Mutations, DNA Damage, and Repair Mechanisms

Vocabulary flashcards covering types of DNA mutations, natural and chemical mutagens, experimental proofs of spontaneous mutation, and accurate versus error-prone DNA repair pathways.

Forward mutation

A mutation that changes a wild-type allele to a different, mutant allele (for example, $A^+ \rightarrow a$ or $b^+ \rightarrow B$).

Reverse mutation (reversion)

A mutation that restores a mutant allele back to the original wild-type allele (for example, $a \rightarrow A^+$ or $B \rightarrow b^+$).

Substitution

A DNA sequence mutation where one base pair is replaced by another base pair.

Transition

A base substitution mutation in which a purine is replaced by another purine, or a pyrimidine is replaced by another pyrimidine.

Transversion

A base substitution mutation in which a purine is replaced by a pyrimidine, or a pyrimidine is replaced by a purine.

Deletion

A mutation resulting in the loss of a block of one or more base pairs from the DNA sequence.

Insertion

A mutation resulting in the addition of a block of one or more base pairs into the DNA sequence.

Indels

A collective term for insertion and deletion mutations, which can range in size from a single base pair to megabases.

Point mutation

A mutation that affects only one or a few base pairs, altering a single gene at a time.

Fluctuation test

An experimental assay devised by S. Luria and M. Delbrück (1943) demonstrating that bacterial resistance mutations arise randomly and spontaneously prior to exposure to a bacteriophage or bactericide, rather than as a physiological response to it.

Replica plating

A technique using a sterile velvet surface to transfer bacterial colonies in the exact same spatial layout to selective plates, verifying that resistant mutants were present before exposure to an antibiotic.

Selective agent

An environmental substance (such as an antibiotic or bactericide) that kills sensitive non-mutant cells and permits only preexisting resistant mutant cells to grow.

Depurination

A spontaneous hydrolytic process occurring approximately $1000$ times per hour per cell that hydrolyzes the bond between a purine base (guanine or adenine) and the sugar-phosphate backbone, leaving an apurinic site.

Deamination

The removal of an amino group ($-\text{NH}_2$) from a base, such as modifying cytosine to uracil, which causes a $C\text{–}G \rightarrow T\text{–}A$ transition mutation after DNA replication.

Thymine dimer

An abnormal covalent linkage formed between adjacent thymine bases on the same DNA strand upon exposure to ultraviolet (UV) light, creating a distortion in the DNA double helix.

8-oxodG (GO)

An oxidized form of guanine created by active oxygen species that mispairs with adenine during replication, resulting in a $G\text{–}C \rightarrow T\text{–}A$ transversion.

$3' \text{ to } 5'$ exonuclease

The proofreading domain of DNA polymerase that detects, excises, and removes mispaired bases from the $3'$ end of a growing DNA strand during replication.

Base tautomerization

The reversible interconversion of a nucleotide base between structural isomers (tautomers) with altered hydrogen-bonding properties, leading to replication errors and point mutations.

Slipped mispairing

A replication slippage mechanism occurring at repetitive trinucleotide sequences where DNA polymerase pauses and the newly synthesized strand slips out to form a loop (causing expansion) or the template strand slips out (causing contraction).

Mutagen

Any physical or chemical agent (such as X-rays or alkylating agents) that increases the mutation rate above the spontaneous background rate.

Base analog

A chemical mutagen with a molecular structure almost identical to a normal DNA base (such as 5-Bromouracil) that incorporates into DNA and causes mispairing during replication.

Hydroxylating agent

A mutagen (such as hydroxylamine) that adds a hydroxyl group ($-\text{OH}$) to a base, causing modified cytosine ($N\text{-4-hydroxycytosine}$) to pair with adenine instead of guanine.

Alkylating agent

A chemical mutagen (such as ethylmethane sulfonate / EMS) that transfers ethyl ($-\text{CH}_2\text{–CH}_3$) or methyl ($-\text{CH}_3$) groups to bases, altering base pairing (e.g., $O\text{-6-Ethylguanine}$ mispairing with thymine).

Deaminating agent

A chemical agent (such as nitrous acid) that removes amino groups ($-\text{NH}_2$), converting cytosine to uracil (pairing with adenine) and adenine to hypoxanthine (pairing with cytosine).

Intercalating agent

A flat, planar molecule (such as proflavin or ethidium bromide) that slips between adjacent base pairs of the DNA double helix, causing single base pair insertions or deletions during replication.

Somatic mutation

A mutation occurring in non-germline body cells that is not transmitted to future generations but can affect individual survival and cause cancer.

Ames test

A biological screening assay used by regulatory agencies to detect potential mutagens and carcinogens by measuring the rate of reversion from $His^-$ to $His^+$ in bacteria exposed to compounds mixed with rat liver enzymes.

Base excision repair (BER)

A repair pathway where DNA glycosylases cleave damaged or incorrect nitrogenous bases (such as uracil) from deoxyribose, followed by AP endonuclease nicking, exonuclease excision, DNA polymerase filling, and DNA ligase sealing.

Nucleotide excision repair (NER)

A repair pathway that removes bulky double helix distortions (such as thymine dimers) through endonuclease incision (e.g., UvrB and UvrC), fragment excision, and replacement synthesis by DNA polymerase and ligase.

Homologous recombination (HR)

An accurate double-strand break repair mechanism that uses an intact homologous chromosome or sister chromatid as a template to direct repair without loss of sequence information.

Nonhomologous end-joining (NHEJ)

A double-strand break repair mechanism where proteins such as KU70, KU80, and $\text{PK}_{\text{cs}}$ protect and rejoin broken DNA ends directly, often resulting in small deletions.

Methyl-directed mismatch repair

A bacterial post-replication repair system where MutS and MutL recognize base mismatches, and MutH nicks the newly synthesized unmethylated strand opposite a methylated $\text{GATC}$ sequence on the parental template strand.

SOS system

An error-prone bacterial repair pathway recruited when replication stalls at DNA lesions, employing specialized 'sloppy' translesion DNA polymerases that insert random bases opposite damaged sites.

Microhomology-mediated end-joining (MMEJ)

An error-prone double-strand break repair pathway similar to NHEJ that removes terminal nucleotides to expose short regions of microhomology, inevitably generating deletions.

Xeroderma pigmentosum

A rare hereditary human disorder caused by inherited mutations in any of seven genes responsible for nucleotide excision repair, leading to an inability to repair UV-induced thymine dimers and a high susceptibility to skin cancer.