1-10 DNA replication & repair

Question 1

Euchromatin

Heterochromatin

Answer 1

Active, lysine acetylation

Silenced/condensed, lysine methylation

Question 2

Formation of replication fork

Answer 2

1. Origin recongition complex (ORC) sits on origin
2. helicase finds to ORC->prereplicatitive comples (pre-RC)= “origin loaded”
3. helicase activated, ORC phosphrylated (to prevent form refiring) and starts unzipping= “origin fired”

Question 3

Leading

Lagging

Answer 3

Continuous

Okazaki fragments with RNA primers and ligase needed, single strand DNA binding proteins attach on to newly unzipped part to protect from degredation until a RNA primer can be put down and DNA polymerase extend/protect

Question 4

Sliding clamp

Answer 4

prevent DNA pol from falling off

Question 5

alpha
delta
epsilon

DNA polymerases

Answer 5

alpha: leading and lagging no 3’-5- exonuclease
delta: primarily lagging strand, has 3-5’ exo
epsilon: primarily leading strand, has 3-5’ exo

exonucleases stall polymerase if incorrect nucleotide added and fix

Question 6

Supercoiling

Answer 6

unwiding DNA helix by helicase results in supercoils that are resolved by topoisomerases

top1: ss knick
top2: double stranded break, uses ATP

Question 7

cohesin rings

Answer 7

hold sister chromatids together

Question 8

Shelterin complex

Answer 8

telomeres has on single stranded DNA side that is long with tandem repeats

during DNA replication, shelterin complex will bind telomere area and wrap up single stranded end to fold back on self so polymerase will continue transcribing

Question 9

Replication of telomeres

Answer 9

Gap remains at end of lagging strand, therefore telomerase with an internally RNA template will bind sequence on template of lagging strange and extend the template strand end of telomere, now DNA polymerase can transcribe this newly extended sequence and leading/lagging strands will match size

Question 10

Methods of DNA damage

Answer 10

1. depurination
2. deamination
3. oxidation

Question 11

Single stranded DNA damage repair

Answer 11

identify, remove, replace, ligate

Types:

1. base excision repair: damage to single base
2. nucleotide excision repair: helix distorting
3. mismatch repair: errors in DNA replication/recombination

Question 12

Double-strand breaks DNA damage repair

Answer 12

identify, rejoin, ligate

Types:

1. NHEJ: mainly in G1 (error prone)
2. Microhomology-mediated end joing: similar to NHEJ cut occurs during s phase (error prone)
3. Homology directed repair: repair during/after DNA replication

Question 13

Error prone methods of DNA repair

Answer 13

NHEJ

MMEJ (Microhomology-mediated end joing)

Question 14

Base excision repair

Answer 14

Ex. deaminated cytosine = appears as Uracil

1. uracil DNA glycosylase removes nitrogen base
2. AP endonuclease and phosphodiestase remove sugar/phosphate
3. DNA pol add new nucleotides, DNA ligase seals

Question 15

Nucleotide excision repair

Answer 15

Ex. pyrimidine dimer, distorts helix

1. Excision nuclease cuts out chunk
2. DNA helicase zips off
3. DNA pol, DNA ligase fix

Question 16

NHEJ

Homologous recombination

Answer 16

Ex. Accidental ds break

1. breaks
2. processing of DNA end by nuclease
3. end joing by ligase
   Therefore: deletion of DNA sequence, low fidelity, G1 phase
4. breaks
5. Processing of broken ends by special nuclease
6. Accurately repairs using undamaged DNA as template
   Therefore; no loss of nucleotides, only S or G2 cuz requires sister chromatid

Question 17

Homologous recombination

Answer 17

Ex. Accidental double strand break

Question 18

BRCA1-associated genome surveillance complex (BASC)

Answer 18

has DNA damage sensing phosphorylations that activate repair machinery or if too severe induces apoptosis to protect self