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MFoM > 06a: DNA Repair > Flashcards

06a: DNA Repair Flashcards

1
Q

The major methylated bases in prokaryotes are (X). The modified bases are called (Y).

A

X = adenine and cytosine

Y = N6-methyladenine and N4-methylcytosine

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2
Q

Why is bacterial DNA methylated?

A

Protection mechanism (methylated DNA won’t be cleaved by bacteria’s own restriction endonucleases)

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3
Q

T/F: methylation in bacteria is maintain after replication, as it is in eukaryotes.

A

True

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4
Q

Methylation of (X) residues in the sequence (Y) in bacteria is involved in mismatch error repair.

A

X = adenine

Y = GATC

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5
Q

The major methylated bases in eukaryotes are (X). The modified bases are called (Y).

A

X = cytosine

Y = 5’-methylcytosine

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6
Q

(X)% of cytosine in eukaryotic DNA is methylated.

A

X = 3-5

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7
Q

5’-methylcytosine in (prokaryotes/eukaryotes) is usually found nearby which other base(s) or in which sequence?

A

Eukaryotes;

Musically found 5’ to a G (so in CG sequence)

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8
Q

T/F: methylation in eukaryotes is heritable.

A

True

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9
Q

(During/after) replication, (X) carries out methylation of daughter strand.

A

After;

X = maintenance methylase

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10
Q

T/F: Methylation of DNA mainly occurs after fertilization.

A

False - methylation sites can be selected during gametogenesis

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11
Q

(Methylated/unmethylated) promoter is expressed.

A

Unmethylated

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12
Q

At 6 weeks of age, (X)-globin gene expressed and (Y)- globin gene not expressed. Does this change?

A 
X = epsilon
Y = gamma

Yes! Reversed at 12 weeks of age

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13
Q

Inactivity of methylated genes (can/can’t) be reversed. If can’t, why not? If can, how?

A

Can; by 5-azacytidine

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14
Q

5-azacytidine functional and structural importance.

A

Reverses methylation of genes.

Cytidine analog with N at 5’ position (that can’t be methylated)

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15
Q

What can 5-azacytidine be treatment for?

A

Beta-thalassemia

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16
Q

When would 5-azacytidine be introduced to the cell for it to carry out function effectively?

A

During replication of DNA (so it can be incorporated into daughter strands)

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17
Q

List some causes of DNA mutation.

A
  1. Replication mistakes
  2. ROS
  3. Chemical damage
  4. Radiation
  5. Deamination of cytosine/5-methylcytosine
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18
Q

Deamination of 5-methylcytosine converts it to which base?

A

Thymine

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19
Q

Deamination of 5-methylcytosine will cause a (X) mutation. A (Y) bp will become a (Z) bp.

A

X = transition point mutation

Y = GC
Z = AT
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20
Q

What’s especially dangerous about a 5-methylcytosine deamination?

A

Thymine isn’t seen as abnormal base by repair enzymes

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21
Q

What defines a transition point mutation?

A

Purine-pyrimidine changes to a different purine-pyrimidine

22
Q

What defines a transverse point mutation?

A

Purine-pyrimidine changes to pyrimidine-purine

23
Q

Which mutations can shift the reading frame of DNA?

A

Insertion or deletion mutations

24
Q

Exposure to UV light can result in (X) of which bases?

A

X = intra-strand dimerization of adjacent thymine a

25
Q

Give example of direct base repair in DNA.

A

Repair of O6-alkylguanine

26
Q

Base modification is found (more/less/about the same) in purines than in pyrimidines.

A

More

27
Q

Why is O6-alkylguanine problematic?

A

High probability of base pairing with thymine (so GC pair becomes GT then AT)

28
Q

(X) repair of O6-methylguanine is carried out by (Y) in prok and (Z) in euk.

A

X = direct

Y = Z = O6-methylguanine DNA methyltransferase (MGMT)

29
Q

How does MGMT work?

A

Direct repair of O6-methylguanine by transferring the methyl from damaged base to itself (self-alkylation)

30
Q

MGMT acts (before/during/after) replication.

A

Before

31
Q

Which repair mechanism used to correct intra-strand thymine dimers in prok?

A

NT excision repair

32
Q

Does NT excision repair require ATP hydrolysis?

A

Yes

33
Q

List steps in prok NT excision repair.

A
  1. UvAB complex scans/finds damage and bends DNA
  2. UvrA leaves and UvrC binds
  3. Endonuclease cuts damaged strand 5’ THEN 3’ to damage
  4. Helicase removes damaged pieces
  5. DNA pol 1 replaces DNA and ligase seals Nick
34
Q

What are the categories of excision repair in prok?

A
  1. NT excision repair

2. Base excision repair

35
Q

Which enzymes carry out base excision repair?

A

DNA-N-glycolases

36
Q

Can uracil be found in DNA?

A

Yes - damage situation (if cytosine is deaminated)

37
Q

If deamination of cytosine isn’t repaired over time, what (transition/transversion) mutation can occur?

A

Transition;

GC goes to AT

38
Q

Which repair mechanism is used in cases of deaminated cytosine? Which enzyme used?

A

Base excision repair by uracil DNA-N-glycosylase

39
Q

Which repair mechanism leaves an apyrimidinic or apurinic site?

A

Base excision repair (glycosylase removes base, but not entire backbone)

40
Q

In base excision repair, is an endonuclease necessary? Why/why not?

A

Yes - apyrimidinic or apurinic endonuclease cuts backbone 5’ to damage

41
Q

Nick translation is part of which prokaryotic repair mechanism?

A

Base excision repair

42
Q

What repair pathways are found in eukaryotes?

A

2 major BER pathways (short and long patch)

43
Q

List, in order, the key players in base excision repair in prok.

A
  1. DNA-N-glycosylase
  2. Abasic endonuclease
  3. DNA pol 1
  4. DNA ligase
44
Q

Mismatch repair in prok is carried out by:

A

MutHLS system

45
Q

(X) is a motor protein that’s involved in (Y) repair.

A 
X = MutHLS
Y = mismatch
46
Q

The parent and daughter strands can be distinguished during (X) repair because:

A

X = mismatch

Parent strand is methylated and MutHLS pulls strands, scanning for the methylation to distinguish the two

47
Q

What sequence is MutHLS searching for to identify parent strand?

A

Methylated Adenine in GATC sequence

48
Q

Do any prokaryotic repair mechanisms use exonucleases?

A

Yes - mismatch repair

49
Q

Which polymerase involved in mismatch repair?

A

DNA polymerase 3

50
Q

MutH, a(n) (X), has what function?

A

X = endonuclease

In mismatch repair, cuts backbone 5’ to G in GATC sequence of daughter strand

51
Q

Does mismatch repair occur in humans?

A

Yes - just different enzymes

MFoM (20 decks)

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