Chapter 13: Synthesis of DNA

DNA replication follows a semiconservative model wherein each newly formed molecule consists of one original strand paired with one recently synthesized strand. The replication fork serves as the active site of synthesis, requiring multiple accessory proteins including helicases that unwind the double helix, topoisomerases that relieve tension, and single-strand binding proteins that prevent reannealing. DNA polymerase catalyzes phosphodiester bond formation exclusively in the five-prime to three-prime direction, creating a continuous leading strand while the opposing lagging strand is synthesized discontinuously as Okazaki fragments that are subsequently ligated together. RNA primers synthesized by primase are essential for initiating polymerase activity, and built-in proofreading mechanisms coupled with specialized mismatch repair pathways ensure replication fidelity. The chapter contrasts prokaryotic replication, illustrated through Escherichia coli with its three polymerases, against eukaryotic replication involving multiple replication origins, nucleosome remodeling, and polymerase-specific roles in nuclear and mitochondrial DNA synthesis. Telomerase, an RNA-dependent polymerase, extends chromosomal termini to counteract progressive shortening, with implications for cellular senescence and cancer cell immortality. DNA repair mechanisms address diverse damage types: nucleotide excision repair targets bulky adducts, base excision repair corrects oxidative and spontaneous lesions, mismatch repair eliminates replication errors, and transcription-coupled repair prioritizes active genes. Clinical pathologies arising from defective repair include xeroderma pigmentosum from impaired nucleotide excision repair, Cockayne syndrome affecting transcription-coupled repair, Lynch syndrome from mismatch repair mutations, and BRCA mutations predisposing to hereditary malignancies. The chapter integrates clinical cases demonstrating pharmacological interventions targeting DNA synthesis and practical disease associations including UV-induced melanoma and tobacco-related carcinogenesis. Homologous recombination via Holliday junction intermediates, chromosomal translocations in cancer, and transposable elements as mobile genetic units conclude the discussion of how genetic material undergoes rearrangement and evolution.