What is the driving force that promotes secondary structure formation of alpha helices and beta sheets? How is this force arranged to makean 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 theinteractions facilitating this effect.

Alpha-helix and beta-sheets are the two most prominent regular secondary structures in protein.…

Answered: What is the driving force that promotes…

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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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.
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'
What is the length in AA’s of the LilP protein? Assume fMet is NOT CLEAVED. Write out the sequence of the polypeptide in AA: use the three letter notation, e.g. Met-Ser-Pro-
How many Alpha helices and beta sheets are in ESR1? What's the percentage of alpha helices and the beta sheets?
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
The infectious prion protein which are believed to cause a neurodegenerative disease by acting as a template to misfold other cellular prion proteins are usually β-helices. Is this correct or not?
Consider the following protein sequence as an α helix: Leu-Lys-Arg-Ile-Val-Asp-Ile-Leu-Ser-Arg-Leu-Phe-Lys-Val. how many turns does this helix make?
Assume that the 3 polypeptide strands shown below form a parallel B-sheet. Select amino acids AA1, AA2, and AA3 so that the parallel B-sheet is amphipathic and remains stable. Glu-lle-Asn-AA1-Cys-Val Ser-AA2-GIn-Leu-Lys-Phe Lys-Met-Cys-Leu-AA3-Val O AA1 = Pro, AA2 = Leu, AA3 = lle O AA1 = Val, AA2 = Leu, AA3 = Asn O AA1 = Ala, AA2 = Gly, AA3 = Leu AA1 = Phe, AA2 = Arg, AA3 = Ala O O
There are different types of helical structures that can be found in proteins (i.e., not only helices). What is common among different types of helices is that the he structure is maintained by intrachain hydrogen bonding between two polypeptide backbone atoms. Oftentimes, at least two intrachain hydrogen bonds need to be formed in order for a helix to start gaining stability. This can be observed from circular dichroism, technique that detects helicity in proteins. Circular dichroism starts detecting helicity in a helical chain only when there are at least two intrachain hydrogen bond formed. If a helical structure is too short such that it only has one intrachain hydrogen bond, the helix is too unstable for the helicity to be accurately detected th circular dichroism. Four different types of helical structures were studied using circular dichroism and the minimum number of residues needed for helicity to become detectable wa determined as summarized in the table below. Minimum number…
List some of the possible combinations of α-helices and βsheets in supersecondary structures.
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?
Proline is known as a beta sheet and alpha helix "breaker ," therefore proline is rarely found in beta sheets or alpha helices. why do you think this is? In your explanation, you should describe the specific molecular interactions necessary for the formation of alpha-helices and beta-sheets. Please be as specific as possible.

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