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M2M Biochemistry and molecular biology > DNA Repair LO > Flashcards

DNA Repair LO Flashcards

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1
Q

Why is DNA the only macromolocule that is repaired?

A

RNA and proteins can be easily replaced but DNA cannot be replaced

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2
Q

what is a mutation?

A

permanent alteration of base sequences in daughter DNA

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3
Q

what are the positives of DNA mutations?

A

responsible for evolution, allelic variations, and polymorphisms in populations that makes us unique

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4
Q

what are the negatives of DNA mutations?

A

cancer and many human diseases

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5
Q

what are the 2 ways change-causing mutations can occur?

A
  1. uncorrected errors made during DNA replication

2. damage (oxidative, cleavage of DNA strand by radiation and chemicals, alkylation, depurianation, deamination etc)

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6
Q

what does deamination of C yield?

A

U

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7
Q

what are the 3 types of mutations?

A

point mutations
insertions
deletions

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8
Q

what is a point mutation?

A

substitution of one base for another

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9
Q

what is an insertion?

A

addition of one or more nucleotides within a DNA sequence

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10
Q

what is a deletion?

A

removal of one or more nucleotides from a DNA sequence

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11
Q

what are 2 examples of direct reversal of DNA damage?

A
  1. ligation of a break in phosphodiester backbone of DNA by DNA ligase
  2. repair of O6-methylguanosine by O6-methylguanosine methyltransferase (MGMT)
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12
Q

what is excision repair?

A

excision of a damaged region followed by precise replacement

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13
Q

what are the 3 types of excision repair?

A
  1. nucleotide excision repair (NER)
  2. base excision repair (BER)
  3. mismatch repair (MMR)
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14
Q

when is nucleotide excision repair (NER) used?

A

lesions that distort DNA structure and block RNA or DNA polymerase movement

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15
Q

how are thymine dimers formed and which process removes them?

A

UV radiation, removed by NER

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16
Q

what are the 2 ways lesions are recognized in NER?

A
  1. global genome NER

2. transcription-coupled NER

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17
Q

how does global genome NER work?

A

proteins recognize distoring DNA lesions in any region of the genome

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18
Q

how does transcription-coupled NER work?

A

recognized distorting DNA lesions in regions that are actively transcribed

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19
Q

what is the process of NER?

A
  1. recognition of damaged site by multi-protein complex
  2. local unwinding of DNA duplex by helicases (bubble of 25 bases)
  3. double incision of damaged strand by two endonucleases (about 30 bp)
  4. fill gap by DNA polymerase
  5. rejoin ends by DNA ligase
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20
Q

what are the 5 common steps in all types of excision repair mechanisms?

A
  1. recognition
  2. endonuclease
  3. nuclease
  4. DNA polymerase
  5. DNA ligase
21
Q

When is base excision repair used?

A

when DNA lesions are missed by NER but do not necessarily block polymerase function or distort DNA structure

22
Q

What genetic diseases result from mutations in the NER pathway?

A 
Cockayne syndrome (CS)
Xeroderma pigmentosum (XP)
Trichothiodystrophy (TTD)
23
Q

which DNA repair system uses glycosylases?

A

Base Excision repair (BER)

24
Q

what does a glycosylase do and what does it form?

A

flips out damaged base from stacked region of DNA, hydrolyzes glycosidic bond forming AP site (apurinic or apyrimidinic)

25
Q

A defect in the global genome NER pathway causes which disease?

A

Xeroderma pigmentosum (XP)

26
Q

a defect in transcription-coupled NER causes which disease?

A

cockayne syndrome (CS)

27
Q

what is the presentation of xeroderma pigmentosum (XP)

A

sun hypersensitivity
skin neoplasms
nuerological degeneration (later)

28
Q

what is the presentation of cockayne syndrome (CS)

A

sun hypersensitivity
premature aging (progeria)
impaired development
neurological degeneration

29
Q

when is mismatch repair used?

A

when there is a mismatch in nucleotides between the parent and daughter strand

30
Q

which protein complexes are used in mismatch repair (MMR)?

A

hMSH (MutS Homologs)

hMLH (MutL Homologs)

31
Q

how does MMR differentiate between parent strand and daughter strand in prokaryotes?

A

daughter strand is not yet methylated

32
Q

how does MMR differentiate between parent strand and daughter strand in eukaryotes?

A

DNA nicks are more abundant on newly replicated strand

33
Q

what disease results from mutations in the MMR mechanism?

A

hereditary non-polyposis colorectal cancer (HNPCC)

34
Q

what is the nick present on the newly synthesized lagging strand that MMR recognizes?

A

transient 5’ DNA ends of okazaki fragments

35
Q

what is the nick present on the newly synthesized leading strand that MMR recognizes?

A

transient presence of ribonucleotides which is processed into nicks by RNase H2

36
Q

what genetic disease accounts for about 5% of all colon cancers?

A

Hereditary non-polyposis colorectal cancer (HNPCC) or Lynch Syndrome

37
Q

when is trans-lesion synthesis used?

A

when there is too much damage to the DNA for the repair systems to function

38
Q

how does trans-lesion synthesis work?

A

cell uses more loosely associated DNA polymerases so that replication can continue

39
Q

what is a downside of trans-lesion synthesis?

A

loosely associated DNA polymerases do not have 3’-5’ exonuclease activity and thus the error rates are 100-10,000 time higher

40
Q

True or False

Mutations will most likely be incorporated into the daughter strand during trans-lesion synthesis?

A

True

41
Q

which double strand break repair system is most accurate and why?

A

homologous recombination because requires extensive sequence homology between broken ends and template DNA

42
Q

What is the most likely mutation to occur during non-homologous end joining (NHEJ)?

A

insertions or deletions

43
Q

which protein is activated by a single strand break?

A

Poly(ADP-ribose) (PARP)

44
Q

what are the 3 functions of Poly(ADP-ribose) (PARP) in single strand break repair?

A
  • amplifies damage signal
  • focal enrichment of repair proteins
  • change in local chromatin structure
45
Q

what does PARP add to signal a single strand break?

A

adds poly(ADP-ribose) chains to proteins

46
Q

what are the 2 main homologous protein kinases used in DNA damage checkpoints?

A

ATM and ATR

47
Q

what is the job of ATM and ATR?

A

initiates sequential recruitment and activation of downstream proteins for DNA repair

48
Q

What would happen if there were mutations disrupting the DNA damage checkpoint in cells?

A

cancers and genomic instability

M2M Biochemistry and molecular biology (19 decks)

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