U01.01.006 DNA replication

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Learning Objectives

Identify the directionality and semiconservative nature of DNA replication.
Distinguish between the roles of DNA Polymerase I and III in prokaryotes.
Master the clinical correlations of Topoisomerase inhibitors and Helicase mutations.
Understand the function of Telomerase in eukaryotes and its role in aging/cancer.

1. The Replication Fork & Machinery

DNA replication occurs in the 5′ → 3′ direction (5ynth3sis). It is semiconservative, meaning each new daughter strand is paired with one original parent strand.

Enzyme	Function	Clinical Note
Helicase	Unwinds the DNA template at the fork.	Deficient in Bloom syndrome (BLM gene).
SSB Proteins	Prevents reannealing or nuclease degradation.	Stabilizes single strands.
Topoisomerases	Relieves supercoils via single (I) or double (II) strand breaks.	Targeted by Fluoroquinolones (prokaryotes) and Etoposide (eukaryotes).
Primase	Makes RNA primer to provide a 3′-OH group.	Essential for DNA Pol III to start.

2. Prokaryotic DNA Polymerases

Prokaryotes utilize two main polymerases for elongation and cleanup:

DNA Polymerase III: The primary elongator. It synthesizes the leading strand and Okazaki fragments.
- Has 3′ → 5′ exonuclease activity for proofreading.
DNA Polymerase I: The “cleanup” crew. It excises the RNA primer using 5′ → 3′ exonuclease and replaces it with DNA.

3. Telomerase: Eukaryotes Only

Since eukaryotic chromosomes are linear, they shorten with each round of replication. Telomerase prevents this loss.

Mechanism: An RNA-dependent DNA polymerase (reverse transcriptase).
Sequence: Adds TTAGGG repeats to the 3′ ends.
Mnemonic: Telomerase TAGs for Greatness and Glory.
Clinical: Upregulated in Cancer; downregulated in Aging/Progeria.

4. Clinical Pharmacology Summary

Topoisomerase I Inhibitors: Irinotecan, Topotecan.
Topoisomerase II Inhibitors: Etoposide, Teniposide.
Chain Terminators: Drugs like Zidovudine (AZT) lack a 3′-OH group, preventing the addition of the next nucleotide.