11. A polypeptide is making a short a-helix. A typical residue in an a-helix is involved in two H-bonds. Ata minimum, how many residues this helix could have?

In an alpha helix, each amino acid residue forms hydrogen bonds with the amino acid located three…

Answered: 11. A polypeptide is making a short…

Biology 2e

2nd Edition

ISBN:9781947172517

Author:Matthew Douglas, Jung Choi, Mary Ann Clark

Publisher:Matthew Douglas, Jung Choi, Mary Ann Clark

Chapter3: Biological Macromolecules

Section: Chapter Questions

Problem 16RQ: The helix and the pleated sheet are part of which protein structure? primary secondary tertiary...

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The helix and the pleated sheet are part of which protein structure? primary secondary tertiary quaternary
6) Proline is not commonly found in the middle of a-helices because its ring structure prevents it from adopting the proper value and because it disrupts the hydrogen-bonding pattern of the helix. Looking at the structure of proline in the amino acid sequence below, suggest how this residue would disrupt the hydrogen-bonding pattern of an a-helix. 'N H R N N H *** R
40.What would you expect about the formation of an alpha-helix for a segment of a protein chain that contains lysine approximately every four residue with all other residues being mostly hydrophobic? A. Helix formation would be favored at low pH B. Helix formation would be favored at high pH C. Helix formation would be favored at neutral pH D. Helix formation would never occur regardless of pH
3. The primary amino acid sequence of a stretch of polypeptide is Asp-Glu-Pro- Lys-His-Arg. Would you expect this portion of the polypeptide to form an alpha helix at PH35? Provide 3 reasons to justify your answer.
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-
4. Do the "Bond X" bonds in Figure 4 involve atoms in the amino acid R groups or in the polypeptide "backbone"/ "main chain" atoms? 5. Given Your Answer To “b," are each of the following statements True or False? Be able to explain your reasoning. o Only very specific primary sequences can form a-helices and B-sheets. o Many different primary sequences can form a-helices and B-sheets. Each arrow depicted in Figure 4D represents consecutive amino acids in the primary sequence of the polypeptide, while the different arrows may be formed from amino acids that are removed from each other in the primary sequence. Each arrow is referred to as a B-strand, and the structure formed through interaction of the B-strands is the B-sheet. In a complete protein, other segments of the protein would connect the different B-strands. 6. Do the "Bond X" bonds in the B-sheet connect atoms from the same B-strand or neighboring strands? TERTIARY STRUCTURE (A) (B) (C) Figure 4-17 Essential Cell Biology 3/e (o…
1. Which of the following structures could the following polypeptide form? And why? The non- polar amino acids are italicized. Gly-Leu-Asp-Glu-lle-Ala-Lys-Ser-Val-Arg-His-Phe-Cys-His-Ala- lle A. A hydrophobic alpha helix B. An amphipathic a- helix C. A hydrophilic a helix D. A hydrophobic B sheet E. An amphipathic B sheet Where would you expect to find the N-term and C-term amino acids in the polypeptide?
4. A polypeptide comprised of 17 amino acid res- idues with the sequence on the right is ob-served by spectroscopic methods to undergo transitions from an a-helix conformation to a B-sheet as a function of pH and concentration. The acetyl and carboxamide groups are attached covalently to deri- vatize the N- and C-terminal residues, respectively, to avoid charge effects of the end groups. CH3CO-ΤAΤΚΑE LLAKYEATΗK-CONH2 (a) ( amino acid residues. Write the sequence of this polypeptide with corresponding 3-letter abbreviations for the (b) At pH < 4 the polypeptide forms an a-helix. (i) ( the helix? and (ii) (: · with respect to the positive and negative ends of the macrodipole? ) What is the direction of the macrodipole of | Are the charges on the N- and C-terminal residues stabilizing or de-stabilizing (c) (* stabilize the helical conformation. What are the most likely protonation states of the side-chains that provide a-helix stabilizing interactions? Use the helical wheel (at the back…
4. A polypeptide comprised of 17 amino acid res- idues with the sequence on the right is ob-served by spectroscopic methods to undergo transitions from an a-helix conformation to a B-sheet as a function of pH and concentration. The acetyl and carboxamide groups are attached covalently to deri- vatize the N- and C-terminal residues, respectively, to avoid charge effects of the end groups. CH3CO-ETATKAELLAKYEATHK-CONH2 (а) amino acid residues. Write the sequence of this polypeptide with corresponding 3-letter abbreviations for the (b) At pH < 4 the polypeptide forms an a-helix. (i) the helix? and (ii) with respect to the positive and negative ends of the macrodipole? What is the direction of the macrodipole of Are the charges on the N- and C-terminal residues stabilizing or de-stabilizing
The amino acids leucine and threonine in general tolerate being in an alpha helix. However having too many of these residues close together may disrupt an alpha helix. Why do you think this occurs?
4. The molecular structure of the last 12 amino acid residues (dodecapeptide) that comprise the C- terminal segment of semaglutide is shown below. NH₂ H₂N NH HO NH NH CH 3 NH CH3 CH 3 NH NH ΝΗ CH3 CH3 O NH H3C NH CH3 a) Determine the sequence of the dodecapeptide in one-letter code: b) Convert your sequence in (a) into three-letter code: H₂N. NH NH NH NH H₂N NH NH NH Im c) How many of the a-carbons in this peptide sequence are chiral? d) How many peptide bonds are in this peptide? e) Predict the overall charge of this peptide at physiological pH. f) A biochemist synthesized the C-terminal dodecapeptide version of semaglutide but found that there were other contaminating peptides. Based on your answer in (4.e), which ion exchange chromatography technique would you use to effectively purify the dodecapeptide from the mixture? (encircle one) anion exchange cation exchange g) Briefly explain your answer in (4.f).
1. Hydrogen bonds can form an alpha helix or beta sheet. The hydrogen atom has a partial positive because of the atom it is covalently bound to. Name the two most common atoms hydrogen bonds within biological systems that give hydrogen a partial positive charge. 2. Are the atoms named in the question above in the backbone of the protein or are they found in R groups? Which R groups? 3. Besides hydrogen, what other atom is involved in the hydrogen bonds in an alpha helix or beta sheet? In other words, hydrogen is interacting with what other atoms when it makes a hydrogen bond? 4. Write out, in order, the full names of the seven amino acids circled in the picture.

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11. A polypeptide is making a short a-helix. A typical residue in an a-helix is involved in two H-bonds. At a minimum, how many residues this helix could have?