#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
#Question id: 725
#Unit 1. Molecules and their Interaction Relevant to Biology
At 25°C values of [θ]222, the mean residue ellipticity at 222 nm, are - 33,000 and -3,000 deg cm2 dmol-1 for a polypeptide existing in α- helical (α) and β-structure (β), respectively. If this polypeptide undergoes a two-state heat-induced α-β transition, and a value of [θ]222 = -15,000 deg cm2 dmol-1 is observed at 60°C, then this observation leads to the conclusion that the α helix conversion to β- structure is:
#Question id: 726
#Unit 1. Molecules and their Interaction Relevant to Biology
The structure of a protein is known from X-ray diffraction studies which gave 30% - helix, 50% -sheet and 20% random coil. Circular dichroism (CD) measurements gave 50% -helix, 40% -sheet and 10% random coil. What could not be a possible explanation for these observations.
#Question id: 727
#Unit 1. Molecules and their Interaction Relevant to Biology
26-residue peptide composed of alanine and leucine shows a circular dichroism (CD) spectrum characteristic of α-helix at 50°C in 5 mM phosphate buffer at pH 7.4. When the peptide solution is cooled gradually to 25°C, and the CD spectra are recorded at different temperatures, the most likely observation will be that