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Nucleotide Metabolism, DNA Structure, and Replication - Coggle Diagram

- - - - DNA: deoxyribose + A, T, G, C
      - RNA: ribose + A, U, G, C
      - Backbone: sugar-phosphate (3' → 5' phosphodiester bonds)
  - - - Right-handed, antiparallel strands
      - A-T and G-C specific base pairing
      - Stabilised by:
      - Hydrogen bonds
      - Hydrophobic effect
      - Base stacking (van der Waals)
  - - - B-DNA: common physiological form
      - A-DNA: dehydrated form
      - Z-DNA: left-handed helix (biological role unclear)
  - - - Negative supercoiling aids in replication, transcription
      - Topoisomerases:
      - Type I: relax supercoils
      - Type II (e.g., DNA gyrase): add negative supercoils using ATP
  - - - DNA wrapped around histone octamer (2× H2A, H2B, H3, H4)
      - H1 binds linker DNA
      - Further compacted into 30 nm fibers
      - Histone tails modulate accessibility
- - - - Semiconservative (Meselson-Stahl experiment)
      - Requires:
      - DNA polymerases
      - Helicases
      - Primase (makes RNA primers)
      - DNA ligase (joins fragments)
      - Topoisomerases (relieves stress)
  - - - Catalyse phosphodiester bond formation
      - Require:
      - Template
      - Primer (free 3' OH)
      - dNTPs
      - Synthesize 5' → 3' direction
      - Proofreading:
      - 3' → 5' exonuclease activity
  - - - DnaA binds origin
      - DnaB helicase unwinds DNA
      - SSB proteins stabilise single-stranded DNA
  - - - Leading strand: continuous synthesis
      - Lagging strand: Okazaki fragments (~1000 bp)
      - DNA ligase seals Okazaki fragments
  - - - More complex due to:
      - Larger genomes
      - Multiple linear chromosomes
      - Multiple origins of replication (~30,000 origins in humans)
  - - - Telomeres: repetitive TTAGGG sequences at chromosome ends
      - Telomerase extends leading strand using its own RNA template
      - Protects against chromosome shortening during replication
      - Telomerase activity low in most somatic cells → aging