Lecutre 27 - DNA Replication and Repair

Question 1

where does DNA replication initiate?

Answer 1

at replication origins

Question 2

what are the 3 stages of DNA replication?

Answer 2

1. initiation
2. elongation
3. termination

Question 3

what are the 6 basic steps of DNA replication?

Answer 3

1. origin unwinding + helicase recruitmen
2. primase loading
3. loading of sliding clamp
4. loading of replicative polymerase
5. bidirectional fork movement
6. completion of replication

Question 4

what does the structure of DNA polymerase resemble?

Answer 4

a right hand

Question 5

what is exonuclease activity?

Answer 5

associated with proofreading

Question 6

polymerase ensures ___ by _____

Answer 6

fidelity by proofreading

Question 7

what does helicase do?

Answer 7

undwinds DNA base pairs

Question 8

what are two types of replicative helicases?

Answer 8

1. bacterial

2. eukaryotic

Question 9

what is the helicase called in eukaryotes?

Answer 9

MCM

Question 10

what are single-stranded binding proteins?

Answer 10

-they can adopt many secondary structures that would make copying by polymerase difficult

Question 11

what is the single stranded binding protein called in eukaryotes? in bacteria?

Answer 11

RPA

SSB

Question 12

what does topoisomerase do?

Answer 12

relieves supercoiling strains

Question 13

where does DNA supercoil?

Answer 13

ahead of the replication fork

Question 14

what does the sliding clamp and loader do?

Answer 14

• clamp loader is an ATPase

- helps to load the clamp onto the template DNA

Question 15

what is the clam in eukaryotes? in bacteria?

Answer 15

• PCNA

- beta protein

Question 16

what do initiator proteins do?

Answer 16

help recognize replication origin

Question 17

what is the initiator protein in eukaryotes? in bacteria?

Answer 17

• ORC

- DnaA

Question 18

what does primase do?

Answer 18

synthesizes short 10-30 nt RNA primer

Question 19

how does the polymerase/primase complex switch?

Answer 19

it switches form primer synthesis to replicative elongation

Question 20

where is the lagging strand synthesized?

Answer 20

in Okazaki fragments

Question 21

what happens to the ends of linear chromosomes during replication?

Answer 21

ends of linear chromosomes are truncated

Question 22

what is the solution to truncated ends?

Answer 22

-telomeric sequences are added

Question 23

what is a cause of truncated ends?

Answer 23

-inability to fill the gap left after the removal of the last RNA primer

Question 24

besides the typical DNA replication error rate, what is another cause of DNA damage?

Answer 24

exposure to radiation or chemical agents

Question 25

what are 2 main types of DNA damages?

Answer 25

1. point mutations | 2. insertions/deletions

Question 26

what are 2 types of point mutations?

Answer 26

1. transitions (purine/ pyrimidine replaced by another purine/pyrimidine) 2. transversion (purine replaced by a pyrimidine or vice versa)

Question 27

what is insertion/deletion?

Answer 27

-one or more nucleotide pairs missing or added

Question 28

how are DNA damage repairs mediated?

Answer 28

by enzymes

Question 29

distortions in ______ causes replication errors

Answer 29

dsDNA

Question 30

bases are subject to ______

Answer 30

natural/unnatural modifications

Question 31

what is the most common type of base damage?

Answer 31

- hydrolytic breakage of the glycosidic bond between a purine and the sugar-phosphate backbone of DNA - leaves a gap which causes substitutions or deletions when the DNA is replicated

Question 32

what are the 4 mechanisms for DNA repair?

Answer 32

1. Mismatch repair (MMR) 2. Base excision repair (BER) 3. Nucleotide excision repair (NER) 4. Translesion synthesie (TLS)

Question 33

what does MMR do?

Answer 33

1. fixes single base errors | 2. fix splipped-strand replication errors

Question 34

what does BER do?

Answer 34

-abasic sites cleaved by AP endonucleases | -

Question 35

what does NER do?

Answer 35

- short stretches of damaged DNA with bulky lesions are removed by NER - followed by resynthesis

Question 36

what can NER be coupled with?

Answer 36

transcription

Question 37

what is TCR?

Answer 37

- transcription coupled repair | - used to repair damaged DNAs that have stalled transcription

Question 38

what is TLS?

Answer 38

- follow the sliding clamp | - switched between normal replication to TLS when a lesion is found

Question 39

how are double-strand breaks (DSB) fixed?

Answer 39

1. homology directed repair | 2. homologous recombination

Question 40

what is homology directed repair

Answer 40

- uses homologous chromosome | - conversion of info in the region of the break to info from the homolog

Question 41

what is homologous recombination?

Answer 41

-exchange large segments of DNA