DNA Replication, Repair, and Recombination

Question 1

Semiconservative replication

Answer 1

1 old strand paired with 1 new strand

Question 2

3 steps of DNA replication

Answer 2

1. Initiation (assembly of replication machinery)
2. Elongation (nucleotides are added to growing chains)
3. Termination (replication machinery disassembles; separation of daughter molecules)

Question 3

Longest step in DNA replication

Answer 3

Elongation

Question 4

DNA polymerase I

Answer 4

Repairs DNA and catalyzes the synthesis of the lagging strand

Question 5

DNA polymerase II

Answer 5

Repairs DNA

Question 6

DNA polymerase III

Answer 6

Major DNA replication enzyme

Question 7

Eta subunit of DNA pol III

Answer 7

3’ -> 5’ exonuclease

Proofreading portion of DNA pol III

Question 8

Beta subunit of DNA pol III

Answer 8

Forms sliding clamp

Portion of DNA pol III that wraps around it

Question 9

How DNA pol III works

Answer 9

Catalyzes formation of a phosphodiester linkage between the dNTP and the growing chain

Question 10

How fast replication takes place

Answer 10

~1000 bp/second

Question 11

Elongation mechanism

Answer 11

Free 3’ -OH attacks the alpha-phosphate of the dNTP

Question 12

Error rate of DNA pol III

Answer 12

Wrong base every 10^5 residues
Exonuclease activity has an error rate of 10^-2
Combined error rate: 10^-7

Question 13

Leading strand vs. lagging strand

Answer 13

Leading strand is constructed as a single sequence
Lagging strand is synthesized discontinuously (Okazaki fragments)
Leading strand is the strand that is synthesized in the same direction as the overall synthesis/unzipping

Question 14

Degradation of RNA primer in Okazaki fragment joining

Answer 14

DNA pol I’s exonuclease activity degrades the RNA primer as it moves

Question 15

Cofactor that DNA ligase uses

Answer 15

NAD+

Question 16

Helicases

Answer 16

Unwind double-stranded DNA

Question 17

Topoisomerases

Answer 17

Remove supercoiling ahead of the replisome

Question 18

Single-strand binding proteins

Answer 18

Prevent premature double-helix reformation

Question 19

Differences between replication in prokaryotes and in eukaryotes

Answer 19

1. Okazaki fragments are shorter in eukaryotes
2. Replication rate is slower in eukaryotes
3. Multiple origins of replication in eukaryotes
4. Eukaryotes have at least 5 different DNA polymerases
5. Eukaryotic DNA replication occurs during the S-phase of the cell cycle

Question 20

Sanger sequencing method

Answer 20

DNA replication is performed in presence of ddNTPs
When ddNTP is incorporated into growing strand, synthesis stops (no 3’ -OH to add onto)
Gel electrophoresis separates out segments with 1 bp in length difference

Question 21

Only class of cellular macromolecules that has repair mechanisms

Answer 21

DNA

Question 22

Hydrolytic deamination

Answer 22

Common type of DNA damage
Converts cytosine into a uracil residue
Repaired by an excision repair mechanism