DNA Structure and Replication

Discovery of DNA Structure

  • Prior knowledge about DNA:
    • Composed of nucleic acids and nucleotides (containing nitrogen bases).
    • Structure includes a polynucleotide chain with polarity (5' to 3') and a sugar-phosphate backbone linked by phosphates.
    • Chargaff's rules:
    • Adenine (A) pairs with Thymine (T).
    • Guanine (G) pairs with Cytosine (C).
  • Rosalind Franklin played a crucial role in discovering the DNA structure but was not recognized due to her gender.

Nucleotides in DNA

  • The nucleotide in DNA is known as deoxyribonucleotide (contains deoxyribose).
  • Comparing DNA and RNA:
    • DNA contains deoxyribose sugar; RNA contains ribose sugar.
    • Carbon 2 in DNA has a single hydrogen (H); in RNA, Carbon 2 is attached to a hydroxyl (OH) group.
  • Structure of nucleotides:
    • Composed of a 5-carbon sugar, phosphate group, and nitrogenous bases (A, G, C, T) attached to Carbon 1.
    • Each sugar is uniquely aligned and forms a polynucleotide chain via phosphodiester bonds linking 3'-OH of one sugar to 5'-phosphate of the next.

DNA Polarity and Structure

  • DNA has a directional nature:
    • 5' end has a free phosphate group.
    • 3' end has a free hydroxyl group.
  • James Watson and Francis Crick are credited for the double helix structure, based on Franklin's findings.
  • Key features of the double helix:
    • Two antiparallel strands (run opposite in polarity).
    • Sugar-phosphate backbones on the outside, paired bases (A, T, G, C) on the inside.
    • Purines (A, G) pair with pyrimidines (C, T) via hydrogen bonds (A-T has 2 H-bonds, G-C has 3 H-bonds, which provides stability).

Bonds and Stability

  • Types of bonds in DNA:
    • Phosphodiester bonds (strong covalent bonds between sugar and phosphate).
    • Hydrogen bonds (weaker compared to phosphodiester bonds).
    • Ionic bonds (strong).
    • Van der Waals forces (weak).
  • DNA contains millions of base pairings, each sequence unique to individuals, encoding information for RNA and protein synthesis.

DNA Replication Process

  • Fast and accurate replication originates at multiple points along the DNA strand.
  • Enzymes involved:
    • DNA Polymerases: Add nucleotides to form new strands.
    • Only add to the 3'-OH end of an existing chain and grow in the 5' to 3' direction.
    • Helicase: Unwinds the DNA double helix.
    • Primase: Synthesizes a short RNA primer necessary for DNA polymerase initiation.
    • Topoisomerase: Prevents DNA from twisting during unwinding.
    • Single-Strand Binding Proteins: Stabilize unwound DNA strands.
    • DNA Ligase: Seals nicks left in the sugar-phosphate backbone after RNA primers are replaced with DNA.

Main Steps of DNA Replication

  1. Unwinding: Helicase unwinds DNA, forming a replication fork.
  2. Single Strand Stabilization: SSB proteins attach to the unwound strands.
  3. Elongation: DNA polymerase III synthesizes new strands using RNA primers as starting points.
  4. Lagging Strand Synthesis: Involves Okazaki fragments, necessitating multiple RNA primers.
  5. Removal of Primers: DNA polymerase I replaces RNA primers with DNA.
  6. Sealing Nicks: DNA ligase completes the assembly by sealing gaps in the DNA strand.

Proofreading and Error Repair

  • DNA polymerase has proofreading capabilities, correcting errors during synthesis.
  • Mismatch repair proteins rectify errors overlooked during replication.

Key Enzymes in DNA Replication

  • Helicase: Unwinds the DNA helix.
  • Topoisomerase: Prevents over-twisting of the DNA.
  • Primase: Initiates RNA primer synthesis.
  • DNA Polymerase III: Principal enzyme for DNA synthesis.
  • DNA Polymerase I: Replaces RNA primers with DNA.
  • Ligase: Joins Okazaki fragments.
  • Single-Stranded Binding Proteins (SSBP): Stabilize unwound DNA strands.

Direction and Structure of DNA Strands

  • Leading Strand: Synthesized continuously in the direction of unwinding (5' to 3').
  • Lagging Strand: Synthesized discontinuously; requires Okazaki fragments to accommodate the opposite direction of unwinding.
  • The leading and lagging strands differ in the orientation of their 5' and 3' ends, maintaining antiparallel configuration.