9. As DNA polymerase forms a new phosphodiester bond, all the following occur EX
ID: 213542 • Letter: 9
Question
9. As DNA polymerase forms a new phosphodiester bond, all the following occur EXCEPT:
a) an amino acid residue accepts the H+ released from 3 1 hydroxyl of deoxyribose.
b) oxygen of 3 1 hydroxyl attacks a phosphoryl group of nucleoside triphosphate.
c) phosphate is displaced and protonated by an acidic amino acid residue.
d) hydrogen bonds between DNA strands help position nucleotides.
e) metal ions lower pKa within the active site to facilitate activation of the '3' O- nucleophile.
10. In the replication fork structure, the strand being synthesized
a) into the fork is the leading strand.
b) away from the fork is the leading strand.
c) in a discontinuous fashion is the leading strand.
d) in a continuous fashion is the lagging strand.
e) None of the answers is correct.
I I . At the POI I active site, the primer 3'-OH is deprotonated and the incoming dNTP is bound as the pyrophosphate leaving group departs. This mechanism is carried out by:
a) side chains of the conserved asparagine residues present at the site.
b) two magnesium ions and does not include any protein side chains at all.
c) magnesium, together with conserved asparagine side chains.
d) a water molecule that is deprotonated.
e) None of the above.
12. Which of the following proteins does NOT contain enzymatic activity?
a) Gyrase
b) DNA ligase
c) Single-strand binding protein (SSB)
d) DNA helicase
e) Primase
13. A biochemist is purifying a new DNA helicase encoded by a pathogenic virus. The enzyme acti vity is readily detected after the first several purification steps that generate fractions a, b, and c, each with successively greater purity. The researcher then puts fraction c on an ionexchange column, and this process generates two new fractions, d and d'. The helicase acti vity cannot be detected in either of the new fractions. However, when fractions d and d are mixed, the activity reappears. The most likely explanation for this is:
a) The helicase is present in both fractions; however, the low concentration results in no activity. Mixing the fractions yields a higher helicase concentration and then acti vity can be observed.
b) The helicase is present one fraction; however, it has additional peptide sequences that must be removed in order for the helicase to assume an active form. An enzyme in the second fraction activates the helicase via proteolytic cleavage.
c) The helicase is present in one fraction and another protein or macromolecule required for helicase activity is present in the other fraction.
d) The helicase is present in one fraction; however, the helicase requires ATP, which is present in the other fraction. When the fractions are mixed, the helicase becomes catalytic again.
e) All of the above are equally likely.
Explanation / Answer
9) All the stated events happen except (a) an amino acid residue accepts the H+ released from the 3' hydroxyl of deoxyribose since H+ released bonds with OH- released from the incoming dNTP and is removed as water.
10) The correct answer (a)
a)The strand being synthesized into the fork is the leading strand.
(b) The strand being synthesized away from the fork is the lagging strand.
(c)The strand being synthesized in a discontinuous manner is the lagging strand.
(d) The strand being synthesized in a continuous manner is the leading strand.
11) The correct answer is (e) None of the answers is correct.
Arginine and Lysine in the O helix are involved in forming salt bridges and neutralizing the negative charge of the triphosphate on the dNTP, tyrosine near the active site play a role in substrate specificity and two magnesium ions also participate in the process.
12) The answer is (c)Single-strand binding protein (SSB)
a) Gyrase- It is an enzyme belonging to the class topoisomerase, which catalyzes ATP-dependent negative supercoiling of the double-stranded closed-circular DNA.
b)DNA ligase- It is an enzyme which catalyzes the ATP/NAD-dependent formation of a phosphodiester bond between DNA single strands in the duplex form.
c)Single-strand binding protein- SSBs bind ssDNA with high affinity in a sequence-independent manner and helps in forming a central nucleoprotein complex substrate for DNA replication, recombination and repair processes.
d)DNA helicase- It is an enzyme catalyzing the separation of duplex DNA into single strands in an ATP-dependent reaction.
e)Primase- It is basically an RNA polymerase which catalyzes the synthesis of a short RNA segment called a primer complementary to a single-stranded DNA template.
13) The correct answer is (e) All the above are equally likely since all these are the probable reasons for the helicase activity not being detected in the fractions.
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