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Flow of genetic information BIOL2010 > DNA Damage and repair > Flashcards

DNA Damage and repair Flashcards

1
Q

What are the types of DNA damage?

A

Replication errors
base tautomers
covalent modification
non covalent interactions

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2
Q

What is a base tautomer?

A

alternative isomeric forms present for a small proportion of time. (keto to enol and amino to imino)

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3
Q

What are the changes in base paring in tautomers?

A

ENOL form of T pairs with G instead of A

IMINO form of A pairs with C instead of T.

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4
Q

What are purines?

A

bases A and G

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5
Q

what are pyrimidines?

A

bases C and T

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6
Q

what is a transition in DNA damage?

A

where the order of purines and pyrimidines are conversed. GC > AT and AT > GC

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7
Q

What is a transversion in DNA damage?

A

order of purines and pyrimidines is reversed. GC > TA or CG

AT > CG or TA

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8
Q

what causes insertions to occur?

A

Strand slippage.

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9
Q

what is cytosine deamiation?

A

hydrolytic deamiation of cytosine to uracil. GC > GU > AU

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10
Q

What is depurination?

A

the loss of a base via hydrolysis. the glycosidic bond between base and sugar breaks leaving an abasic site (AP site - apurinic/apyrimidinic site)

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11
Q

what is alkylation and what can this do to base pairing?

A

It is the addition of CH3 groups to DNA bases that can cause the bases to bind to different bases.

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12
Q

What can induce the formation of thymine dimers adjacent to eachother?

A

UV

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13
Q

What does nitrous acid (HNO2) do to bases?

A

can cause oxidative deamiation of adenine to hypoxanthine which pairs with C. oxidative damage to guanine produces 8-Oxoguanine that pairs with A instead of C.

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14
Q

What is a frameshift mutation?

A

a mutation caused by the addition or deletion of a base pair or base pairs in the DNA of a gene resulting in the translation of the genetic code in an unnatural reading frame from the position of the mutation to the end of the gene.

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15
Q

what can cause frameshift mutations

A

intercalating agents like flat aromatic compounds such as acridine.

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16
Q

How can DNA damage be tested for?

A

AMES TEST. a short term bacterial test to identify mutagens.

17
Q

What does Aflotoxin B do and where is it made?

A

is produced by a mold that grows on peanuts and is activated by liver cytochrome P450 to form a reactive species that modifies guanine leading to mutations. Causes GA to TA transversions.

18
Q

What are types of DNA repair?

A

Direct repair which acts directly on the damaged base.

base excision repair that removes the base.

nucleotide excision repair removing the damaged nucleotide

mismatch repair by excision of a long strand containing the mistake

19
Q

what about DNA makes it possible to repair or replace damaged DNA?

A

DNA has a double stranded helix structure where information is stored on both strands.

20
Q

Give an example of direct reversal (demthylation)

A

the demethylation of methylguanine via mthylguanine-DNA methyl transferase. (MGMT)

it transfers a methyl group from the alkkylated G onto a Cysteine resitude in enzymes active site.

(not really an enzyme as its irreversible)

alkylated form of MGMT is a transcription activator upregulating synthesis of other repair proteins,

21
Q

How are thymine dimers repaired?

A

UvrABC excinuclease cut out a section 8 bases on the 5’ side and 4 bases on the 3’ side of the lesion. the gap is then filled with POL I and sealed with ligase.

22
Q

What is the eynzyme used in nucleotide excision repair? how does it work.

A

A multienzyme complex which is a hetrotrimer composed of two UvrA and one UvrB which first detect DNA damage. UvrA dimer is then replaced by UvrC where the UvrBC complex does the repair.

8 bases on 5’ side and 4 on 3’ side cut out and filled with POL I and ligase.

23
Q

What is different in eukaryotes for nucleotide excision repair?

A

More complex process with 25+ proteins.

XPC (UvrA) recognises legion.
XPA and XPD (UvrB) open and binds the DNA.
RPA (single stranded binding protein) stabalises the open complex.
ERCC1-XPF and XPG (UvrC) create incisions and remove the oligonucleotide.

24
Q

How is Uracil removed?

A

AP (apyrimidinic) endonuclease cuts between the posphate backbone.
Uracil–N-glycosylase cuts Uracil bas

gap is filled in by DNA POL I (nick translation) and sealed by ligase.

Uracil-N-glycosylase does not discriminate between U opposite G or U opposite A.

25
Q

How does Uracil-D-glycosidase discriminate between U and T?

A

steric clash of mthyl group with Tyr residue.

26
Q

what enzyme is used to repair mismatches of T and U from GT and GU mismatches.

A

Thymidine-DNA gycosylase removes T and U from GT and GU.

U-D-glycosylase can repaurGu mismatch.

27
Q

How do Mismatches of T arrise?

A

T opposite G arises from deamiation of 5-methyl-C

28
Q

How is 8-oxo-G repaired ?

A
  1. prevent incoporation of base. MutT breaks down 8-oxo-GTP to 8-oxo-GMP + PPi
  2. Removal of 8-oxo-G from DNA (base excision repair done by MutM)
  3. removal of A from GA and oxo-G.A pairs. MutY.
29
Q

What is the process for long patch repair (MutHLS)

A

MutS recognises and binds to the mismatch.
MutH binds to DNA which is hemimethylated at DAM (DNA adenine methylase) methylation sites (GATC). enables differentiation of methylated parent and unmethylated daughter strands

MutS and MutH then linked by MutL.

MutH cuts the unmethylated strand and DNA segment is removed.

30
Q

What is the SOS response?

A

when there is DNA damage RecA binds to the single stranded regions with the damage and this activates the clevage of LexA. it is a repressor protein but when its cleaved it causes teh increased transcription of repair proteins.

31
Q

What is non homologous end joining?

A

usually results in deletion of one or two base pairs but since such a large proportion of the human genome is non coding this may not necessarily be harmful.

ends are directly ligated.

32
Q

what is homologous recombination?

A

damaged/broken DNa is repaired by a comparison with the otehr chromosome in a diploid cell.

33
Q

what is the function of p53

A

it is tumour suppressor protein.

acts by regulating cell cycle and activating DNA repair proteins

holds the cell cycle at the G1/S regulation point and can initiate apoptosis id the DNA damage proves irreparable.

34
Q

Xeroderma pigmentosum is a disease involved in DNA repair. What does it cause?

A

individuals show dry parchment like skin (xeroderma) and many freckles (pigmentosum)

increased UV light sensitivity.

1000 fold increased risk of skin cancer

it is caused by an inherited defect in one of eight distinct genes responsible for components of the NER complex. (Nucleotide excision repair)

35
Q

What is hereditary non polyposis colon cancer (HNPCC) caused by?

A

defects in the human equivalent of the MutHL MMR system (MSH2 and MLH1) which leads to the accumilation fo mutations throughout the genome. in time genes controlling proliferation get affected.

36
Q

when homology directed repair of dsDNA break on teh BCRA1 and 2 genes are affected what disease can occur?

A

Familial breast/ovarian cancer.

37
Q

what occurs in the spontaneous deamination of cytosine to uracil?

A

Water reacts with the top of the cytosine ring and removes NH2 group and replaces it with a keto group, creating Uracil

38
Q

UV induced dimers of adjacent thymines does what to the helical strucuture and why?

A

a cyclobutene ring forms between the thymines. they still pair with adenosine but the helical structure changes.

Flow of genetic information BIOL2010 (4 decks)

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