Notes on DNA Structure, Packaging, and Replication

Acknowledgement

  • Acknowledge the Traditional Owners of the land: Wurundjeri People of the Kulin Nation.
  • Respect to Elders: past, present, and emerging.
  • Recognition of connection to Wurundjeri Country and commitment to respect Indigenous heritage.

Topic Learning Objectives

  1. Basic Properties of DNA:
    • Understand nucleotides, complementary base pairing, double-strand helix structure.
  2. DNA Packaging and Regulation:
    • Explore how DNA is organized within the cell.
  3. DNA Replication Process:
    • Describe the enzymes involved in DNA replication and their functions.
  4. Leading vs Lagging Strand Replication:
    • Compare and contrast replication on leading and lagging strands.

Introduction to DNA, Chromosomes, and Genome

  • DNA Structure:
    • Eukaryotic DNA consists of two complementary strands of nucleotides.
    • Nucleotides include:
    • Guanine (G)
    • Adenine (A)
    • Cytosine (C)
    • Thymine (T)
    • Covalent bonds form the sugar-phosphate backbone with orientation indicated by 5’ and 3’ ends.

Genome

  • Definition:
    • Complete set of genes or genetic material in a cell or organism.
  • Usage of DNA:
    • Chromosomes carry genes, which are segments of DNA that encode for proteins.

Chromosome Organization

  • DNA Hybridization:
    • Visualizes chromosomes and their structure as per karyotypes.
  • Coding vs Non-Coding DNA:
    • Only 1% of DNA codes for proteins.
    • Exons: coding regions.
    • Introns: noncoding regions.
    • Regulatory DNA sequences control gene expression and protein production.

Cell Cycle and DNA Replication

  • Cell Cycle Phases:
    • Interphase: Genes expressed, chromosomes replicated.
    • M-phase: Chromosomes condense and divide.
  • Specialized DNA Regions:
    • Replication origin, centromere, telomere.

DNA Packaging

  • Nucleosome Formation:
    • Nucleosomes compact DNA extensively (e.g., Chromosome 22 contains 48 million nucleotide pairs).
  • Chromatin Types:
    • Euchromatic: less condensed (active).
    • Heterochromatic: more condensed (inactive).

DNA Replication Mechanism

  • Enzymes in Replication:
    • Helicase: Unwinds the double-stranded DNA.
    • SSB Proteins: Stabilize separated strands.
    • DNA Polymerase: Synthesizes new DNA strands in the 5’ to 3’ direction.
  • Replication Fork:
    • Multiple enzymes operate at replication forks to synthesize daughter strands.
    • Lagging strand synthesized in fragments (Okazaki fragments).

Leading vs Lagging Strand

  • Leading Strand:
    • Synthesized continuously in the 5’ to 3’ direction.
  • Lagging Strand:
    • Synthesized as Okazaki fragments, requires RNA primer (made by DNA primase) to start synthesis.
    • Fragments joined by DNA ligase post-synthesis.

DNA Polymerase Functions

  • Proofreading Ability:
    • Exonucleolytic proofreading increases fidelity during DNA replication (errors decreased to 1 in 10 billion).

Telomere Maintenance

  • Function of Telomeres:
    • Composed of repeated sequences (e.g., GGGTTA).
    • Telomerase replenishes telomeric sequences during cell division, counteracting the potential shortness from incomplete replication at lagging strands.
  • Reverse Transcriptase Activity:
    • Uses RNA template to extend the lagging strand, allowing for complete DNA synthesis.