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LSM2232 > DLW06 - DNA Repair > Flashcards

DLW06 - DNA Repair Flashcards

1
Q

State the importance of DNA repair

A
  1. Minimises the need for cell killing
  2. Reduces mutations and replication errors.
  3. Reduces the persistence of DNA damage
  4. Increases stability of the genome
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2
Q

List the purines that you know.

A

Adenine, Guanine

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3
Q

List the pyrimidines that you know

A

Cytosine, Thymine, Uracil

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4
Q

State the two spontaneous mechanisms of DNA damage.

A

Depurination and deamination

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5
Q

Define the term “transition” in terms of DNA damage.

A

Transition involves the replacement of a purine or a pyrimidine with another purine or pyrimidine respectively.

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6
Q

Define the term “transversion” in terms of DNA damage.

A

Transversions involve the replacement of a purine with a pyrimidine or vice versa.

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7
Q

Depurination more frequently than depyrimidination. TRUE or FALSE?

A

TRUE.

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8
Q

Deamination of adenine yields … which binds to …

A

hypoxanthine; cytosine

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9
Q

Deamination of guanine yields …

A

xanthine

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10
Q

Deamination of cytosine yields … which binds to …

A

uracil; adenine

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11
Q

Deamination of thymine yields …

A

nothing. Thymine is unable to undergo deamination.

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12
Q

Name the mutagen which causes deamination.

A

Nitrous acid, HNO2.

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13
Q

Deamination of methylated cytosine yields … which binds to …

A

thymine; adenine

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14
Q

State the possible effect of deamination

A

Substitution mutations

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15
Q

State the possible effect of depurination

A

Deletion mutations.

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16
Q

Briefly describe pyrimidine dimerisation.

A

When cells are exposed to UV irradiation, two pyrimidine bases will form a dimer. Dimerisation occus between two adjacent thymine/cytosine bases.

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17
Q

State the three alkylating agents covered.

A
  1. Nitrogen mustard
  2. EMS
  3. MNNG
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18
Q

State the effect of nitrogen mustard on DNA.

A

Nitrogen mustard cross-links DNA at N7 of guanine, resulting in chromosomal breaks.

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19
Q

State the effect of EMS on DNA.

A

Reaction of guanine with EMS results in O6-ethylguanine, which can pair with either cytosine or thymine.

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20
Q

State the efffect of MNNG on DNA.

A

Reaction of guanine with MNNG results in O6-methylguanine, which can pair with either cytosine or thymine.

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21
Q

How do deletion and insertion mutations arise?

A

They are generated by intercalating agents. Intercalating agents increase the distance between two consecutive base pairs. Deletions are also caused by depurination.

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22
Q

What is a missense mutation?

A

A missense mutation is a point mutation that results in a different amino acid.

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23
Q

What is a nonsense mutation?

A

A nonsense mutation results in a premature stop codon

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24
Q

What is a silent mutation?

A

A silent mutation does not result in a change of amino acid.

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25
Q

What is the Ames test?

A

The Ames test can be used to assess the mutagenicity of compounds.

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26
Q

Describe the procedure for an Ames test.

A
  1. His- auxotrophs are prepared and mixed with a mutagen and a non-mutagen control.
  2. Both cultures are then plated on agar medium lacking histidine.
  3. The number of colonies that have regained their ability to metabolise histidine correlate to the mutagenic ability of the mutagen.
27
Q

What is meant by the term “auxotroph”?

A

An auxotroph is a mutant strain that has lost the ability to synthesise a nutrient

28
Q

Define what is meant by the term “direct repair”

A

Direct repair entails a direct reversal of the damage. This pathway is widespread in all except placental mammals.

29
Q

Define what is meant by the term “excision repair”

A

Excision repair involves the recognition and removal of a damaged base or an incorrect sequence.

30
Q

State the two forms of excision repair.

A
  1. Base excision repair

2. Nucleotide excision repair.

31
Q

Define what is meant by the term “mismatch repair”

A

Mismatch repair involves the scrutiny for apposed bases that do not pair properly. Mismatches arise during DNA replication, and are corrected for by distinguishing between the old and the new strand.

32
Q

Define what is meant by the term “recombination repair”

A

Recombination repair is a mode of filling a gap in one of the strands of duplex DNA by retrieving a homologous single strand from another duplex.

33
Q

Define what is meant by “nonhomologous end-joining”

A

NHEJ repairs double stranded breaks when no homologous strands are available.

34
Q

There are four main DNA repair systems in place. List them.

A
  1. Repair of DNA synthesis errors.
  2. Repair of DNA modifications.
  3. Repair of replication fork barriers
  4. Repair of DNA breaks.
35
Q

Recall that DNA polymerase III possesses its own proofreading ability. However, this is not enough. Why?

A

Complementary base pairing is often not enough to determine fidelity.
Rare tautomeric forms of the four bases occur transiently, which may cause anomalous base pairing.

36
Q

State the anomalous base-pairings due to tautomerisation of the four bases.

A
  1. rare cytosine - adenine

2. rare guanine - thymine

37
Q

Name the system involved in mismatch repair in E. coli

A

MutSLH

38
Q

How is the cell able to distinguish between a newly synthesised strand of DNA versus the template strand?

A

Fully methylated DNA intiates DNA replication. As such, the daughter strand will not have a methylated adenine and is treated as the “new strand”.

39
Q

Describe the process of mismatch repair, using the MutSLH system as an example

A
  1. Two copies of Mut S bind to the mismatch.
  2. Two copies of Mut L bind to each Mut S and induce the bending of DNA in an ATP dependent process.
  3. MutH endonuclease makes a nick on the 5’ side of unmethylated GATC.
  4. UvrD (helicase), in conjunction with exonuclease, removes the defective strand.
  5. DNA polymerase III resynthesises the correct strand.
40
Q

Describe the repair of pyrimidine dimers.

A

The reaction involves a photoreactivation enzyme (PRE) photolyase that cleaves bonds between pyrimidine dimers. This reaction is blue-light dependent and does not occur in placental mammals.

41
Q

Mammals are unable to use blue light to fix pyrimidine dimers. TRUE or FALSE?

A

TRUE.

42
Q

State the function of DNA glycosylases.

A

DNA glycosylases cleaves the glycosidic bond between the deoxyribose sugar and the base, resulting in an apurinic or apyrimidinic site.

43
Q

State the enzymes involved in base excision repair.

A
  1. DNA glycosylase
  2. AP endonuclease
  3. Phosphodiesterase
  4. DNA polymerase I
  5. DNA ligase
44
Q

State the most common DNA glycosylase

A

Uracil DNA glycosylase

45
Q

List at least four examples of DNA glycosylases

A
  1. Uracil DNA glycosylase
  2. Hypoxanthine DNA glycosylase
  3. 3-methyladenine DNA glycosylase
  4. 8-oxoguanine DNA glycosylase
46
Q

Briefly describe the process of base excision repair

A
  1. A deaminated base is recognised.
  2. The corresponding DNA glycosylase removes the base, resulting in an apurine or apyrimidine.
  3. AP endonuclease and phosphodiesterase removes the sugar phosphate, resulting in a single nucleotide gap.
  4. DNA polymerase I adds a new nucleotide
  5. DNA ligase seals the nick.
47
Q

Base excision repair is responsible for correcting which kind of DNA damage?

A

Deamination and depurination.

48
Q

Nucleotide excision repair is responsible for correcting which kind of DNA damage?

A

Pyrimidine dimers and other DNA lesions in which the bases are displaced.

49
Q

Nucleotide excision repair is an ATP-dependent process. TRUE or FALSE?

A

TRUE.

50
Q

State the proteins involved in nucleotide excision repair in E. coli.

A

UvrA, UvrB, UvrC, and UvrD

51
Q

Briefly describe the process of nucleotide excision repair.

A
  1. UvrAB recognises the DNA damage
  2. UvrBC nicks DNA on both sides of the DNA damage
  3. UvrD unwinds the marked region, releasing the damaged strand.
  4. A correct sequence is synthesised.
52
Q

State the two conditions in humans that impair the ability to repair UV-induced lesions.

A
  1. Xeroderma pigmentosum (XP)

2. Cockayne syndrome (CS)

53
Q

Name the DNA polymerases involved in lesion bypass in E. coli

A

DNA polymerase IV and V

54
Q

Translesion polymerase are often the first mode of lesion repair in E. coli. TRUE or FALSE?

A

FALSE. They are invoked as a last resort as part of the SOS response.

55
Q

Name the eukaryotic translesion DNA polymerases

A

DNA pol eta and DNA pol zeta

56
Q

State the two ways in which double stranded breaks can be repaired

A
  1. Homologous recombination

2. NHEJ

57
Q

List the proteins involved in homologous recombination repair of DNA

A
  1. RecBCD and RecA

2. RuvA, B and C

58
Q

Briefly describe the NHEJ pathway for DNA repair

A

NHEJ repair is common in mammalian somatic cells, however, is generally used as an emergency repair.
NHEJ repair involves Ku (a key protein), and is able to ligate blunt ends of duplex DNA.
The bases near the ends of the break, however, suffer deletion.

59
Q

State the DNA repair system affected in xeroderma pigmentosum patients.

A

Nucleotide excision repair

60
Q

State the DNA repair system affected in hereditary nonpolyposis colorectal cancer patients.

A

DNA mismatch repair

61
Q

State the DNA repair system affected in Bloom’s syndrome patients.

A

Repair of DSBs by homologous recombination

62
Q

State the DNA repair system affected in Fanconi anaemia patients.

A

Repair of DSBs by homologous recombination

63
Q

State the DNA repair system affected in heriditary breast cancer patients.

A

Repair of DSBs by homologous recombination

LSM2232 (9 decks)

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