DNA Replication - Vocabulary Review

Vocabulary flashcards covering the major terms and concepts from the DNA replication lecture notes.

DNA

The double-stranded genetic material composed of four nucleotides (A, T, C, G) held together by base pairing; stores hereditary information and serves as the template for replication.

DNA Replication

The process that copies the genome to produce two identical DNA duplexes; it is semiconservative and bidirectional.

Chromosome

A DNA-containing structure that is replicated to yield two identical duplexes, each containing one parental strand and one newly synthesized daughter strand.

Free nucleotides

Individual nucleotide substrates that are added to growing DNA chains during replication.

DNA polymerase

Enzymes that synthesize new DNA by adding nucleotides in the 5′ to 3′ direction; key players in replication (e.g., Pol III and Pol I in bacteria).

Adenine

A purine base in DNA that pairs with thymine via two hydrogen bonds.

Thymine

A pyrimidine base in DNA that pairs with adenine via two hydrogen bonds.

Cytosine

A pyrimidine base in DNA that pairs with guanine via three hydrogen bonds.

Guanine

A purine base in DNA that pairs with cytosine via three hydrogen bonds.

Replication fork

The Y-shaped region where the DNA double helix is unwound and replication occurs.

Helicase

Enzyme that unwinds the DNA double helix by breaking hydrogen bonds between bases.

Leading strand

The DNA strand synthesized continuously toward the replication fork in the 5′ to 3′ direction.

Lagging strand

The DNA strand synthesized discontinuously away from the replication fork as Okazaki fragments.

Origin of replication

A specific DNA sequence where replication begins; bacteria typically have a single origin, while eukaryotes have multiple origins.

OriC

The origin of replication in E. coli; about 245 base pairs, AT-rich, containing three 13-mer sequences and four 9-mer sequences.

Semiconservative replication

Each new DNA duplex contains one parental strand and one newly synthesized strand.

Bidirectional replication

Replication that proceeds in both directions from an origin, forming a replication bubble with two forks.

Meselson-Stahl experiment

A classic 1958 experiment using 15N and 14N to test DNA replication models; results supported semiconservative replication.

DnaA

Bacterial initiator protein that binds the 9-mer origin sequences and helps start replication at oriC.

DnaB

Helicase that unwinds DNA at the origin; moved to the fork by DnaC.

DnaC

Helicase loader that delivers DnaB helicase to the origin to initiate unwinding.

Primase (DnaG)

RNA polymerase that synthesizes RNA primers to provide starting points for DNA synthesis and helps assemble the primosome.

RNA primer

Short RNA sequence that provides the 3′-OH for DNA polymerases to begin synthesis.

DNA polymerase III

Main bacterial DNA polymerase that elongates new DNA strands; highly processive and part of the holoenzyme at the replisome.

DNA polymerase I

Bacterial polymerase that removes RNA primers and fills in gaps with DNA; has 5′–3′ exonuclease activity.

Okazaki fragment

Short DNA segments synthesized on the lagging strand, later joined by DNA ligase.

DNA ligase

Enzyme that joins Okazaki fragments by sealing the remaining nicks in the sugar-phosphate backbone.

Single-stranded binding protein (SSB)

Protein that stabilizes single-stranded DNA to prevent reannealing during replication.

Topoisomerase

Enzyme that relieves DNA supercoiling by cutting and rejoining DNA strands during replication.

Tau protein

Part of the bacterial clamp-loading system; tethers two DNA polymerase III cores in the replisome.

Replisome

The multi‑protein complex at a replication fork that carries out DNA synthesis, including DNA Pol III and associated factors.

Clamp loader (RFC)

Complex that loads sliding clamps onto DNA to increase polymerase processivity; in bacteria the analogous system involves the beta clamp and related factors.

Sliding clamp

Protein ring that encircles DNA and tethers DNA polymerase to the template to enhance processivity (beta clamp in bacteria; PCNA in eukaryotes).

PCNA

Proliferating Cell Nuclear Antigen; the sliding clamp used in eukaryotic DNA replication.

Tau protein (relevant to replication)**

See Tau protein above; serves to coordinate two polymerase cores at the replication fork.

Autonomously replicating sequence (ARS)

Eukaryotic origin of replication in yeast; recognized as a replication initiation site; characteristic ARS elements determine origin activity.

Telomeres

Repetitive DNA sequences at the ends of linear chromosomes that protect gene-rich regions from erosion during replication.

Telomerase

Ribonucleoprotein enzyme that extends telomeres using an RNA template; maintains telomere length in germ cells and some stem cells.

End replication problem

Problem that lagging-strand primer removal creates a shortened chromosome end; telomeres and telomerase help solve it.

Replication bubble

Expanded region of DNA created as replication proceeds from an origin in both directions, containing two replication forks.

Pulse-chase labeling

Experiment showing bidirectional replication by tracking incorporation of radioactive labels over time; symmetry around origins indicates bidirectional movement.