DNA replication, Damage, and repair

Flashcards cover key topics from the lecture notes: DNA structure, replication mechanics, enzymes, experiments, and telomeres.

What is the DNA structure proposed by Watson and Crick in 1953?

A double helix with two antiparallel chains; the sugar–phosphate backbone is on the outside; bases pair via hydrogen bonds (A–T and G–C).

How long is one turn of the DNA double helix?

3.4 nanometers.

What forms the backbone of DNA?

The sugar–phosphate backbone.

What are the two grooves in the DNA double helix called?

Deep groove and shallow groove.

What type of bonds stabilize the DNA base pairs?

Hydrogen bonds between purines and pyrimidines.

What is the central dogma of molecular biology as described by Crick?

Information flows from DNA to RNA to protein (transcription and translation); reverse transcription can occur in some viruses.

Name the three main RNA types involved in translation.

mRNA, tRNA, and rRNA.

When was the central dogma concept established?

1957 (Crick’s discussion of the central dogma).

What is reverse transcription?

Synthesis of DNA from an RNA template, as in retroviruses.

What is the approximate base-pairing error rate of DNA replication before proofreading?

About 1 base per 10^5 base pairs.

How does proofreading by DNA polymerase affect the error rate?

Reduces it about 100-fold (to around 10^-7 per bp).

What is the role of DNA repair in replication fidelity?

Further reduces errors to about 10^-9 per base pair.

Who demonstrated semi-conservative DNA replication?

Matthew Meselson and Franklin Stahl.

What isotopes were used in the Meselson-Stahl experiment?

Heavy nitrogen 15N initially, then switched to 14N.

What are the three replication models tested in Meselson-Stahl?

Conservative, semi-conservative, and dispersive.

What pattern after one generation supported semi-conservative replication?

Two DNA duplexes, each with one heavy and one light strand.

What is a replication bubble?

A region where parental strands separate and synthesis occurs, with two replication forks.

Which enzyme unwinds DNA at the replication fork?

Helicase (uses ATP).

What is the primary DNA polymerase for replication in E. coli?

DNA polymerase III.

What are Okazaki fragments?

Short DNA fragments synthesized on the lagging strand (about 1–2 kb in bacteria).

Which enzyme removes RNA primers and fills the gaps in prokaryotes?

DNA polymerase I (with 5′→3′ exonuclease and 3′→5′ exonuclease activities).

What is the Klenow fragment?

A proteolytic fragment of DNA polymerase I containing polymerase and 3′→5′ exonuclease activities.

What is the role of the sliding clamp in DNA replication?

The β-subunit dimer that encircles DNA to increase polymerase processivity.

What is PCNA?

Proliferating cell nuclear antigen, the eukaryotic sliding clamp.

What is the function of the clamp loader (γ complex)?

Loads the sliding clamp onto DNA and helps assemble the polymerase; not part of the fork long-term.

How fast can the DNA polymerase III holoenzyme synthesize DNA?

About 1,000 nucleotides per second.

Why do lagging-strand synthesis loops form?

To replicate the lagging strand discontinuously in the 5′→3′ direction while the fork moves.

What are terminator sites in bacterial replication?

TerA–TerF sequences where Tus binds to arrest replication forks.

Which enzyme disentangles daughter duplexes after termination?

Topoisomerase IV.

What is oriC?

The origin of replication in E. coli.

What proteins form the E. coli primosome?

DnaB helicase, DnaG primase, and DnaC loader (assembled with DnaA at oriC).

What is the role of DnaA in origin melting?

DnaA binds to dnaA boxes and, with HU, helps melt DNA to form an open complex, enabling DnaB binding.

What happens after the open complex forms in E. coli replication initiation?

DnaB binds, DnaC facilitates, and primase is recruited to form the primosome.

What is SV40 origin–initiated replication and which protein initiates it?

SV40 origin uses the viral large T antigen to bind and unwind DNA; priming is carried out by the host primase with polymerase α.

What are ARS elements in yeast?

Autonomously replicating sequences that function as origins of replication (ARS1 has regions A, B1, B2, B3).

Which polymerases replicate DNA in eukaryotes?

Pol δ and Pol ε; Pol α has primase activity; Pol β for repair; Pol γ replicates mitochondrial DNA.

What is the role of PCNA in eukaryotes?

A ring-shaped clamp that increases polymerase processivity by encircling DNA.

What are single-stranded DNA-binding proteins (SSBs) for?

Stabilize and protect single-stranded DNA and prevent it from re-annealing.

What is the role of DNA gyrase?

A topoisomerase II enzyme that relieves torsional strain by introducing negative supercoils.

What is the telomere?

Repeated DNA sequences at chromosome ends that protect chromosomes from degradation.

Who won the 2009 Nobel Prize for telomeres research?

Elizabeth H. Blackburn, Carol W. Greider, and Jack W. Szostak.

What enzyme extends telomeres?

Telomerase, an RNA-dependent DNA polymerase.

What is shelterin?

A protein complex (TRF1, TRF2, POT1, TIN2, RAP1, TPP1) that protects telomeres.

What is a T-loop?

A loop structure formed at telomeres where the overhang invades the duplex.

What roles do TRF1 and TRF2 play at telomeres?

TRF1 binds double-stranded telomere DNA and bends it; TRF2 stabilizes the D-loop.

What is the role of POT1?

Binds the single-stranded telomere overhang.

Why is telomere maintenance important?

Prevents chromosome ends from being degraded and protects genome integrity through replication.

What is the typical pattern of DNA replication in bacteria regarding identically copied molecules after replication?

Two identical DNA molecules are produced, one for each daughter cell.