Theme 1C: DNA replication and Repair

Question 1

What are the three models of DNA replication?

Answer 1

1. Semiconservative: each daughter strand is paired with complementary parental strand.
2. Conservative: after replication. both daughter strands pair up.
3. Dispersive: Daughter strand has mixture of parental strand and newly synthesized DNA.

Question 2

At which end can DNA synthesis occur?

Answer 2

Nucleotide can only be added to the new strand at the 3’ end of parental strand. DNA synthesis occurs at a 5’-3’ direction.

Question 3

What is the energy source of the phosphodiester bonds?

Answer 3

Hydrolysis of pyrophosphates. see ppt for figure.

Question 4

What is sugar/group is required for DNA polymerase to synthesize a new strand?

Answer 4

The OH 3’ end for synthesis, either from strand or DNA primer.

Question 5

How many active sites does DNA polymerase have?

Answer 5

One, but can catalyze reactions for all four base-sugars.

Question 6

Name all the DNA replication enzymes?

Answer 6

1. Repliosome: molecular machine of enzymes that replicate DNA.
2. Helicase: unwinds the double helix by break H-bonds
3. Primase: synthesize RNA primers for DNA polymerase
4. Single-strand binding protein: stabilizes ssDNA before replication by preventing reannealling so the strands serve as template.
5. DNA topoisomerase/syrase: removes super coils
6. DNA polymerase III: synthesizes DNA by adding nucleotides to the new DNA strand.
7. DNA polymerase I: removes RNA primer and fills the gaps with DNA.
8. Sliding clamp: attaches DNA polymerase III to DNA template, replication is more efficient.
9. DNA ligase: joins the ends of DNA segments by forming phosphodiester bonds.

Question 7

What are replication forks?

Answer 7

Sites of DNA synthesis.

Question 8

What is a nick?

Answer 8

Single DNA strands that break in the phosphodiester bonds that need to be repaired.

Question 9

What is a two types of synthesis strands?

Answer 9

Leading strand (continuous), lagging strand (discontinuous).

Question 10

What are the fragments of the lagging strands called?

Answer 10

Okazaki fragments.

Question 11

What are the three parts DNA replication for bacterial chromosomes?

Answer 11

1. Initiation: Unwinding and separation of the two template DNA strands at origin of replication site.
2. Elongation: synthesis of two strands simultaneously from DNA polymerase.
3. Termination: DNA replication stops at termination site (for circular) or at end of chromosome (linear DNA).

Question 12

What the unique aspects of DNA replication for eukaryotic chromosomes?

Answer 12

1. Much larger genomes and linear chromosomes
2. Multiple origins of replication along chromosomes so that DNA replication be completed during S phase.
3. DNA replication proceeds in opposite directions away from the origin.
4. Complications replicating the ends of linear chromosomes.

Question 13

Whats the problem with replicating ends of linear chromosomes?

Answer 13

RNA primer initiates DNA synthesis, which means the 3’ end is not replicated.

Question 14

Where is telomerase found?

Answer 14

Generally only found in gamete, cancer and stem cells.

Question 15

What direction is exonuclease?

Answer 15

3’ to 5’