In-depth Notes on Cellular Information Structure

The Structural Basis of Cellular Information: DNA, Chromosomes, and the Nucleus

Chemical Nature of the Genetic Material

• 1869: Johann Friedrich Miescher discovers DNA.
• Observation: Walther Flemming observes chromosomes during cell division.

Genes and Protein

• Pre-1940s Belief: Genes were thought to consist of proteins due to their complexity.
• Shift in Understanding: Important evidence emerged confirming that DNA is the true genetic material.

Griffith and Avery's Experiments

Griffith's Experiment

• Pathogenic Study: Frederick Griffith analyzes pneumonia-causing bacteria.
  • S-strain: Causes fatal infections in mice (smooth appearance).
  • R-strain: Non-pathogenic (rough appearance).
• Experiment: Heat-killed S-strain mixed with living R-strain injected into mice results in death, indicating transformation.
• Conclusion: R-strain converts to S-strain, demonstrating genetic transformation.

Avery's Experiment

• Focus: Identifies the transforming material using Griffith's findings.
• Process: Various components of heat-killed S bacteria destroyed (lipids, proteins, RNA), but only destruction of DNA prevents transformation.
• Conclusion: DNA is confirmed as the transforming agent.

DNA Structure

• Structure: Antiparallel, double-stranded polymer of deoxyribonucleotides.
• Base Pairing: A pairs with T and G pairs with C (complementary sequences).
• Replication: One strand can serve as a template for the other.

Key Features of DNA Structure

• Grooves: Major and minor grooves formed by twisting.
• Orientation: Strands run antiparallel (5' to 3' direction).
• Length Measurement: DNA length is commonly measured in kilobases (kb).

Supercoiling of DNA

• Formation: DNA can form supercoiled structures, crucial for compaction.
  • Positive Supercoil: DNA twisted in the same direction.
  • Negative Supercoil: DNA twisted in the opposite direction.
• Topoisomerases: Enzymes that manage supercoiling by introducing breaks in the DNA.
  • Type I: Creates single-strand breaks.
  • Type II: Creates double-strand breaks (e.g., DNA gyrase).

Denaturation and Renaturation of DNA

• Denaturation: Separation of DNA strands induced by heat or pH changes.
  • Monitored through changes in light absorption (260 nm).
• Renaturation: Cooling allows strands to reform; useful in hybridization techniques.
  • FISH: Technique using fluorescent probes to identify specific DNA sequences.

DNA Packaging in Eukaryotes

• Chromatin Formation: DNA wraps around histone proteins, creating nucleosomes (146 bp of DNA per core particle).
• Chromatin Structure: Organized into fibers and ultimately chromosomes; compacting important for cellular organization.

Heterochromatin and Euchromatin

• Heterochromatin: Densely packed, found at centromeres and telomeres, important for chromosome structure.
• Euchromatin: Less compact, active in transcription.

Repeated DNA Sequences

• Types: Includes tandemly repeated DNA (satellite DNA) and interspersed repeated DNA (transposable elements).
  • LINES: Long interspersed nuclear elements
  • SINEs: Short interspersed nuclear elements (e.g., Alu sequences).

Nuclear Structure and Function

• Nucleus: Key site for DNA replication and transcription in eukaryotic cells.
  • Contains nuclear pores for transportation between the nucleus and cytoplasm; NPC is formed by nucleoporins.
• Transport Mechanisms:
  • Small particles diffuse freely.
  • Large proteins require nuclear localization signals (NLS) for active transport across nuclear pores.

Nuclear Localization Signals (NLS)

• Characteristics: Typically 8-30 amino acids long, rich in proline, lysine, and arginine.
• Function: NLS directs proteins into the nucleus; certain sequences are sufficient for this localization.

Export Mechanism

• RNA Export: Mediated by adaptor proteins with nuclear export signals (NES), recognized by exportins for transport out of the nucleus.