DNA Synthesis

Question 1

What is a replication origin and what happens?

Answer 1

Replication origins is the specific site on DNA where DNA replication is initiated.
DNA at the origin unwinds to form a replication bubble and allows access to the replication machinery.

Question 2

What are the differences between a bacterial cell cycle and a mammalian cell cycle?

Answer 2

The bacterial cell cycle takes 20-30 minutes and consists of M-Phase and S-Phase.
The mammalian cell cycle takes 16-24 hours and consists of M-Phase, G1, S-Phase and G2.
It takes longer as the eukaryotic cells have a larger number of chromosomes

Question 3

What are the types of DNA polymerases in bacteria?

Answer 3

I = repair
II = repair
III = replication

Question 4

What are the types of DNA polymerases in a eukaryotic cell?

Answer 4

α = synthesises the RNA primer, initiates DNA synthesis and the lagging strand (replication)
β = repair DNA (replication)
γ = replicate mitochondrial DNA (mitochondrion)
δ = synthesises the leading strand, filling DNA gaps after the removal of the primer (replication)
ε = repair DNA

Question 5

How does DNA polymerase function and what are some key features?

Answer 5

• acts only in a 5’ to 3’ direction
• utilises complementary base pairing to synthesise DNA
• requires a DNA template, a DNA/RNA primer (requires a -OH group to start adding carbons to the 3’ ends), four deoxyribonucleoside triphosphate building blocks and Mg2+ ions
• also has a proofreading function

Question 6

How does dNTPs looks like and what do they do?

Answer 6

Basically a nucleotide with two extra phosphate groups attached to the phosphate group.
The two phosphate groups or pyrophosphate deattaches from the molecule by a hydroxyl group (from another nucleotide) attacking the first phosphate group.
A phosphodiester bond forms between the phosphate group and the hydroxyl group of another nucleotide forming a sugar backbone.

Question 7

What happens at the replication fork?

Answer 7

A replication fork will appear at the replication origin.
The parental strand will separate (anti-sense)
On the 5’-3’ strand (leading strand), DNA polymerase will cause a continuous strand to be made- the complementary strand.
However on the other strand, DNA polymerase will be working in the opposite direction (lagging strand), meaning behind it, the strand will be opening up while moving forward.
This forms okazaki fragments and replication has to reinitiated again and again.

Question 8

What are the DNA replication enzymes?

Answer 8

• helicase = separates the bases into single strands
• topoisomerase = goes in-front of helicase and gets rid of the coils that helicase can cause
• primase = lays down some RNA (3–OH)
• DNA binding proteins = stabilises the DNA strand by stopping recombination of the two strands
• Replicative DNA polymerase = repair fragments and takes out RNA
• DNA ligase = splices the fragments together

Question 9

How does the DNA polymerases’ proofreading system work?

Answer 9

The proofreading system and mismatch repair system is there to ensure that DNA replication proceeds with high fidelity.
Error rate is extremely low due to:
-error rate is 1 in 10^8 due to base pairing and proofreading function
-the mismatch repair system corrects most errors and this is conserved across most species.

Question 10

What are the different DNA replication inhibitors?

Answer 10

• antibacterial agent= ciprofloxacin, levofloxacin and novobiocin (gyrase inhibitor)
• antitumor agent= etoposide, doxorubicin and mitoxantrone (topo II inhibitors)
• antiviral (AIDS)= zidovudine, tenofovir, lamivudine (reverse-transcriptase inhibitors)