DNA Replication, Damage, and Repair

Question 1

DNA synthesis begins at origins of replication, which are __rich.

__directional replication forks with both leading and lagging strand synthesis proceed away from the origins to form replication bubbles.

Answer 1

AT-rich origins of replication

Bidirectional replication forks form growing replication bubbles

Question 2

Compare and contrast leading strand vs lagging strand

Answer 2

• BOTH synthesize 5’ to 3’.
• Leading strand synthesis is processive and continuous
  
  • Synthesize toward the fork
  • Lays down one 5’ RNA primer across from the template’s 3’ end.
• Lagging strand synthesis is nonprocessive and discontinuous
  
  • Synthesize away from the fork in okazaki fragments
  • Has to keep laying down multiple 5’ RNA primers at the fork –> Requires removal/fill in of primers and ligase

Question 3

Helicase unwinds

Topoisomerase relieves torsional stress

What do single-stranded DNA binding proteins do?

Answer 3

Bind single-stranded DNA to stabilize and prevent them reannealing

Question 4

Primase

Answer 4

Lays down RNA primers to create free 3’OH ends

Question 5

RNAase

Answer 5

removes RNA primers

Question 6

Polymerases synthesize new strands at ____ ends of primers using existing parental DNA template

Answer 6

Synthesize at free 3’OH ends of primers

Question 7

How does replication prevent a high rate of mutations?

Answer 7

3’->5’ Exonuclease proofreading function of polymerase to detect & correct errors

Question 8

What is the issue for replication at telomeres?

Answer 8

The last lagging strand RNA primer is placed at the end of the linear chromosome, so removing it means there’s no 3’OH group needed to start an Okazaki fragment to fill in that space.

–> Lagging strand template would get degraded and shortened

Question 9

Telomerase

Answer 9

Uses an internal RNA primer that is complementary antiparallel to telomeric sequences to prevent shortening of lagging strand

1. Extend the lagging strand template
2. Fills in the lagging strand, using the extended template

Question 10

How do ZDV, acyclovir, and gancyclovir inhibit DNA replication?

Answer 10

They all incorporate an analog that lacks a free 3’OH group –> terminates replication

Question 11

Endogenous sources of DNA damage

Answer 11

DNA synthesis problems

Depurination, demaination, lack of proofreading, ROS

Question 12

Exogenous types of DNA damage

Answer 12

Ionizing X ray radiation

UV light (thymidine dimers)

Environmental chemicals

Question 13

Transitions vs Transversions

Answer 13

Transitions: purine to purine, or pyrimidine to pyrimidine

Transversions: purine to pyrimidine, or pyrimidine to purine

Question 14

Base excision repair

Answer 14

• Occurs for spontaneous endogenous changes causing minor distortions
  
  • Deamination: 5MeC to Thymine
• Base excision mechanism

Question 15

Nucleotide excision repair

Answer 15

• Used when UV light causes thymidine dimers –> detect large lesions or stalled transcriptional complexes
• Patch excision emchanisms
• XP & Cockayne syndrome

Question 16

Mismatch excision repair

Answer 16

• Used for unfixed DNA replication errors
• Patch excision
• Colorectal cancer

Question 17

How do cells form resistance to anti-cancer drugs like cisplatin?

Answer 17

Cisplatin causes DNA adduction to try to kill cancerous cells.

These cells will over-express the gene for XP-F (an NER protein) to repair damaged DNA –> drug resistance

Question 18

What type of damage causes melanomas?

Answer 18

Melanomas caused by inability to detect or repair exogenous UV-induced thymine dimers or chemical-induced DNA damage via NE

Question 19

XP vs Cockayne

Answer 19

• Xeroderma Pigmentosum & melanomas result from mutations to XP genes in the NER pathway
  
  • Cancer from sunlight or other chemical damage
• Cockayne: premature aging disease resulting from inactive genes involved in transcription-coupled repair (ERCC8 & ERCC6)