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Genes, Genomes and Biomedical Implications > DNA Repair > Flashcards

DNA Repair Flashcards

1
Q

What can DNA damage be?

A

spontaneous or mutagen-induced

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2
Q

Give examples of spontaneous DNA damage

A
  • depurination
  • deamination
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3
Q

Give examples of mutagen-induced DNA damage

A
  • pyrimidine dimers
  • alkylation
  • substitution
  • deletions/insertions
  • frameshift mutations
  • DSBs
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4
Q

What are the 2 DNA related point mutations?

A
  • transitions (purine or pyrimidine is replaced by another)
  • trasversions (purine is replaced by a pyrimidine or vice versa)
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5
Q

What happens if depurination or deamination are left uncorrected?

A

deletion or substitution of base pairs during DNA replication

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6
Q

What does nitrous acid do?

A

oxidatively deaminate primary amines, producing transition mutations

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7
Q

What recognises unnatural nucleotides?

A

specific DNA glycosylases

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8
Q

When does DNA mispairing occur?

A

when methylated C is converted to T by deamination

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9
Q

When do pyridine and thymine dimers form?

A

when cells are exposed to UV irradiation

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10
Q

What are alkylating agents?

A

chemicals that add an alkyl group to another molecule

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11
Q

What do intercalating agents do?

A

generate insertion/deletion mutations and increase the distance between 2 consecutive base pairs

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12
Q

What does replication of DNA with insertion/deletion mutations do?

A

generate deletion or insertion of one or more nucleotides in the newly synthesised DNA i.e. frameshift mutation

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13
Q

What is Ames test used for?

A

to assess mutagenicity of compounds using bacterial strain Salmonella typhimurium which is unable to grow and form colonies in a medium lacking histidine

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14
Q

What are the 5 main DNA repair pathways?

A
  • direct repair
  • excision repair
  • mismatch repair
  • recombination repair
  • non homologous end joining
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15
Q

What are the 4 types of DNA repair systems in bacteria?

A
  • repair of synthesis errors
  • repair of DNA modifications
  • repair of replication fork barriers by translesion synthesis
  • repair of breaks in DNA by homologous recombination and non-homologous end joining
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16
Q

What does proofreading by DNA pol do?

A

decrease errors introduced during DNA synthesis by 1000-fold

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17
Q

What does mismatch repair in E. coli do?

A

correct errors that remain after proofreading and reduce errors by a further 100-fold

18
Q

What does mismatch repair involve in E. coli?

A

the MutSLH system, which depends on the methylation of selected A residues in GATC to distinguish newly synthesised vs template DNA

19
Q

What are the 5 steps of mismatch repair in E. coli?

A
  1. MutH binds to the dam site and MutS recognises that there is a mismatch
  2. MutL bind to the MutS (ATPS)
  3. after the MutS has recognised the damage, it communicates to MutH which becomes activated as a nuclease
  4. it cleaves the newly synthesised unmethylated strand and acts in the same way as an NER
  5. DNAPIII then synthesises a new strand, ensuring the correct nucleotides are used
20
Q

What are the targets for Dam methylase after replication?

A

GATC sequences

21
Q

What does photoreactivation repair do?

A

remove pyrimidine dimers via a light-dependent reaction

22
Q

Where does photoreactivation repair occur?

A

bacteria but not placental mammals

23
Q

What are photolyases?

A

photo-reactivating enzymes made up of 2 tightly bound chromophores that repair pyrimidine dimers by using light energy and a very rapid photochemical reaction

24
Q

What are the 5 steps of photoreactivation repair?

A
  1. enzyme binds to DNA containing pyrimidine dimer
  2. absorbs visible light (300-500nm) using second chromophore
  3. energy transferred to FADH2
  4. FADH2 transfers electron to pyrimidine dimer
  5. pyrimidine dimer splits into monomeric form
25
Q

What does BER do?

A

remove only the damaged base via DNA glycosylase

26
Q

What does DNA glycosylase do?

A

cleave the glycosidic bond leaving an apurinic or apyrimidinic site

27
Q

What are the 4 enzymes involved in BER?

A
  • AP endonuclease
  • DNA pol I
  • DNA ligase
  • DNA glycosylase
28
Q

What does NER involve in E. coli?

A
  • ATP
  • UvrABCD proteins
29
Q

What is UvrA?

A

ATPase that recognises damage with 2 ATP binding sites that binds damaged DNA

30
Q

What is UvrB?

A

monomer with helicase motifs but no ATPase or helicase activity that is activated by UvrA

31
Q

What is UvrC?

A

nuclease monomer that binds ssDNA non-specifically and does not interact with UvrA or B in solution

32
Q

What are the 4 steps of NER in E. coli?

A
  1. UvrA recognises damage and binds with UvrB
  2. UvrA is released and UvrC binds
  3. UvrC nicks DNA on both sides of damage
  4. UvrD unwinds region, releasing damaged strand
33
Q

Give examples of conditions in which UV-induced DNA lesions cannot be repaired

A
  • xeroderma pigmentosum
  • Cockayne syndrome
34
Q

What happens when a lesion is encountered during replication?

A

DNA Pol III is replaced by error-prone translesion DNA polymerase, Pol IV or Pol V

35
Q

What does translesion DNA polymerase do?

A

extend DNA synthesis beyond thymine dimer independent of base pairing and has no proofreading exonuclease activity

36
Q

Where is DSB repair by non-homologous end joining (NHEJ) common?

A

mammalian somatic cells

37
Q

What does Ku do?

A

splice the 2 fragments together at the break site

38
Q

What are the 4 stages of NHEJ?

A
  1. end recognition by Ku heterodimers
  2. processing of DNA ends
  3. limited repair synthesis
  4. ligation
39
Q

How can the replication fork collapse?

A

through homologous recombination repair

40
Q

When are DSBs produced?

A
  • replication fork encountering an ss nick in the template DNA
  • ionising radiation
  • replication errors
  • oxidising agents

Genes, Genomes and Biomedical Implications (15 decks)

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