DNA Replication and Recombination

Vocabulary flashcards covering prokaryotic and eukaryotic DNA replication mechanisms, enzymes, key experiments, and homologous recombination.

Conservative Replication

A proposed model of DNA replication where the original double helix is completely conserved and two newly synthesized strands come together to form a second double helix.

Semiconservative Replication

The accepted model of DNA replication where each replicated DNA molecule consists of one original parental strand and one newly synthesized strand.

Dispersive Replication

A proposed model of DNA replication where parental strands are cleaved and dispersed into new double helices, producing a patchwork hybrid of old and new DNA in every strand.

Meselson-Stahl Experiment

A 1958 experiment using heavy ($^{15}\text{N}$) and light ($^{14}\text{N}$) nitrogen isotopes with equilibrium density gradient centrifugation in E. coli to prove that DNA replication is semiconservative.

Equilibrium Density Gradient Centrifugation

A method using a heavy salt solution spun in a centrifuge at high speeds to establish a density gradient that separates molecules based on density, such as heavy ($^{15}\text{N}$) and light ($^{14}\text{N}$) DNA.

Taylor-Woods-Hughes Experiment

A 1957 experiment using root tips of broad bean (Vicia faba) labeled with radioactive $^3\text{H}$-thymidine and autoradiography to demonstrate semiconservative DNA replication in eukaryotes.

Autoradiography

A technique that visualizes radioactively labeled molecules within cells or tissues by exposing radioisotope emissions on x-ray or photographic film.

Origin of Replication

A specific nucleotide sequence in a genome where DNA unwinding begins and replication is initiated.

Replication Fork

The Y-shaped region formed when the strands of a DNA double helix are unwound during active replication.

Replicon

The specific length of DNA replicated following a single initiation event at one origin of replication.

oriC

The single origin of replication site on the circular chromosome of E. coli.

Ter

The specific termination region on a bacterial chromosome where two migrating replication forks meet to end replication.

DNA Polymerase I

A bacterial enzyme that possesses $5'\rightarrow 3'$ polymerization, $3'\rightarrow 5'$ exonuclease proofreading, and $5'\rightarrow 3'$ exonuclease activity used to excise RNA primers and fill resulting DNA gaps.

DNA Polymerase II

A bacterial DNA polymerase involved in DNA repair and restarting replication after damaged DNA halts synthesis; possesses $5'\rightarrow 3'$ polymerization and $3'\rightarrow 5'$ exonuclease activity.

DNA Polymerase III

The primary bacterial holoenzyme responsible for $5'\rightarrow 3'$ elongation of the polynucleotide strand in vivo; possesses $3'\rightarrow 5'$ exonuclease activity for proofreading.

Fidelity

The overall accuracy with which a DNA polymerase replicates DNA, directly dependent on its proofreading capability.

Alpha Subunit ($\alpha$)

The core subunit of bacterial DNA Polymerase III responsible for catalytic $5'\rightarrow 3'$ polymerization.

Epsilon Subunit ($\epsilon$)

The core subunit of bacterial DNA Polymerase III responsible for $3'\rightarrow 5'$ exonuclease proofreading activity.

Theta Subunit ($\theta$)

The core subunit of bacterial DNA Polymerase III responsible for core assembly.

Beta Subunit ($\beta$)

The sliding clamp structure of DNA Polymerase III that acts as a processivity factor, preventing core enzyme dissociation from the template strand.

Gamma Complex ($\gamma$)

The sliding clamp loader complex of DNA Polymerase III responsible for loading the $\beta$ sliding clamp onto DNA at the primer-template junction.

Subunits of DNA Polymerase III Holoenzyme

The 10-subunit complex consisting of core subunits ($\alpha$, $\epsilon$, $\theta$), clamp loader complex ($\gamma$, $\delta$, $\delta'$, $\chi$, $\nu$), sliding clamp ($\beta$), and dimerization subunit ($\tau$).

DnaA

The initiator protein encoded by the dnaA gene that binds to oriC, destabilizes and opens the double helix, exposes single-stranded DNA, and recruits DNA helicase.

DNA Helicase

A hexameric protein composed of DnaB subunits in bacteria that unwinds the double helix by breaking hydrogen bonds using energy from ATP hydrolysis.

Single-Stranded Binding Proteins (SSBPs)

Proteins that bind specifically to single-stranded DNA to stabilize its open conformation and prevent secondary structure formation.

DNA Gyrase

A bacterial topoisomerase enzyme that relieves supercoiling torque ahead of the replication fork by making and resealing single- or double-stranded cuts in DNA.

Primase

An RNA polymerase recruited by helicase that synthesizes a short RNA primer ($10\text{--}12$ nucleotides) to supply the free 3'-OH required by DNA polymerase for elongation.

Leading Strand

The DNA strand synthesized continuously in the $5'\rightarrow 3'$ direction toward the replication fork, requiring only a single RNA primer.

Lagging Strand

The DNA strand synthesized discontinuously away from the replication fork in short Okazaki fragments, each requiring its own RNA primer.

Okazaki Fragments

Short segments of newly synthesized DNA produced discontinuously on the lagging strand that are later joined together.

DNA Ligase

An enzyme that seals nicks in the sugar-phosphate backbone by forming phosphodiester bonds between adjacent Okazaki fragments.

Tus-Ter Complex

A protein-DNA complex formed when Tus protein binds to Ter sites in E. coli, halting helicase movement and stalling the replication fork to terminate replication.

Autonomously Replicating Sequences (ARSs)

Eukaryotic origins of replication found in yeast ($250\text{--}400$ per genome) containing an 11-bp consensus sequence flanked by initiation elements.

Origin Recognition Complex (ORC)

A six-protein complex in eukaryotes that binds to origins of replication during early G1 phase, tagging them for initiation and ensuring DNA replicates only once per cell cycle.

DNA Polymerase Alpha ($\text{Pol } \alpha$)

A eukaryotic DNA polymerase with low processivity responsible for synthesizing RNA/DNA primers during replication initiation on leading and lagging strands.

DNA Polymerase Delta ($\text{Pol } \delta$)

A eukaryotic DNA polymerase responsible for lagging strand elongation, proofreading, repair, and recombination.

DNA Polymerase Epsilon ($\text{Pol } \epsilon$)

A eukaryotic DNA polymerase responsible for leading strand elongation, proofreading, repair, and recombination.

Polymerase Switching

The event in eukaryotic replication where low-processivity $\text{Pol } \alpha$ dissociates after primer synthesis and is replaced by $\text{Pol } \delta$ or $\text{Pol } \epsilon$ for high-speed elongation.

Chromatin Assembly Factors (CAFs)

Proteins that move along with the eukaryotic replication fork to assemble histones into nucleosomes immediately behind newly synthesized DNA.

Telomeres

Repetitive DNA sequences at the terminal ends of linear eukaryotic chromosomes that cap chromosome ends and protect them from degradation and improper double-strand break repair.

Telomerase

A ribonucleoprotein enzyme that uses an internal RNA template to extend the 3' end of telomeres, resolving the end-replication problem in germ and stem cells.

TERC

Telomerase RNA Component; the internal RNA molecule within telomerase that acts as the template for synthesizing telomeric DNA repeat sequences.

TERT

Telomerase Reverse Transcriptase; the catalytic protein subunit of telomerase that synthesizes DNA using an RNA template.

Homologous Recombination

The exchange of genetic material between two homologous double-stranded DNA molecules at equivalent positional sites.

Heteroduplex DNA

A hybrid double-stranded DNA region created during recombination containing one strand from each of two homologous chromosomes, held together by a bridge structure.

Branch Migration

The lateral movement of a DNA cross-bridge along homologous chromosomes during recombination, breaking and reforming hydrogen bonds to expand heteroduplex length.

Holliday Structure

An intermediate planar cross-shaped (chi form) structure formed during homologous recombination when crossed DNA duplexes bend prior to strand resolution.