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Biochemistry > DNA modification and repair > Flashcards

DNA modification and repair Flashcards

1
Q

Major methylated bases in prokaryotes

A

N6-methyladenine and N4-methylcytosine

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2
Q

Goal of methylation in bacteria

A

Protect DNA from cleavage by endonucleases

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3
Q

Methylated base in eukaryotes

A

5’ methylcytosine

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4
Q

Where is methylated cytosine usually found?

A

C residues 5’ to G, i.e. 5’- CG -3’

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5
Q

When are methylation sites selected?

A

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

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6
Q

Which protein carries out methylation during DNA synthesis?

A

Maintenance methylase

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7
Q

How does methylation control gene expression via promoters?

A

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

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8
Q

5-azacytidine

A

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

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9
Q

Methylation of which residue is involved in mismatch error correction.

A

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

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10
Q

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

A

It becomes thymine

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11
Q

Point mutation

A

Change in a single base pair

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12
Q

Transition mutation

A

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

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13
Q

Transverse mutation

A

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

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14
Q

Intercalating agents

A

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

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15
Q

Which mutations will shift the reading frame?

A

Deletion or insertion mutations

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16
Q

What mutation does UV light typically cause?

A

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

17
Q

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

A

8-oxoguanine

18
Q

Which base can 8-oxoguanine mispair with?

A

Adenine

19
Q

Methylation or ethylation agents typically cause modifications of which bases?

A

Purines, for example O6-alkylguanine.

20
Q

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

A

Thymine

21
Q

MGMT

A

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

22
Q

Which DNA polymerase is involved in NER in prokaryotes?

A

DNA pol I

23
Q

Repair proteins involved in NER in prokaryotes

A

UvrA, UvrB, and UvrC

24
Q

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

A

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

25
Q

Two mechanisms of NER in eukaryotes

A

Global genome and transcription coupled

26
Q

Which proteins are involved in NER in eukaryotes?

A

XP proteins, named after xeroderma pigmentosum

27
Q

Which type of mutation affects mainly pyrimidines?

A

Ultraviolent radiation

28
Q

Which type of mutation is caused by O6-alkylguanine

A

GC to AT. This is a transition mutation.

29
Q

Base excision repair protein

A

DNA-N-glycosylase

30
Q

Deamination of cytosine will turn it into?

A

Uracil

31
Q

DNA polymerase involved in prokaryotic base excision repair

A

DNA pol I

32
Q

Two mechanisms of BER in eukaryotes

A

Short patch (similar to prokaryotes) and long patch

33
Q

Which proteins does long patch BER involve?

A

DNA pol delta, epsilon; FEN-1; PCNA

34
Q

Which subunit proofreads for mistakes during DNA replication in eukaryotes?

A

DNA pol III ε subunit

35
Q

MutHLS

A

Prokaryotic mismatch repair system

36
Q

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

A

GATC

37
Q

Which polymerase fills in the DNA for mismatch repair?

A

DNA pol III

Biochemistry (6 decks)

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