DS DNA repair

Question 1

double stranded DNA break

Answer 1

when the phosphodiester backbone of both strands breaks the DNA duplex

Question 2

how do DS DNA breaks occur

Answer 2

naturally through:
1. meiosis
2. immune diversity, VDJ recomobination
3. DNA replication
4. Insertion of retrovisru or retrotransposons into genomic DNA
Ionizing radiation:
1. cosmic rays
2. cosmuc radiation
3. ionizing radiation
4. medical tests and treatment

Question 3

How are DS breaks sensed?

Answer 3

1. ataxia telegiectasia mutated (ATM)

2. ataxia telangiectasia and RAD3 (ATR)

Question 4

how are DS breaks repaired?

Answer 4

1. DNA non-homologous end jointing (NHEJ)

2. homologous recombination (HR)

Question 5

NHEJ

Answer 5

imperfect
loss of nucleotides
occurs throughout the cell cycle

Question 6

HR

Answer 6

perfect repair
requires sister chromatid
limited to S and G2 of cell cycle

Question 7

NHEJ involved proteins

Answer 7

1. Ku recognizes DS break
2. Ku recruits DNA PKcs
3. uses nuclease to remove damaged DNA (Ku, DNA PKcs, Artemis)
4. polymerase to fill gaps
5. repair finished with ligase to restore phosphodiester backbone on both strands

Question 8

NHEJ is not a linear process

Answer 8

lots of possible outcomes, like:

1. repaired dsDNA
2. two DNA ends with partially processed top and bottom strands
3. gapped structure with partially processed bottom strand

Question 9

NHEJ has

Answer 9

heterogeneity after repair

typically causes deletions/insertions or imperfect healing

Question 10

Homologous recombination between homologous chromosomes is essential for

Answer 10

progression through meiosis–assures genetic diversity in gametes

Question 11

HR in germ cells:

Answer 11

bias to use homolog and resolve via DSBR

to ensure recombination

Question 12

HR in somatic

Answer 12

bias to use sister chromatid and resolve via SDSA

to avoid recombination and LOH

Question 13

Key steps of ds DNA repair

Answer 13

Sense
signal transduction: ATM
Response
either DNA repair or Cell death

Question 14

types of next gen sequencers

Answer 14

illumina

pacific biosciences

Question 15

difference in illumine and pacific biosciences

Answer 15

both optical
pacific long reads
illumine short reads
pacific: high error rates, cheap, short time
illumina: low error rates, expensive, long time

Question 16

next gen sequencing is

Answer 16

1. direct sequencing of cDNA products
2. identify mutations and modifications
3. dynamic range

Question 17

issues that affect SNP calling

Answer 17

coverage
error rate
ploidy