Topic 6 (DNA Damage and Repair) Flashcards

1
Q

Define DNA damage

A

Any modification of DNA that changes its coding properties or normal function in transcription or translation

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2
Q

What can DNA damage lead to?

A

Mutations and genetic instability

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3
Q

True/False? Mutations arise solely by chance

A

False. They may be induced by chemicals and UV as well

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4
Q

What is the evolutionary tradeoff of mutations?

A

They may increase fatality or may increase biodiversity

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5
Q

What are the three types of DNA damage?

A

Mutation, recombination, and transposons

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6
Q

Why is recombination a way in which the genome can change?

A

Unequal crossing over results in gene deletion/duplication

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7
Q

What are the two mechanisms inducing DNA mutations?

A

Replication errors and chemical modifications

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8
Q

What are examples of chemical modifications to DNA which result in mutations?

A

Deamination, depurination/depyrimidination, oxidation, alkylation, nitrous acid, radiation, intercalating agents, and base analogs

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9
Q

What are the types of mutations that can occur due to errors in DNA replication?

A

Point mutations and frameshift mutations

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10
Q

Give 3 examples of point mutations

A

Missense, nonsense, and silent

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11
Q

Give 2 examples of frameshift mutations. How does each occur?

A

Deletion; slippage of template during replication
Insertion; slippage of daughter strand during replication

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12
Q

In what tautomeric form are Adenine and Cytosine found in usually?

A

Amino

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13
Q

In what tautomeric form are Guanine and Thymine found in usually?

A

Keto

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14
Q

How many hydrogen bond donors and acceptors are there in an amino to imino tautomerization?

A

Amino: 2 acceptors, 1 donor
Imino: 2 acceptors, 1 donor (different locations)

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15
Q

How many hydrogen bond donors and acceptors are there in a keto to enol tautomerization?

A

Keto: 2 donors, 1 acceptor
Enol: 2 donors, 1 acceptor (different location)

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16
Q

What changes about the hydrogen bond donors/acceptors in tautomerization?

A

Two donors/acceptors switch to the other kind (donor to acceptor and acceptor to donor), so number of donors and acceptors stays the same

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17
Q

The enol form of T can base pair with: __________. What does this form following 2 cycles of replication? Transition or transversion?

A

Keto form of G; TA to CG; transition

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18
Q

The enol form of G can base pair with: __________. What does this form following 2 cycles of replication? Transition or transversion?

A

Keto form of T; GC to AT; transition

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19
Q

The imino form of A can base pair with: __________. What does this form following 2 cycles of replication? Transition or transversion?

A

Amino form of C; AT to GC; transition

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20
Q

The imino form of C can base pair with: __________. What does this form following 2 cycles of replication? Transition or transversion?

A

Amino form of A; CG to TA; transition

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21
Q

What is a transition mutation?

A

Purine to purine/pyrimidine to pyrimidine (CG to TA)

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22
Q

What is a transversion mutation?

A

Purine to pyrimidine/pyrimidine to purine (CG to GC or AT)

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23
Q

What is a lesion vs a mutation?

A

Lesion is a single base change but its still paired with the correct base. Mutation is a double-stranded discrepency

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24
Q

What are the steps in creating point mutations?

A
  1. Incorrect nucleotide incorporated by DNA Pol (lesion)
  2. Mismatched base is not repaired and undergoes replication (mutation)
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25
Q

What is a K53X?

A

Lysine 53 changed to a stop codon (nonsense mutation)

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26
Q

What are the three stop codons? What colour name is associated with each?

A

UAA; ochre
UGA; opal
UAG; amber

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27
Q

Why is a mutation at codon 53 on the mature transcript at position 257 on genomic DNA?

A

Genomic DNA includes introns

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28
Q

What is an E6V mutation? What sickness is associated with this?

A

Glutamate 6 to Valine is a missense mutation; sickle cell anemia

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29
Q

What are indels caused by?

A

Aberrant DNA recombination or DNA Pol slippage during replication

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30
Q

What is a reading frame?

A

A contiguous, non-overlapping three-nucleotide codon in DNA or RNA

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31
Q

What is a frameshift mutation?

A

A mutation that changes the reading frame (3bp mutation/deletion preserve reading frame)

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32
Q

What are trinucleotide repeat/expansion disorders? Give an example

A

Expansion of repeats of CAG, CGG, GAA, and CTG; Huntington’s disease (expansion of CAG)

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33
Q

What is fragile X syndrome caused by?

A

Expanded CGG repeats in FMR1 (200-1000 results in disease)

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34
Q

What strategy can be used to determine the number of triplet repeats in the fragile X locus?

A

Gel electrophoresis (larger band = more repeats)

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35
Q

In what 4 ways can chemical damage occur to DNA?

A
  1. Hydrolysis of water (depurination/depyrimidination)
  2. Electrophilic attack of backbone by alkylating agents
  3. ROS (hydrogen peroxide hydroxyl radicals, etc.)
  4. Irradiation
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36
Q

What is deamination?

A

Removal of an amine group

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37
Q

Which bases can be deaminated? Why?

A

CAG all have amine groups

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38
Q

Deamination of C into (product) causes a (transition/transversion) into (new pairing)

A

U; transition; CG to TA

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39
Q

Deamination of A into (product) causes a (transition/transversion) into (new pairing)

A

Hypoxanthine; transition; AT to GC

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40
Q

Deamination of G into (product) causes a (transition/transversion) into (new pairing)

A

Xanthine; no change; no change

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41
Q

Deamination of 5-Me-C into (product) causes a (transition/transversion) into (new pairing)

A

T; transition; CG to TA

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42
Q

What is the biproduct of deamination?

A

Ammonia

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43
Q

DNA hydrolysis causes what kind of chemical damage?

A

Depurination/depyrimidination

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44
Q

What causes depurination/depyrimidination? What is the product?

A

Hydrolysis of the glycosidic bond; apurinic/apyrimidinic site

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45
Q

What is the result of a depurination/depyrimidination?

A

Base loss or base pair transition

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46
Q

What may occur in an abasic site?

A

Sugar backbone isomerizes to the open aldehyde form, which is unstable and vulnerable to nucleophilic attack

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47
Q

What produces ROS?

A

Metabolism, cellular respiration, radiation

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48
Q

Oxidation of T by ROS produces (product) which (impact)

A

Thymine glycol; blocks DNA Pol due to steric hindrance

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49
Q

Oxidation of G by ROS produces (product) which (impact)

A

8-oxo-G; pairs with A (transversion), GC to TA

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50
Q

What are the highly reactive sites of A and G for alkylating damage?

A

N3 and O6, respectively

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51
Q

Where are alkyl groups added to bases?

A

Nucleophilic positions

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52
Q

Methylation of A by SAM results in?

A

DNA functioning like RNA

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53
Q

Nitrous acid causes:

A

Deamination of CAG (NOT 5-Me-C)

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54
Q

Sodium nitrate and bisulfite are _______ that cause _______

A

Food preservatives; deamination

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55
Q

True/False? Chemical modifications cannot occur simultaneously on a single base due to steric hindrance

A

False. Multiple modifications may occur simultaneously on a single base

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56
Q

Which modifications may occur to a single nucleotide base simultaneously?

A

Oxidation, alkylation, and deamination

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57
Q

What is the likelihood of a T-T CPD forming over a C-C CPD?

A

T-T»T-C>C-T>C-C

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58
Q

What causes CPDs?

A

UV radiation

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59
Q

In the case of T-C and C-C dimers, what are these called instead of CPDs?

A

6-4PPs, or 6-4 pyrimidone photoproducts

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60
Q

What is a CPD?

A

Cyclobutane pyrimidine dimer caused by the condensation of two double-bonded C5:C6 atoms on adjacent pyrimidine dimers

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61
Q

What is the most common CPD?

A

T-T (thymine dimer)

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62
Q

What does it mean when CPDs and 6-4PPs are called intra-strand crosslinks?

A

They form chemical bonds within their own strand, not the complimentary strand

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63
Q

What happens to the shape of the DNA when a thymine dimer forms?

A

It introduces a bend/kink in the DNA

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64
Q

What happens to DNA replication machinery upon encountering a pyrimidine dimer?

A

DNA Pol stalls

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65
Q

In the presence of radical O2, how is DNA radiosensitivity effected?

A

Increased

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66
Q

What does ionizing radiation cause the formation of? What is the most important species and how is it formed?

A

Excited and ionized molecules; ROS (H2O2, OH radical, O2 radical) formed by radiolysis of water

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67
Q

What can ROS cause?

A

Base loss, strand breaks, and DNA-protein crosslinks

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68
Q

What are intercalating agents?

A

Chemical that mimics base pairs and inserts between stacked bases, which destabilizes the DNA helix, which then causes frame shift mutations by making indels

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69
Q

Provide 4 examples of intercalating agents

A

Proflavin, acridine orange, ICR-191, and ethidium bromide

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70
Q

What is hydroxylation?

A

The addition of a hydroxyl group to the amino of cytosine

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71
Q

Hydroxylation of cytosine produces:

A

Hydroxylaminocytosine (HC)

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72
Q

Hydroxylaminocytosine forms hydrogen bonds with (base), resulting in a (base pair) after two rounds of replication. This is a (transition or transversion)

A

A; C-G to T-A; Transition

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73
Q

The keto form of 5-BrU base pairs with (base), causing a (base pair) after two rounds of replication. This is a (transition or transversion)

A

A; no change (T-A); neither

74
Q

The enol form of 5-BrU base pairs with (base), causing a (base pair) after two rounds of replication. This is a (transition or transversion)

A

G; T-A to C-G; transition

75
Q

What is 5-bromouracil?

A

A thymine analog

76
Q

What is 2-amino purine?

A

An adenine analog

77
Q

2-AP base pairs with (base), causing a (base pair) after two rounds of replication. This is a (transition or transversion)

A

T; no change (A-T); neither

78
Q

Where does alkylation most readily occur?

A

Nucleophilic centers

79
Q

True/False? Electrophilic centers are subject to attack by alkylating agents

A

False. Nucleophilic centers

80
Q

The protonated form of 2-AP base pairs with (base), causing a (base pair) after two rounds of replication. This is a (transition or transversion)

A

C; A-T to G-C; transition

81
Q

True/False? G-C rich regions are preferred for alkylation

A

True

82
Q

Which atoms of guanine and adenine, respectively, are the most commonly alkylated?

A

N7 and O6 of guanine, N3 of adenine

83
Q

Provide 7 examples of alkylating agents

A

EMS, EES, MNNG, nitrosamine, nitrosurea, cigarette smoke, and environmental pollution

84
Q

The O-4-ethylthymine base pairs with (base), causing a (base pair) after two rounds of replication. This is a (transition or transversion)

A

G; TA to CG; transition

85
Q

The O-6-ethylguanine base pairs with (base), causing a (base pair) after two rounds of replication. This is a (transition or transversion)

A

T; GC to AT; transition

86
Q

Interstrand crosslinking and DNA-protein crosslinking can be caused by:

A

UV, ionizing radiation, and bifunctional alkylating agents, such as psoralens

87
Q

What is psoralen?

A

A naturally occurring bifunctional alkylating agent that intercalates adjacent pyrimidines and is sensitive to light

88
Q

What is psoralen used in? Why?

A

Psoralen UVA (PUVA) treatment for skin problems, such as psoriasis, eczema, and vitiligo. It stops all cell division when photoactivated

89
Q

What are two types of DNA damaging agents with potential in chemotherapy? Provide an example for each

A

Alkylating agents (psoralen) and cross-linkers (cis-platin)

90
Q

True/False? Nucleotide excision repair (NER) is general to many types of DNA damage

A

True

91
Q

When does direct reversal of DNA damage occur?

A

Occurs for very common types of damage, like for mismatches, pyrimidine dimers, and methylation

92
Q

Describe the pathway of cis-platin

A

Cancer cells (fast-dividing cells) are more likely to pick up cis-platin. It is taken into the cell, and either causes DNA damage, mitochondrial DNA damage (causes leakage of CytC, which causes apoptosis)

93
Q

When does base excision repair (BER) occur?

A

Cytosine deamination to U

94
Q

Why is the mismatch repair system (MMR) highly conserved?

A

Mismatches can occur in both prokaryotes and eukaryotes, so it’s needed in both

95
Q

What is the limitation of MMR?

A

Indels cannot be repaired

96
Q

Which strand carries the lesion recognized by MMR?

A

The daughter strand

97
Q

What is the replication error rate of DNA Pol III (prokaryotic)?

A

10^-6

98
Q

What is the function of Dam methylase?

A

Identifies newly synthesized strand and methylates adenine residues on the sequence GATC on the new strand

99
Q

The sequence (GATC) Dam methylase recognizes is:

A

Palindromic

100
Q

How is the parental strand distinguished from the daughter stand?

A

Transient hemimethylation (daughter strand is not methylated but parental is)

101
Q

Describe the sequence of events in the MMR system in prokaryotes

A
  1. DNA Pol III synthesizes new strand
  2. MutS recognizes mismatched distortion and forms a complex with MutL
  3. Formation of a DNA loop and bidirectional scanning by the MutS/L complex
  4. Complex recruits MutH to cleave the nearest unmethylated GATC sites (endonuclease)
  5. MutS/L recruits UvrD (helicase II) to unwind DNA in the direction of the mismatch and an exonuclease degrades the displaced DNA strand to create a single-stand gap
  6. ssDNA is coated in single-stranded binding proteins (SSB) and DNA Pol III and ligase fill and seal the gap
102
Q

Which exonuclease is recruited when the hemimethylated GATC is on the 3’ side of the mismatch?

(hint: which strand is the methylated GATC located on?)

A

5’ to 3’ (RecJ or exonuclease VII)

103
Q

Which exonuclease is recruited when the hemimethylated GATC is on the 5’ side of the mismatch?

(hint: which strand is the methylated GATC located on?)

A

3’ to 5’ (exonuclease I or X)

104
Q

True/False? Eukaryotic cells have MutS and MutL

A

False. They have structural and functional analogs, but not MutS/L themselves

105
Q

Which MMR machinery do eukaryotic cells lack homologs for?

A

MutH and Dam methylase

106
Q

True/False? Eukaryotic MMR uses relative strand methylation to distinguish between new and old strands

A

False. Further research needed

107
Q

What is a CPD photolyase?

A

A single polypeptide chain found in all cells except placental mammals (us) that contain 2 non-covalently bound chromophores that utilize UV to catalyze monomerization of thymine dimers

108
Q

What wavelength light is used in direct reversal of thymine dimers?

A

400nm

109
Q

What coenzymes are used by CPD photolyase?

A

FADH and either MTHF or 8-HDF

110
Q

What is the function of the coenzymes used in CPD photolyase?

A

MTHF or 8-HDF absorb light and transfer the energy to FADH to cleave the cyclobutane ring

111
Q

Which gene encodes CPD photolyase?

A

phr (photoreactivation)

112
Q

What level of phr expression is seen in wildtype cells? LOF mutants?

A

Low expression; very low expression

113
Q

What is the phenotype of LOF phr mutants?

A

UV sensitivity, lack of CPD photolyase activity, slow growth rate, low viability

114
Q

Describe the sequence of events following CPD photolyase activation

A
  1. CPD photolyase binds thymine dimers in the presence of UV
  2. Dimer is flipped into the active site pocket
  3. MTHF absorbs a photon, transfers excitation energy to FADH- in the catalytic site
  4. Excited state FADH- transfers an electron to dimer and splits it into 2 T’s
  5. Electron returns to flavin radical to form FADH- and the enzyme dissociates
115
Q

Describe the direct reversal of O6-meG by DNA methyltransferase

A

Transfer of methyl group to a Cys residue on O6-meG DNA methyltransferase

116
Q

Methylation of the O6 on guanine results in a (base pair), which is a (transition/transversion) mutations, which is repaired by (enzyme)

A

GC to AT, transition, DNA methyltransferase

117
Q

True/False? Direct repair of O6-meG is found in all organisms except placentals

A

False. All organisms

118
Q

What kind of enzyme is DNA methyltransferase in terms of it’s processivity?

A

Suicide, it can only perform the reversal once before degradation, so it has low processivity

119
Q

What kind of mutations is base excision repair used to repair?

A

Single damaged nucleotides and ssDNA breaks that lack a ligatable junction

120
Q

Describe BER in prokaryotes

A
  1. DNA glycosylase recognizes damaged base and hydrolyzes the N-beta-glycosyl bond between the base and pentose, creating an abasic site
  2. ssDNA is cleaved at the abasic site by AP endonuclease
  3. A segment of DNA 3’ of the break site is removed and patched by DNA Pol I and ligase
121
Q

Where does AP endonuclease cleave the DNA relative to the abasic site?

A

5’

122
Q

Describe what is meant by the nick translation activity exhibited by DNA Pol I. When is this activity used?

A

Movement of where the nick is located on the DNA (first made at the abasic site and is moved 3’ of the original site after polymerization); prokaryotic BER

123
Q

True/False? After BER in prokaryotes, ligase seals the cut a couple of nucleotides 3’ of the initial DNA damage site

A

True

124
Q

True/False? There is only one type of “universal” DNA glycosylase that can recognize any type of damaged base

A

False. There are different glycosylases for different bases; ex. Uracil DNA Glycosylase (UDG) operates specifically to remove uracil from DNA

125
Q

UNG detects:

A

ssU, U:G, and U:A

126
Q

TDG detects:

A

Thymine

127
Q

MPG detects:

A

7-meA, 3-meA, 7-meG, 3-meG

128
Q

OGG1 detects:

A

8-oxo-G

129
Q

MYH detects:

A

A:G, A:8-oxo-G

130
Q

NTH1 detects:

A

T-glycol, C-glycol

131
Q

Describe BER in eukaryotes

A
  1. DNA Glycosylase detects
  2. AP endonuclease nicks

3a. Long patch: flap endonuclease is recruited to remove the displaced 5’ terminus
4a. DNA pol fills the gap and ligase seals it

3b. Short patch: Pol beta removes only the abasic pentose
4b. Pol beta fills the gap and ligase seals it

132
Q

Why do prokaryotes and eukaryotes have different BER pathways?

A

Eukaryotes lack 5’-3’ exonucleases

133
Q

How does DNA glycosylase recognize DNA damage if the bases face inwards?

A

The presence of a kink in the minor groove can be detected, so the damaged base is then flipped into the active site of the enzyme

134
Q

True/False? DNA glycosylase bends DNA when it is removing a damaged base. This temporarily disrupts the adjacent base pairs

A

False. They are not disrupted because the DNA isn’t bent significantly

135
Q

What is different about the type of DNA damage repaired in BER vs NER?

A

BER repairs single nucleotides while NER repairs bulky bases

136
Q

Describe NER in prokaryotes

A
  1. UvrA and UvrB complex scans DNA helix for damage
  2. UvrA dissociates when damage is detected and UvrB melts the two strands and recruits UvrC excinuclease
  3. UvrC makes incisions on the backbone on the 5’ and 3’ sides of the damaged bases to create a 12-13 nucleotide ssDNA gap
  4. UvrD is a helicase and releases the 12-13nt fragment
  5. DNA Pol I and ligase fill and seal the gap
137
Q

What type of enzyme is UvrC?

A

Excinuclease

138
Q

What type of enzyme is UvrD?

A

Helicase

139
Q

Describe NER in eukaryotes

A
  1. XPC recognizes the lesion
  2. XPB and XPD are recruited and separate the DNA to form an ssDNA bubble
  3. RPA binds to the bubble and positions XPF and XPG nucleases on either side of the lesion
  4. 24-32 nt fragment is displaced and PCNA clamp recruits DNA Pol and ligase to fill and seal
140
Q

Describe transcription-coupled DNA repair (TCR)

A
  1. RNA Pol recognizes damage and stalls
  2. Stalled complex recruits NER proteins, which release RNA Pol and repair the DNA
141
Q

Which regions are subject to the greatest DNA repair by TCR?

A

Genomic regions that are most highly transcribed

142
Q

What is xeroderma pigmentosum (XP)? What is it caused by?

A

An autosomal recessive disorder resulting from a defective NER system, which means cells can’t repair UV damage, so skin cells are extremely photosensitive (early skin cancer)

143
Q

What are the seven types of chromosome rearrangement?

A

Terminal deletion
Interstitial deletion
Unequal crossing over
Ring
Isochromosome
Robertsonian translocation
Insertion

144
Q

What is terminal deletion?

A

Deletion of the end of a chromosome

145
Q

What is interstitial deletion?

A

The deletion of a fragment within the chromosome

146
Q

What is a ring rearrangement of chromosomes?

A

Ends are deleted and new ends are joined

147
Q

What is an isochromosome?

A

One end of the chromosome replaces the other end (longer arm replaces the shorter arm so now you have a chromosome with two long arms)

148
Q

What is Robertsonian translocation?

A

Translocation of a chromosome arm onto another arm

149
Q

What is insertion?

A

A fragment from one chromosome translocates to another

150
Q

Why do carriers of a chromosomal inversion not show a mutant phenotype?

A

They have a balanced rearrangement

151
Q

What is a balanced arrangement?

A

Genes stay the same but change locations within the chromosome

152
Q

What produces unbalanced chromosomes?

A

Crossing over of a paracentric inversion

153
Q

What makes offspring with unbalanced chromosomes inviable?

A

Some may be acentric or dicentric, which causes issues in cell division, and they may have gene duplication and/or deletion

154
Q

Describe normal vs. balanced

A

Normal: genes occur in specific order (ABCD)
Balanced: genes occur in a different order but retain function (ACBD)

155
Q

How many balanced:unbalanced:inviable gamates are produced after crossing over of paracentric inversion loops?

A

2:0:2

156
Q

How many balanced:unbalanced:inviable gamates are produced after crossing over of pericentric inversion loops?

A

2:2:0

157
Q

Carriers of balanced arrangements usually produce gametes containing _______ chromosomes

A

Unbalanced

158
Q

Describe balanced vs. unbalanced chromosomes

A

Balanced: same number of genes, same or different order as wildtype, retain one centromere
Unbalanced: Have gene deletion/insertion, but retain one centromere

159
Q

Where are the gene duplications/deletions found on unbalanced chromosomes?

A

At the ends of the chromosome

160
Q

Paracentric vs pericentric inversion loops?

A

Pericentric includes the centromere, paracentric does not and occurs between the same arm of the chromosome

161
Q

What are the two repair mechanisms for a double stranded breaks that result in full repair?

A

Synthesis dependent strand annealing (SDSA) and double-stranded break repair (DSBR)

162
Q

True/False? SDSA can only result in a noncrossover event

A

True

163
Q

True/False? DSBR can only result in a noncrossover event

A

False. Both crossover and noncrossover

164
Q

When does NHEJ occur?

A

When a sister chromosome is unavailable for DSBR

165
Q

Describe the steps of NHEJ

A
  1. Double-stranded break occurs
  2. Ku70/80 binds at each DNA end
  3. DNA PKcs are recruited and the two ends are ligated together
166
Q

Why are indels common with NHEJ?

A

Repaired ends don’t always reproduce the sequence before the break

167
Q

What is TLS?

A

Translesion DNA synthesis

168
Q

Describe TLS

A
  1. DNA Pol III stalls when it encounters a lesion at the replication fork and dissociates
  2. Pol IV is recruited to polymerize across the lesion
  3. Pol IV dissociates and the replisome is rerecruited
169
Q

Why is Pol IV recruited during TLS?

A

A low-fidelity polymerase that lacks 3’-5’ exonuclease activity is needed so that the DNA can still be synthesized and the mutation is repaired later

170
Q

Summarize the damage type and enzymes used for MMR

A

Replication errors; MutS, MutL, MutH (E. coli), MSH, MLH, and PMS (humans)

171
Q

Summarize the damage type and enzymes used for photoreactivation

A

Pyrimidine dimers; DNA photolyase

172
Q

Summarize the damage type and enzymes used for BER

A

Damaged base; DNA glycosylase, AP endonuclease

173
Q

Summarize the damage type and enzymes used for NER

A

Pyrimidine dimer and bulky adduct on base; UvrA, UvrB, UvrC, UvrD (E. coli), XPC, XPA, XPD, XPF, and XPG (humans)

174
Q

Summarize the damage type and enzymes used for DSBR

A

Double stranded breaks; RecA (E. coli)

175
Q

Summarize the damage type and enzymes used for TLS

A

Pyrimidine dimer, apurinic site, or bulky adduct on base; Y-family DNA Pol (UmuC or Pol IV)

176
Q

Alkylation can be repaired by which mechanisms?

A

BER, alkyltransferases (ex. DNA methyltransferase), and NER

177
Q

Depurination can be repaired by which mechanisms?

A

BER

178
Q

Pyrimidine dimers can be repaired by which mechanisms?

A

CPD photolyase, NER

179
Q

Deamination can be repaired by which mechanisms?

A

BER

180
Q

Double stranded breaks can be repaired by which mechanisms?

A

DSBR, NHEJ, SDSA

181
Q

Direct reversal of DNA damage can be seen in which mechanisms?

A

MMR, photoreactivation (photolyases), and removal of methyl groups (methyltransferases)