DNA Replication - Key Terms (Lecture Notes)

Vocabulary flashcards covering key terms and definitions from the DNA replication lecture notes.

DNA

Double-stranded molecule of nucleotides with a sugar–phosphate backbone and base pairs A–T and G–C; antiparallel strands.

Nucleotide

Basic unit of DNA consisting of a sugar (deoxyribose), a phosphate group, and a nitrogenous base.

Base pairing rules

Adenine pairs with thymine (2 hydrogen bonds); guanine pairs with cytosine (3 hydrogen bonds).

DNA replication

Process that copies the entire genome to produce two identical DNA molecules.

DNA synthesis

General polymerization of nucleotides into a polynucleotide; not necessarily genome-wide replication.

Origin of replication (ori)

DNA region where replication begins; often AT-rich to ease strand separation.

oriC (in E. coli)

Bacterial origin of replication containing multiple DnaA boxes; ~245 bp long.

DnaA

Initiator protein that binds 9 bp repeats and uses ATP to melt the origin DNA.

DnaC

Loader protein that delivers the DnaB helicase to the replication origin.

DnaB helicase

Enzyme that unwinds the DNA duplex to create replication forks.

DnaG primase

RNA polymerase that synthesizes short RNA primers (~10 nt) at the fork.

Primosome

Complex including primase and helicase assembled at the replication fork.

Single-stranded binding protein (SSB)

Protein that binds exposed ssDNA to prevent reannealing; forms a tetramer and binds cooperatively.

DNA polymerase III holoenzyme

Main bacterial replicative polymerase; multi-subunit complex with high processivity and multiple cores.

β clamp (sliding clamp)

Protein ring that encircles DNA to tether Pol III and increase processivity.

Clamp loader (γ complex)

Protein complex that loads the β clamp onto DNA at the primer end using ATP.

Pol III core (αεθ)

Subunit assembly of the Pol III core: α (polymerase), ε (3′–5′ exonuclease proofreading), θ (accessory).

3′–5′ exonuclease

Proofreading activity that removes mispaired nucleotides from the 3′ end.

5′–3′ exonuclease

Exonuclease activity used in nick translation to remove RNA primers and replace with DNA (Pol I).

Klenow fragment

Large C-terminal fragment of Pol I containing polymerase and 3′–5′ exonuclease activities; N-terminal fragment has 5′–3′ exonuclease.

Pol I

DNA polymerase with 5′–3′ polymerase, 3′–5′ proofreading exonuclease, and 5′–3′ nick translation activity.

RNA primer

Short RNA segment synthesized by primase to initiate DNA synthesis.

rNTP

Ribonucleoside triphosphates; cannot be directly incorporated into DNA due to 2′-OH steric clash.

dNTP

Deoxyribonucleoside triphosphates; substrates for DNA synthesis.

Uracil in DNA

Uracil (U) should be absent from DNA; can arise from dUTP incorporation or cytosine deamination and leads to mutations.

Uracil-DNA glycosylase (UNG)

Enzyme that removes uracil from DNA, creating an abasic site for repair.

AP endonuclease (xthA)

Cuts DNA at abasic sites to enable repair after UNG action.

Nicks

Single-strand breaks in the DNA backbone; gaps between Okazaki fragments that are sealed by ligase.

Okazaki fragment

Short DNA fragments synthesized on the lagging strand; later joined by ligase.

Lagging strand

DNA strand synthesized discontinuously in the 5′→3′ direction away from the fork via Okazaki fragments.

Leading strand

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

DNA ligase

Enzyme that seals nicks between Okazaki fragments by forming phosphodiester bonds.

Termiation (Ter/Tus system)

Mechanism to stop forks; Ter sites bind Tus to block fork progression in a directional manner.

Topoisomerase IV

Relieves catenation near termination by decatenating interlinked chromosomes.

DNA gyrase

Topoisomerase II that relieves positive supercoiling ahead of the fork by introducing negative supercoils.

Dam methylase (dam)

DNA adenine methyltransferase that methylates adenine in GATC sequences to regulate initiation.

GATC methylation

Site-specific methylation pattern used to time initiation; hemimethylation after replication delays reinitiation.

SeqA

Protein that binds hemimethylated GATC sites to prevent premature initiation and help with sequestration to the membrane.

Replication timing in E. coli

Origin fires once per cell cycle; new rounds can start before previous replication finishes (overlapping rounds).

Eukaryotic replication similarities

Uses helicases, SSBs, RNA primers, and multiple DNA polymerases for leading and lagging strands.

Eukaryotic replication differences

Occurs in the nucleus with linear chromosomes; many origins; slower polymerases; leading/lagging polymerases not tightly linked; no Pol with 5′–3′ exonuclease activity.

Pol α-primase (eukaryotes)

Primase–polymerase complex that initiates DNA synthesis with RNA primers and has limited processivity.

Pol ε and Pol δ (eukaryotes)

Main leading- and lagging-strand polymerases with high processivity; lack 5′–3′ exonuclease activity.

Okazaki fragment length (eukaryotes vs prokaryotes)

Eukaryotic Okazaki fragments are short (~165 nt); prokaryotic fragments are much longer (~2000 nt in notes).