw the structure of Phe-Ser-Met-Glu, and indicate where the peptide bonds are.
Match the following statements about protein structure with the proper levels of organization. (i) Primary structure (ii) Secondary structure (iii) Tertiary structure (iv) Quaternary structure (a) The three-dimensional arrangement of all atoms (b) The order of amino acid residues in the polypeptide chain (c) The interaction between subunits in proteins that consist of more than one polypeptide chain (d) The hydrogen-bonded arrangement of the polypeptide backbone.
24. The sidechain of the amino acid serine is -CH2-OH. Serine is classified as this type of amino acid (side chain): a) hydrophobic and nonpolar b) hydrophilic and polar c) acidic d) basic
24. What is the quaternary structure of a protein? Do all proteins have quaternary structure?
3. A. Briefly discuss the four levels of structure in proteins. Knowing that the 3-dimensional shape of a protein is important to its function, discuss on a qualitative basis whether the changes below will likely alter the function of a protein, justifying your answer with why or why not. B. What would happen to a protein's functionality if a serine residue were replaced with threonine? C. What would happen if serine were replaced with leucine? D. What would happen if serine were replaced with cysteine? E. What would happen if aspartic acid were replaced with tryptophan in the part of the protein (an enzyme) that serves as an active site to catalyze a reaction? F. What would happen if aspartic acid were replaced with tryptophan in a non-active site?
2. Calculate the pI of the following primary structure of protein A) Lys- Gly- Ala- Gly B) Lys- Gly-Ala-Glu C) His- Gly- Ala- Glu D) Glu- Gly- Ala -Glu E) Gln-Gly-Ala-Lys
What level of protein structure is determined by the following:(a) Peptide bonds between amino acids?(b) Hydrogen bonds between backbone carbonyl oxygen atoms and hydrogen atoms attached to backbone nitrogen atoms?(c) R group interactions that may involve Van der Waalsforces, ionic interactions, or hydrogen bonds?
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%3; 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-Gln- 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 (h) Which of the peptides would migrate the closest to the cathode in isoelectric focusing? (i) Which of the three peptides would migrate the furthest away from the cathode in isoelectric focus-…
In the following diagram of a portion of a protein, label the types of interactions that are shown. What level of protein structure are these interactions producing?
6

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