DNA Replication Mechanisms and Replisome Dynamics in E. coli

Vocabulary practice flashcards covering DNA replication machinery, replisome components, supercoiling topology, fidelity mechanisms in E. coli, and sequence tracing applications.

DNA Polymerase

An enzyme involved in DNA replication that links nucleotides together to synthesize a new DNA polymer.

DNA Polymerase III Core

The catalytic portion of DNA Polymerase III in E. coli that synthesizes DNA by adding deoxynucleotides to the 3'-OH end of a pre-existing primer strand.

Replication Bubble

An unwound region of duplex DNA formed at the origin of replication that expands bidirectionally as new nascent DNA is synthesized.

Helicase

An enzyme that converts energy from ATP hydrolysis into physical work to denature duplex DNA, binding to a single strand and moving in the 5' to 3' direction.

Single-Strand Binding Protein (SSB)

A protein that binds to and protects single-stranded DNA exposed during replication fork progression.

Linking Number ($Lk$)

The total topological winding number of a closed-circular or anchored DNA duplex, given by the formula $Lk = Tw + Wr$, where $Tw$ is twist and $Wr$ is writhe.

DNA Gyrase

A Type II topoisomerase in E. coli that hydrolyzes ATP to cut both strands of duplex DNA and pass an adjacent duplex through, reducing writhe ($Wr$) and linking number ($Lk$) by $2$ to relieve positive supercoils ahead of the replication fork.

Type I Topoisomerase

An enzyme that cleaves one strand of a DNA duplex and ligates it around the partner strand without ATP hydrolysis, altering the linking number ($Lk$) by $1$.

Primase

An RNA polymerase that synthesizes short RNA primers ($< 20$ residues) on a single-stranded DNA template to provide a starting 3'-OH group for DNA polymerase.

Primosome

A functional complex formed by primase physically bound to helicase at the replication fork.

Sliding Clamp

A ring-shaped protein dimer composed of two copies of the DNA Polymerase III $\beta$ subunit that encircles duplex DNA to tether the core polymerase to the template, dramatically increasing processivity.

Clamp Loader

An enzyme complex that uses ATP hydrolysis energy to open the sliding clamp ring and assemble it onto a primer-template duplex.

Leading Strand

The nascent DNA strand synthesized continuously in the 5' to 3' direction toward the unwinding replication fork.

Lagging Strand

The nascent DNA strand synthesized discontinuously in the 5' to 3' direction away from the replication fork as a series of Okazaki fragments.

$\tau$ Subunit (Tether)

A component of DNA Polymerase III consisting of two $\tau$ subunits that links both core polymerases to helicase to coordinate synchronized progress at the replication fork.

DNA Polymerase I (DNAP I)

A multifunctional repair polymerase possessing 5'-to-3' polymerization, 3'-to-5' proofreading exonuclease, and 5'-to-3' primer-removal exonuclease domains.

DNA Ligase

An enzyme that joins nicks in the phosphodiester backbone between adjacent Okazaki fragments using energy from ATP or $\text{NAD}^+$ hydrolysis.

Processivity

The ability of a DNA polymerase to catalyze consecutive nucleotide additions without falling off the template strand.

Fidelity

The accuracy of DNA replication, represented by a low rate of nucleotide misincorporation during synthesis.

Proofreading

A 3'-to-5' exonuclease activity in replication polymerases that removes mismatched terminal nucleotides from the 3' end of the nascent strand prior to continued extension.

Klenow Fragment

A proteolytic cleavage product of DNA Polymerase I that retains 5'-to-3' polymerization and 3'-to-5' proofreading exonuclease activities but lacks the 5'-to-3' primer-removal exonuclease domain.

Woolly Dog

An extinct dog breed kept by Coast Salish peoples whose woolly hair was utilized alongside mountain goat fibers to weave traditional blankets (~1830s), as demonstrated by genetic and proteomic sequencing.