Biochemistry: Concepts and Connections (2nd Edition)
2nd Edition
ISBN: 9780134641621
Author: Dean R. Appling, Spencer J. Anthony-Cahill, Christopher K. Mathews
Publisher: PEARSON
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Chapter 6, Problem 5P
Give two reasons to explain why a proline residue in the middle of an a helix is predicted to be destabilizing to the helical structure.
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Give two reasons to explain why a proline residue in the middle of an αhelix is predicted to be destabilizing to the helical structure.
Consider a short peptide that forms an alpha-helix within a larger protein structure. Suppose that one glutamate residue at some specific position in the helix were mutated to a leucine residue. The mutation could either make the helix more stable, or less stable.
i) Describe two situations in which a Glu-to-Leu mutation could make the helix more stable.
ii) Describe two situations in which the Glu-to-Leu mutation could make the helix less stable.
Explain briefly the basis for the stabilizing and destabilizing effect in all cases.
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.
Chapter 6 Solutions
Biochemistry: Concepts and Connections (2nd Edition)
Ch. 6 - Prob. 1PCh. 6 - Bovine pancreatic trypsin inhibitor (BPTI; Figure...Ch. 6 - A schematic structure of the subunit of...Ch. 6 - In the protein adenylate kinase, the C-terminal...Ch. 6 - Give two reasons to explain why a proline residue...Ch. 6 - Consider a small protein containing 101 amino acid...Ch. 6 - a. Based on a more conservative answer to Problem...Ch. 6 - The following sequence is part of a globular...Ch. 6 - a. A protein is found to be a tetramer of...Ch. 6 - Under physiological conditions, the protein...
Ch. 6 - Theoretical and experimental measurements show...Ch. 6 - The peptide hormone vasopressin is used in the...Ch. 6 - A protein gives under conditions of buffer...Ch. 6 - A protein gives a single band on SDS get...Ch. 6 - It has been postulated that the normal...Ch. 6 - Below are shown two views of the backbone...Ch. 6 - Do you expect a Pro Gly mutation in a...Ch. 6 - Rank the following in terms of predicted rates...Ch. 6 - Shown below are two cartoon views of the small...Ch. 6 - Prob. 20PCh. 6 - In most cases, mutations in the core of protein...Ch. 6 - A Leu Ala mutation at a site buried the core of...Ch. 6 - Disulfide bonds have been shown to stabilize...Ch. 6 - Cartoon renderings of the proteins Top 7 and adaH2...
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Need a deep-dive on the concept behind this application? Look no further. Learn more about this topic, biochemistry and related others by exploring similar questions and additional content below.Similar questions
- 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'arrow_forwardEstimate 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.arrow_forwardA synthetic polypeptid made up of L-glutamic acid residues is in a random coil configuration at pH 7.0 but changes to alpha helical when the pH is lowered to 2.0. Explain this pH-dependent conformational transition.arrow_forward
- Certain polypeptide sequences that show a pronounced tendency to dimerize in an antiparallel coiled-coil structure exhibit an exact repetition of leucine every 7 residues. If you also know that the a helix is distorted somewhat from its usual 3.6 residues/turn in coiled coils, propose a mechanism for the dimerization. What does this suggest that the residue/turn value might be in a coiled coil?arrow_forwardTo visualize the spatial arrangement of amino acid residues in an a-helix, it is helpful to imagine you are looking down the long axis of the helix, just as you would look down a soda straw. Viewed in this orientation, the residues form a circle, with each residue offset from its neighbor by 100 degrees. This representation is called a helical wheel. Use the circle below to indicate the position of each residue around the helix of the enzyme lysozyme. NH ...Arg - Cys - Glu- Leu - Ala Ala - Ala Met-Lys COO- The first two amino acids, Arg-1 and Cys-2, are shown as an example. Arg-1 O Glu-3 Which amino acid in the polypeptide is the first to pass the origin (i.e., which amino acid passes Arg- 1 first, completing one full circle)? Select the best answer. O Leu-4 O Ala-5 O Ala-6 O Ala-7 Met-8 O Lys-9 100° O none of the above Cys-2arrow_forwardA schematic diagram of the helical structure of cytochrome b562 is reproduced below. Thisprotein belongs to the family of -proteins that have a four-helix bundle. Number the helices 1 – 4according to their N C direction. Indicate relative orientations of the macrodipoles of helices 1 – 4adjacent to the diagram of cytochrome b562. Remember that according to the definition of a dipolethat the arrow points towards the positive end.arrow_forward
- Given the structures of the ribonucleotides as (shown in Image A) and deoxyribonucleotides (as shown in Image B), Draw the structure of the polyribonucleotide UAGCCUG and the structure of thepolydeoxyribonucleotide CGTAGAT.arrow_forwardAt physiological pH (i.e. 7.4), polylysine assumes a random structure in solution. Given that the pKa for the e-amino group of lysine is 10.5, under what conditions would you expect polylysine to form an a-helix? Explain your reasoning. Under what conditions would you expect polyglutamate to form an a-helix, given that the pKa for the side-chain COOH group is 4.3?arrow_forwardUsing 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.arrow_forward
- For the structure shown on the figure - qualitatively draw Ramachandran plot. Assume a mixture of right and left handed helices. How would the plot change if only left handed helices were present?arrow_forwardPfCRT is found to have 10 peaks on a hydropathy plot given its primary sequence. Researchers also noted that each peak is comprised of about 30 amino acids. The digestive vacuole membrane is 45Å in Plasmodium species. Explain why researchers conclude there are 10 transmembrane helices from these two pieces of data.arrow_forwardDraw and label the following RNA tetranucleotide: 5’phosphoryl-A-2’O-methyl-C-U-G-3’-phosphatearrow_forward
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