06a: DNA Repair

Question 1

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

Answer 1

X = adenine and cytosine

Y = N6-methyladenine and N4-methylcytosine

Question 2

Why is bacterial DNA methylated?

Answer 2

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

Question 3

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

Answer 3

True

Question 4

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

Answer 4

X = adenine

Y = GATC

Question 5

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

Answer 5

X = cytosine

Y = 5’-methylcytosine

Question 6

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

Answer 6

X = 3-5

Question 7

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

Answer 7

Eukaryotes;

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

Question 8

T/F: methylation in eukaryotes is heritable.

Answer 8

True

Question 9

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

Answer 9

After;

X = maintenance methylase

Question 10

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

Answer 10

False - methylation sites can be selected during gametogenesis

Question 11

(Methylated/unmethylated) promoter is expressed.

Answer 11

Unmethylated

Question 12

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

Answer 12

X = epsilon
Y = gamma

Yes! Reversed at 12 weeks of age

Question 13

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

Answer 13

Can; by 5-azacytidine

Question 14

5-azacytidine functional and structural importance.

Answer 14

Reverses methylation of genes.

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

Question 15

What can 5-azacytidine be treatment for?

Answer 15

Beta-thalassemia

Question 16

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

Answer 16

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

Question 17

List some causes of DNA mutation.

Answer 17

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

Question 18

Deamination of 5-methylcytosine converts it to which base?

Answer 18

Thymine

Question 19

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

Answer 19

X = transition point mutation

Y = GC
Z = AT

Question 20

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

Answer 20

Thymine isn’t seen as abnormal base by repair enzymes

Question 21

What defines a transition point mutation?

Answer 21

Purine-pyrimidine changes to a different purine-pyrimidine

Question 22

What defines a transverse point mutation?

Answer 22

Purine-pyrimidine changes to pyrimidine-purine

Question 23

Which mutations can shift the reading frame of DNA?

Answer 23

Insertion or deletion mutations

Question 24

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

Answer 24

X = intra-strand dimerization of adjacent thymine a

Question 25

Give example of direct base repair in DNA.

Answer 25

Repair of O6-alkylguanine

Question 26

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

Answer 26

More

Question 27

Why is O6-alkylguanine problematic?

Answer 27

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

Question 28

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

Answer 28

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

Question 29

How does MGMT work?

Answer 29

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

Question 30

MGMT acts (before/during/after) replication.

Answer 30

Before

Question 31

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

Answer 31

NT excision repair

Question 32

Does NT excision repair require ATP hydrolysis?

Answer 32

Yes

Question 33

List steps in prok NT excision repair.

Answer 33

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

Question 34

What are the categories of excision repair in prok?

Answer 34

1. NT excision repair | 2. Base excision repair

Question 35

Which enzymes carry out base excision repair?

Answer 35

DNA-N-glycolases

Question 36

Can uracil be found in DNA?

Answer 36

Yes - damage situation (if cytosine is deaminated)

Question 37

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

Answer 37

Transition; GC goes to AT

Question 38

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

Answer 38

Base excision repair by uracil DNA-N-glycosylase

Question 39

Which repair mechanism leaves an apyrimidinic or apurinic site?

Answer 39

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

Question 40

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

Answer 40

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

Question 41

Nick translation is part of which prokaryotic repair mechanism?

Answer 41

Base excision repair

Question 42

What repair pathways are found in eukaryotes?

Answer 42

2 major BER pathways (short and long patch)

Question 43

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

Answer 43

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

Question 44

Mismatch repair in prok is carried out by:

Answer 44

MutHLS system

Question 45

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

Answer 45

``` X = MutHLS Y = mismatch ```

Question 46

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

Answer 46

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

Question 47

What sequence is MutHLS searching for to identify parent strand?

Answer 47

Methylated Adenine in GATC sequence

Question 48

Do any prokaryotic repair mechanisms use exonucleases?

Answer 48

Yes - mismatch repair

Question 49

Which polymerase involved in mismatch repair?

Answer 49

DNA polymerase 3

Question 50

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

Answer 50

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

Question 51

Does mismatch repair occur in humans?

Answer 51

Yes - just different enzymes