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LS 3 Midterm 2 > Lecture 10: Mutability and DNA Repair > Flashcards

Lecture 10: Mutability and DNA Repair Flashcards

1
Q

Transition (base substitution)

A

Replace base with one having the same chemical properties (purine to purine or pyrimidine to pyrimidine)

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2
Q

Transversion (base substitution)

A

Replace base with one having different chemical properties (purine to pyrimidine or vice versa)

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3
Q

Purines

A

A and G

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4
Q

Pyrimidines

A

C and T

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5
Q

What are indels?

A

Base addition/insertions: one or more nucleotides added

Base deletion: one or more nucleotides deleted

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6
Q

What kind of mutations to indels cause?

A

Frameshift mutations

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7
Q

Silent mutation

A

Nucleotides sequence changes but polypeptide sequence does not

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8
Q

Missense mutation

A

Change in nucleotide sequence causes change in AA sequence

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9
Q

Nonsense mutation

A

Premature stop codon (TAA, TAG, TGA)

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10
Q

What is a conservative missense mutation?

A

Altered AA is in same group as the one it replaced (e.g., lysine to arginine; both are basic)

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11
Q

What is a non-conservative missense mutation?

A

Altered AA is in a different group than the one it replaced (e.g., Phe to Ser is nonpolar to polar)

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12
Q

4 causes of spontaneous cleavage of chemical bonds in DNA

A

(1) Genotoxic chemicals in environment
(2) Chemical byproducts of normal cellular metabolism
(3) Environmental agents like UV light and ionizing radiation
(4) Copying errors by DNA polymerase during replication

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13
Q

What happens in deamination of 5-methyl cytosine?

A

Amino group is replaced with O, and molecule becomes thymine

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14
Q

What happens in deamination of cytosine?

A

Amino group replaced with O, and molecule becomes uracil (bad bc DNA doesn’t have uracil)

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15
Q

Which base is exempt from deamination?

A

Thymine

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16
Q

What happens in depurination?

A

Guanine or adenine are released from the DNA strand

17
Q

Base substitution (and types)

A

Change of one base to another: transitions and transversions

18
Q

Possible effect of depurination

A

Deletion mutation

19
Q

Cause and effect of thymine dimers

A

Caused by UV light, effect is that DNA assumes rigid structure (interfering with DNA replication and RNA transcription)

20
Q

Basis of Ames Test

A

When His-/- cells added to dish with mutagen, it makes them His+/+ and allows them to grow

21
Q

What are base analogs and what do they do? Give one example.

A

Similar in structure to bases, but cause mutation if they pair with actual base (e.g., 5-bromouracil is similar to cytosine so will pair with guanine)

22
Q

What do intercalating agents do?

A

Get into DNA structure and destroy it

23
Q

3 examples of intercalating agents

A

ethidium, proflavin, acridine orange

24
Q

What ability allows some DNA polymerases to proofread?

A

3’ to 5’ exonuclease activity (they have an exonuclease site, distinct from the polymerase site)

25
Q

What does E. coli Dam methylase do?

A

Methylates A residues of GATC sequence, only on template strands (if mistake is made, cell knows to remove newly synthesized strand since the old one is correct and methylated)

26
Q

Basis of translesion DNA synthesis

A

When replicative DNA pol finds mistake, translesion DNA pol replaces it (lacks proofreading ability), continues synthesis, and then replicative pol comes back

27
Q

What happens in photoreactivation?

A

DNA photolyase (activated by UV light) breaks thymine dimers

28
Q

What does methyl transferase do (with regards to DNA repair)?

A

Removes unwanted methyl groups between base pair

29
Q

Basis of base excision repair

A

Glycosylates remove damaged bases (one nucleotide only)

30
Q

Which enzymes remove the sugar phosphate in base excision repair in prokaryotes?

A

AP endonuclease and phosphodiesterase

31
Q

What common mismatch is almost always caused by deamination of 5-methyl cytosine?

A

G-T (the T is the wrong one, should be C instead)

32
Q

What enzymes cut/remove the DNA backbone during base excision repair in eukaryotes?

A

APEI cuts 5’ end, then AP lyase removes deoxyribose phosphate

33
Q

Nucleotide excision repair: order of proteins recruited

A

XP-C and 23B, TFIIH, XP-G and RPA, XP-F, DNA polymerase delta/epsilon, DNA lipases

34
Q

Nucleotide excision repair: which protein cuts 3’ end and which one cuts 5’ end?

A

XP-F cuts 5’ and XP-G cuts 3’

35
Q

Function of RAD51 in homologous recombination

A

Forms nucleoprotein filaments on exposed 3’ ends of damaged strands, which search for homologous sequences in sister chromatids

36
Q

Homologous recombination: order of molecules recruited

A

ATM kinase (activated by break), BRCA1 and BRCA2, RAD51, RAD54 and RAD52, DNA polymerase, DNA ligation

37
Q

NHEJ: order of molecules used

A

Ku70/80, DNA protein kinase, Artemis (exonuclease), DNA ligase

LS 3 Midterm 2 (4 decks)

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