#Question id: 719
#Unit 1. Molecules and their Interaction Relevant to Biology
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?
#Question id: 720
#Unit 1. Molecules and their Interaction Relevant to Biology
How would a homopolymer of alanine be more likely to form an alpha helix in water or in a hydrophobic medium?
#Question id: 721
#Unit 1. Molecules and their Interaction Relevant to Biology
Addition of urea leads to a two-state transition between α-helix and random coil conformation. It has been observed that [θ]222 of the polypeptide is -11000 deg cm2 dmol-1 in the presence of 6M urea. Initially it was observed that tile values of mean residue ellipticity at 220 nm ([θ]220) are -36000, and +4000 deg cm2 dmol-1 for α-helix, and random coil conformations of this polypeptide. The percentage of the polypeptide in α-helix conformation is:
#Question id: 722
#Unit 1. Molecules and their Interaction Relevant to Biology
The structure of alpha helix is stabilized by hydrogen bonds between the hydrogen atom attached to the electronegative nitrogen atom of a peptide linkage and the electronegative carbonyl oxygen atom of the fourth amino acid on the amino-terminal side of that peptide bonds. Within the helix, every peptide bond (except those close to each end of the helix) participates in such hydrogen bonding. Each successive turn of the helix is held to adjacent turns by three to four hydrogen bonds, conferring significant stability on the overall structure. Which of the following are correct statements regarding these findings?
A. At the ends of a helical segment, there are always three or four amide carbonyl or amino groups that participate in this stabilised helical pattern of hydrogen bonding.
B. Helix ends are exposed to the surrounding solvent, where they hydrogen-bond with water, or other parts of the protein may cap the helix to provide the needed hydrogen-bonding partners.
C. Helix can form in polypeptides consisting of either L- or D-amino acids but a D-amino acid will disrupt a regular structure consisting of L-amino acids, and vice versa.
D. The most stable form of a helix consisting of L-amino acids is left-handed.
E. 310 helix occupies similar place as turns in Ramachandran plot due to its confirmation
#Question id: 723
#Unit 1. Molecules and their Interaction Relevant to Biology
Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PPII or PGII ) are frequently found in proteins, they are not considered as equivalent secondary structure elements. Which of the following statements are correct about PP and PGs.
A. PGII -like helices form hexagonal bundles which appear to fulfill the criterion of a (largely) saturated hydrogen-bonding network of the main-chain groups
B. main chain NH and CO groups of the central PGII -helix are saturated by either intra- or intermolecular hydrogen-bonds, resulting in a self-contained hydrogen-bonding network
C. The formation of the right-handed PPI helix is possible only with proline residues because of the required cis conformation.
D. PPII helices seem to be stabilized by main chain-water hydrogen bonds (in the absence of main chain- main chain H-bonds), and tend to have a regular pattern of hydrogen bonds with water. After this, it is not surprising, that PPII helices are found mostly on the protein surface.
#Question id: 724
#Unit 1. Molecules and their Interaction Relevant to Biology
In 1988, Richardson and Richardson observed that certain amino acid residues are statically favored as the amino-terminal caps for the alpha helices in 45 globular proteins. Which of the following statement stand correct with stability of helix?
A. The introduction of a negatively charged side chain at the N-cap, which can neutralize the partial dipole created by the unpaired amide protons, has been shown to increase stability
B. In particular, Gly is often observed at the both C-cap position and N-cap positions
C. In particular, Gly is often observed at the C-cap position only
D. In particular, Gly is often observed at the C-cap position, Asn at the N-cap position, Pro at the Ncap+1 and Asp and Glu at N2 and N3