Genetics Lecture 4: DNA Repair Mechanisms and Consequences of Mutations

Vocabulary practice flashcards covering prokaryotic and eukaryotic DNA repair mechanisms (direct reversal, BER, NER, MMR, NHEJ, HR, and SOS bypass), associated human diseases, and the molecular genetics of Mendel's pea mutants.

DNA Polymerase I Activities

The three enzymatic functions of bacterial DNA polymerase I: $5' \rightarrow 3'$ polymerase activity for gap filling, $3' \rightarrow 5'$ exonuclease activity for proofreading, and $5' \rightarrow 3'$ exonuclease activity for RNA primer removal.

Cyclobutane Pyrimidine Dimer (CPD)

A covalent DNA lesion (photodimer) between adjacent pyrimidines formed as a result of exposure to ultraviolet (UV) radiation.

CPD Photolyase

A flavoprotein enzyme that directly binds to and splits cyclobutane pyrimidine dimers in a light-dependent repair process called photoreactivation, utilizing methenyltetrahydrofolate (MTHF) as a cofactor.

$O^6$-Methylguanine Methyltransferase (MGMT)

A direct reversal repair enzyme that transfers an alkyl group from position $O^6$ of guanine directly to a cysteine residue in its active site, resulting in irreversible inactivation and degradation of the protein.

AlkB Family Dioxygenases

A group of direct reversal repair enzymes that remove alkyl adducts from nucleobases via oxidative dealkylation without requiring DNA backbone cleavage or synthesis.

Base Excision Repair (BER)

A DNA repair pathway that corrects minor, non-bulky damage to bases (caused by methylation, deamination, oxidation, or spontaneous loss) by removing the defective base prior to nicking the backbone.

DNA Glycosylase

An enzyme in base excision repair that hydrolyzes the N-glycosidic bond linking an abnormal or damaged base to the deoxyribose sugar, generating an abasic (AP) site.

AP Site (Apurinic/Apyrimidinic Site)

A location in DNA where a purine or pyrimidine base is missing, leaving only the sugar-phosphate backbone, which is recognized and cleaved by AP endonuclease.

5-Methylcytosine Mutation Hot Spots

DNA sites frequently identified by Jeffrey Miller that are highly vulnerable to transition mutations because deamination of 5-methylcytosine produces thymine, which is not recognized by uracil-DNA glycosylase.

$\text{UvrA}_2\text{UvrB}_2$ Complex

A bacterial multi-protein scanning assembly in nucleotide excision repair wherein a $UvrA$ dimer binds upstream of DNA damage and loads $UvrB$ to detect helix distortions.

UvrC

A prokaryotic endonuclease recruited by $UvrB$ that makes dual incisions in the damaged DNA strand, cleaving $4\text{--}5$ nucleotides $3'$ and $8$ nucleotides $5'$ to the lesion.

UvrD (Helicase II)

A prokaryotic helicase that unwinds and releases the excised damaged single-stranded oligonucleotide during bacterial nucleotide excision repair and mismatch repair.

Transcription-Coupled NER (TC-NER)

A subpathway of nucleotide excision repair triggered when RNA polymerase stalls at a lesion during transcription, recruiting the CSA and CSB proteins.

Global Genomic Repair (GGR)

A subpathway of nucleotide excision repair that scans the entire genome for helix-distorting damage, initiated by sensor complexes including DDB1-XPE and XPC-HR23B.

TFIIH

A 10-subunit general transcription and repair factor containing the helicases XPB and XPD that unwinds DNA around a lesion during eukaryotic nucleotide excision repair.

XPF-ERCC1 and XPG

Structure-specific endonucleases in eukaryotic NER that carry out dual incisions on the damaged strand ($5'$ incision by XPF-ERCC1 and $3'$ incision by XPG) to release an oligonucleotide of approximately $30$ nucleotides.

Mismatch Repair (MMR)

A post-replication repair pathway that recognizes and fixes base-base mispairs and small indels missed by DNA polymerase proofreading, lowering the error rate from $10^{-7}$ down to $10^{-9}$.

Hemimethylated DNA

Newly replicated prokaryotic DNA in which the adenine in the GATC sequence of the parental strand is methylated by adenine methylase while the daughter strand is not yet methylated, directing MMR to the correct strand.

MutS

A mismatch repair protein that scans DNA, recognizes base mismatches, and determines the incorrect base configuration.

MutH

A sequence- and methylation-specific endonuclease in bacterial mismatch repair that selectively nicks the unmethylated nascent DNA strand containing the replication error.

Non-Homologous End Joining (NHEJ)

The major error-prone pathway for repairing double-strand DNA breaks that directly processes and ligates broken chromosome ends without using a homologous template.

Ku70/Ku80 Heterodimer

A ring-shaped protein complex that binds directly to the ends of double-strand breaks and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs).

Artemis

An endonuclease recruited and phosphorylated by DNA-PKcs in non-homologous end joining to trim and process damaged ends of DNA double-strand breaks for ligation.

Synthesis-Dependent Strand Annealing (SDSA)

A mitotic homologous recombination mechanism that repairs double-strand breaks using an undamaged sister chromatid as a template without crossover products.

MRN Complex

A protein complex composed of Mre11, Rad50, and Nbs1 that binds broken ends of double-strand breaks and mediates $5'$ end trimming to expose single-stranded $3'$ overhangs.

Rad51

A recombinase protein that binds exposed single-stranded $3'$ DNA tails to form a nucleoprotein filament capable of searching for homology and performing strand invasion.

D-Loop (Displacement Loop)

A DNA structure formed during homologous recombination when an invading single-stranded $3'$ overhang displaces the homologous strand of an intact sister chromatid duplex.

SOS Response

An inducible emergency DNA damage-tolerance response in E. coli regulated by RecA filamentation at stalled forks that allows survival by upregulating error-prone bypass polymerases.

DNA Polymerase V ($\text{UmuD}'_2\text{C}$)

An error-prone, lesion-bypass DNA polymerase in E. coli lacking proofreading activity, induced by the SOS response to replicate past replication-blocking DNA lesions.

PCNA Monoubiquitination

A post-translational regulatory modification catalyzed by Rad6 on proliferating cell nuclear antigen that facilitates a switch from high-fidelity replicative polymerases to translesion bypass polymerases.

Xeroderma Pigmentosum (XP)

An autosomal recessive disorder caused by defective nucleotide excision repair proteins characterized by extreme UV sensitivity and a high incidence of early skin cancer and malignant melanoma.

Cockayne Syndrome

A genetic condition caused by mutations in the TC-NER proteins CSA or CSB where stalled RNA polymerases trigger apoptosis instead of repair, producing dwarfism, deafness, learning difficulties, and premature aging without increased cancer risk.

Mendel's Le Gene

The pea plant gene governing stem length (tall vs. dwarf); the recessive dwarf allele (le) carries a single base change ($\text{G} \rightarrow \text{A}$) causing an alanine-to-threonine substitution at position $229$ in a gibberellin synthesis enzyme.

Mendel's R Gene

The pea plant gene controlling seed shape (round vs. wrinkled); the recessive wrinkled allele (r) results from a transposon insertion interrupting the starch branching enzyme gene.

Mendel's A Gene

The pea plant gene controlling flower color (purple vs. white); the recessive white allele (a) contains a $\text{G} \rightarrow \text{A}$ splice-site mutation that produces a truncated bHLH transcription factor.

Mendel's I Gene

The stay-green (SGR) gene in peas that regulates cotyledon color; the recessive mutant allele (i) fails to degrade chlorophyll, resulting in persistent green cotyledons instead of yellow.