DNA Replication: Models, Enzymes, and Telomere Maintenance

Criteria for Genetic Material

1) Store information, 2) Replicate, 3) Express information, 4) Allow variation by mutation.

Semiconservative Replication

The correct model of replication where each new DNA molecule contains one old (parental) strand and one newly synthesized strand.

Conservative Replication

An incorrect model where the original double helix remains intact and a completely new double helix is created.

Dispersive Replication

An incorrect model where both strands of both daughter molecules contain a mix/patchwork of old and new DNA.

Meselson & Stahl Experiment

Experiments that used heavy and light nitrogen isotopes to prove that DNA replicates semi-conservatively.

Replicon

A unit of DNA that is replicated; bacteria usually have one (the whole chromosome), while eukaryotes have many per chromosome.

Origin of Replication

The specific sequence/site on a chromosome where DNA replication begins.

oriC

The single origin of replication found in the E. coli (bacterial) chromosome.

Bidirectional Replication

Replication that proceeds in both directions from the origin, creating two replication forks moving away from each other.

Theta Replication

The mode of replication in circular bacterial chromosomes, named because the intermediate structure resembles the Greek letter theta.

DnaA (Initiator Protein)

Proteins that bind to the origin (oriC) and cause a short section of DNA to unwind, allowing helicase to load.

DNA Helicase

The enzyme that breaks hydrogen bonds to unwind the DNA helix; it requires ATP.

Single-Stranded DNA-Binding Proteins (SSBs)

Proteins that bind to the exposed single strands of DNA to keep them open and prevent hairpins (secondary structures) from forming.

DNA Gyrase

A Topoisomerase II enzyme in bacteria that relieves the supercoiling/torque ahead of the replication fork by making double-strand breaks; requires ATP.

Topoisomerase I

An enzyme that makes single-strand breaks to relieve supercoiling; does not require ATP.

DNA Primase

An enzyme that synthesizes short RNA primers (10-60 nucleotides) to provide a 3'-OH group for DNA polymerase to start synthesis.

RNA Primer

A short segment of RNA complementary to the DNA template, required because DNA polymerase cannot start from scratch.

3'-OH Group

The chemical group required at the end of a strand for DNA polymerase to add a new nucleotide.

DNA Polymerase III

The main replication enzyme in E. coli; it is a holoenzyme that elongates DNA (5' to 3') and proofreads (3' to 5').

Holoenzyme

A complex enzyme made up of multiple subunits (e.g., DNA Pol III).

Beta Clamp (Sliding Clamp)

A subunit of DNA Polymerase III that forms a ring around the DNA, keeping the polymerase attached for long stretches of synthesis.

5' to 3' Polymerase Activity

The direction in which DNA polymerase synthesizes a new strand (adding bases to the 3' end).

3' to 5' Exonuclease Activity

The "proofreading" ability of DNA polymerases to move backward and remove an incorrectly inserted nucleotide.

5' to 3' Exonuclease Activity

The ability to remove nucleotides in the forward direction (specifically used by Pol I to remove RNA primers); unique to DNA Pol I.

DNA Polymerase I

The bacterial enzyme that removes RNA primers (5' to 3' exonuclease) and fills the gap with DNA (5' to 3' polymerase).

Leading Strand

The strand synthesized continuously in the same direction that the replication fork is moving.

Lagging Strand

The strand synthesized discontinuously (in short bursts) in the opposite direction of the replication fork.

Okazaki Fragments

Short DNA fragments produced on the lagging strand.

DNA Ligase

The enzyme that seals the "nick" (phosphodiester bond break) in the sugar-phosphate backbone between Okazaki fragments.

Trombone Model

The model where the lagging strand template loops out so that the two core enzymes of the DNA Pol III dimer can move in the same physical direction.

Replication Licensing Factor (RLF)

Proteins in eukaryotes that mark origins during G1 to ensure each origin fires only once per cell cycle (prevents re-replication).

Nucleosomes

Eukaryotic DNA packaging units (histones) that must disassemble before the replication fork and reassemble quickly behind it.

DNA Polymerase Alpha

Eukaryotic polymerase that initiates synthesis and possesses primase activity.

DNA Polymerase Delta

Eukaryotic polymerase responsible for synthesizing the lagging strand.

DNA Polymerase Epsilon

Eukaryotic polymerase responsible for synthesizing the leading strand.

RNAse H

The eukaryotic enzyme responsible for degrading RNA primers (similar function to Pol I's exonuclease in bacteria).

The "End Problem"

The issue in linear chromosomes where the removal of the last RNA primer at the 5' end of the lagging strand leaves a gap that cannot be filled.

Telomeres

Repetitive DNA sequences (e.g., TTAGGG in vertebrates) at the ends of eukaryotic chromosomes that protect them from degradation.

G-Rich Overhang

The single-stranded extension at the very end of the telomere (3' end) that folds back to form a protective loop.

Telomerase

A ribonucleoprotein enzyme that extends telomeres; it uses an internal RNA template to add DNA repeats to the chromosome end.

Reverse Transcription

The process of making DNA from an RNA template; this is the catalytic activity of telomerase.

Senescence

A state of permanent cell cycle arrest (aging) that occurs when telomeres become too short.

Werner Syndrome

A premature aging disorder caused by a mutation in the WRN gene (RecQ helicase), leading to defective telomere maintenance.

Dolly the Sheep

The first cloned mammal (from a somatic cell); she had shorter telomeres and showed signs of premature aging (arthritis, lung disease).

Cancer Cells

Cells that often reactivate telomerase to maintain telomere length, allowing them to divide indefinitely (immortality).