Lecture 26: Mutation, Mutagens, Repair

Transition

purine to purine or pyrimidine to pyrimidine

Transversion

pyrimidine to purine or purine to pyrimidine

Nonsynonymous

mutation alters the animo acid sequence of protein

• missense and neutral

Missense

changes in amino acid that may alter protein function or protein is non-functional

Neutral

change in amino acid that doesn’t affect protein function

Nonsense

changes codon so it becomes a codon stop

• ex) GAG mutates to UAG

Synonymous (Silent)

codes for the same amino acid

• ex) AGG mutates to CGG but both are Arginine anyways

Readthrough

stop codon is changes to a codon that codes for amino acids resulting in a larger protein

Exact Reversion

causes normal codon to be put back into position

• AAA —> GAA —> AAA

  Lys Glu Lys

Equivalent Reversion

restores normal phenotype but the DNA sequence after the equivalent reversion isn’t exactly the same as normal

• UCC —> UGC —> AGC

  Ser Cys Ser

Intragenic

mutations that occur within the same gene

Intergenic

mutations that occur in different genes to restore normal phenotype

Depurination

results in a purinic site where the glycosidic bond is removed at either G or A bases

Wobble Base Pairing

mispairing because of flexibility in helix; results in transitions after replication

Frameshift Mutation

occurs when one or more base pairs of DNA are inserted into the gene which shifts the reading frame of all codons from one involved in the change and onwards, so this can alter start and stop sites

Intercalating Agents

agents like proflavine, ethidium bromide, and acridine orange can slide in between the base pairs of the DNA, distorting the helix and causing template slippage during replication

Pyrimidine Dimers

• occur between two pyrimidines that are adjacent to each other on the same strand of double stranded DNA.

• UV light can cause these to form.

• Most of us have a repair mechanism that catch and repair a large proportion of these dimers.

• Individuals with the disorder Xeroderma pigmentosum are lacking a repair mechanism for these dimers resulting in a high frequency of skin cancer among these individuals.

Direct Repair of Pyrimidine Dimers (in bacteria)

Corrects structure of abnormal nucleotide without replacing the nucleotide

• Enzyme Photolyase absorbs light and clips dimer

• Enzyme is released from the DNA, restoring the normal DNA sequence.

Mismatch Repair

identify improperly paired base pairs and to remove them

• Exonucleases remove an area of the new strand from the methylated sequence to the mismatch.

• fills in the gap and DNA polymerase ligase seals the nick

Nucleotide Excision Repair

repair many types of DNA damage and is found in prokaryotes and eukaryotes.

• An enzyme complex (UVR Endonuclease) recognizes the distortion in the helix due to the abnormal situation

• Strands of DNA are separated and held apart by SSB

• Enzyme cleaves sugar phosphate bonds on both sides of lesion removing several nucleotides including the defective area

• DNA polymerase fills in gap

• DNA ligase seals nick

Base Excision Repair

Glycosylase recognizes and removes defective base resulting in an AP site

• glycosylase/specific modified base (uracil, 7-methylguanine, etc.)

• AP endonuclease cleaves the phosphodiester bond next to the missing base (causes a nick) and then removes the rest of the nucleotide

• DNA polymerase fills in the gap

• DNA ligase seals the nick

Double Stranded Break Repair

Homologous Recombination Repair

• Uses the sister chromatid to repair the break

• Uses the many of the same enzymes as homologous recombination in meiosis

• BRCA1, BRCA2

Nonhomologous end joining

• Often used in G1

• Joins broken ends

• often leads to translocations, deletions and insertions

Translesion DNA Repair

Specialized polymerases that can bypass lesions on the DNA during replication

• polymerases often make errors and allow replication to proceed at the cost of introducing mutations

Point vs Frameshift Mutation

Frameshift mutations occur when one or more base pairs of DNA are inserted/deleted into the gene

Point mutation occurs when one base pair is substituted for another

Some chemicals that cause transitions are

• base analogs

• alkylating agents

• deamination

• hydroxylamine

Some chemicals that cause transversions are

• aflatoxin

• 8-oxygaunine