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BIO 226 > 6 DNA damage, repair, and mutations > Flashcards

6 DNA damage, repair, and mutations Flashcards

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1
Q

what are somatic mutation

A

mutations in body that only impact you

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2
Q

What are germinal mutations

A

get transmitted to further generation

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3
Q

what are 2 ways tp get a mutant DNA sequence

A

DNA damage –> turns into mutant DNA
DNA Repair messes up and created a mutant DNA

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4
Q

what is the origin and frequency of mutation

A

○ Mostly from replication errors
○ Polymerase makes mistakes

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5
Q

what are some causes of spontaneous mutation rate

A

○ Genome characteristics
○ Cell age

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6
Q

what are induced mutations

A

○ Happens in higher frequency
○ From known chemical and physical reagents
○ Base analogs
§ Imposter nucleuotides
○ Hydroxylating, alkylation, deaminating agents
○ UV and ionizing radiation

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7
Q

what are 3 types of mutations

A

○ SBP (single base pair)
○ SNP (single nucleotide polymorphism)
○ Point mutations (SNP and SBP)

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8
Q

what are 3 types of point mutations

A
  • Transition mutations
  • Transversion mutations
  • Indels
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9
Q

what is a transition Point mutation

A

□ Purine –> purine (A=G, G=A)
□ Pyr –> pyr (A=T, T=A)

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10
Q

what is a transversion point mutation

A

□ Purine <–> pyrimidine

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11
Q

what is an indel point mutation

A

Deletion or insertion of a base

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12
Q

what are synonymous mutations

A

○ Silent mutations = nothing happens

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13
Q

what are non-synonymous mutations (sense)

A

○ Missense mutations = code for a diff AA
○ Nonsense mutations = changes to a stop codon (likely severe)

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14
Q

what is a frameshift mutation

A
  • Frameshift = removal, addition, or substitution
    ○ Disrupts triplet reading frame
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15
Q

what does a non-coding region mutation do

A

Affects gene expression

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16
Q

what is slippage

A

Polymerase accidentally moves on the dna up or down causing insertion or deletion on strand its synthesizing

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17
Q

what are 6 types of nucleotide mispairing

A
  • tautomers
  • ionization
  • wobble bases
  • depurination
  • deamination
  • oxidative damage
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18
Q

what is a tautomer

A

Isomeric changes in chemical shape

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19
Q

what is ionization in nucleotide mispairing

A

Gain or loss of electrons changes binding pattern (ex. T binds to G)

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20
Q

what are wobble bases in nucleotide mispairing

A

Can sometimes fuck up

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21
Q

what is depurination of nucleotide mispairing

A

Removal of a purine
Stops replication and transcription

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22
Q

what is deamination

A

Removal of amine (NH2) grp
Alters base pairing

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23
Q

what is oxidative damage

A

□ Directly breaks DNA dbl strand

24
Q

what are induced mutation (what is the inducer)

A

○ Mutagen: chemical or physical force that increases chance of mutation
§ Replace alter or damage base in dna

25
Q

what are sometypes of chemical and physical mutations

A

Chemical
- alkylating agents
- reactive oxygen species
- intercalating agents
- Base analogs
Physical
- UV/Ionizing radiation

26
Q

what happens when UV light hits a DNA strand

A

○ Covalently links neighbouring pyrimidines
○ Stops replication
○ Results in transition mutations

27
Q

what happens when ionizing radiation hit DNA

A

○ “lightning bolts hitting DNA”
- Likely to cause actual breaks in DNA

28
Q

what is an alkylating agent in chemical mutagens

A

addition of alkyl grp to a nucleotide
- disrupts correct base pairing

29
Q

what is a base analog in chemical mutagens

A

Chemically similar to ATCG(imposter)
- can be incorrectly incorporated into DNA polymerase

30
Q

what is a intercalating agent (mutagen)

A

Inserts between base pairs
- distorts dbl helix
- increases slippage

31
Q

what is an Abasic site

A

○ Nucleotide been removed and theres jus a hole in the DNA

32
Q

what is the non bulky DNA damage and the bulky DNA damage

A

NON-BULKY
- alkylation
- oxidation
- deamination
- depurination
BULKY
- pyrimidine dimer
- bulky adduct
- base mismatch
- loop
- dbl strand break

33
Q

what is a revertant

A

WT that have been mutants and are now WT again

34
Q

what is the mutagenicity ratio (MR)

A

total # revertants / # spontaneous revertants

35
Q

if a compound has no mutagenic effect the MR is

A

~ 1

36
Q

if a compound shows signs of being mutagenic the MR is

A

MR > 1

37
Q

if a compound kills the cell the MR is

A

MR < 1

38
Q

How can we fix the non-bulky damage in DNA

A

Base excision repair

39
Q

how can we fix a pyrimidine dimmer and a bulk adduct

A

Nucleotide excision repair
- (pyrimidine dimmer can also be fixed by direct repair)

40
Q

what does the mechanism of mismatch repair fix ?

A

base mismatch and loop

41
Q

what does non-homologous end joining repair ?

A

double stranded break

42
Q

what are the steps taken when DNA has been damaged

A
  • surveillance(detect errors)
  • Excision (Find mistake and cut it out)
  • polymerization (replace what was cut)
  • strand ligation (reconnect bonds in repaired stand)
43
Q

what is direct repair

A

○ Some errors can be reverted by using specific enzymes because they happen so often

44
Q

what is base excision repair

A

○ One of the simplest way to repair
○ Detection and excision
§ Enzyme removes the whole error
§ Cut strand with endonuclease to allow DNA entry to fix
§ Polymerase replaces error with correct base
§ Can replace 1 base or a whole chunk

45
Q

what is nucleotide excision repair

A

For larger damage that affects multiple base pairs
§ Damage detection
□ Global genome surveillance finds
□ Look for stalled RNA polymerase
§ Strand separation
□ Helicase opens DNA
§ excision
□ Endonuclease cuts out whole chunk
§ Polymerization
□ Polymerase fixes
§ Ligation
□ Glued back together by DNA ligase

46
Q

what is mismatch repair (what does it look for)

A

○ Uses concept of DNA methylation
○ Detection
§ Template strand has a methyl group and new strand doesn’t so we know which one is right

47
Q

what are double stranded breaks

A

○ Most serious of damage
○ Affects both strands so theres no template

48
Q

what are 2 ways to fix a double stranded break

A

homologous recombination (HR), non homologous End Joining (NHEJ)

49
Q

what are traits of homologous recombination (HR)

A

§ Uses homo chromos as template
§ Active post DNA replication
§ More error proof

50
Q

what are traits of non homologous End Joining (NHEJ)

A

§ DNA strands join independent of complementarity
§ Active in dividing and non dividing cells
§ Doesn’t req template strand
§ More prone to errors
§ DNA strands jus glued together

51
Q

how does NHEJ work

A

○ Detection
§ Proteins bind to end to supress further damage
○ Strand resection
§ Recruit of kinase and nuclease proteins to make blunt ends
○ Polymerization
§ Polymerase fills end for ligation (sticky ends)
§ Does not add bases (no template)
○ Ligation
§ Ligates the 2 sticky ends together

52
Q

how does HR repair work

A

○ Detection
§ Same way NHEJ
○ Strand resection
§ Cuts back from break
§ Creates 3’ overhangs (sticky ends)
○ Strand exchange/invastion
§ Seperates double stranded DNA
§ Forms a Displacement loop (D-Loop)
○ Polymerization
§ Missing DNA copied from template
○ 2 complex pathways from here
§ Synthesis dependant strand annealing pathway (SDSA)
§ Double strand break repair pathway (DSBR)

53
Q

what is Synthesis dependant strand annealing pathway (SDSA)

A
  • both strands broken
  • One broken strand “invades” a matching DNA strand to use as template.
  • The broken strand copies the missing DNA using the intact strand as guide.
  • The newly made DNA strand separates and sticks back to its original partner strand.
  • No Crossing-Over: Unlike other repair methods, SDSA does not swap large sections of DNA between chromosomes, avoiding genetic changes.
54
Q

what is Double strand break repair pathway (DSBR)

A

It’s like repairing a torn rope by using a similar rope to guide the fix, but sometimes parts of the ropes get exchanged.

55
Q

what is the only repair mechanism that doesnt use a polymerase

A

Direct repair
- uses enzymes

56
Q

TF NHEJ doesnt use a template strand and HR does

A

T

BIO 226 (10 decks)

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