Lecture 4: DNA Replication, Repair, and Recombination 2

Question 1

What factors cause a need for DNA damage to be repaired?

Answer 1

Replication errors and accidental lesions that occur in the genome.

Question 2

Fewer then how many accidental base changes result in a permanent mutation?

Answer 2

1/1000 accidental base changes

Question 3

Fill in the Blank:

Spontaneous deamination of C to U occurs at _____ bases/day.

Answer 3

100 bases/day

Question 4

Fill in the blank:

_____ purine bases are lost every day due to a spontaneous reaction called _____.

Answer 4

5000; depurination

Question 5

What bond is broken in depurination?

Answer 5

Hydrolysis of the N-glycosyl linkage.

Question 6

What type of DNA damage can cause covalent linkage between two adjacent pyrimidines (T-T or C-T)?

Answer 6

UV Radiation

Question 7

Can exposure to reactive forms of O₂ in the cell or chemicals in the environment cause DNA damage.

Answer 7

Hell Yes

Question 8

What happens if a deaminated C is changed to U and it is not fixed during DNA replication? Also, what happens if a purine base is depurinated and not fixed during DNA replication?

Answer 8

Lead to either a deletion or a base pair substitution in the daughter strand.

**look at slide 6 for a nice figure**

Question 9

What types of DNA repair mechanisms do we have?

Answer 9

• Base excision repair
• Nucleotide excision repair
• Transcription-coupled repair
• Double-strand break repair
  
  • non-homologous end joining
  • homologous recombination

Question 10

What do DNA glycosylases do and in which form of DNA repair are they involved with?

Answer 10

• each recognize a specific type of altered base and catalyzes its removal
  
  • at least 6 different types
• Base Excision Repair

Question 11

What do DNA glycosylases do if they find an incorrect base during their mediated “flipping out” of bases from the helix to check them?

Answer 11

cleaves glycosyl bond connecting the base and sugar

Question 12

In base excision repair, what do AP endonuclease and phosphodiesterase do after DNA glycosylase has cleaved the glycosyl bond between the base and the sugar?

Answer 12

They cut the phosphodiester backbone; damage is removed and the gap is repaired.

**DNA polymerase adds a new nucleotide and then DNA ligase seals the nick**

Question 13

True or False:

Both deaminated cytosines and depurinated purines are fixed via the same mechanism in base excision repair.

Answer 13

False - Depurinations are directly repaired beginning with AP endonuclease. Deaminated cytosines are repaired by the same process, but it is proceeded by DNA glycosylase activity to remove the sugar from the base.

Question 14

What can nucleotide excision repair do that base excision repair cannot?

Answer 14

• Differs in how damage is removed.
• Can repair any bulky lesion.
  
  • e.g., chemically-induced and thymine dimers

Question 15

How does nucleotide excision repair check for DNA damage?

Answer 15

• A multienzyme complex scans DNA for distortion in double helix instead of specific base exchange.

Question 16

Once distortion in the double helix is found by nucleotide excision repair multienzyme complex, how does the repair occur?

Answer 16

• Cleaves phosphodiester backbone on both sides; DNA helicase peels lesion-containing strand away.
• Large gap is repaired by DNA polymerase and ligase.

Question 17

What is transcription-coupled repair?

Answer 17

Cells can preferentially direct DNA repair to sequences that are being actively transcribed by linking RNA polymerase with DNA repair.

**sequences that urgently need repair**

Question 18

Stopped on Slide 12