DNA Replication and Recombination

Comprehensive vocabulary flashcards covering the molecular mechanisms, enzymatic machinery, experiments, and structural features of bacterial and eukaryotic DNA replication and genetic recombination.

Nucleosome

A bead-like structure of chromatin consisting of DNA wrapped around an octamer core of eight histone proteins, producing a packing ratio of $10:1$.

Chromatin

The complex of DNA, histone proteins, and non-histone scaffold proteins that forms eukaryotic chromosomes.

Semiconservative Replication

A mode of DNA replication in which the two strands of the parental double helix separate, and each original strand serves as a template to direct the synthesis of a complementary new strand, yielding daughter duplexes composed of one old strand and one new strand.

Alternative Modes of DNA Replication

The three proposed hypothetical models of DNA duplication: conservative (parental duplex remains entirely intact while directing synthesis of an all-new duplex), semiconservative (each daughter duplex contains one old and one new strand), and dispersive (daughter duplexes consist of a patchwork of old and newly synthesized DNA fragments).

Meselson-Stahl Experiment

A 1958 experiment using $^{15}\text{N}$ (heavy) and $^{14}\text{N}$ (light) isotope labeling in E. coli with cesium chloride gradient centrifugation, proving experimentally that DNA replicates semiconservatively.

Taylor-Woods-Hughes Experiment

A 1957 study on the broad bean (Vicia faba) using radioactive $^3\text{H}\text{-thymidine}$ and autoradiography to demonstrate that eukaryotic chromosome replication is semiconservative.

Replication Fork

The Y-shaped region where the parental DNA double helix is locally unwound into two single template strands to permit bidirectional DNA synthesis.

Replicon

A unit of DNA replicated from a single origin of replication; in E. coli, it encompasses the entire circular genome of $4.6\,\text{million base pairs}$.

oriC

The specific bacterial origin of replication sequence in E. coli, measuring $245\,\text{base pairs}$ in length.

ter

The designated termination region on the circular bacterial chromosome where the two bidirectional replication forks converge and replication ceases.

DNA Helicase

An enzyme (encoded by dnaB in E. coli) that breaks hydrogen bonds between bases to unwind the parental double helix at the replication fork.

DNA Gyrase

A type II topoisomerase (composed of subunits encoded by gyrA and gyrB) that introduces double-stranded breaks and reseals DNA to relax positive supercoiling ahead of the replication fork.

Single-Stranded Binding Proteins (SSBPs)

Monomeric proteins encoded by the ssb gene that bind selectively to exposed single-stranded DNA to prevent the strands from prematurely re-annealing.

Primase

An RNA polymerase encoded by dnaG that synthesizes a short RNA primer complementary to the DNA template to provide a free $3'\text{-OH}$ group for DNA polymerase elongation.

Leading Strand

The newly synthesized DNA strand elongated continuously in the $5' \rightarrow 3'$ direction toward the advancing replication fork.

Lagging Strand

The newly synthesized DNA strand synthesized discontinuously in the $5' \rightarrow 3'$ direction away from the replication fork, forming Okazaki fragments.

Okazaki Fragments

Short discontinuous stretches of DNA synthesized on the lagging strand template (~$1000\text{--}2000\,\text{bp}$ in bacteria; ~$100\text{--}150\,\text{bp}$ in eukaryotes) discovered by Reiji and Tsuneko Okazaki.

DNA Ligase

An enzyme encoded by the lig gene that catalyzes phosphodiester bond formation between adjacent Okazaki fragments to seal nicks in the sugar-phosphate backbone.

DNA Polymerase I

A single-polypeptide enzyme ($928\,\text{amino acids}$, encoded by polA) present at $400\,\text{molecules/cell}$ possessing $5' \rightarrow 3'$ polymerase, $3' \rightarrow 5'$ exonuclease (proofreading), and unique $5' \rightarrow 3'$ exonuclease activity used to excise RNA primers and fill gaps.

DNA Polymerase III Holoenzyme

The primary multisubunit replicative complex in E. coli ($15\,\text{molecules/cell}$) that carries out the bulk of continuous and discontinuous elongation during chromosomal DNA replication.

$\alpha$ Subunit (Pol III)

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

$\epsilon$ Subunit (Pol III)

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

$\beta$ Subunit (Pol III)

The homodimeric sliding clamp subunit of the DNA Polymerase III holoenzyme that encircles DNA to serve as a processivity factor.

$\gamma$ Complex (Pol III)

A group of five subunits ($\gamma, \delta, \delta', \chi, \nu$) that acts as the sliding DNA clamp loader, placing the $\beta$ clamp onto the DNA template.

$\tau$ Subunit (Pol III)

The holoenzyme subunit that dimerizes two catalytic Pol III core enzyme complexes at the replication fork.

Proofreading

The enzymatic check performed by the $3' \rightarrow 5'$ exonuclease activity of replicative DNA polymerases, removing incorrectly paired bases and reducing error rates from $1\,\text{in}\,10^7$ to $1\,\text{in}\,10^9$.

Mismatch Repair

A post-replicative DNA repair process where specialized proteins scan newly synthesized double helices to identify, excise, and correct mispaired bases that escaped proofreading.

Excision Repair

A repair pathway where repair enzymes detect damaged bases, excise the damaged lesion, and DNA Polymerase I synthesizes replacement DNA.

Polymerase Switching

The eukaryotic process occurring during replication initiation where low-processivity DNA Polymerase $\alpha$ is replaced by high-processivity Polymerase $\delta$ on the lagging strand or Polymerase $\epsilon$ on the leading strand.

DNA Polymerase $\alpha$

A eukaryotic DNA polymerase that synthesizes RNA/DNA primers required to initiate DNA replication.

DNA Polymerase $\delta$

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

DNA Polymerase $\epsilon$

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

DNA Polymerase $\gamma$

The eukaryotic DNA polymerase dedicated to the replication and repair of mitochondrial DNA.

Telomeres

Repetitive tandem DNA sequences (such as $\text{TTAGGG}$ in humans and $\text{TTGGGG}$ in Tetrahymena) at the ends of linear eukaryotic chromosomes that preserve chromosomal integrity and solve the end-replication problem.

Telomerase

A ribonucleoprotein reverse transcriptase consisting of an RNA component (TERC) that acts as a template and a catalytic protein component (TERT) that extends the $3'$ G-rich overhang of chromosome ends.

Hayflick Limit

The finite number of cell divisions (~$40\text{--}60$ times) that normal human somatic cells can complete before entering cellular senescence due to telomere shortening.

Holliday Structure (chi form)

An X-shaped four-way DNA intermediate formed during homologous recombination after strand displacement, ligation, branch migration, and $180^\circ$ duplex rotation.

Branch Migration

The lateral movement of the crossover junction (cross bridge) along two homologous paired DNA duplexes during genetic recombination.