2. DNA Replication and Repair

Question 1

Polymerases

Answer 1

Enzymes that synthesize nucleic abides by forming PDE bonds, PPi is released

Question 2

Nucleases

Answer 2

Hydrolyze PDE bonds:

• Exonucleases: remove nucleotides from ends
• Endonucleases cut within nucleic acid

Question 3

Required primer DNA polymerase and RNA polymerase

Answer 3

DNA: RNA (or DNA) primer
RNA: None

Question 4

Proofreading activity polymerases

Answer 4

DNA: Yes (exonuclease 3’->5’), RNA: No

Question 5

Helicase

Answer 5

Breaks hydrogen bonds

Question 6

Single stranded DNA binding protein (SSB)

Answer 6

Prevents reassociation of DNA and protects from degradation by nucleases

Question 7

Primase

Answer 7

Synthesizes (10bp) RNA primer

Question 8

DNA polymerase III

Answer 8

Begins synthesizing DNA in 5’->3’ direction

Question 9

Leading strand & Lagging strand

Answer 9

Leading = continuously (move to replication fork)
Lagging = Okazaki fragments (move from replication fork)

Question 10

RNAase H + uncharacterized DNA polymerase (delta)

Answer 10

Removes primers in eukaryotes + fills the gap

Question 11

DNA Polymerase I

Answer 11

Removes primers in prokaryotes + fills gap

Question 12

DNA Ligase

Answer 12

Seals the nicks between Okazaki fragments

Question 13

DNA Gyrase (topoisomerase II)

Answer 13

Provides swivel

Question 14

Quinolones, function + examples

Answer 14

Block activity of topoisomerase

Levofloxacin, ciprofloxacin, moxifloxacin

Question 15

Nalidixic acid

Answer 15

Kills bacteria by inhibiting DNA gyrase

Question 16

Etoposide, teniposide

Answer 16

Inhibitors of eukaryotic topoisomerase II

Question 17

Eurkaryotic DNA polymerases

Answer 17

Alfa and delta: leading and lagging strand
Gamma: replicates mitochondrial DNA
Beta and epsilon: DNA repair
Epsilon: can substitute for delta

Question 18

Telomeres

Answer 18

Repetitive sequence at ends of linear DNA

Question 19

Telomerase (only in eukaryotes)

Answer 19

RNA template, reverse transcriptase activity (hTRT). Only present in embryonic cells, germ cells and stem cells, not in somatic cells. Seen in cancer cells

Question 20

Inhbition of reverse transcriptase meds

Answer 20

AZT, ddC and ddI

Question 21

Reverse transcriptase activity in eurkaryotes

Answer 21

• Telomerase (hTRT)

- Retrotransposons (residual viral genomes in human DNA)

Question 22

AZT (HIV treatment)

Answer 22

1. Converted to triphosphate derivative, substrate
2. Azide instead of normal hydroxyl group: prevents further replication by causing chain termination. (Reverse transcriptase does not have proofreading activity)

Question 23

p53

Answer 23

Prevents damaged cells from entering S phase. Associated with Li Fraumeni syndrome and solid tumors

Question 24

ATM

Answer 24

Kinase essential for p53 activity.

Question 25

Ataxia telangiectasia

Answer 25

Inactivated ATM, hypersensitivity to X-rays and predisposition to lymphomas

Question 26

Rb

Answer 26

Retinoblastoma gene, negative regulator cell cycle, binds to E2F and repress transcription of genes

Question 27

Thymine dimers

Answer 27

Caused by UV light

Question 28

Remove thymine dimers

Answer 28

By nucleotide excision-repair mechanism (excision endonuclease, aka excinuclease)

Question 29

Cytosine deamination makes..

Answer 29

Cytosine -> Uracil

Question 30

Removal of uracil by..

Answer 30

Uracil glycosylase enzyme, then recognized by AP endonuclease that removes damaged sequence (loss of purine or pyrimidine)

Question 31

Maintain DNA fidelity in G2

Answer 31

Mismatch repair enzymes MSH2, MLH1

Question 32

Maintain DNA fidelity G1->S

Answer 32

Rb, p53

Question 33

Maintain DNA fidelity in S phase

Answer 33

DNA polymerase proofreading

Question 34

Maintain DNA fidelity in G1/G0 phase

Answer 34

Thymine dimer repair (XP, nucleotide excision repair)

Question 35

Xeroderma pigmentosum (4)

Answer 35

- Autosomal recessive (1/250,000) - Extreme sensitive to sunlight, skin freckling, ulcerations, skin cancer - Most common deficiency in excinuclease enzyme - Measure enzyme level in white blood cells

Question 36

Heriditary nonpolyposis colorectal cancer

Answer 36

- Aka Lynch syndrome - Deficiency to repair mismatched base pairs (hMLH1 or hMSH2) - Can inherit one copy, somatic mutation later - Intestinal cells high cell division rate

Question 37

Microsatellite instability

Answer 37

Short tandem repeats, usually in noncoding regions, e.g. TGTGTG. If mismatch repair lacks, number of repeats at locus will vary.