Question 1

The enzyme that removes the RNA primer from the Okazaki fragment is:

Accepted Answer

The enzyme that removes the RNA primer from the Okazaki fragment is DNA polymerase I, which also simultaneously fills in the gap left behind by the RNA primer.

Question 2

All of the following are characteristic of replication of the E. coli circular chromosome EXCEPT:

Accepted Answer

The unwinding of the duplex DNA is not driven by the translocation of the DNA polymerase. Instead, it is driven by DNA helicase, which separates the two strands of DNA at the replication fork. The DNA polymerase then adds nucleotides to the new strand in a 5' to 3' direction, using the existing strand as a template.

Question 3

DNA polymerases share all of the following characteristics EXCEPT:

Accepted Answer

DNA polymerases vary in their processivity, with some having high processivity and others having low processivity, depending on their role in DNA replication and repair. Processivity refers to the number of nucleotides a polymerase can add before dissociating from the DNA template.

Question 4

Removal of RNA primer and replacement with DNA is carried out by:

Accepted Answer

Removal of RNA primers and replacement with DNA is carried out by DNA polymerase I in prokaryotes, which has both exonuclease and polymerase activity. It is capable of digesting RNA and replacing it with DNA in the 5' to 3' direction, ultimately leading to the synthesis of a continuous DNA strand.

Question 5

SSBs are:

Accepted Answer

SSBs (single-stranded DNA binding proteins) bind to single-stranded DNA and prevent it from re-annealing with another complementary strand. They play a crucial role in DNA replication, recombination, and repair.

Question 6

The termination of DNA replication in E. coli occurs when ____ protein binds the ____ locus on the DNA and acts as a ____.

Accepted Answer

The termination of DNA replication in E. coli occurs when Tus protein binds the Ter locus on the DNA and acts as a contrahelicase, preventing helicase from unwinding the DNA duplex and stopping replication. Option A is incorrect because DnaC is an initiation protein, DnaG is a primase, and gyrase is involved in supercoiling. Option B is incorrect because there is no tag locus on the DNA, and polymerase is involved in replication, not termination. Option E is incorrect because SSB is a single-strand binding protein, primer is a short RNA sequence that initiates DNA replication, and RNA polymerase is not involved in DNA replication termination.

Question 7

All are characteristics of Okazaki fragments EXCEPT:

Accepted Answer

Okazaki fragments are typically 100 to 200 nucleotides long in eukaryotes and about 1000 to 2000 nucleotides long in prokaryotes, not 20-30 nucleotides as stated in option D.

Question 8

A pair of β-subunits of DNA polymerase III form a ____ to tether the polymerase to the template thus increasing the ____ of the polymerase.

Accepted Answer

The sliding clamp formed by a pair of β-subunits of DNA polymerase III tethers the polymerase to the template, increasing its processivity or ability to stay bound to the template and synthesize long stretches of DNA without dissociating.

Question 9

The degree to which the enzyme remains associated with the template through successive cycles of nucleotide addition is referred to as:

Accepted Answer

The term processivity refers to the ability of an enzyme to remain associated with its substrate/template through successive cycles of catalysis without dissociating. In the context of DNA polymerases, processivity refers to the ability of the polymerase to remain associated with the DNA template strand and synthesize a long chain of nucleotides without dissociating.

Thus, the correct answer is A) processivity.

Question 10

E. coli DNA polymerase I has ____ distinct catalytic active site(s) on its single polypeptide chain.

Accepted Answer

E. coli DNA polymerase I has 3 distinct catalytic active sites on its single polypeptide chain: a 5'→3' polymerase activity, 3'→5' exonuclease (proofreading) activity, and 5'→3' exonuclease activity.

Question 11

All occur during DNA replication in E. coli EXCEPT:

Accepted Answer

Primase (DnaG) does not specifically bind to a GC-rich region of dsDNA in oriC; instead, it synthesizes RNA primers that are necessary for DNA polymerase to initiate synthesis. The initiation of replication involving oriC is more directly associated with the binding and activity of DnaA and other factors, not primase.

Question 12

DNA is replicated by a ____ mechanism.

Accepted Answer

DNA replication occurs via a semi-conservative mechanism, in which each strand of DNA serves as a template for the synthesis of a new complementary strand. This results in two identical double-stranded DNA molecules, each composed of one original (parental) strand and one newly synthesized (daughter) strand. The dispersive, conservative, and liberal mechanisms are hypothetical models of DNA replication that have been discounted by experimental evidence.

Question 13

Eukaryotic cells have replication regions called ____ that occur every ____ kbp and the units of replication are called ____.

Accepted Answer

Eukaryotic cells have replication regions called replicators that occur every 3-300 kbp and the units of replication are called replicons. None of the other options accurately describe these features of eukaryotic DNA replication.

Question 14

All are properties of DNA polymerase III EXCEPT:

Accepted Answer

DNA polymerase III is responsible for incorporating most of the nucleotides in the lagging strand (A), contains a 3' to 5' exonuclease activity (C), is a large protein complex containing more than five subunits (D), and has much greater processivity than DNA polymerase I (E). Therefore, the incorrect statement is B, as DNA polymerase III synthesizes most of the lagging strand and aids in the synthesis of the leading strand.

Question 15

Which of the following is NOT true regarding E. coli replication on the lagging strand?

Accepted Answer

E. coli replication on the lagging strand is primarily carried out by DNA polymerase III, not DNA polymerase I. DNA polymerase I mainly participates in post-replication repair and primer removal.

Question 16

The enzyme that seals nicks in dsDNA where a 3'-OH and 5'-phosphate are juxtapositioned is:

Accepted Answer

DNA ligase is responsible for sealing nicks in dsDNA where a 3'-OH and 5'-phosphate are juxtapositioned. DNA polymerase I is involved in DNA repair and synthesis, DNA gyrase is involved in regulating the supercoiling of DNA, DNA polymerase III is the main DNA synthesizing enzyme in prokaryotes, and primerase is responsible for synthesizing RNA primers during DNA replication.

Question 17

E. coli DNA polymerase I has all of the following characteristics EXCEPT:

Accepted Answer

E. coli DNA polymerase I requires a primer to initiate DNA synthesis; it cannot start DNA synthesis de novo.

Question 18

Enzymes that catalyze the unwinding of DNA double helix are:

Accepted Answer

Helicases are enzymes that catalyze the unwinding of DNA double helix. They are responsible for separating the two strands of DNA, allowing for replication, transcription, and repair processes to occur. Topoisomerases, ligases, gyrases, and polymerases are all enzymes involved in DNA metabolism, but they do not specifically catalyze the unwinding of the double helix.

Question 19

3'-Exonuclease activity of DNA polymerase I of E. coli has all the characteristics EXCEPT:

Accepted Answer

The 3'-exonuclease activity is not faster than the polymerase activity, in fact, it is slower. The removal of nucleotides that do not base pair at the 3'-end of the growing chain helps to correct errors made during polymerization and is therefore an important aspect of DNA polymerase I function.

Question 20

All are correct about DNA gyrase in E. coli EXCEPT:

Accepted Answer

DNA gyrase in E. coli works by introducing negative supercoiling into DNA to overcome torsion stress. It also hydrolyzes ATP during its reaction mechanism and removes positive supercoiling introduced by the DnaB protein. However, it does not break a single phosphoester bond in one strand of dsDNA. Instead, it breaks both strands of DNA and passes another segment of DNA through the break before resealing the break.

Quiz 28: Dna Metabolism: Replication, Recombination, and Repair