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imed2004 > Mutation Repair + Epigenetics 1 > Flashcards

Mutation Repair + Epigenetics 1 Flashcards

1
Q

What is base excision repair?

A

Base is removed and replaced with a DNA poilymerase and then a ligase sticks backbone together

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2
Q

What happens in nucleotide excision repair?

A

2 pathways:

Global Genomic Repair (GGR): Damaged strand recognized -> Damaged DNA sequence removed -> DNA polymerase repairs

Transcription-coupled (TC-NER): Damaged strand halts transcription at that point -> Proteins are recruited to form a stalled transcription complex -> Damaged strand removed -> damaged strand replaced

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3
Q

What kind of process is nucleotide excision repair?

A

Complex process requiring many proteins which cause disease if mutated (such as cockayne syndrome and xeroderma pigmentosum)

This process involves up to 30 nucleotides being removed from damaged strand

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4
Q

What kind of problems does nucleotide excision repair fix?

A

Removes bulky lesions such as pyrimidine dimers and other mutations causing distortions in DNA structure

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5
Q

How important is nucleotide excision repair?

A

It is a highly conserved pathway from bacteria to man which makes it very important for DNA fidelity

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6
Q

Which proteins are damaged in cockayne syndrome?

A

The proteins that form a complex with RNA polymerase during transcription

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7
Q

What proteins are damaged during xeroderma pigmentosum?

A

The helicase proteins that are part of the TFIIH complex which is important for DNA polymerase acitivty during nucleotide excision repair

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8
Q

What is TFIIH?

A

A large protein complex (10 subunits) which has DNA polymerase activity during nucleotide excision repair

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9
Q

What is RPA?

A

A single stranded DNA-binding protein that binds to template strand for nucleotide excision repair

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10
Q

Which DNA is most often repaired by nucleotide excision repair mechanisms?

A

Actively transcribed genes, this is because repair is coupled to transcription.

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11
Q

Why is nucleotide excision repair so necessary?

A

Lots of eukaryotic cells don’t divide and so DNA can’t be repaired in same way as bacteria.

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12
Q

Which strand is repaired more quickly?

A

The template strand. Lesions in other strand are not repaired as quickly because they will be repaired before DNA replication.

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13
Q

What happens if both DNA strands are damaged so that one cannot act as a template in repair?

A

Different repair mechanisms are used:

Either through non-homologous end joining

or Homologous directed repair

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14
Q

What kind of mutagens cause double stranded DNA damage?

A

Ionising radiation results in double strand breaks.

Interstrand crosslinks result when 2 DNA strands become covalently bonded which is highly toxic because it causes replication blocks.

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15
Q

What kind of medication cause crosslinks?

A

Chemotherapeutic drugs

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16
Q

What is homologous directed repair (aka strand dependent annealing)?

A

Homologous chromosome is used as a template for repair.

Error-free repair of double strand breaks

17
Q

How does HDR occur?

A

End trimming by 5’ endonuclease exposes ssDNA overhangs coated by SSB forming nucleoprot filaments

Sister chromatid is disconnected and the damaged DNA uses that disconnected strand as a template strand for new DNA synthesis

DNA synthesis occurs on both strands to fill overhangs with the correct DNA in the 5’ - 3’ direction.

Ligation seals the gap

18
Q

What is the consequence of defective DNA repair?

A

It is a cause for a few genetic diseases.

Affects a wide variety of body systems

Share constellation of common traits, notably a predisposition to cancer

19
Q

What are the symptoms of xeroderma pigmentosum?

A

Freckle-like spots on skin, extreme sensitivity to UV light

Predisposition to skin cancer

Defect in nucleotide excision repair (proteins that bind to RNA polymerase when it is stopped)

20
Q

What are the symptoms of cockayne syndrome?

A

Dwarfism

Sensitivity to light

Premature aging (fatal)

Deafness

Eye disorders

Mental retardation

Defect in nucleotide excision repair (TFIIH helicase proteins)

21
Q

What does epigenetics mean?

A

The structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states

22
Q

How does epigenetics get controlled?

A

Chemical tags are added or subtracted on DNA nucleotides/histones:

DNA methylation

Histone acetylation

Phosphorylation

Ubiquitination

23
Q

How are epigenetics inherited?

A

Some genetic tags are passed down through generations. (Some tags are removed from chromsomes during zygote formation but some remain which make some traits heritable)

24
Q

What are the implications for epigenetics in identical twins?

A

Epigenetic tags form on each twin resulting in different traits with age.

Epigenetic tags can have such a huge effect on twins that one can develop a disease while the other does not.

25
Q

What 3 chromatin changes can alter gene transcription?

A

Modification of histone proteins

Chromatin remodelling

DNA methylation

26
Q

How are histones arranged?

A

Nucleosomes are arranged as octamers of histone proteins with protruding N-terminal ends.

147 bp of coiled DNA wrapped around histones 2 each of the 4 core histones H2A, H2B, H3, and H4

27
Q

What does H1 do?

A

it is a linker protein that is bound to DNA between the nucleosomes

28
Q

What does modifying histone tails do to expression of chromosomal regions?

A

They act as epigenetic marks that control expression of chromosomal regions (Controlled by transcription factors)

29
Q

How are epigenetic markers controlled in daughter cells?

A

Parental nucleosomes with modified histones split and half the daughter nucleosomes have modified histones as a result.

Parental pattern of histone modifications is re-established by enzymes (reader-writer complexes) that recognize the same modifications they catalyze

30
Q

How do we know that histones are a mix of old and new proteins?

A

Experiments were done using isotopically-labelled histones

31
Q

What is the histone code?

A

Histone N-terminal tails have a number of different modifications that form a code which tells us chromatin state (active or inactive)

32
Q

What modifications are common for H2A?

A

Lysine residue acetylation (lots of lysine residues in this region)

33
Q

What does acetylation do to DNA?

A

It separates histone proteins from each other to create proteins that can be actively transcribed.

Deacetylation has the opposite effect making nucleosomes more compact

34
Q

What do reader, writer, and eraser proteins do to acetyl groups?

A

Reader: They read acetyl groups

Writer: Add acetyl groups

Eraser: Remove acetyl groups

35
Q

Which amino acid residues get acetylated in histones?

A

Lysine residues

36
Q

What does acetylation do?

A

Acetylation decreases affinity of histones for DNA

37
Q

How are histones acetylated?

A

Histone acetylase and histone deacetylase enzymes add/remove acetyl groups

38
Q

What happens to histones near active genes?

A

They are hyperacetylated

imed2004 (22 decks)

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