BIOL 4210 – Lecture 06: DNA Replication, Repair, and Recombination

Question-and-answer flashcards covering initiation/completion of DNA replication, origins, methylation, replication licensing, histone inheritance, telomeres/telomerase/shelterin/t-loops, and major DNA repair pathways (BER, NER, translesion synthesis, DSB repair by NHEJ and HR) as presented in Lecture 06.

How is DNA replication initiated in prokaryotes like E. coli, and what feature characterizes the origin of replication?

The origin is AT-rich; initiator proteins destabilize the DNA to open the helix, followed by recruitment of helicases and DNA primase, then DNA polymerases to the leading and lagging strands.

What is the replication origin situation in human chromosomes?

Human chromosomes have many origins of replication; origins are activated with a pre-replicative complex, and ORC phosphorylation cycles regulate firing; the exact DNA sequences marking human origins are not fully defined.

What role does DNA methylation play in prokaryotic origins of replication?

Origins must be methylated on both strands; after DNA synthesis methylation is slow, so origins are hemimethylated during replication, creating a refractory period before reinitiation.

Explain origin licensing in eukaryotes and what remains unclear about human origins.

A pre-replicative complex forms and ORC phosphorylation controls origin firing; origins are licensed to fire once per cell cycle. In humans, it is still not clear which DNA sequences mark origins.

How are histones inherited during DNA replication?

H3–H4 tetramers are randomly inherited by each daughter; H2A–H2B dimers dissociate ahead of the replication fork and mix with newly synthesized histones; chaperones NAP1 and CAF1 help assemble histones onto both daughter strands with the sliding clamp.

What is telomerase and what is its role at chromosome ends?

Telomerase is a DNA polymerase that carries its own RNA template and extends telomere repeats at chromosome ends to protect them from loss and fusion.

What are telomeres and why are they important?

Telomeres protect the ends of chromosomes and prevent chromosome fusions, especially during double-strand break repair.

What is a t-loop and which protein complex protects chromosome ends?

A t-loop is a protective loop structure at the end of a chromosome; shelterin forms a protective cap that guards chromosome ends from DNA repair proteins.

What is base excision repair (BER) and which enzymes initiate and complete it?

BER fixes small base damage via a glycosylase that removes the damaged base, followed by AP endonuclease and phosphodiesterase removing the sugar–phosphate, then DNA polymerase and ligase fill and seal.

What is nucleotide excision repair (NER) and what kind of lesions does it remove?

NER repairs bulky lesions such as thymine dimers; a damage-recognition complex unwinds DNA and endonucleases remove about 30 base pairs around the lesion, followed by synthesis to fill the gap.

What causes thymine dimers and how are they repaired?

Thymine dimers are caused by UV irradiation (UVB); similar dimers can form between neighboring pyrimidines (e.g., T+C, C+C) and are repaired predominantly by NER.

What is translesion DNA synthesis and what are its trade-offs?

Translesion polymerases bypass heavily damaged DNA when high-fidelity polymerases stall; they lack exonuclease proofreading and are more error-prone, synthesizing short runs before high-fidelity polymerases resume.

What are the two main pathways for repairing double-strand breaks (DSBs)?

Nonhomologous end joining (NHEJ) and homologous recombination (HR).

What is nonhomologous end joining (NHEJ)?

Directly ligates broken ends after processing; can involve end trimming and is efficient but error-prone.

What is homologous recombination (HR) and why is it high-fidelity?

HR uses a sister chromatid as a repair template; relies on base pairing and DNA hybridization, leading to accurate repair of DSBs.

What is the concept of origin licensing and how does it enforce once-per-cycle firing?

Licensing involves formation of a pre-replicative complex and regulated ORC phosphorylation to ensure origins fire only once per cell cycle.

What is the role of shelterin and what other structure protects chromosome ends?

Shelterin forms a protective cap on chromosome ends; a t-loop also protects the ends from DNA repair proteins.

What do Table 5-3 endogenous DNA lesions illustrate about damage and repair?

They list endogenous lesions arising from normal chemical reactions (e.g., depurination, deamination, oxidation) and show that many are repaired within 24 hours in a diploid mammalian cell.

Why are glycosylases important in DNA repair?

Glycosylases recognize and remove damaged bases by cleaving the N-glycosidic bond, initiating base excision repair.

What is the sequence of events in base excision repair after a deaminated base is removed?

A glycosylase removes the damaged base, then AP endonuclease and phosphodiesterase remove the sugar-phosphate, and DNA polymerase plus ligase fill and seal the gap.

What triggers deamination-related mutations and how are they detected by repair systems?

Deamination yields unnatural bases (e.g., uracil or thymine from 5-methylcytosine) that are recognized and removed by specific glycosylases, preventing mutations.