DNA Replication Detailed Notes

DNA Replication Overview

Interphase Steps in Cell Cycle

• G1 (Gap 1): Growth phase where the cell prepares for DNA synthesis.
• S (Synthesis): DNA replication occurs; each chromosome is replicated to form sister chromatids.
• G2 (Gap 2): Cell continues to grow and prepares for mitosis.
• M (Mitotic Phase): Includes mitosis and cytokinesis, leading to cell division.

Structure of DNA

• Double Helix: Comprised of two anti-parallel strands.
  • Strands are connected by hydrogen bonds between nitrogenous bases.
• Base Pairing: Specific pairing between bases:
  • Adenine (A) pairs with Thymine (T)
  • Cytosine (C) pairs with Guanine (G)
• Bonding: Covalent phosphodiester bonds connect the sugar-phosphate backbone.
• Dimensions:
  • Distance between base pairs is 0.34 nm.
  • Helix makes a full turn every 3.4 nm.

DNA Strand Orientation

• Strands run in opposite directions (anti-parallel):
  • One strand runs 5’ to 3’ and the other runs 3’ to 5’.
• 3' Hydroxyl and 5' Phosphate ends determine directionality.

Bonding Mechanisms

• Covalent Bonds: Strong bonds that form the backbone of DNA.
• Hydrogen Bonds: Weaker bonds between complementary bases facilitating strand separation during replication.
  • 2 hydrogen bonds between A-T.
  • 3 hydrogen bonds between C-G.

DNA Replication Process

• Semi-Conservative Replication:
  • Each new DNA molecule consists of one old (parent) strand and one new strand.
• Enzymes Involved in DNA Replication:
  • DNA Polymerase III: Main enzyme; adds nucleotides to the growing strand at a rate of 1000 bases/second.
  • DNA Polymerase I: Involved in editing, repairing, and primer removal at a rate of 20 bases/second.
• Origin of Replication: Multiple sites along DNA for simultaneous replication.

Energy Requirements for Replication

• Nucleoside Triphosphates (dNTPs) provide energy due to high-energy bonds.
  • Energy is released during the incorporation of dNTPs into the DNA strand.

Proofreading and Error Correction

• High Fidelity: DNA polymerase proofreading reduces error rates significantly from 1 in 10,000 to 1 in 100 million.
  • Nuclease Enzymes: Cut damaged DNA, which is then repaired by DNA polymerases.
  • DNA Ligase: Seals nicks in the DNA after repairs.

Speed and Accuracy of Replication

• E. coli can replicate 5 million base pairs in under an hour, demonstrating high efficiency.
• Human Cells replicate 6 billion bases in just a few hours with a similar accuracy.
  • Average error rate is approximately 1 error per 100 million bases.
  • Results in about 30 errors per cell cycle.

Leading and Lagging Strands

• Leading Strand: Continuously synthesized in the direction of replication fork opening.
• Lagging Strand: Synthesized discontinuously as Okazaki fragments, requiring multiple priming events.