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2B genetics and evolution > R7 DNA damage and repair > Flashcards

R7 DNA damage and repair Flashcards

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1
Q

What is a DNA lesion ?

A

breaks or other chemical changes that affect the structure of the helix, ultimately preventing transcription

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2
Q

What are some examples of DNA lesions ?

A

ss breaks, ds breaks, bulky adduct (covalently linked), interstrand crosslink, base mismatch, base alkylation

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2
Q

What effect can UV have on DNA ?

A

cause thymines to form dimers (bond to one another)

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3
Q

What effect can ionising radiation have on DNA ?

A

ss and ds breaks

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4
Q

What effect can alcohol have on DNA ?

A

interstrand crosslinks

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5
Q

What effect can oxidative damage have on DNA ?

A

oxidised bases, ROS - reactive oxygen species

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6
Q

What effect can mechanical stress have on DNA ?

A

ds breaks during mitsosis

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7
Q

What process is the biggest source of DNA lesions

A

DNA replication

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8
Q

How does the unpacking of chromatin affect the chances of lesions ?

A

Increases, as the proteins in chromatin protect from UV and IR

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9
Q

How can DNA polymerase increase the chance of lesions occurring ?

A

May miss or add nucleotides or mismatch them, damaged nucleotides can be used, ribonucleotides are incorporated or not removed from RNA primers

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10
Q

How do unpaired bases affect the chances of lesions occurring ?

A

they are exposed to bases and ROS

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11
Q

How is ssDNA affected by lesions ?

A

more prone to breakage due to mechanical stress

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12
Q

What happens if lesions are not repaired or repaired incorrectly ?

A

Mutation(s) will occur

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13
Q

What type of lesions does the cell recognise ?

A

DNA free ends (not telomeres), ssDNA accumulation and persistence, base pairing incorrectly, the bases not being A,T,G,C, not having deoxyribose

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14
Q

How is an extra nucleotide base repaired by the cell

A

Nuclease removes the structural damage then polymerase fills the gap then ligase seals the nick

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15
Q

How is a thymine dimer repaired by the cell ?

A

Photolyase (light-activated enzymes) cleaves the bond between thymines during times of high UV

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16
Q

How does an extra nucleotide/ mismatch affect the replication process ?

A

they will be paired up on one strand leading to a mutation, this would be the same for mismatch

17
Q

How may a RNA nucleotide affect the replication process?

A

cause mismatch in the daughter strand

18
Q

How may an oxidised guanine affect the replication process?

A

oxo-G can pair with A, when repaired by cut and patch the G will be removed and replaced with a T, leading to a mutation in both strands

19
Q

What is the cut and patch mechanism ?

A

Nuclease removes a nucleotide, polymerase adds one, ligase seals the nick

20
Q

How can a dsBreak be caused?

A

broken replication fork, unseperated sister chromatids in mitosis, ionising radiation, some chemicals (chemotherapeutic)

21
Q

How is an ICL caused ?

A

endogenous metabolites (acetaldehyde), chemicals (chemotherapeutic drugs)

22
Q

How is a dsbreak repaired ?

A

Ligation of broken ends, homologous recombination (the breakage is compared to a non-broken homologous chromosome and copied)

23
Q

What can ligation of a dsbreak cause ?

A

addition or deletion at the site of breakages which is error prone

24
Q

What can homologous recombination cause ?

A

Erroneous repair

25
Q

What is erroneous repair in terms of DSB ?

A
  • telomeres added to a break (causing the loss of the acentromeric arm and a shorter chromosome),
  • reciprocal translation - the broken end joins to another strand
  • dicentric chromosomes - another chromosome binds to the broken end, making an unstable double chromosome, the chromosome then has 2 centromeres so the spindle fibres pull at them both, leading to more breakages
26
Q

What is GCR ?

A

Gross chromosomal rearrangement:
- large deletions, large insertions, large inversions, translocation

arises from erroneous DSB repair

27
Q

what is aneuploidy ?

A

more than one abnormal chromosome

28
Q

What is common in cancer cells that may be caused by erroneous dsb repair ?

A

aneuploidy, GCR

29
Q

How is ICLs repaired ?

A

they cannot be transcribed as the DNA strands cannot be separated

in proliferating cells it may block sister chromatid segregation in mitosis

may be converted to DSB then repaired as a DSB

sometimes induced in anti-cancerous therapy

30
Q

What is the bacterial SOS response ?

A

During serious DNA damage, ssDNA accumulates and activates SOS regulons

This causes:
- replication to continue, cell division inhibitors are activated, filamentous cells with many chromosome copies are made

  • homologous recombination genes activated
  • trans lesion synthesis (TLS) DNA polymerase genes activated allowing for mutagenesis (gene mutation in base order). the polymerase uses the damage template strand adding the wrong bases
  • delayed cell division allows time to repair DNA before dividing
31
Q

What is mutagenesis ?

A

The change in base order leading to a mutant forming

32
Q

Where are the DNA damage checkpoints in the cell cycle?

A

G1 - so DSB cannot go into S
Intra-S checkpoints - replication fork problems means the late origin is not fired
G2 - there is ssDNA, mitosis is then blocked

33
Q

What is the DNA damage response based on ?

A

PTMs, transcription activation plays a minor role

34
Q

Why is blocking the next stage of the cell cycle important ?

A

Allows time for repair

35
Q

What two processes must happen before a mutation is acquired ?

A

lesion formation, escaping repair

36
Q

How can we work on the probability of mutations?

A

multiple the probability of lesions, and probability of escaping correct repair

external stimuli may change the probability, UV increases the chance of lesions

37
Q

How can mutation rates be increased ?

A

Exposure to high UV, then placed in the dark so photolyase isn’t activated

38
Q

what can increase the chance of acquiring lesions ?

A
  • DNA polymerase loses its proofreading activity
  • Wrong nucleotide incorporated
  • Helicase loses function, forks break more often
  • Mitochondria are leaking, more ROS in the nucleus
39
Q

What increases the probability of escaping repair ?

A
  • Mutations lead to higher mutation rates due to higher probability of unrepaired or incorrectly repaired damage.
  • Mutations in DNA damage checkpoint genes
  • Mutations in chromosome segregation genes (mitotic spindles)
40
Q

What is somatic mosaicism ?

A

the acquiring of mutations in somatic cells leading to only some areas being affected - cannot be inherited

BRCA is an example of this

41
Q

Why might a replication fork be stalled ?

A

DNA damage (ss breaks, ds breaks, abbducts), G-quadruplexes (lots of G), fork collision, not enoguh free nucleotides, helicase and polymerase loose function, R-loops (RNA, DNA hybrids), failure for topioisomerase, lack of checkpoints, DNA-binding proteins, crosslinks

2B genetics and evolution (26 decks)

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