Genetics: Linkage, DNA Replication, Repair, Bacterial Genetics, and Transcription

Vocabulary practice flashcards covering genetic linkage, three-point mapping, chi-square linkage tests, DNA history, replication, bacterial gene transfer, DNA repair pathways, and eukaryotic transcription/gene expression.

Gene Linkage

The tendency of two or more genes located close together on the same chromosome to be inherited together during gamete formation rather than assorting independently.

Recombination (Crossing-Over)

The breakage and reciprocal exchange of genetic material between homologous chromatids during Prophase I of meiosis, producing non-parental allele combinations.

Recombination Frequency (RF)

The proportion of recombinant progeny relative to total progeny, where a $1\%$ recombination frequency is defined as $1\text{ map unit (m.u.)}$, representing the physical distance between linked loci.

Genetic Marker

A detectable gene, allele, or natural DNA sequence polymorphism (such as eye color mutations in flies or DNA variations in humans) used to identify and map the chromosomal position of specific loci.

Double Crossover (DCO)

The rarest phenotypic class observed in a three-point test cross, occurring when two separate crossover events take place between three linked markers simultaneously, which identifies the middle gene.

Chi-Square ($\chi^2$) Test for Linkage

A statistical test that evaluates whether observed phenotypic offspring counts deviate significantly from expected Mendelian ratios under the null hypothesis of independent assortment ($\text{unlinked}$ genes).

Griffith's Transforming Principle (1928)

The phenomenon demonstrated by Frederick Griffith wherein heat-killed pathogenic $S\text{ strain}$ bacteria transfer genetic material into live nonpathogenic $R\text{ strain}$ bacteria, transforming them into virulent pathogens.

Hershey-Chase Experiment (1952)

An experiment using bacteriophages labeled with radioactive $^{32}\text{P}$ for nucleic acids and $^{35}\text{S}$ for proteins, demonstrating that injected DNA, and not the viral protein coat, constitutes the genetic material.

Chargaff's Rules (1950)

Empirical rules stating that while DNA base composition varies between species, within any given species, the concentration of adenine equals thymine ($\%A = \%T$) and guanine equals cytosine ($\%G = \%C$).

Antiparallel Strands

The arrangement of the two complementary strands in a DNA double helix, where one strand runs in the $5' \rightarrow 3'$ direction and the other runs opposite in the $3' \rightarrow 5'$ direction.

Semiconservative Replication

The mechanism confirmed by Meselson and Stahl (1958) using $^{15}\text{N}$ and $^{14}\text{N}$ density gradient centrifugation, where each newly synthesized DNA molecule retains one intact parental strand and one newly assembled daughter strand.

Okazaki Fragments

Short segments of newly synthesized DNA formed discontinuously along the lagging strand during replication, measuring roughly $1000\text{--}2000\text{ nucleotides}$ in prokaryotes and $100\text{--}200\text{ nucleotides}$ in eukaryotes.

Auxotroph

A mutant microorganism that has lost the ability to synthesize an essential organic compound (e.g., $phe^-$ cannot synthesize phenylalanine) and requires it as a supplement to survive on minimal media.

Prototroph

A wild-type bacterium designated with a plus superscript (e.g., $phe^+$) capable of synthesizing all required organic nutrients independently from minimal medium ($MM$).

Replica Plating

A microbiological technique that uses a velvet-covered disk to transfer identical colony patterns from a master plate to various supplemented agar plates to detect auxotrophic mutants.

Bacterial Conjugation

The unidirectional transfer of genetic material between bacteria occurring via direct cell-to-cell contact mediated by hollow protein tubes called pili.

Fertility Factor ($F\text{ Factor}$)

An extrachromosomal circular DNA plasmid containing genes for pilus assembly (including $tra$ genes) that enables a donor $F^+$ bacterium to conjugate and transfer plasmid DNA to an $F^-$ recipient.

Streptomycin Resistance ($Str^R$)

A genetic condition caused by a mutation in a protein of the bacterial $30\text{S}$ ribosomal subunit that blocks streptomycin binding, allowing continued protein synthesis in the presence of the antibiotic.

DNA Polymerase Proofreading

The intrinsic $3' \rightarrow 5'$ exonuclease activity of DNA polymerases that excises incorrectly paired nucleotides during replication, improving fidelity from an error rate of $1\text{ in }10{,}000$ to $1\text{ in }10{,}000{,}000\text{ bases}$.

Photolyase

An ancient, light-dependent DNA repair enzyme found in plants and bacteria that directly reverses UV-induced pyrimidine (thymine) dimers without using a template strand; non-functional in humans.

DNA Mismatch Repair (MMR)

A post-replication excision-repair pathway that corrects mispaired nucleotides missed by polymerase proofreading, lowering the net DNA replication error rate to approximately $1\text{ in }10\text{ billion bases}$.

Strand Discrimination (MMR)

The mechanism identifying which DNA strand carries the error during mismatch repair, relying on unmethylated adenines in $\text{GATC}$ sites cut by $MutH$ in E. coli, or transient single-strand nicks in eukaryotes.

Non-Homologous End Joining (NHEJ)

A direct, error-prone DNA repair pathway that rejoins double-strand DNA breaks without using a homologous chromosome template, frequently leading to insertion or deletion mutations.

Homologous Recombination (HR) Repair

A high-fidelity double-strand break repair mechanism that uses an intact homologous chromosome or sister chromatid sequence as a template to accurately resynthesize damaged DNA.

Ribozyme

An RNA molecule possessing enzymatic catalytic activity, the discovery of which earned Sidney Altman and Thomas Cech the 1989 Nobel Prize in Chemistry.

RNA World Hypothesis

The evolutionary hypothesis proposing that RNA was the primordial genetic and functional material on Earth because it can simultaneously store genetic information and catalyze biochemical reactions.

Promoter

A regulatory DNA region located upstream ($5'$) of the transcription start site ($+1$) where general transcription factors and RNA polymerase bind to initiate transcription.

TATA Box

An ancient, highly conserved promoter consensus sequence ($\text{TATAAAA}$) found in prokaryotes, archaea, and eukaryotes that binds TATA-binding protein to orient RNA polymerase II at the exact start site.

Transcription Factors

Proteins that bind to specific promoter or enhancer motifs to modulate and regulate the recruitment of RNA polymerase and the transcription rate of target genes.

Operon

A prokaryotic genetic regulatory unit discovered by François Jacob and Jacques Monod consisting of multiple co-regulated, functional genes controlled coordinately by a single promoter.

5' Cap (7-Methylguanylate)

A modified guanine residue linked to the $5'$ end of eukaryotic pre-mRNA through an unconventional $5' \rightarrow 5'$ triphosphate bridge, protecting the nascent transcript from exonuclease digestion.

Poly(A) Tail

A stretch of $100\text{--}200$ adenine nucleotides added to the cleaved $3'$ end of eukaryotic pre-mRNA by poly(A) polymerase following cleavage $10\text{--}36\text{ nucleotides}$ downstream of the $\text{AAUAAA}$ recognition motif.

RNA Splicing

The post-transcriptional process within the eukaryotic nucleus wherein non-coding intervening sequences (introns) are excised from primary transcripts and coding regions (exons) are joined together.

Untranslated Region (UTR)

Transcribed sequences located at the $5'$ ($5'\text{ UTR}$) and $3'$ ($3'\text{ UTR}$) ends of mature mRNA that are not translated into amino acids but govern transcript stability, localization, and translational control.

Enhancer

A cis-acting regulatory DNA sequence that can be located far from a gene's promoter and binds specific transcription factors to dramatically increase transcription efficiency (e.g., the $ZRS$ limb enhancer).