DNA replication, Damage, and repair

Vocabulary flashcards covering key terms from the lecture notes on DNA structure, replication mechanisms, enzymes, and telomere biology.

DNA

Deoxyribonucleic acid; the genetic material composed of two antiparallel polynucleotide chains forming a double helix.

DNA double helix

Watson–Crick structure with two complementary strands wound around each other and bases paired inside.

Phosphodiester backbone

The sugar–phosphate chain that forms the structural backbone of each DNA strand.

Hydrogen bond

A noncovalent interaction stabilizing base pairs in DNA (A–T with two bonds, G–C with three).

Major groove

The deeper (more accessible) groove along the DNA double helix where proteins often bind.

Minor groove

The shallower groove along the DNA helix.

Purine

A two-ring nitrogenous base (adenine or guanine).

Pyrimidine

A single-ring nitrogenous base (cytosine or thymine).

Adenine–thymine (A–T) pairing

Purine–pyrimidine base pair stabilized by two hydrogen bonds.

Guanine–cytosine (G–C) pairing

Purine–pyrimidine base pair stabilized by three hydrogen bonds.

DNA polymerase III

Main bacterial enzyme that synthesizes new DNA strands during replication.

DNA polymerase I

Enzyme with polymerase and exonuclease activities; removes RNA primers and processes Okazaki fragments.

Klenow fragment

Proteolytic fragment of DNA polymerase I retaining polymerase and 3′→5′ exonuclease activities.

DNA ligase

Enzyme that seals nicks to join Okazaki fragments on the lagging strand.

Primase

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

RNA primer

Short RNA segment (~10–12 nt) that provides a 3′-OH for DNA synthesis.

Beta clamp (β-subunit)

Sliding clamp that tethers DNA polymerase to DNA to increase processivity.

PCNA

Proliferating cell nuclear antigen; eukaryotic sliding clamp analogous to the β-clamp.

Gamma complex

Clamp loader that loads the sliding clamp onto DNA, enabling processive replication.

Holoenzyme

Complete multi-subunit enzyme complex performing replication (e.g., Pol III holoenzyme).

Leading strand

DNA strand synthesized continuously toward the replication fork.

Lagging strand

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

Okazaki fragment

Short DNA fragment synthesized on the lagging strand and later joined by ligase.

Replication fork

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

Bidirectional replication

DNA replication proceeding in two directions from the origin.

Origin of replication (oriC)

DNA sequence where replication starts in bacteria; initiates replisome assembly.

Replicon

DNA segment under the control of a single origin of replication.

Semiconservative replication

Each daughter DNA molecule contains one old strand and one new strand.

Meselson–Stahl experiment

Classic experiment showing semiconservative DNA replication using heavy isotopes.

Heavy nitrogen 15N

Isotope used to label DNA to distinguish old and new strands in Meselson–Stahl experiments.

CsCl gradient ultracentrifugation

Technique to separate DNA by density, revealing replication patterns.

Theta replication

Bidirectional replication in circular DNA producing a theta-shaped intermediate.

SSB (single-strand DNA-binding proteins)

Proteins that stabilize unwound single-stranded DNA during replication.

Helicase

Enzyme that unwinds the DNA double helix at the replication fork using ATP.

DNA gyrase

Bacterial topoisomerase that relieves torsional strain by introducing negative supercoils.

Topoisomerase

Enzymes that relieve DNA supercoiling and torsional strain during replication.

DnaA

Bacterial initiator protein that binds oriC and promotes origin melting.

DnaB

Helicase that unwinds DNA at the replication fork in bacteria.

DnaC

Helicase loader that facilitates DnaB loading onto DNA.

HU protein

Nucleoid-associated protein aiding origin opening and DNA structure in bacteria.

Primosome

Complex including primase that coordinates primer synthesis at origins.

DnaG

Bacterial primase that synthesizes RNA primers.

SV40 large T antigen

Viral protein that initiates replication at the SV40 origin by recruiting host factors.

ARS (Autonomously Replicating Sequence)

Yeast DNA sequence acting as an origin of replication in plasmids.

ARS1

A key yeast origin region within ARS1 important for plasmid stability.

Telomere

Repeated DNA sequences at chromosome ends that protect genome integrity.

Telomerase

Reverse transcriptase–RNA enzyme that extends telomeres by adding repeats.

Shelterin

Protein complex protecting telomeres; includes TRF1, TRF2, POT1, TPP1, RAP1.

TRF1

Telomeric repeat-binding factor 1 that binds double-stranded telomere DNA.

TRF2

Telomeric repeat-binding factor 2 that stabilizes telomeric structures like the D-loop.