Chapter 3: DNA Replication

Comprehensive vocabulary flashcards covering the molecular mechanisms of prokaryotic and eukaryotic DNA replication, including replication models, polymerases, initiation, elongation, lagging strand processing, telomere maintenance, and nucleosome assembly.

Conservative Model

A proposed model of DNA replication in which one daughter cell inherits a chromosome consisting entirely of old parental DNA and the other daughter cell inherits a chromosome of entirely newly synthesized DNA.

Dispersive Model

A proposed model of DNA replication where parental double-stranded DNA fragments and replicates, mixing and matching to form a mosaic of old and new regions in both daughter cells.

Semi-conservative Model

The confirmed mechanism of DNA replication in which the parental double-stranded DNA separates and each daughter cell receives one parental strand and one newly replicated strand.

Meselson-Stahl Experiment

A 1958 experiment that grew E. coli in $^{15}\text{N}$ and transferred them to $^{14}\text{N}$; after 1 replication cycle, DNA had an intermediate density band, and after 2 cycles showed two distinct bands (one intermediate and one fully $^{14}\text{N}$), supporting the semi-conservative model.

Taylor, Woods, and Hughes Experiment

An experiment conducted with the root tip of Vicia faba using radioactive thymidine; in the second generation of cell division, one chromatid per chromosome was labeled and one was normal, demonstrating semi-conservative chromosome replication in eukaryotes.

DNA Polymerase I

An E. coli enzyme discovered by Arthur Kornberg in 1955 (originally called the Kornberg enzyme) that removes RNA primers via $5' \rightarrow 3'$ exonuclease activity and replaces them with DNA, while also containing $3' \rightarrow 5'$ exonuclease proofreading capability.

dNTP (Deoxyribonucleoside Triphosphate)

High-energy nucleotide precursors (dATP, dTTP, dGTP, and dCTP) attached to the $3'\text{-OH}$ group of a growing DNA chain; cleavage of two of their three phosphate groups ($\text{P-P}$) releases the energy required to catalyze phosphodiester bond formation.

DNA Polymerase Chain Elongation

The enzymatic addition of an incoming dNTP from its $5'\text{-phosphate}$ group to the free $3'\text{-OH}$ group of a preexisting polynucleotide chain, requiring magnesium ions ($\text{Mg}^{2+}$) and synthesizing exclusively in the $5' \rightarrow 3'$ direction.

$3' \rightarrow 5'$ Exonuclease Activity

A proofreading mechanism found in DNA Polymerases I and III where mispaired terminal nucleotides are recognized, excised, and replaced before forward DNA synthesis resumes, drastically reducing errors.

$5' \rightarrow 3'$ Exonuclease Activity

An enzymatic activity unique to DNA Polymerase I that removes nucleotides from the $5'$ end of a DNA strand or degrades an RNA primer ahead of the enzyme during primer replacement.

DNA Polymerase III

The primary enzyme complex responsible for synthesizing the leading and lagging DNA strands in E. coli; it consists of a core of 3 polypeptides and a complete functional holoenzyme containing 6 additional polypeptides.

Origin of Replication (oriC)

A $245\text{ bp}$ region in E. coli where replication begins; it contains four $9\text{ bp}$ binding sites and three $13\text{ bp}$ AT-rich sequences that denature to form a replication bubble.

DnaA (Initiator Protein)

An initiator protein encoded by the dnaA gene in E. coli that binds to the $9\text{ bp}$ consensus repeats of oriC and denatures the adjacent $13\text{ bp}$ AT-rich sequences to allow replication fork assembly.

DNA Helicase (DnaB)

An enzyme loaded onto DNA that untwists the double helix bidirectionally from the origin by breaking hydrogen bonds between base pairs, powered by ATP hydrolysis.

DNA Primase

An enzyme that binds to DNA helicase to form a primosome and synthesizes short $5\text{--}10\text{ nucleotide}$ RNA primers complementary to the template strand to provide a free $3'\text{-OH}$ group for DNA Polymerase III.

Primosome

A protein complex formed by the physical association of DNA helicase and DNA primase at the replication fork.

SSB (Single-Stranded Binding) Proteins

Proteins that bind to exposed single strands of template DNA to stabilize them and prevent them from reannealing or reforming a double strand.

DNA Gyrase

A topoisomerase in E. coli that relieves torsional tension ahead of the moving replication fork by introducing negative supercoils to counteract positive supercoiling.

Leading Strand

The continuously replicated DNA strand that is extended by DNA Polymerase III in the $5' \rightarrow 3'$ direction toward the replication fork, requiring only a single RNA primer.

Lagging Strand

The discontinuously replicated DNA strand synthesized in short segments in the $5' \rightarrow 3'$ direction away from the replication fork, requiring repeated RNA priming.

Okazaki Fragments

Short stretches of newly synthesized DNA formed discontinuously on the lagging strand that are later joined together into a continuous strand.

DNA Ligase

An enzyme that seals single-stranded nicks in the phosphodiester backbone between adjacent Okazaki fragments after RNA primers have been replaced by DNA Polymerase I.

Joining of Okazaki Fragments

The multistep maturation process on the lagging strand where DNA Polymerase III dissociates, DNA Polymerase I removes the RNA primer and fills the gap with DNA, and DNA ligase seals the remaining single-stranded nick.

Replisome

A complex macromolecular assembly of key replication proteins that loops the lagging strand over the helicase to keep DNA Polymerase III adjacent to each new Okazaki fragment site for coordinated synthesis.

Rolling Circle Replication

A specialized replication mechanism used by plasmids and circular viral chromosomes (such as bacteriophage $\lambda$) where a nick in the positive strand initiates continuous synthesis at the $3'$ end, displacing the $5'$ end to produce linear multimeric DNA.

Replicon

A unit of chromosomal DNA replicated from a single origin of replication; eukaryotic chromosomes possess multiple replicons to ensure the entire genome is replicated in a timely manner.

Temporal Ordering of Replication Initiation

The programmed activation of replication units along eukaryotic chromosomes over time throughout S phase, where individual origins initiate bidirectionally at different time points rather than simultaneously.

ARSs (Autonomously Replicating Sequences)

Conserved origin DNA sequences in yeast that initiate eukaryotic DNA replication by recruiting the initiator complex.

ORC (Origin Recognition Complex)

A multi-protein complex that acts as the initiator protein in eukaryotes by binding to replicators (such as ARSs) during the G1 phase of the cell cycle.

Licensing Factors

Proteins synthesized in G1 that bind to the ORC to assemble the pre-replicative complex (pre-RC) and load helicase, ensuring that each origin initiates replication only once per cell cycle before being inactivated by CDK phosphorylation.

Pol $\alpha$ (alpha) / Primase

A eukaryotic enzyme complex that initiates new strands by synthesizing a hybrid RNA/DNA primer composed of approximately $10\text{ nt}$ of RNA followed by $10\text{--}20\text{ nt}$ of DNA.

Pol $\varepsilon$ (epsilon)

A major eukaryotic replicative DNA polymerase responsible for synthesizing the continuous leading strand from the hybrid primer.

Pol $\delta$ (delta)

A major eukaryotic replicative DNA polymerase responsible for synthesizing the discontinuous lagging strand and extending Okazaki fragments until it displaces the downstream RNA/DNA primer.

FEN1 (Flap Endonuclease 1)

A eukaryotic nuclease that cleaves and removes the single-stranded RNA/DNA flap generated when Pol $\delta$ displaces the preceding primer during Okazaki fragment maturation.

DNA2

A eukaryotic nuclease/helicase recruited when a displaced primer flap is too long, shortening the flap sequence so that FEN1 can complete its removal.

End-Replication Problem

The dilemma encountered at the extreme ends of linear eukaryotic chromosomes where removal of the terminal RNA primer leaves an unreplicated single-stranded gap at the $5'$ end of the new strand, threatening chromosome shortening with each cell cycle.

Telomerase

A ribonucleoprotein reverse transcriptase (TERT) containing an integral RNA molecule that elongates the $3'$ overhang of chromosome ends by adding species-specific tandem telomere repeat sequences without using genomic DNA templates.

Nucleosome Assembly

The post-replicative packaging of newly synthesized DNA into chromatin, beginning with the binding of an $H3\text{-}H4$ tetramer to the daughter duplex, followed by the histone chaperone-assisted addition of two $H2A\text{-}H2B$ dimers.