How do beneficial mutations arise?
randomly
What are the different classifications of point mutations?
synonymous, missense, nonsense, frameshift, promoter, polyadenylation splice site, DNA replication mutation
transition mutation
purine for purine or pyrimidine for pyrimidine
transversion mutation
purine for pyrimidine or pyrimidine for purine
Which is more common in nature, transversions or transitions?
transitions
forward mutation
mutations that alters a wild-type allele and turns it into a mutant
reverse mutation or reversion
mutations that alters a mutant back to its wild type
true reversion
exactly reverses the mutation
intragenic reversion
second mutation within the gene that restores wild type (or near) function
second site reversion
takes place at a second location to restore the wild type
also known as a suppressor mutation
strand slippage
the DNA polymerase temporarily dissociated and then reattaches to resume replication, and it leads to increased or decreased numbers of repeating nucleotides
Incorrect base is incorporated:
DNA CYCLE 1
- error gets incorporated
DNA CYCLE 2
- if not repaired here, then the change becomes permanent and the base becomes incorporated in a mutation
Depurination
loss of a purine by breakage of the covalent bond at the carbon that links the sugar and nucleotide base. This forms an apurinic site, and if not repaired, DNA polymerase will put an adenine into the site during replication
most frequent spontaneous chemical changes affecting DNA
deamination
loss of an amino group from a nucleotide base, and it is replaced with an oxygen, forming uracil. DNA mismatch repair will recognize uracil as RNA and replace it with cytosine
consequences of UV radiation on DNA
induces chromosomes breaks
How does the Ames test work, and what conclusions can be drawn from it?
Two different mutants exposed to S9 extract (detoxifying liver enzymes), which then diffuse outwards, either creating many revertant colonies or few/none. The more colonies compared to the control the more mutations than expected by the spontaneous mutation rate
If there is a statistically significant difference in the number of colonies on the experimental compared to control plate – the compound (or metabolized compound) is likely mutagenic
base exision repair
removal of an incorrect or damaged DNA base and repair by synthesis of a new strand segment (nick translation)
Nucleotide excision repair (NER)
removal of a strand segment containing DNA damage and replacement by new DNA synthesis
Mismatch repair
removal of DNA base-pair mismatch by excision of a segment of the newly synthesized strand followed by resynthesis of the excised segment
Nick translation
essentially identical to the process that removes and replaces RNA primer during DNA replication. Creates a small break in th esugar-phosphate backbone and replaces several nucleotides and DNA ligase seals it back up.
Non-homologous end joning
Ends of the break will be trimmed so that they become blunt and ligase joins them together. Some nucleotides are lost
Synthesis-dependent strand annealing
Uses the sister chromatid as a template strand. It needs to happen while there are two strands.
Translesion DNA synthesis
damage tolerance mechanism that allows to bypass DNA lesions. DNA pol III switches with a different, more flexible, DNA polymerase, which adds nucleotides (no proof-reading ability), and normal replication resumes with DNA pol III
p53 pathway
decides the cell’s fate when damage is sensed: either pause for repair in G1 or induce apoptosis
