The yeast Gal4 transcription activator comprises two domains: a DNA binding domain and an activation domain. The DNA-binding domain allows Gal4 to bind to appropriate DNA sequences located near genes that are required for metabolism of the sugar galactose. The activation domain binds to components of the transcriptional machinery (including RNA polymerase), attracting them to the promoter, so the regulated genes can be turned on. In the absence of Gal4, the galactose genes cannot be turned on. When Gal4 is expressed normally, the genes can be maximally activated. When Gal4 is massively overexpressed, however, the galactose genes are turned off. Choose correct explanation for this regulation?

A. In order for Gal4 to work properly, the DNA-bound Gal4 recruits many proteins, including RNA polymerase, to the promoter.

B. When there is too much Gal4 in the cell, the free and DNA-bound Gal4 will compete for the limited quantities of these other components.

C. In the presence of excess Gal4, those components are tied up in unproductive complexes with free Gal4, thereby preventing their recruitment to the promoter.

D. cells that massively overexpress Gal4 grow poorly because of the reduced availability of critical components of the transcription machinery.

E. Over concentration of Gal4 prevent suppressors to bind with DNA

#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

#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.