DNA Repair

Question 1

What are the 3 general steps of DNA repair?

Answer 1

Irregularity is detected, abnormal DNA is removed, normal DNA is synthesized

Question 2

What is Depurination a result of?

Answer 2

Cleavage of glycosidic bond between deoxyribose and a purine base.

Question 3

What is deamination?

Answer 3

The hydrolytic conversionof a DNA cytosine to a uracil.

Question 4

What is oxidation (DNA damage context)

Answer 4

Oxidation of a guanine to 8-oxoguanine or thymine to thymine glycol

Question 5

What is non-enzymatic methylation?

Answer 5

Accomplished by S-adenosyl methionine

Question 6

Prolonged UV radiation can result in thymine dimers, what enzyme can repair it? What type of repairs can be fix it?

Answer 6

Photolyase. Can be repaired by direct repair or nucleotide excision repair

Question 7

What is photoreactivation?

Answer 7

Direct repair: Photolyase binds to the thymine dimers in the dark and then when light is present, the enzyme breaks the bonds linking the rings. It then disassociates in the dark.

Question 8

What is nucleotide excision repair?

Answer 8

In E.coli, UVrA / UVrB recognizes the dimer as damaged DNA and uses ATP hydrolysis to bend the DNA and cleave around the damaged DNA and removes it. Polymerase and ligase replace the DNA with new DNA using the other strand as a template

Question 9

Mutations causing nucleotide excision repair pathways can cause what disease ?

Answer 9

Xeroderma pigmentosa, extreme sensitivity to sunlight and have a very high risk of developing skin cancer.

Question 10

What is the danger of altered bases?

Answer 10

Altered bases can be mispaired and result in changes that are passed to the next generation. Ionizing radiation can make OxoGuanine and Nitrosamines can make O6-methyl guanine these can mismatch to Adenine or Thymine leads to mutagenesis

Question 11

How is O6-methylG damage reversed?

Answer 11

Direct repair, one enzyme, methyltransferase, removes the methyl group.

Question 12

When cytosine is replaced with uracil what kind of rxn is it?

Answer 12

Deamination

Question 13

What is depurination?

Answer 13

Guanine is removed via hydrolytic rxn and leaves an abasic site. Guanine and adenine = purines

Question 14

What is the bond between a sugar and a base?

Answer 14

Glycosidic

Question 15

Whats the general process of base excision repair fix AP sites?

Answer 15

DNA Glycosylase cuts the glycosidic bond and removes uracil and leaves AP site. The AP site recruits endonucleases and cuts around the site . DNA pol I and ligase fill the gap.

Question 16

During replication what can repair a mismatched base pair?

Answer 16

DNA pol I

Question 17

In prokaryotes, if a mismatched base isnt repaired by DNA pol I, a bulge forms and what happens next?

Answer 17

The bulge recruits Mut S, Mut L comes in to link Mut S to Mut H and finds GATC, Mut H identifies the unmethylated (new) strand and forms nick, exonuclease helicase and SSB remove the damaged DNA region and pol III synthesizes new strand

Question 18

What are the steps of Homologous Recombination? Whats happening at each step?

Answer 18

1. Resection the 5’ ends. 2. Strand invasion. 3 Holliday junction formation. 4. Branch Migration. 5. Holliday Junction resolution. 6. Damaged DNA reparied.

Question 19

Holliday junctions, whats the difference between crossover and non-crossover

Answer 19

Crossover is when all 4 strands exchange genetic material, anything less is non-crossover. It just depends on what enzyme performs what type of cut.

Question 20

What is trans-lesion synthesis?

Answer 20

For regions that arent important and dont code for anything, damaged DNA halts Pol III synthesis and Translesion polymerase incorporates bases independent of base pairing, TL Pol disassociates and DNA pol III comes back and finishes synthesis

Question 21

What is loss of heterozygosity?

Answer 21

When a diploid cell loses the normal allele on one chromosome due to inactivation, deletion, or being non-functional