You identify a section of 2 beta strands in a protein crystal structure. When you identify theprimary sequence spanning the residues from the beginning to the very end of the two betastrands, you notice there are two G and one P residues separating the two strands. Which is mostlikely to be true?The two beta strands are likely right-handed.The two beta strands are likely left-handed.O The two beta strands are likely anti-parallel.O The two beta strands are likely parallel.

The linear arrangement of amino acids in beta strands, an usual secondary structure in proteins,…

Answered: You identify a section of 2 beta…

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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Shown below are two cartoon views of the small globular protein StrepG inwhich an α helix is packed against a four-strand β sheet. The sheet is madeup of two “β-hairpins” (a β-hairpin is a “β-turn-β” structure). Refer to theimages and answer the questions that follow: (a) Identify the locations of the N- and C-termini of StrepG.(b) Indicate the orientation of the helical macrodipole, showing the (δ+)and (δ-) ends of the macrodipole.(c) How many residues are in the helix?(d) Do you predict that the α helix and β sheet are amphiphilic or not?Briefly explain.(e) The following two peptides are part of the primary sequence of StrepG.Based on your answer to part (d), which one is more likely to correspondto the α helix? Which is most likely to be part of a β-hairpin? Explainyour choice.Peptide #1: DAATAEKVFKQYAND or Peptide #2: VDGEWTYDDATKTFTV
Amino acids project from each polypeptide backbone in a β-sheet in an alternating fashion (oneabove the plane and the next below the plane – see Fig 3.8B). Consider the following proteinsequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg-Leu-Lys-Ile-Arg-Phe-Glu.a. Is there a pattern to these amino acids? If so, what is it? b. What does this sequence of amino acids mean for the hydrophobicity/hydrophilicity of theresulting β-sheet? c. Can you make a prediction about how the β-sheet will be arranged in higher levels of protein structure? If so, what prediction would you make?
Using a copy of a helical wheel (attached to the end) plot the amino acids of the helix on the helical wheel. Is there any evidence of the helix as a whole being amphipathic or having a “sidedness"? Explain yes or no. Are the amino acid side chains in close proximity of one another or staggered to minimize steric hinderance between side chains? Explain the pattern you observe.
For determining the crystal structure, a short sequence of histidine residues is sometimes attached to the N- or C-terminus of the protein. What is the purpose of this?
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.
Consider the following in light of the concept of levels of structure (primary, secondary, tertiary, quaternary) as defined for proteins. (a) What level is shown by doublestranded DNA? (b) What level is shown by tRNA? (c) What level is shown by mRNA?
(a) Tropomyosin, a 70-kDa muscle protein, is a two-stranded α -helical coiled coil. Estimate the length of the molecule. (b) Suppose that a 40- residue segment of a protein folds into a two-stranded antiparallel β structure with a 4-residue hairpin turn. What is the longest dimension of this motif?
Which amino acid replacement would result in the biggest structural change in a protein if a Cys residue was replaced with Ser or Phe amino acid, and why?
The pi-helix is a rare secondary structural element in proteins that resembles an alpha helix but has slightly different properties. Notably, hydrogen bonds within a pi-helix display a repeating pattern in which the backbone C=O of residue i hydrogen bonds to the backbone HN of residue i+5. Based on this information, which of the following are true? Select all that apply. O The hydrogen bonding distance between C=O and NH groups remains unchanged between pi-helices and alpha-helices The torsion angles of amino acids found in pi-helices are the same as those found in alpha-helices Pi-helices have a smaller rise per residue compared to alpha- helices Pi-helices have fewer residues per turn compared to alpha-helices Pi-helices have more residues per tůrn compared to alpha-helices Pi-helices are left handed
If an Arg residue in a protein was replaced with either Lys or Glu amino acid, whichsubstitution would you expect to result in the greatest structural change and why?
Estimate the length, in nm, of the four identical beta-strands drawn in blue in panel (B) of the image below, if they consists of only the amino residues of the two alpha-helices highlighted in purple in panel (A) of the image below. Assume that the amino acid residues of the two alpha-helices combined were folded in four beta-strands of identical length.
Peptides and small proteins fold spontaneously in aqueous solution at room temperature. Thus, for a small protein in water, we can say ΔG FOLD < 0. Denoting the unfolded protein as Unf and the folded protein as Fld, we can write the following equation:Unf(aq)--DELTA G FOLD----> Fld(aq)Considering the transition from the unfolded state (in which there are many possible conformations) to the folded state (only one conformation), there is clearly a decrease in the entropy of the protein. However, protein folding is (correctly) described as an entropically driven process.a) Resolve this apparent paradox by identifying the enthalpy (ΔH) and entropy (−TΔS)components involved in protein…

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