DNA Replication and Recombination

Vocabulary flashcards covering the mechanisms, models, enzymes, and fidelity of bacterial and eukaryotic DNA replication as well as homologous recombination.

Semiconservative replication

The mechanism of DNA replication in which each newly formed DNA molecule consists of one original parental strand and one newly synthesized strand.

Equilibrium density gradient centrifugation

A technique used by Meselson and Stahl that separates molecules based on density using a heavy salt solution spun at high speeds for several days, distinguishing $^{15}\text{N}$-labeled DNA from $^{14}\text{N}$-labeled DNA.

Theta replication

A mode of circular DNA replication, demonstrated by John Cairns, where unwinding at a single origin generates a replication bubble and fork(s) resembling the Greek letter $\theta$, ultimately yielding two circular DNA molecules.

Rolling-circle replication

A specialized replication mechanism found in some bacteriophages and the F plasmid initiated by a break in one nucleotide strand, using the intact inner strand as a template to displace the broken strand and produce multiple circular DNA molecules.

Linear eukaryotic replication

Replication in eukaryotic linear chromosomes initiated bidirectionally at multiple origins occurring every $20{,}000$ to $300{,}000$ base pairs, ending when adjacent replication bubbles fuse to form two linear DNA molecules.

Replicon

An individual unit of DNA replication containing an origin of replication; theta and rolling-circle models utilize a single replicon, whereas linear eukaryotic chromosomes contain many replicons.

Deoxyribonucleoside triphosphate (dNTP)

The nucleotide monomer building block whose $5'\text{-phosphate}$ group is attacked by the $3'\text{-OH}$ group of an existing DNA strand; cleavage of two phosphates provides the energy needed to form a phosphodiester bond.

Leading strand

The DNA strand that undergoes continuous synthesis in the $5' \rightarrow 3'$ direction, proceeding in the same direction as replication fork unwinding and requiring only a single initial primer.

Lagging strand

The DNA strand synthesized discontinuously in short stretches in the direction opposite to replication fork movement, requiring a new primer at the beginning of each fragment.

Okazaki fragments

The short segments of DNA produced by discontinuous synthesis along the lagging-strand template during replication.

Initiator protein (DnaA)

A bacterial protein that binds to the origin of replication ($\text{oriC}$) and causes a short stretch of DNA to unwind, allowing helicase and other single-strand-binding proteins to attach.

DNA helicase

An enzyme that breaks hydrogen bonds between nucleotide strands at the replication fork, binding to the lagging-strand template in bacterial cells and translocating in the $5' \rightarrow 3'$ direction.

Single-strand-binding (SSB) proteins

Proteins that attach to exposed single-stranded DNA to stabilize it and prevent secondary structures (such as hairpins) from forming during unwinding.

DNA gyrase

A bacterial topoisomerase that moves ahead of the replication fork, cleaving and resealing double-helical DNA to relieve torsional strain and torque created by unwinding.

DNA primase

An RNA polymerase enzyme that synthesizes a short RNA primer to provide an initial free $3'\text{-OH}$ group required for DNA polymerases to attach DNA nucleotides.

DNA polymerase III

The primary bacterial replication enzyme in E. coli that possesses $5' \rightarrow 3'$ polymerase activity and $3' \rightarrow 5'$ exonuclease activity to elongate new nucleotide strands with high processivity.

DNA polymerase I

A bacterial DNA polymerase with $5' \rightarrow 3'$ polymerase, $3' \rightarrow 5'$ exonuclease, and unique $5' \rightarrow 3'$ exonuclease activity, which allows it to remove RNA primers and replace them with DNA nucleotides.

DNA ligase

An enzyme that seals nicks in the sugar-phosphate backbone by forming a phosphodiester bond between the $5'\text{-phosphate}$ of one nucleotide and the adjacent $3'\text{-OH}$ of another, joining Okazaki fragments.

Replication licensing factor

A eukaryotic cell cycle protein that marks origin of replication sites to ensure that DNA replication initiates precisely once per cell cycle.

DNA polymerase $\alpha$ (alpha)

A eukaryotic DNA polymerase that possesses primase activity and functions in the initiation of nuclear DNA synthesis as well as DNA repair.

DNA polymerase $\delta$ (delta)

A eukaryotic DNA polymerase possessing $5' \rightarrow 3'$ polymerase and $3' \rightarrow 5'$ exonuclease activities that completes lagging-strand synthesis of nuclear DNA, DNA repair, and translesion DNA synthesis.

DNA polymerase $\epsilon$ (epsilon)

A eukaryotic nuclear DNA polymerase with $5' \rightarrow 3'$ polymerase and $3' \rightarrow 5'$ exonuclease activities that carries out leading-strand synthesis.

DNA polymerase $\gamma$ (gamma)

A eukaryotic DNA polymerase with $5' \rightarrow 3'$ polymerase and $3' \rightarrow 5'$ exonuclease activities dedicated to the replication and repair of mitochondrial DNA.

Telomerase

A ribonucleoprotein enzyme that provides an internal RNA template complementary to G-rich telomeric repeats to extend the $3'$ protruding ends of linear eukaryotic chromosomes, preventing end-shortening.

Holliday junction

A cross-shaped intermediate structure formed during homologous recombination when single strands from homologous DNA duplexes break, cross over, and join the opposite duplex.

Branch migration

The lateral movement of a Holliday junction along homologous DNA molecules as two nucleotide strands exchange positions, extending the region of heteroduplex DNA.

Heteroduplex DNA

A double-stranded DNA molecule formed during homologous recombination that contains nucleotide strands originating from two distinct homologous chromosomes.