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1. Molecular Biology > DNA Polymerases in DNA repair > Flashcards

DNA Polymerases in DNA repair Flashcards

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1
Q

List the five enzymes involved in DNA rreplication.

A

DNA helicase

DNA primase

DNA polymerase

DNA ligase

Nuclease

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2
Q

What does nuclease do?

A

Removes and incorrect nucleotides

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3
Q

What are the three main polymerases used in prokaryotic DNA replication?

A

DNA pol I

DNA pol II

DNA pol III

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4
Q

What does DNA pol II primarily do?

A

Repair

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5
Q

What does DNA pol III primarily do?

A

DNA synthesis

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6
Q

What does DNA pol I do in the forward direction?

2

A

Exonuclease activity

Nick translation (random nicks in DNA)

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7
Q

Define DNA damage.

A

Any alteration to DNA that distorts its geometry

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8
Q

What causes DNA damage?

2

A

Endogenous agents

Exogenous agents

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9
Q

Give two examples of endogenous damage.

A

Replication errors

Metabolism

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10
Q

Give three examples of exogenous damage.

A

Toxins

Chemicals

UV radiation

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11
Q

Characterise DNA damage.

A

Single strand damage (SSD)

Double strand damage (DSD)

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12
Q

What does the type of DNA damage depend on?

A

Depends on the type of agent and the severity of the agent that caused the damage

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13
Q

What causes SSD damage?

3

A

Endogenous replication errors

Oxidative chemicals

Non-ionising radiation e.g. UV

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14
Q

What causes DSD damage?

2

A

Antitumor agents e.g. Cisplatin

Ionising radiation e.g. Gamma rays

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15
Q

What are the five types of single strand damage?

A

Base Mismatch

Depurination

Deamination

Thymine dimers

Bulky adducts

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16
Q

What is base mismatch SSD?

A

Distorted geometry of DNA (associated with errors in replication)

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17
Q

What is depurination SSD?

A

Reaction resulting in the removal of Purines A or G

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18
Q

What is deamination SSD?

A

Loss of an amino group from Cytosine to produce uracil or loss from Adenine to produce hypoxanthine

19
Q

What is formed when cytosine loses an amino acid?

A

Uracil

20
Q

What is formed when adenine loses an amino acid?

A

Hypoxanthine

21
Q

What is thymine dimers SSD?

A

Covalent linkage of 2 adjacent thymines together (associated with UV radiation)

22
Q

What is bulky adducts SSD?

2

A

Occur due to DNA intercalalting agents such as anticancer agent Cisplatin

Cisplatin binds to bases and forms bulky lesions in the DNA helix

23
Q

What is a mutation?

A

Randomly produced permanent change in a sequence of DNA

24
Q

When can a single permanent mutation severely compromise an organism’s fitness?

A

If the change occurs in a vital position in the DNA sequence

25
Q

What happens if a mutation occurs in a protein coding portion of DNA?

A

A protein with an altered amino acid sequence will result -> defective protein

26
Q

Give an example of a disease caused by a mutation of the DNA resulting in incorrect amino acid sequence of a protein.

A

Sickle cell anaemia

27
Q

What are the three repair processes for SSD?

A

Mismatch repair (MMR) for repairing

Base excision repair (BER)

Nucleotide excision repair (NER)

28
Q

What is MMR?

A

Repairs rare mistakes made during DNA replication process (endogenous) that escape DNA polymerase III and I proofreading

29
Q

What is BER?

A

Repair of modified DNA bases from depurination or deamination

30
Q

What is NER?

A

Repair of bulky lesions and distortions in DNA

31
Q

Explain how MMR works.

4

A

Replication machines makes a copying mistake

Mismatch base pair occurs

Mismatch repair proteins recognise the mismatch and remove the new strand

Missing strand is now resynthesized

32
Q

How does MMR repair a nick?

2

A

DNA mismatch repair proteins recognise a nick in DNA

DNA pol I repairs the nick and replaces the DNA at the cleaved site

33
Q

How does Ber-Base Excision repair work?

5

A

A DNA glycosylase recognises a damaged base and cleaves between the base from
the deoxyribose in the backbone leaving an AP site

An AP endonuclease cleaves the phosphodiester backbone near AP site creating a
nick in the strand

Phosphodiesterase removes the AP sugar and phosphate

DNA Pol I replaces the damaged bases

The phosphodiester nick is sealed with DNA ligase

34
Q

What does DNA glycosylase do?

2

A

Recognises a damaged base

Cleaves between the base from the deoxyribose in the backbone leaving an AP site

35
Q

What does AP endonuclease do?

A

Cleaves the phosphodiester backbone near AP site creating a

nick in the strand

36
Q

What does Phosphodiesterase do?

A

Removes the AP sugar and phosphate

37
Q

How does Ner-Nucleotide Excision Repair work?

A

Damaged DNA recognised and removed by one of a variety of different nucleases

Nucleases first scan and cleave the phosphodiester bonds that join damaged nt to rest of DNA molecule.

Results in small gap on 1 strand of DNA double helix

Repair DNA polymerase II binds to 3’ OH end of cut DNA strand and fills the gap

Nick remains in sugar-phosphate backbone until it is sealed by DNA ligase

38
Q

Give an example of a nuclease

A

The UvrABC endonuclease enzyme complex
consisting of four Uvr proteins: UvrA, UvrB, UvrC, and UvrD (DNA
helicase II))

39
Q

What is UvrABC?

A

An endonuclease enzyme complex
consisting of four Uvr proteins: UvrA, UvrB, UvrC, and UvrD (DNA
helicase II))

40
Q

What does UvrABC do?

A

Scan and cleave the phosphodiester bonds that join damaged nt to rest of DNA molecule.

41
Q

What does the cleavage of a phosphodiester bond do?

A

Results in small gap on 1 strand of DNA double helix

42
Q

What fills the gap caused by UvrABC?

A

Repair DNA Polymerase II

43
Q

What is the final step in repair of a nick?

A

DNA ligase seals the nick

1. Molecular Biology (12 decks)

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