Topic 6 Flashcards
True or false: most mutations are harmful
True
- Cells have repairing mechanisms to correct changes in genetic materials
Mutations and repairing mechanisms have to maintain a balance between…
Organismal survival and biodiversity (variation in the DNA)
What are the 3 types of DNA damage?
- Gene mutation (spontaneous or induced by mutagens)
- Recombination (likely causing chromosomal arrangements)
- Transposable elements
Unequal crossing over leads to what?
Leads to the insertion/deletion of certain genes
What are the 2 mechanisms inducing DNA mutations?
- Replication errors
- Chemical modifications
Deamination (chemical modification that leads to DNA mutations)
Removal of an amino group
Depurination/depyrimidination leads to… (chemical modification that leads to DNA mutations)
Base loss
Oxidation (chemical modification that leads to DNA mutations)
Electron loss
Alkylation (chemical modification that leads to DNA mutations)
Transfer of an alkyl (CH3-) group
Nitrous acid (that is found in food preservatives) can induce what?
DNA damage
Energy-rich radiations cause what? (chemical modification that leads to DNA mutations)
Inter-base, inter-strand crosslinkings, and strand breaks
Intercalating agents can cause what?
DNA damage
Base analogs can cause what?
DNA damage
What 2 mutations are caused by replication errors?
- Point mutations (e.g. missense, nonsense mutations)
- Frameshift mutations
Slippage of template during replication leads to…
Deletion
Slippage of new strand during replication leads to…
Addition
Number the nucleotides on slide 9
In what tautomeric form are nucleotides usually found? (2)
Amino and keto
When amino form of nucleotide tautomerizes into imino form, what happens to the hydrogen bond donors and acceptors?
Hydrogen bond donor from amino becomes a hydrogen bond acceptor, while one of the deprotonated nitrogens becomes a hydrogen bond donor
When keto form of nucleotide tautomerizes into enol form, what happens to the hydrogen bond donors and acceptors?
Hydrogen bond acceptor on carbonyl becomes a hydrogen bond donor, while hydrogen bond donor on one of the protonated nitrogens becomes a hydrogen bond acceptor
Enol form of Thymine can base pair with…
Keto form of guanine
Enol form of guanine can base pair with…
Keto form of thymine
Imino form of adenine can base pair with…
Amino form of cytosine
Imino form of cytosine can base pair with…
Amino form of adenine
Transition mutation
purine -> purine or pyrimidine -> pyrimidine
Transversion mutation
purine -> pyrimidine or pyrimidine -> purine
Describe how substitution point mutations occur in two steps
Step 1: incorrect nucleotide is incorporated by DNA polymerase during replication -> mismatching (mismatch is called a lesion)
Step 2: Mismatched base is not repaired and undergoes DNA replication -> mutation
What does it mean if you read about an E6V mutation in a research article?
Glutamate mutates at codon (amino acid) 6 to Val
teg-1 (oz230) mutation changes AAG to UAG at codon 53. However, this corresponds to position 257 on genomic DNA, rather than 159. Why?
The position 259 includes all the introns
Frameshift mutation
A mutation changes the reading frame of codons during protein synthesis
Indel mutations that occur in multiples of 3 base pairs…
Preserve the reading frame of the gene
Slippage of DNA polymerase during DNA replication can cause…
Several diseases
What do Trinucleotide Repeat/Expansion Disorders involve?
Involve expansion of repeats of CAG, CGG, GAA and CTG
Huntington’s chorea
Expansion of CAGs (codon for glutamine)
Describe Fragile X syndrome
- The most common form of hereditary mental retardation with a frequency of 1/1500 males and 1/2500 females
- (CGG)n repeats in Fragile-X syndrome gene, FMR1
- Progressive expansion from generation to generation
How can triplet expansion diseases be diagnosed?
The number of triplet repeats in the fragile X locus can be determined by length analysis of PCR products
- because repeats increase the length of DNA
What are the 4 main types of chemical damage that can damage DNA?
- Hydrolytic reactions with H2O to damage nucleotides and the phosphodiester backbone of DNA.
- Electrophilic attack of DNA backbone by alkylating agents.
- Reaction with oxygen species, such as hydrogen peroxide, hydroxyl radicals, superoxide radicals, etc…
- Alteration of DNA structure by irradiation, such as X ray and UV
Cytosine deamination results in…
Uracil
Adenine deamination results in…
Hypoxanthine
Guanine deamination results in…
Xanthine
5-Methylcytosine deamination results in…
Thymine
Which modified bases can base pair with cytosine?
Hypoxanthine and Xanthine
Which nucleotide cannot deaminate?
Thymine
What results in base loss by depurination or depyrimidination?
Hydrolytic reaction cleaves glycosyl bond between the nitrogenous base and the deoxyribose to create an abasic (AP) site
- Under physiological conditions, depurination occurs at ~5000 bases/cell/day
The (open/closed) form of deoxyribose has an unstable 3’phosphodiester bond; therefore, hydrolysis may result in…
Open, may result in strand break and base loss
What produces reactive oxygen species (ROS)?
Cellular metabolism, such as cellular respiration in the mitochondria and detoxification in the liver, and ionization radiation
ROS can oxidize thymine to what? What does this result in?
Thymine glycol, this blocks DNA polymerase (due to steric hinderance)
ROS can oxidize guanine to what? What does this result in?
8-oxoguanine, this changes a GC base pair to an AT base pair because 8-oxoguanine can base pair with adenine.
Alkylating agents (CH3-) come from what?
Cigarette smoke and environmental pollutions
What positions does alkylation on Thymine occur most readily?
C=O of C2, N3 and C=O of C4
What positions does alkylation on Adenine occur most readily?
N1, N3, N7, amine on C6
What positions does alkylation on Cytosine occur most readily?
C=O of C2, N3 and amine on C4
What positions does alkylation on Guanine occur most readily?
N1, N2, N3, N7, C=O on C6
What are the highly reactive sites for alkylation in all of the bases?
N3 of A, O6 of G and N7 of G
S-adenosylmethionine (SAM)
The biological methyl group donor that can accidentally react with DNA to methylate A to give N6-methyladenine (m6A) -> DNA functions like RNA
Sodium nitrate (NaNO3) and bisulfite (HSO3-) used as food preservatives causes…
Deamination of guanine to xanthine, cytosine to uracil and adenine to hypoxanthine
True or false: guanine deaminating to xanthine causes a mutation
False, because hypoxanthine also hydrogen bonds with cytosine so there’s overall no change.
True or false: multiple potential chemical modifications can occur simulatenously on a single base
True
Cyclobutane pyrimidine dimers (CPD)
Condensation of two double-bonded C5=C6 atoms on adjacent pyrimidine bases that distort the DNA double helical structure (UV-induced)
Most common CPD
Thymine dimers
(6-4) pyrimidine photoproducts (6-4PPs)
Formation of a single covalent bond between the 6 position of one pyrimidine and the 4 position of the adjacent pyrimidine on the 3’ side (UV-induced)
CPD and 6-4 Photoproduct are (inter/intra) strand crosslinking
Intra
Ionizing radiations induce (inter/intra)base crosslinks
Inter
The formation of a pyrimidine dimer introduces a…
Bend or kink in the DNA
On encountering a pyrimidine dimer during replication…
The DNA polymerase stalls
Ionizing radiation causes…
The formation of excited and ionized molecules
- The most important are species formed by radiolysis of water, forming products capable of causing oxidative damage