Lecture 4 Flashcards

0
Q

Mutations doe not only occure because of mistakes in replication

A

spontaneous DNA damage

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1
Q

What needs to be repaired in DNA

A

replications errors

accidental lesions

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2
Q

What is the spontaneous reaction to which 5000 purines are lost every day?

A

depurination

hydrolysis of the N-glycosyl linkage

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3
Q

What spontaneously occurs with 100 C to U bases/ day?

A

damination

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4
Q

What is caused by UV readation from the sun, or chemicals in the environment?

A

Produce a covalent linakge btw two adjacent pyrimidines (T-T) or (C-T)
purimidine dimers

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5
Q

What if DNA goes unrepaired?

A

deletion or base pair substitution in the duaghter strand

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6
Q

Base excision repair

A

Takes out the base, small repair

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7
Q

BER, six different types

- each recognizes a specific type of altered base and catalyzes its removal

A

DNA glycosylases

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8
Q

BER… Enzyme probes for damage by…

A

flipping out of base from helix to check if it is correct

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9
Q

BER, What happens if DNA glycosylases find an incorrect base?

A

cleaves glycosyl bond connecting base w sugar

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10
Q

BER What cuts the phosphodiester backbone to remove and repair gap?

A

AP endonuclease and phosphodiesterase

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11
Q

BER what are directly reapired begging w AP endonuclease?

A

depurinations

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12
Q

BER What adds new nucleotides/

A

DNA polymerase

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13
Q

What seals nick in DNA

A

DNA ligase

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14
Q

nucleotide excision repair…

A

repairs any bulky lesion like those chemically induced and thymine dimers

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15
Q

How does NER work?

A

a multienzyme complex scans DNA for distortion in double helix instead of specific base change

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16
Q

What does NER cleave?

A

phosphodiester backbone on both sides; DNA helicase peels lesion containg strand away

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17
Q

With NER what is the large gap repaired by?

A

DNA polymerase and ligase

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18
Q

Transcription coupled repair

A

cells can preferentially direct DNA repair to sequences that are being actively transcribed by linking RNA polymerase with DNA repair
- sequences that urgentyl need repair

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19
Q

TCR repairs by?

A

RNA plymerase stalls at lesions and directs repair machinery there

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20
Q

How does TCR work with BER, NER and others to repair genes?

A

Repairs genes that are being expressed when the damage occurs

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21
Q

What is TCR specific too?

A

the strand being transcribed

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22
Q

TCR

A

Non- transcribed strand repaired at the same rate as DNA not being trnascribed

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23
Q
  • defect in transcritipon coupled repair
  • growth retardation, skeletal abnormalitites, sensitivty to light
  • RNA polymerase is permanetely stalled at sites of damage in importnat genes
A

Cockayne’s syndrome

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24
Q

Damage detection

A

optimal for constructed remair
two strands=backup copy
all 4 bases are distinct so damage is obvious
RNA is not primary bc C and U would not be able to tell defect

25
Q

special problem with methylated cytosines in vertebrate DNA

A

occurs at CpG sequences

associtated with inactive genes

26
Q

deamination of methyl-C produces

A

T mismatched with G

27
Q

what recognizes and removes the T

A

special DNA glycosylase

  • repairs ineffectvie
  • only 3% of C nucleotides in human genome are methylated, but it counts for 1/3 of all point mutaionts associated with inherited hjman diseases
28
Q

Causes of double stranded breaks

A

ionizing, radiation, replication errors, oxidizing agents and other metabolites

29
Q

if double stranded break is left un repaired

A

chromosomes would break into smaller fragments and be lost

30
Q

how does DSB repair work?

A

non hologous end joining brings broken ends together and rejoins by DNA ligation; one or more nucleotides will be lost
-predominates in humnas and is genreally ok since so little of genome is protein coding

31
Q

Damage delays the cell cycle

A

very importnat to maintian intact and undamaged DNA from one gnereation to the next

32
Q

ensure the completion of one stage in the cell cycle before the next can begin

A

checkpoints

33
Q

Presnend of DNA damage triggers various checkpoints

A
  • blocks entry from G1 into S phase
  • Slows down progression through S phase
  • blocks transition from G2 to M phase
  • goves the cell extra time to repair DNA damage
34
Q

homologous recombination

A

genetic exchange btw a pair of homolgous DNA sequences

35
Q

Repair of double stnrad breaks

A

homologous recombination

-especially at stalled or broked replicaiton forks

36
Q

exhange of genetic informaiton to create new combinations of gnetic sequences

A

homologous recombination

-crossing over and gene converstion in meiosis

37
Q

homologous recombination mechanical role

A

assuring accurate chromosome segregation

38
Q

HR to repair stalled or broken replication fork

A
  • exchange takes place btw similar sequences … process requries base pairing but it doesnt have to be a perfect match
  • replication fork will collapse and break when nick is encountered
  • 5’ exonucleauses chews back parental strand to prepare for strand invation
39
Q

pairs single standed DNA with complementary strand in different double standed helix
-forms a region of heteroduplex DNA

A

strand invasion

40
Q

What happens in stand invasion

A
  • strands break/dissociates

- dAN synthessi continues as replication fork restarts

41
Q

What guides homolougus recombination?

A

base-pariing

42
Q

HR

A

must be sequences that are similar

43
Q

DNA dboule helix reforming from its spearated single strands

A

hybridizatino also called renaturation

44
Q

once a region of homology is found,

A

the single strands rapidly pair up

45
Q

creates a double helix from strands that orginate from different moclecules

A

heteroduplex DNA

46
Q

What allows single stranded DNA pairing with homologous double helix

A

Rec A

47
Q

What requires a single stranded DNA

A

DNA hybridization

-freed from pariing with complement so it can pair with the 2nd strand

48
Q

How is the singld stranded invading strand directed?

A

RecA(Rad51 in eukaryotes) and other proteins

49
Q

What happeds after the strand is guided to the SS

A

DNA synapsis reaction

  • beinds cooperatively to SS DNA and holds it together with the double helix until homologous seqence is foudn
  • SS searches via an unaknown mechanism
50
Q

once homologous sequnce is identified…

A

strand invasion occurs, fomring heteroduplex

51
Q

Once strand invations occurs, the point of exchang can move through?

A

Branch migration

52
Q

Branch migration

A

unpaired region of one single strand displaces a paired region on the other
-happens spontaneously in both directions or can be catalyzed by special helicase to move in one direction

53
Q

non-homologous end joinging

A
  • no template requried
  • creates a mutation at the site of repair
  • can also create translocation
54
Q

homologous recombination repair

A
  • uses daught DNA duplex as template
  • no loss or alteratioon of DNA at repair site
  • can repair other tiypes of DNA damage
  • very versatile
  • mechanism and proteins conserved in all organisms
55
Q

Repairing double stranded breaks by HR not at a replicaiton fork

A
  • 5’ ends degraded by exonucleases
  • one 3’ end invades homologous template and primes repair DNA synthesis
  • gaps are filled in and ligated
  • the newly synthesized 3’ end of the inading strand is then able to anneal to the other orgiinal 3; overhang in the dmaged chromsome through complementary base pairing
56
Q

homologous recombination in meiosis is slightly different

A

has many portine and sturcurual compononets in common

57
Q

Regulation of homologous recombination

A
  • accurate repair process can still casue problmes for a cell
  • use of a non functioning homolog to repair the other homolog
58
Q

What is a danger of homologous recombination?

A

loss of heterozygosity

  • critcal first step in cancer development
  • rare occurance
59
Q

prevention of repair in the absnece of damage

A

repair proteins dispersed thoughout the cell

-after damage, repair occurs in factories or foci at the sites of damage

60
Q

Regulation of homologous recombination of absence of damage

A

Brca2 maintains Rad51(recA) inactive

-mutations in BRAC2 leads to increase of breast cancer

61
Q

localization of repair proteins to DNA damage

A

fibroblasts Xrayed to produce double strand breaks

-