06a: DNA Repair Flashcards Preview

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Flashcards in 06a: DNA Repair Deck (51):
1

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

X = adenine and cytosine

Y = N6-methyladenine and N4-methylcytosine

2

Why is bacterial DNA methylated?

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

3

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

True

4

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

X = adenine

Y = GATC

5

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

X = cytosine

Y = 5'-methylcytosine

6

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

X = 3-5

7

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

Eukaryotes;
Musically found 5' to a G (so in CG sequence)

8

T/F: methylation in eukaryotes is heritable.

True

9

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

After;

X = maintenance methylase

10

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

False - methylation sites can be selected during gametogenesis

11

(Methylated/unmethylated) promoter is expressed.

Unmethylated

12

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

X = epsilon
Y = gamma

Yes! Reversed at 12 weeks of age

13

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

Can; by 5-azacytidine

14

5-azacytidine functional and structural importance.

Reverses methylation of genes.

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

15

What can 5-azacytidine be treatment for?

Beta-thalassemia

16

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

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

17

List some causes of DNA mutation.

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

18

Deamination of 5-methylcytosine converts it to which base?

Thymine

19

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

X = transition point mutation

Y = GC
Z = AT

20

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

Thymine isn't seen as abnormal base by repair enzymes

21

What defines a transition point mutation?

Purine-pyrimidine changes to a different purine-pyrimidine

22

What defines a transverse point mutation?

Purine-pyrimidine changes to pyrimidine-purine

23

Which mutations can shift the reading frame of DNA?

Insertion or deletion mutations

24

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

X = intra-strand dimerization of adjacent thymine a

25

Give example of direct base repair in DNA.

Repair of O6-alkylguanine

26

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

More

27

Why is O6-alkylguanine problematic?

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

28

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

X = direct

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

29

How does MGMT work?

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

30

MGMT acts (before/during/after) replication.

Before

31

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

NT excision repair

32

Does NT excision repair require ATP hydrolysis?

Yes

33

List steps in prok NT excision repair.

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

What are the categories of excision repair in prok?

1. NT excision repair
2. Base excision repair

35

Which enzymes carry out base excision repair?

DNA-N-glycolases

36

Can uracil be found in DNA?

Yes - damage situation (if cytosine is deaminated)

37

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

Transition;

GC goes to AT

38

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

Base excision repair by uracil DNA-N-glycosylase

39

Which repair mechanism leaves an apyrimidinic or apurinic site?

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

40

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

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

41

Nick translation is part of which prokaryotic repair mechanism?

Base excision repair

42

What repair pathways are found in eukaryotes?

2 major BER pathways (short and long patch)

43

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

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

44

Mismatch repair in prok is carried out by:

MutHLS system

45

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

X = MutHLS
Y = mismatch

46

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

X = mismatch

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

47

What sequence is MutHLS searching for to identify parent strand?

Methylated Adenine in GATC sequence

48

Do any prokaryotic repair mechanisms use exonucleases?

Yes - mismatch repair

49

Which polymerase involved in mismatch repair?

DNA polymerase 3

50

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

X = endonuclease

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

51

Does mismatch repair occur in humans?

Yes - just different enzymes