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Molecular biology > Mutation and repair > Flashcards

Mutation and repair Flashcards

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1
Q

what is a point mutation?

A

mutation that involved a change in a single base

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2
Q

what is a missense mutation

A

a point mutation that causes a codon to change into a different codon

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3
Q

what is a nonsense mutation?

A

a point mutation that causes a codon to change into a stop codon

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4
Q

what is an indel mutation

A

insertion of deletion of base(s), cause frameshift

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5
Q

what is frameshift

A

when a base(s) is inserted or deleted, the subsequence nucleotides are all shifted up by one, causing all the codons to be out of phase

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6
Q

what are mutagens

A

external factors that cause mutations e.g.:

  • viruses
  • UV
  • chemicals
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7
Q

what can cause error during translation

A

for example:

  • mispairing of amino acid to tRNA by aaRS (aminoacyl tRNA synthetase)
  • misparing of codon to anticodon by ribosome
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8
Q

DNA is prone to spontaneous & externally-induced lesions, what are leisons?

A
  • damage/error in a base in dsDNA
  • still can be corrected because complimentary base pair stores original information
  • if not correct will lead to mutation after replication (original information lost)
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9
Q

what are some of the reactions that cause leisons?

A
  • Oxidative deamination
  • Depurination
  • Thymine dimerisation
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10
Q

describe oxidative deamination

A
  • C change to U
  • by free radicals
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11
Q

describe depurination

A
  • A (or G) loses its base, resulting in a hole
  • glycosidic bond between base and ribose broken
  • by spontaneous hydrolysis
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12
Q

describe thymine dimerisation

A

2 adjacent thymines dimerise to form a cyclobutane dimer

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13
Q

5-bromouracil (5BrU) is a potent mutagen, how?

A
  • Unlike ‘normal’ bases, 5BrU equilibrium mix is even-ish, rather than heavily biased to keto form
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14
Q

what does keto-5BrU pair to

A

A

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15
Q

what does enol-5BrU pair to

A

G

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16
Q

How does 5BrU cause mutation?

A
  1. first, for example there is a T:A base pair
  2. replication occurs, keto-5BrU as a free nucleotide comes in and pair with A
  3. next round of replication, keto-5BrU has tautomerised and become enol-5BrU, so pairs with incoming G
  4. another round of replication, G pairs with C
  5. results in G:C base pair, original information (T:A) lost
17
Q

how can small leisions where a base is altered in DNA be repaired?

A
  • base excision
  • DNA glycocylase recognises altered base (different DNA glycocylases recognise different kinds of damage, e.g. uracil DNA glycocylase checks for U, which is a deaminated C)
  • DNA glycocylase hydrolyses glycosidic bond between base and sugar, removing the base
  • AP endonuclease and phosphodiesterase cuts out the sugar phosphate with a missing base
  • DNAP then synthesise DNA to repair the hole
  • ligase seals sugar phosphate backbone
18
Q

what is AP endonuclease

A

an enzyme that recognizes and cuts out any site in the DNA helix that contains a deoxyribose sugar with a missing base

19
Q

How does the cell know which base is incorrect?

A
  • cell can know which strand is parental
  • DNA repair has to happen at the same time as DNA replication or else original information is lost
20
Q

how does the distinction between daughter strand and parental strand occur?

A

in lagging strand:

  • obvious because lagging strand has multiple okazaki fragments and primers

in leading strand:

  • parental strand has more methylation due to age, this can be detected and allow recognised
21
Q

how can large leisions be repaired?

A
  • nucleotide excision
  • homologous recombination
22
Q

how does nucleotide excision occur?

A

bacteria:

  • multienzyme complex recognise a lesion (e.g. pyrimidine dimer), one cut is made on each side of the lesion
  • DNA helicase then removes the entire portion of the damaged strand, leaves the gap of 12 nucleotides

humans:

  • damaged DNA is recognized
  • helicase unwinds the DNA duplex locally
  • excision nuclease cleaves on either side of the damage, leaving a gap of about 30 nucleotides

both humans and bactera:

  • DNAP repairs gap, ligase seals backbone
23
Q

what is a truncated mRNA

A
  • an mRNA which transcription has not been completed => does not have stop codon
  • RNAP is error prone, sometimes stops aruptly, mRNA without a stop codon
24
Q

what would a truncated mRNA cause?

A
  • truncated mRNA does not have stop codon
  • release factors recognise stop codon, without stop codon, mRNA cannot be released from ribosome
  • ribosome is stalled, rendered useless
25
Q

what do prokaryotes use to deal with truncated mRNA?

A
  • tmRNA = transfer messenger mRNA
  • a tRNA and mRNA hybrid
  • tRNA domain can bind to peptidyl transferase active sites
  • mRNA domain of tmRNA can bind to SSU where truncated mRNA would be
  • mRNA domain of tmRNA encodes degradation tag
26
Q

(prokaryotes) How does tmRNA deal with truncated mRNA

A
  • stalled ribosome recruited by EF-Tu
  • EF-Tu:
    • shuffles tRNA domain of tmRNA to A site, and mRNA domain of tmRNA is pushed into SSU where mRNA is
    • truncated mRNA removed
    • hydrolyse one GTP
  • EF-G:
    • continues translation so that the petidyl group translated from truncated mRNA is transfered onto tmRNA
    • the codons on mRNA domain of tmRNA is translated until stop codon is reached and tmRNA is then released
  • specific sequence in mRNA domain of tmRNA taggs polypeptide produced for degradation by protease
27
Q

which two points must fidelity be maintained during translation?

A
  • ribosome decoding: codon:anticodon
  • tRNA aminoacylation: tRNA: amino acid
28
Q

how does aaRS (aminoacyl tRNA synthetase) maintain fidelity during tRNA aminoacylation?

A
  • chances of aaRS picking up the wrong tRNA is small because tRNA is large, can be readily recognised by many of its features (e.g. anticodon)
  • chances of aaRS picking up the wrong amino acid is high because amino acids are small and can be similar (e.g. valine and isoleucine)
    • aaRS has esterase proofreading site to deal with this problem, reducing error to 10-5 per amino acid
29
Q

describe how the esterase proofreading site may help IleRS (isoleucine tRNA synethetase) to not accidentally add valine to tRNA

A
  • esterase proofreading site is smaller than aminoacylation site, can only accomodate valine
  • if valine is accidentally added, esterase proofreading site (which only valine can fit in) will remove valine
  • because esterase proofreading site can only accomodate valine, isoleucine will not be removed by it

Molecular biology (8 decks)

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