Topic 6 (DNA Damage and Repair) Flashcards
Define DNA damage
Any modification of DNA that changes its coding properties or normal function in transcription or translation
What can DNA damage lead to?
Mutations and genetic instability
True/False? Mutations arise solely by chance
False. They may be induced by chemicals and UV as well
What is the evolutionary tradeoff of mutations?
They may increase fatality or may increase biodiversity
What are the three types of DNA damage?
Mutation, recombination, and transposons
Why is recombination a way in which the genome can change?
Unequal crossing over results in gene deletion/duplication
What are the two mechanisms inducing DNA mutations?
Replication errors and chemical modifications
What are examples of chemical modifications to DNA which result in mutations?
Deamination, depurination/depyrimidination, oxidation, alkylation, nitrous acid, radiation, intercalating agents, and base analogs
What are the types of mutations that can occur due to errors in DNA replication?
Point mutations and frameshift mutations
Give 3 examples of point mutations
Missense, nonsense, and silent
Give 2 examples of frameshift mutations. How does each occur?
Deletion; slippage of template during replication
Insertion; slippage of daughter strand during replication
In what tautomeric form are Adenine and Cytosine found in usually?
Amino
In what tautomeric form are Guanine and Thymine found in usually?
Keto
How many hydrogen bond donors and acceptors are there in an amino to imino tautomerization?
Amino: 2 acceptors, 1 donor
Imino: 2 acceptors, 1 donor (different locations)
How many hydrogen bond donors and acceptors are there in a keto to enol tautomerization?
Keto: 2 donors, 1 acceptor
Enol: 2 donors, 1 acceptor (different location)
What changes about the hydrogen bond donors/acceptors in tautomerization?
Two donors/acceptors switch to the other kind (donor to acceptor and acceptor to donor), so number of donors and acceptors stays the same
The enol form of T can base pair with: __________. What does this form following 2 cycles of replication? Transition or transversion?
Keto form of G; TA to CG; transition
The enol form of G can base pair with: __________. What does this form following 2 cycles of replication? Transition or transversion?
Keto form of T; GC to AT; transition
The imino form of A can base pair with: __________. What does this form following 2 cycles of replication? Transition or transversion?
Amino form of C; AT to GC; transition
The imino form of C can base pair with: __________. What does this form following 2 cycles of replication? Transition or transversion?
Amino form of A; CG to TA; transition
What is a transition mutation?
Purine to purine/pyrimidine to pyrimidine (CG to TA)
What is a transversion mutation?
Purine to pyrimidine/pyrimidine to purine (CG to GC or AT)
What is a lesion vs a mutation?
Lesion is a single base change but its still paired with the correct base. Mutation is a double-stranded discrepency
What are the steps in creating point mutations?
- Incorrect nucleotide incorporated by DNA Pol (lesion)
- Mismatched base is not repaired and undergoes replication (mutation)
What is a K53X?
Lysine 53 changed to a stop codon (nonsense mutation)
What are the three stop codons? What colour name is associated with each?
UAA; ochre
UGA; opal
UAG; amber
Why is a mutation at codon 53 on the mature transcript at position 257 on genomic DNA?
Genomic DNA includes introns
What is an E6V mutation? What sickness is associated with this?
Glutamate 6 to Valine is a missense mutation; sickle cell anemia
What are indels caused by?
Aberrant DNA recombination or DNA Pol slippage during replication
What is a reading frame?
A contiguous, non-overlapping three-nucleotide codon in DNA or RNA
What is a frameshift mutation?
A mutation that changes the reading frame (3bp mutation/deletion preserve reading frame)
What are trinucleotide repeat/expansion disorders? Give an example
Expansion of repeats of CAG, CGG, GAA, and CTG; Huntington’s disease (expansion of CAG)
What is fragile X syndrome caused by?
Expanded CGG repeats in FMR1 (200-1000 results in disease)
What strategy can be used to determine the number of triplet repeats in the fragile X locus?
Gel electrophoresis (larger band = more repeats)
In what 4 ways can chemical damage occur to DNA?
- Hydrolysis of water (depurination/depyrimidination)
- Electrophilic attack of backbone by alkylating agents
- ROS (hydrogen peroxide hydroxyl radicals, etc.)
- Irradiation
What is deamination?
Removal of an amine group
Which bases can be deaminated? Why?
CAG all have amine groups
Deamination of C into (product) causes a (transition/transversion) into (new pairing)
U; transition; CG to TA
Deamination of A into (product) causes a (transition/transversion) into (new pairing)
Hypoxanthine; transition; AT to GC
Deamination of G into (product) causes a (transition/transversion) into (new pairing)
Xanthine; no change; no change
Deamination of 5-Me-C into (product) causes a (transition/transversion) into (new pairing)
T; transition; CG to TA
What is the biproduct of deamination?
Ammonia
DNA hydrolysis causes what kind of chemical damage?
Depurination/depyrimidination
What causes depurination/depyrimidination? What is the product?
Hydrolysis of the glycosidic bond; apurinic/apyrimidinic site
What is the result of a depurination/depyrimidination?
Base loss or base pair transition
What may occur in an abasic site?
Sugar backbone isomerizes to the open aldehyde form, which is unstable and vulnerable to nucleophilic attack
What produces ROS?
Metabolism, cellular respiration, radiation
Oxidation of T by ROS produces (product) which (impact)
Thymine glycol; blocks DNA Pol due to steric hindrance
Oxidation of G by ROS produces (product) which (impact)
8-oxo-G; pairs with A (transversion), GC to TA
What are the highly reactive sites of A and G for alkylating damage?
N3 and O6, respectively
Where are alkyl groups added to bases?
Nucleophilic positions
Methylation of A by SAM results in?
DNA functioning like RNA
Nitrous acid causes:
Deamination of CAG (NOT 5-Me-C)
Sodium nitrate and bisulfite are _______ that cause _______
Food preservatives; deamination
True/False? Chemical modifications cannot occur simultaneously on a single base due to steric hindrance
False. Multiple modifications may occur simultaneously on a single base
Which modifications may occur to a single nucleotide base simultaneously?
Oxidation, alkylation, and deamination
What is the likelihood of a T-T CPD forming over a C-C CPD?
T-T»T-C>C-T>C-C
What causes CPDs?
UV radiation
In the case of T-C and C-C dimers, what are these called instead of CPDs?
6-4PPs, or 6-4 pyrimidone photoproducts
What is a CPD?
Cyclobutane pyrimidine dimer caused by the condensation of two double-bonded C5:C6 atoms on adjacent pyrimidine dimers
What is the most common CPD?
T-T (thymine dimer)
What does it mean when CPDs and 6-4PPs are called intra-strand crosslinks?
They form chemical bonds within their own strand, not the complimentary strand
What happens to the shape of the DNA when a thymine dimer forms?
It introduces a bend/kink in the DNA
What happens to DNA replication machinery upon encountering a pyrimidine dimer?
DNA Pol stalls
In the presence of radical O2, how is DNA radiosensitivity effected?
Increased
What does ionizing radiation cause the formation of? What is the most important species and how is it formed?
Excited and ionized molecules; ROS (H2O2, OH radical, O2 radical) formed by radiolysis of water
What can ROS cause?
Base loss, strand breaks, and DNA-protein crosslinks
What are intercalating agents?
Chemical that mimics base pairs and inserts between stacked bases, which destabilizes the DNA helix, which then causes frame shift mutations by making indels
Provide 4 examples of intercalating agents
Proflavin, acridine orange, ICR-191, and ethidium bromide
What is hydroxylation?
The addition of a hydroxyl group to the amino of cytosine
Hydroxylation of cytosine produces:
Hydroxylaminocytosine (HC)
Hydroxylaminocytosine forms hydrogen bonds with (base), resulting in a (base pair) after two rounds of replication. This is a (transition or transversion)
A; C-G to T-A; Transition