DNA Structure and Replication

DNA Structure - Helix Blueprint

• DNA: Deoxyribonucleotide polymer; genetic blueprint.
• Components: Deoxyribose, phosphate, N-bases (A,T,G,C).
  • Purines: Adenine (A), Guanine (G) (📌 Pure As Gold).
  • Pyrimidines: Cytosine (C), Thymine (T) (📌 CUT Py).
• Nucleoside: Base + Sugar. Nucleotide: Base + Sugar + Phosphate.
• 5'-3' Phosphodiester bonds form backbone.
• Watson-Crick B-DNA: Right-handed double helix.
  • Antiparallel strands.
  • Complementary base pairing (Chargaff's rules):
    • A=T (2 H-bonds)
    • G≡C (3 H-bonds)
    • Purines (A+G) = Pyrimidines (T+C)
• Dimensions (B-DNA):
  • ~10.5 base pairs/turn.
  • Pitch: 3.4 nm/turn.
  • Diameter: 2 nm.
• Major & minor grooves: Sites for protein binding.

⭐ B-DNA: right-handed helix; 10.5 bp/turn, pitch 3.4 nm. Z-DNA: left-handed.

DNA Packaging - Chromatin Coils

• DNA (~2m) compacts into nucleus (~10µm) through hierarchical coiling.
• Nucleosome ("beads-on-a-string"): Fundamental unit.
  • DNA (146 bp) wraps ~1.65 times around a histone octamer (2 each of H2A, H2B, H3, H4).
  • H1 histone (linker histone) binds to linker DNA and the nucleosome, aiding compaction.
  • Forms a 10-11 nm fiber.
• Solenoid:
  • Helical coiling of 6 nucleosomes per turn.
  • Forms a 30 nm fiber.
• Higher-order packaging: 30 nm fiber forms loops (300 nm), then scaffolds (700 nm), ultimately condensing into a metaphase chromosome (1400 nm).

⭐ Histones are rich in basic amino acids (Lysine and Arginine), giving them a net positive charge that facilitates binding to the negatively charged DNA backbone.

DNA Replication - Copy Machine

DNA replication is a semi-conservative process, ensuring each daughter DNA molecule has one parental and one newly synthesized strand. It occurs primarily during the S-phase of the cell cycle.

• Key Steps & Enzymes:
  • Initiation:
    • Origin of Replication (ORI): Specific DNA sequences where replication begins.
    • Helicase: Unwinds DNA double helix at replication fork (ATP-dependent).
    • Single-Strand Binding Proteins (SSBPs): Stabilize unwound single-stranded DNA (ssDNA).
    • Topoisomerases: Relieve supercoiling ahead of fork (e.g., DNA gyrase in prokaryotes).
  • Elongation:
    • Primase: Synthesizes short RNA primers.
    • DNA Polymerase III: Main prokaryotic synthesizing enzyme (5'→3' activity), requires RNA primer.
      • Leading strand: Continuous synthesis towards the fork.
      • Lagging strand: Discontinuous synthesis (Okazaki fragments) away from the fork.
    • DNA Polymerase I: Prokaryotic; removes RNA primers (5'→3' exonuclease activity), fills gaps with DNA.
  • Termination:
    • DNA Ligase: Joins Okazaki fragments on lagging strand, seals nicks in the phosphodiester backbone.

⭐ DNA replication is typically bidirectional from the origin, creating two replication forks. Prokaryotes usually have a single ORI, while eukaryotes possess multiple ORIs to ensure timely replication of larger genomes.

Replication Fidelity & Telomeres - Proof & Protect

• Replication Fidelity (Error Prevention):
  • DNA Pol III (prok.) & Pol δ/ε (euk.) 3'→5' exonuclease activity.
  • Mismatch Repair (MMR): Corrects residual errors. Proteins: MutS/L/H (prok.), MSH/MLH/PMS (euk.).
  • Achieves error rate of $1 \times 10^{-9}$ to $1 \times 10^{-10}$.
• Telomeres (Chromosome End Caps):
  • Repetitive DNA (human: TTAGGG) at chromosome ends; prevent gene erosion.
  • Counteract "end replication problem" (incomplete lagging strand synthesis).
  • 
• Telomerase (Maintains Telomeres):
  • Ribonucleoprotein enzyme (reverse transcriptase activity).
  • Contains RNA template (TERC) & catalytic subunit (TERT).
  • Adds telomeric repeats. High in germ, stem, cancer cells. Low in somatic cells (→ Hayflick limit).
  • ⭐ > Telomerase inhibition is a therapeutic target in cancer treatment.

High‑Yield Points - ⚡ Biggest Takeaways

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