40.What would you expect about the formation of an alpha-helix for a segment of a proteinchain that contains lysine approximately every four residue with all other residues being mostlyhydrophobic?A. Helix formation would be favored at low pHB. Helix formation would be favored at high pHC. Helix formation would be favored at neutral pHD. Helix formation would never occur regardless of pH

Two types of secondary structures are abundant in protein: alpha helix and beta sheets. The alpha…

Answered: 40. What would you expect about the…

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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81. You have used the primary amino acid sequence of a newly identified protein (of unknown function) to make a hydropathy plot. From this plot you believe it might be a transmembrane receptor. This is because the plot tells a. the secondary structure is likely made up of several B sheets. b. the secondary structure is likely made up of a-helices. c. the protein would be readily hydrolyzed if in an aqueous environment. d. on average, there are a lot of hydrophobic amino acids in the protein. e. there are several hydrophobic areas interspersed with short hydrophilic stretches. you that 82. You are studying a mutant type of garter snake known for its odd slithering movement. You isolated the mutated gene and this morning you just got the results from your DNA sequencing. What would be your first step towards determining the potential function of the protein encoded by this gene? a. Use X-ray crystallography to determine the tertiary structure of the protein. b. Use computer programs that…
-novel protein is described that functions best at pH 10.5, and contains a beta strand on one side. The authors report that at pH 10.5 this beta strand's interaction with an alpha helix is stabilized by an ionic interaction. a. Beneath each pair of amino acid names, draw out the structures for the two amino acids at pH 10.5 Asp-Arg Asn-Gln Cys-Glu b. Which of these pairs would be the best candidates for the ionic interaction at pH 10.5? (circle your choice): Asp-Arg Asn-Gln Leu-Gly C. Explain your choice in part b (25 words or less)
Consider the hypothetical serine protease in the image, which shows the specificity pockets. The S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1' pocket is deep and hydrophobic. Suggest a 3-amino acid sequence that this protease would cleave and indicate between which sites the peptide bond would be broken. S2 Which sequence would this protease cleave? O Leu-Val-Arg Arg-Val-Leu Val-Leu-Arg Val-Arg-Leu O Leu-Arg-Val O Arg-Leu-Val W Ma étv N 894
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.
3b) Both a-helical 2° structure and b-pleated sheet 2° structure result from the same type of interaction; briefly explain in your own words why you might observe an a-helix in one region of a protein and a b-pleated sheet in another region of the same protein.
1. What is the length in AA’s of the LilP protein? Assume fMet is NOT CLEAVED. 2. Write out the sequence of the polypeptide in AA: use the three letter notation, e.g. Met-Ser-Pro-
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'
46. The SH2 protein domain has 2 binding sites: one for ________ and one for _________. A. Phosphotyrosine; {a}- methyltyrosine B. C- Terminus; N-terminus C. Phosphotyrosine; flanking amino acids D. Alpha Helices; Beta-Pleated Sheets
An unspecified protein contains a 15-residue long α-helix with the following sequence: WEANIKQRLSTMGEYKQCHANG a. How many full turns are there in this α-helix? b. What is the length of the helix (in Angstroms) in the direction of the helix axis? c. How many hydrogen bonding interactions would be there in this α-helix? d. If it was a 310 helix instead with a helical pitch of 6 Å, is it long enough to span the 30 Å bilayer? Calculate and explain.
Which of the three 20-amino-acid sequences listed below in the single-letter amino acid code is the most likely candidate to form a transmembrane region (α helix) of a transmembrane protein? Explain your answer.A. I T L I Y F G N M S S V T Q T I L L I SB. L L L I F F G V M A L V I V V I L L I AC. L L K K F F R D M A A V H E T I L E E S
Alpha-helices have 3.6 amino acid residues per turn, ie a helix 36 amino acids long would form 10 turns, and The axial distance between adjacent residues is 3.5 Angstroms. Beta-helices have two residues per repeat unit which gives the beta-strand a 7 Angstrom pitch. This compares with the alpha-helix where the axial distance between adjacent residues is only 1.5 Angstroms. Then how many residues in an alpha-helix conformation would it take to traverse the same distance as 10 residues in beta-strand conformation?
Consider an a-helix secondary structure.a. Propose a 12-residue amino acid sequence that(assuming it folded intoan a-helix) would yield a structure in which six of the residues, each with an ionizable side-chain were within a 135° region on one face of the helix, and use an appropriate diagram to support your choice of sequence.b. Would it be possible to generate an especially stable helix by correctly choosing the charges on the side-chains? Please justify your answer.

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