DNA Synthesis and Replication - Vocabulary (E. coli)

Vocabulary-style flashcards covering key terms, enzymes, structures, and concepts from the DNA synthesis and replication notes.

DNA polymerase III

Principal E. coli replication enzyme; synthesizes DNA 5'→3' with high processivity (holoenzyme); main chromosome replication enzyme.

DNA polymerase I

DNA repair and Okazaki fragment processing; has 5'→3' exonuclease activity to remove RNA primers and fill gaps; slower than Pol III.

DNA ligase

Enzyme that seals nicks in the DNA backbone to join Okazaki fragments; ATP-dependent in bacteria.

Helicase

Enzyme that unwinds the DNA duplex using ATP, forming replication forks; often a hexamer that moves along DNA.

Primase

RNA polymerase that synthesizes short RNA primers to start DNA synthesis.

SSB proteins

Single-strand DNA-binding proteins that stabilize unwound DNA during replication.

Topoisomerases

Enzymes that relieve DNA supercoiling by cutting and rejoining DNA; include Type I (cuts one strand) and Type II (cuts both strands).

DNA gyrase

Bacterial Type II topoisomerase that introduces negative supercoils; ATP-dependent and essential for fork progression; antibiotic target.

Replication fork

Y-shaped region where the DNA is unwound and new DNA is synthesized.

Theta replication

Bidirectional replication of circular DNA, forming theta-shaped intermediates.

oriC

Origin of chromosomal replication in E. coli.

dnaA

Initiation factor that binds oriC to start replication.

dnaE

Pol III α subunit; catalytic core of Pol III holoenzyme.

dnaG

Primase; synthesizes RNA primers for DNA synthesis.

dnaI

Initiation protein at oriC (involved in start of replication).

dnaL

Gene encoding DNA ligase.

dnaN

Pol III β clamp; sliding clamp that increases DNA polymerase processivity.

dnaQ

Pol III ε proofreading subunit; 3'→5' exonuclease activity.

dnaS

UTPase; involved in DNA replication processes.

dnaX

Pol III holoenzyme γ subunit; contributes to holoenzyme assembly/dimerization.

dnaZ

Pol III τ subunits; enable dimerization of the polymerase on the two strands.

holA

Pol III δ subunit.

holB

Pol III δ' subunit.

holC

Pol III χ subunit.

holD

Pol III ψ subunit.

holE

Pol III θ subunit.

gyrA

DNA gyrase α subunit (Topo II component).

gyrB

DNA gyrase β subunit (Topo II component).

ssb

Single-strand DNA-binding protein; stabilizes unwound DNA.

polA

DNA polymerase I gene; encodes Pol I enzyme.

polB

DNA polymerase II gene; encodes Pol II.

rep

ATP-dependent helicase involved in unwinding DNA.

Lk

Linking number; fixed value in circular DNA; Lk = Twist (T) + Writhe (W).

T

Twist; number of helical turns (duplex twists) in DNA.

W

Writhe; number of duplex self-crossings (supercoiling geometry).

Lk0

Relaxed linking number; state with W = 0 (no supercoiling).

Positive supercoiling

Overwinding of DNA; Lk > Lk0; +W.

Negative supercoiling

Underwinding of DNA; Lk < Lk0; −W.

σ (sigma)

Superhelical density; σ = (Lk − Lk0)/Lk0; normalizes supercoiling independent of length.

Topoisomerase I

Type I topoisomerase; makes single-strand breaks to change Lk by ±1; moves DNA toward relaxed form.

Topoisomerase II

Type II topoisomerase; makes double-strand breaks to pass duplex through; ATP-dependent; can introduce/remove supercoils.

Topoisomerase IV

Type II topoisomerase in bacteria that decatenates interlinked daughter chromosomes after replication.

Decatenation

Process of separating interlinked (catenated) daughter DNA molecules after replication.

Catenane

Interlinked DNA rings formed after replication of circular chromosomes.

Okazaki fragments

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

RNA primer

Short RNA segment that provides a 3' OH for DNA polymerase to start synthesis.

RNAse H

Enzyme that degrades RNA in RNA-DNA hybrids; alternative primer-removal method.

Primer removal by Pol I

Pol I removes RNA primers via 5'→3' exonuclease and fills with DNA.

Pulse-chase experiments

Experimental approach to track synthesis and maturation of DNA fragments over time (Okazaki study).

3H-TTP

Tritiated thymidine used to label newly synthesized DNA in pulse-chase experiments.

Alkaline lysis

Method to lyse cells under alkaline conditions to analyze DNA fragments (Okazaki study).

Leading strand

DNA strand synthesized continuously toward the replication fork.

Lagging strand

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

Bidirectional synthesis

Replication proceeds in two directions from the origin.

Replication bubble

Region where DNA is unwound around an origin, forming a bubble with forks.

Denaturation

PCR step: separation of DNA strands at high temperature (e.g., 95°C).

Annealing

PCR step: primers bind to complementary sequences (e.g., ~55°C).

Extension

PCR step: DNA polymerase extends from primers (e.g., 72°C).

Taq polymerase

Heat-stable DNA polymerase used in PCR; from Thermus aquaticus.

dNTPs

Deoxynucleotide triphosphates; building blocks for DNA synthesis (dATP, dCTP, dGTP, dTTP).

Primer

Short nucleic acid sequence used to initiate DNA synthesis.

Template DNA

DNA strand used as a template for synthesis.

PCR

Polymerase Chain Reaction; method to exponentially amplify DNA.

Leading/lagging distinctions

Leading is continuous; lagging is discontinuous with primers and fragments.