please answer the following question in the picture, thanks in advance. 1. a. What is the role of these bond of the polypeptide in determining the secondary structure of theprotein124Ab. Why don't amino acids Pro and Gly involved in the formation of a-helix or B-sheet structure?What is the secondary structure of the polypeptide part where those amino acid residues located?

Protein is made up of polypeptides. Polypeptides are the polymer of amino acids and these amino…

Answered: 1. a. What is the role of these bond of…

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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1) what is the net charge of the amino acid leucine of it is on the C-terminus end and why? 2) if the amino acid was changed to lysine on the c-terminus end explain why and what the net charge would be?.
What is a helix-turn-helix motif? secondary structure in which an α helix is separated from a β sheet by a loop supersecondary structure in which an α helix is separated from another α helix by a turn supersecondary structure in which a β sheet is separated from a helix by a turn secondary structure in which two right-handed α helices are intertwined secondary structure in which two left-handed α helices are intertwined
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.…
SYNZIPS are a-helices that can be used in synthetic biology to create coiled-coil interactions between two different proteins. SYNZIP1 is around 47 amino acids in length. If each turn in an a-helix is 3.6 residues in length and each turn is 5.4 Å in length, how long is SYNZIP1? Keep in mind that 1 Å = 10 nm. Present your answer in nm.
What is the driving force that promotes secondary structure formation of alpha helices and beta sheets? How is this force arranged to make an alpha helix or beta sheet? What promotes turns or kinks in these structures? You can describe and/or draw it but please show what are the interactions facilitating this effect.
Consider the following peptide to answer the questions below: A M A K K E S H I F T A I D E What is the total charge of this peptide at pH = 5? What is the N terminal amino acid (full name)? C terminal amino acid? How many fragments would result if this peptide underwent proteolytic cleavage with V-8 protease and what are these fragments (list them)? Would this peptide be a candidate to form an alpha helix? Why or why not
1. Explain why the primary structure sequence -Lys-Leu-Trp-Asp- may promote a-helix formation while the sequence -Lys-Leu-Trp-Arg- may inhibit it.
The domain of a protien is approximately 350 residues in length. what is length (in A°) of this domain? if this same peptide segment were a true alpha helix, how long would it be? if the same segment were beta sheet, what would its length be?
The diagram to the right illustrates the inter-actions of the amino acid side chains of two a-helical polypeptide strands in a coiled-coil, viewed end-on and projected along the helix axes from the N-terminal to the C-terminal end. Are the macrodipoles of the two a- helices oriented parallel or anti-parallel? For this projec- tion is the positive end of the macro-dipole in the sur- face of the paper or below the surface? f C b g e d a' a d' g b' f'
1. Consider the following α helix from myoglobin at pH 7. Gln-Gly-Ala-Met-Asn-Lys-Ala-Leu-Glu-His-Phe-Arg-Lys-Asp-Ile-Ala-Ala-Lys-Tyr(a) Label amino acids in the polypeptide above as follows: p for polar and uncharged, np for non polar, – for negatively charged, and + for positively charged.(b) How many complete turns are there in this helix?(b) Which side chains are likely to be on the side of the helix that faces the aqueous solvent? Why?(c) Which side chains are likely to face the interior of the protein? Why?
Given the polypeptide chain below: Ala-Arg-Val-His-Asp-Gln 1. What is the N-terminus? 2.What is the C-terminus?
How long is a fully extended peptide chain that contains the same number of amino acids?(The distance between consecutive amino acids in a fully extended chain is 3.5 Å; the repeat distance ofan a-helix is 5.4 Å.)

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