DNA modification and repair

Question 1

Major methylated bases in prokaryotes

Answer 1

N6-methyladenine and N4-methylcytosine

Question 2

Goal of methylation in bacteria

Answer 2

Protect DNA from cleavage by endonucleases

Question 3

Methylated base in eukaryotes

Answer 3

5’ methylcytosine

Question 4

Where is methylated cytosine usually found?

Answer 4

C residues 5’ to G, i.e. 5’- CG -3’

Question 5

When are methylation sites selected?

Answer 5

During gametogenesis and embryogenesis during periods of demethylation and de novo methylation.

Question 6

Which protein carries out methylation during DNA synthesis?

Answer 6

Maintenance methylase

Question 7

How does methylation control gene expression via promoters?

Answer 7

Methylated promoters are not expressed. This is how temporal expression of globin genes is controlled.

Question 8

5-azacytidine

Answer 8

Cytidine analog that can be metabolized into dCTP and incorporated into DNA structure. It can reverse methylation.

Question 9

Methylation of which residue is involved in mismatch error correction.

Answer 9

Methylation of A in the sequence 5’–GATC–3’

Question 10

What does deamination of 5-methylcytosine do to the base?

Answer 10

It becomes thymine

Question 11

Point mutation

Answer 11

Change in a single base pair

Question 12

Transition mutation

Answer 12

Purine-pyrimidine base pair is changed to a different base pair. For example, CG to TA.

Question 13

Transverse mutation

Answer 13

Purine-pyrimidine base pair is switched to pyrimidine-purine base pair. For example, CG to GC

Question 14

Intercalating agents

Answer 14

Fit between adjacent base pairs of the double helix. Examples include ethidium bromide and doxorubicin.

Question 15

Which mutations will shift the reading frame?

Answer 15

Deletion or insertion mutations

Question 16

What mutation does UV light typically cause?

Answer 16

Intrastrand dimerization of adjacent thymines. Either a cyclobutane or 6-4 photoproduct

Question 17

Which oxidized base is the most abundant from ROS-related oxidation of DNA?

Answer 17

8-oxoguanine

Question 18

Which base can 8-oxoguanine mispair with?

Answer 18

Adenine

Question 19

Methylation or ethylation agents typically cause modifications of which bases?

Answer 19

Purines, for example O6-alkylguanine.

Question 20

Which base does O6-alkylguanine have a high probability of being paired with?

Answer 20

Thymine

Question 21

MGMT

Answer 21

Directly repairs O6-alkylguanine in prokaryotes and eukaryotes. Self-alkylates to restore guanine.

Question 22

Which DNA polymerase is involved in NER in prokaryotes?

Answer 22

DNA pol I

Question 23

Repair proteins involved in NER in prokaryotes

Answer 23

UvrA, UvrB, and UvrC

Question 24

Which complex cuts both sides of the dimer in pk NER?

Answer 24

UvrBC complex. Cuts at 3’ end, then 5’ end.

Question 25

Two mechanisms of NER in eukaryotes

Answer 25

Global genome and transcription coupled

Question 26

Which proteins are involved in NER in eukaryotes?

Answer 26

XP proteins, named after xeroderma pigmentosum

Question 27

Which type of mutation affects mainly pyrimidines?

Answer 27

Ultraviolent radiation

Question 28

Which type of mutation is caused by O6-alkylguanine

Answer 28

GC to AT. This is a transition mutation.

Question 29

Base excision repair protein

Answer 29

DNA-N-glycosylase

Question 30

Deamination of cytosine will turn it into?

Answer 30

Uracil

Question 31

DNA polymerase involved in prokaryotic base excision repair

Answer 31

DNA pol I

Question 32

Two mechanisms of BER in eukaryotes

Answer 32

Short patch (similar to prokaryotes) and long patch

Question 33

Which proteins does long patch BER involve?

Answer 33

DNA pol delta, epsilon; FEN-1; PCNA

Question 34

Which subunit proofreads for mistakes during DNA replication in eukaryotes?

Answer 34

DNA pol III ε subunit

Question 35

MutHLS

Answer 35

Prokaryotic mismatch repair system

Question 36

Which sequence is unmethylated in the daughter strand and clues MutHLS in on which base is mismatched?

Answer 36

GATC

Question 37

Which polymerase fills in the DNA for mismatch repair?

Answer 37

DNA pol III