DNA Replication (Eukaryotes and Viruses) - Vocabulary Flashcards

Vocabulary-style flashcards covering key terms and concepts from the lecture notes on eukaryotic DNA replication, telomere biology, mitochondria, and viral replication.

DNA replication

Process of copying the genome prior to cell division; in eukaryotes it is tightly linked to the cell cycle and must occur only once per cycle.

Origins of replication

DNA regions where replication begins; arise from Autonomously Replicating Sequences (ARS) and are spaced roughly 30 kb apart (range 10 on small chromosomes to thousands on large ones).

Autonomously Replicating Sequences (ARS)

DNA sequences that contain origins of replication in yeast and other organisms.

AT-rich consensus sequence (A region) in yeast

Origin motif: 5'- T/ATTTAYRTTTT/A -3', where Y = pyrimidine and R = purine.

Origin Recognition Complex (ORC)

Protein complex that binds to the A region to license origins in G1.

Licensing factors

Accessory proteins that accumulate in the nucleus during G1 to license replication origins.

Cdc6

Licensing factor that binds to ORC during G1.

Cdt1

Licensing factor that binds to ORC with Cdc6 to load the helicase onto DNA.

Mcm2-7 (helicase)

Helicase complex loaded onto double-stranded DNA during licensing; two helicases are loaded by Cdt1.

Pre-replication complex (pre-RC)

Assembler of ORC, licensing factors and Mcm2-7 formed in G1 before activation.

Activation (S phase)

Process that activates the pre-RC to form the active initiation complex and replisome.

Replisome progression complex

Protein assembly that contains polymerases and other factors to drive DNA elongation.

DNA polymerase α (Pol α)

Enzyme with primase activity and polymerase activity; lacks 3’-5’ exonuclease and is not highly processive until PCNA is loaded.

PCNA (sliding clamp)

Proliferating cell nuclear antigen that increases DNA polymerase processivity during synthesis.

Replication Factor C (RFC)

Clamp loader that loads PCNA onto primer/DNA to enable high-processivity synthesis by other polymerases.

DNA polymerase δ (Pol δ)

Lagging-strand polymerase; associates with PCNA and has proofreading activity.

DNA polymerase ε (Pol ε)

Leading-strand polymerase; associates with PCNA and has proofreading activity.

DNA polymerase β (Pol β)

Polymerase involved in DNA repair rather than replication.

DNA polymerase γ (Pol γ)

Polymerase that replicates mitochondrial DNA (mtDNA).

3’-5’ exonuclease activity

Proofreading activity present in some DNA polymerases but absent in Pol α.

FEN1 (Flap Endonuclease-1)

Enzyme that cleaves 5’ RNA flaps created during Okazaki fragment processing.

RNase H2

Enzyme that removes most RNA primers, leaving a single ribonucleotide for final processing.

DNA ligase

Enzyme that seals nicks after primer removal and gap filling during maturation of Okazaki fragments.

End replication problem

Issue with linear chromosomes where the lagging strand loses terminal information due to RNA primer removal.

Telomeres

DNA repeats at chromosome ends (TTAGGG) that protect genes from loss; the last 20–200 nt are single-stranded.

TTAGGG repeats

Telomeric repeat sequence found at chromosome ends in many eukaryotes.

Hayflick limit

Limit to somatic cell division (~40 divisions) due to telomere shortening and eventual senescence.

Telomerase

Ribonucleoprotein that extends telomeres; contains an RNA template (~450 nt) with sequence CUAACCUAAC.

Telomerase RNA template (CUAACCUAAC)

RNA component that provides the template for telomere repeat synthesis.

Telomere elongation

Process by which telomeres are extended by telomerase, delaying end-replication shortening.

mtDNA

Mitochondrial DNA; circular genome present in multiple copies per mitochondrion.

DNA polymerase γ (Pol γ)

Polymerase that synthesizes the leading strand of mtDNA.

RNA Okazaki fragments

RNA-primed short fragments used on the lagging strand of mtDNA during replication.

Unidirectional replication

mtDNA replication proceeds in one direction with a single replication fork.

Bacteriophages

Viruses that infect bacteria; some utilize rolling circle replication to synthesize DNA.

Rolling circle replication

Mechanism for circular genomes where a nick serves as a primer and the strand is displaced as synthesis proceeds.

Sigma (σ) replication

Rolling-circle-like replication mechanism observed in some bacteriophages.

Nick (as primer)

DNA break used as a primer in rolling circle replication to initiate synthesis.

RNA genomes

Viruses with RNA genomes that encode an RNA-dependent RNA polymerase (RNA replicase) and often lack proofreading.

RNA replicase

RNA-dependent RNA polymerase encoded by RNA viruses for genome replication.

Plus-strand RNA

Positive-sense RNA that can be directly copied to minus-strand RNA during replication.

Self-priming

Ability of some RNA genomes to prime replication without an external primer.

Retroviruses

RNA viruses (e.g., HIV) that reverse-transcribe RNA into DNA for integration into the host genome.

Reverse transcriptase

Enzyme that synthesizes DNA from an RNA template in retroviruses.

RNase H

Enzyme that degrades RNA in RNA-DNA hybrids during reverse transcription.

tRNALys primer

Primer used by reverse transcriptase to initiate DNA synthesis in HIV.

Integration

Process of synthesizing a second DNA strand and integrating the viral DNA into the host genome.