DNA Replication, Repair and Recombination 2 (Lec 4)

Question 1

What is depurination?

Answer 1

spontaneous reaction where purine bases are lost

Question 2

How often does spontaneous deamination of C to U occur?

Answer 2

100 bases/day

Question 3

In regards to DNA damage, UV radiation from sun can produce covalent linkage between what two bases?

Answer 3

adjacent pyrimidines

T-T or C-T

Question 4

What does Base Excision Repair entail?

Answer 4

DNA glycosylases that recognize a specific type of altered base and catalyzes its removal; enzyme mediated “flipping out” of base from the helix; If it finds an incorrect base it cleaves glycosyl bond connecting base with sugar; AP endonuclease and phosphdiesterase cut phosphodiester backbone - damage is removed and gap is repaired

Question 5

What does Nucleotide Excision Repair entail?

Answer 5

can repair any bulky lesion like chemically-induced and thymine dimers; a multi enzyme complex scans DNA for distortion in double helix instead of specific base change; cleaves phosphodiester backbone on both sides; DNA helices peels lesion containing strand away; large gap is repaired by DNA polymerase and ligase

Question 6

What does Transcription-coupled repair entail?

Answer 6

cells can preferentially direct DNA repair to sequences that are being actively transcribed by linking RNA polymerase with DNA repair: RNA polymerase stalls at lesions and directs repair machinery there; it’s specific for the strand being transcribed

Question 7

Every deamination event forms and unnatural base which proves a possible reason why RNA is not the hereditary information because….

Answer 7

deaminated cytosine and natural Uracil are indistinguishable

Question 8

Why are methylated cytosines problematic?

Answer 8

Occur at some CpG sequences, associated with inactive genes

Deamination of methyl-C produces T mismatched with G

Question 9

How is methylated cytosine fixed

Answer 9

a special DNA glycosylase recognizes it and removes the T

Question 10

What does double strand break repair entail?

Answer 10

non-homologous end joining brings broken ends together and rejoins by DNA ligation

Question 11

What causes double-strand breaks?

Answer 11

ionizing radiation, replication errors, oxidizing agents and other metabolites

Question 12

What is homologous recombination?

Answer 12

genetic exchange between a pair of homologous DNA sequences

Question 13

How does homologous recombination repair stalled or broken replication fork?

Answer 13

replication fork is moved back and then broken, an exonuclease then degrades the 5’ end

Question 14

What happens during strand invasion in homologous recombination?

Answer 14

single stranded DNA is paired with complementary strand in different double-stranded helix, forms a region of heteroduplex DNA

Question 15

What is hybridization?

Answer 15

DNA double helix reforming from its separated single strands

Question 16

What does RecA do?

Answer 16

allows single-stranded DNA pairing with homologous double helix

Question 17

DNA hybridization requires double or single-stranded DNA?

Answer 17

single-stranded

Question 18

Once homologous sequence is identified, what happens?

Answer 18

strand invasion

Question 19

What is branch migration?

Answer 19

unpaired region of one single strand displaces a paired region on the other

Question 20

True or False?
branch migration can happen simultaneously in both direction or can be catalyzed by special helicase to move in one direction

Answer 20

true

Question 21

Compare non-homologous end joining and homologous recombination

Answer 21

non-homologous end joining: no template required, creates a mutation at the site of repair, can also create translocations

homologous recombination: uses daughter DNA duplex as template, no loss or alteration of DNA at repair site, can repair other types of DNA damage

note: both of these repair processes are for double-strand breaks