DNA Replication II

Question 1

Components required for DNA synthesis

Answer 1

dNTPs
DNA fragment template
DNA polymerase
Mg2+
free 3' OH

Question 2

Roles and properties of DNA polymerase

Answer 2

phosphodiester bond
3’ OH to 5’ phosphate
Pyrophosphate released
complimentary base pairing

Question 3

Acyclovir (guanine analog)

Answer 3

viral enzyme thymidine kinase

lack 3’ OH

Question 4

Cytosine arabinoside (cytrarabine)

Vidarabine (adenosine arabinoside)

Answer 4

planar conformation at 3’ OH

DNA kinks

Question 5

DNA polymerase III

Answer 5

cytosine can have tautomeric activity
3’ - 5’ proofreading exonuclease activity
Activated by improper H-bonding

Question 6

Theta replication

Answer 6

bacterial cells
1 double stranded circle - plasmid
1 ORI (origin of replication)
Entire genomer

Question 7

Rolling-Circle model - prokaryote DNA replication

Answer 7

Bacteriophage: viral take over

Unrolls as it replicates vs. unpeeling like a sticker in theta replication

Question 8

Initial of DNA Replication (prokaryotes)

Answer 8

Initiator (DNAa) - breaks H-bonds, bubble formation
DNA helicase (DNAb) - primosome formation
Helicase inhibitor(DNAc) - helicase delivery/activation
DNA primase - primer
DNA polymerase I - remove primer, exonuclease, repair. (lagging strand)
DNA polymerase III - synthesis (leading strand)
SSB protein - prevent re-annealing

Question 9

OriC

Answer 9

A-T rich
13-mer & 9-mer
DNAa binding

Question 10

Initiation of replication at OriC

Answer 10

Initiator(DNAa) to 9-mer
Strand seperation at 13mer
Helicase inhibitor(DNAc) delivers helicase(DNAb)
Helicase clamps ss DNA with SSB
Helicase unwinds ds DNA

Question 11

RNAseH and FEN-1

Answer 11

removes the RNA primer in eukaryotes

Question 12

DNA polymerase III (prokaryotes)

Answer 12

okazaki fragments & leading strand

Question 13

DNA polymerase I (prokaryotes)

Answer 13

removes RNA primer

Question 14

DNA ligase

Answer 14

seals nicks
uses ATP
link monophosphate to 3’ OH

Question 15

Follow up care to Okazaki fragments

Answer 15

DNA Pol I (prokaryote) or RNAseH & FEN-1 (eukaryotes) remove primer
gap filled by a DNA Pol I & III
Ligase joins

Question 16

Clamp Protein

Answer 16

holds DNA Pol III
recognized ds DNA
triggering its release then DNA Pol III release

Question 17

Supercoiling control

Answer 17

DNA gyrase(prokaryote)
DNA topoisomerase (eukaryotes)

Question 18

Ciprofloxacin

Answer 18

quinolone drug
inhibits bacterial DNA gyrase - allows supercoiling
URI & UTI Tx

Question 19

Telomeres

Answer 19

repeating terminal DNA sequences

maintained by telomerase, via reverse transcriptase (RNA –> DNA)

Question 20

DNA Replication:

Prokaryotes vs. Eukaryotes

Answer 20

1 vs. many ORI
Pol 1, 2, 3 vs alpha, beta, gama, delta
S phase vs. S-G phase
removal of primer: Pol 1 vs RNAaseH & FEN1

Question 21

Prokaryotic DNA polymerases

Answer 21

1 - removal RNA primer, replace with DNA

3 - sun leading & lagging strand

Question 22

Eukaryotic DNA Polymerases

Answer 22

Alpha - Syn RNA primer leading & lagging. Primes. DNA syn. Low processivity.
Delta - Syn DNA leading/lagging. High processivity. 3’-5’ proofreading.

Question 23

Pol beta & gama

Answer 23

DNA repair

Mithochondria genome replication

Question 24

Camptothecin

Answer 24

inhibits topoisomerase I

nicks one strand in ds DNA to fix supercoiling

Question 25

Etoposide

Answer 25

inhibits topisomerase II

breaks both backbones to fix supercoiling

Question 26

Actinomycin D (Dactinomycin)

Answer 26

phenoxazone ring intercalates between adjacent guanine-cytosine bases
prevents DNA replication by preventing ss DNA formation and inhibits RNA transcription(strand seperation)