AP Biology: DNA Replication – Enzymes, Semi?Conservative, Leading/Lagging Strand, Okazaki Fragments

DNA Replication – Enzymes, Semi?Conservative, Leading/Lagging Strand, Okazaki Fragments

Concept Summary

• DNA replication: Process by which a cell duplicates its DNA before division, ensuring genetic continuity.
• Semi-conservative model: Each new DNA molecule consists of one parental strand and one newly synthesized strand, confirmed by Meselson-Stahl.
• Helicase: Enzyme that unwinds the DNA double helix at the replication fork by breaking hydrogen bonds between bases.
• DNA polymerase III: Primary enzyme synthesizing new DNA strands in the 5’?3’ direction, requiring a primer to initiate.
• Okazaki fragments: Short, discontinuous DNA segments synthesized on the lagging strand, later joined by DNA ligase.

Core Questions

WHAT (definitional)

Q: What is semi-conservative replication? A: A replication model where each daughter DNA molecule retains one original strand and one newly synthesized strand. Trap/Clarification: Not dispersive (random fragments) or conservative (both strands new); Meselson-Stahl’s density-gradient experiments proved semi-conservative.

Q: What are Okazaki fragments? A: Short DNA segments (100–200 nucleotides in eukaryotes) synthesized discontinuously on the lagging strand. Trap/Clarification: They are not found on the leading strand; their existence explains lagging-strand synthesis.

WHY (causal/explanatory)

Q: Why is primase essential for DNA replication? A: DNA polymerase III cannot initiate synthesis de novo; primase synthesizes a short RNA primer to provide a 3’-OH group for elongation. Trap/Clarification: Primase is an RNA polymerase, not DNA polymerase; the primer is later replaced with DNA.

Q: Why is the lagging strand synthesized discontinuously? A: DNA polymerase III can only add nucleotides in the 5’?3’ direction, but the lagging strand’s template runs 3’?5’, requiring backstitching via Okazaki fragments. Trap/Clarification: The lagging strand is not slower—it’s the directionality of synthesis that forces discontinuity.

HOW (process/application)

Q: How does DNA ligase join Okazaki fragments? A: Ligase catalyzes the formation of a phosphodiester bond between the 3’-OH of one fragment and the 5’-phosphate of the next, sealing the nick. Trap/Clarification: Ligase cannot add nucleotides; it only seals pre-existing gaps (unlike polymerase).

Q: How is the leading strand synthesized? A: Continuously in the 5’?3’ direction toward the replication fork, requiring only one RNA primer. Trap/Clarification: The leading strand is not synthesized faster—it’s the mechanism (continuous vs. discontinuous) that differs.

CAN (conditions/possibilities)

Q: Can DNA polymerase III proofread errors? A: Yes; its 3’?5’ exonuclease activity removes mismatched nucleotides during synthesis. Trap/Clarification: Proofreading occurs during replication, not after (unlike mismatch repair).

Q: Under what conditions does DNA replication occur bidirectionally? A: In most prokaryotes and eukaryotes, replication initiates at origins and proceeds in both directions (forming two replication forks). Trap/Clarification: Bidirectional replication is not universal (e.g., some viruses replicate unidirectionally).

Quick Facts & Traps

• Fact: DNA polymerase I removes RNA primers (5’?3’ exonuclease) and replaces them with DNA, but not the primary synthesizer (that’s Pol III).
• Trap: "DNA polymerase synthesizes DNA in the 3’?5’ direction."-Reality: All DNA polymerases synthesize only 5’?3’; the template is read 3’?5’.
• Fact: Topoisomerase relieves supercoiling ahead of the replication fork by breaking and rejoining DNA strands (e.g., gyrase in prokaryotes).
• Trap: "Okazaki fragments are only in prokaryotes."-Reality: They occur in both prokaryotes and eukaryotes, but are shorter in eukaryotes (~100–200 nt vs. ~1000–2000 nt).
• Fact: Telomerase extends eukaryotic lagging-strand templates to prevent chromosome shortening, using an RNA template.
• Trap: "All cells have telomerase."-Reality: Most somatic cells lack telomerase; it’s active in germ cells, stem cells, and cancer cells.

Rapid-Fire True/False

• Statement: The leading strand requires multiple RNA primers. Answer: FALSE Why the common mistake happens: Confusion with the lagging strand’s discontinuous synthesis; the leading strand needs one primer.

• Statement: Helicase breaks phosphodiester bonds to unwind DNA. Answer: FALSE Why the common mistake happens: Helicase breaks hydrogen bonds between bases; phosphodiester bonds are cleaved by nucleases (e.g., topoisomerase).

• Statement: DNA replication is error-free due to proofreading. Answer: FALSE Why the common mistake happens: Proofreading reduces errors (~1 in 10?), but mismatch repair and other systems further correct mistakes.