DNA Structure, Chromosomes, and DNA Replication: Key Concepts and Mechanisms

Chapter 16: DNA & Chromosomes

Key Experiments in DNA Discovery

The identification of DNA as the genetic material was established through a series of landmark experiments.

• Avery-Griffith's Experiments: Demonstrated that DNA is the substance responsible for transformation in bacteria.

• Hershey-Chase Experiment: Used bacteriophages to show that DNA, not protein, is the genetic material.

• Chargaff's Rules: Established that the amount of adenine equals thymine and the amount of guanine equals cytosine in DNA.

• Watson & Crick Model: Proposed the double helix structure of DNA based on X-ray diffraction data and chemical analysis.

Features of DNA Structure

DNA is a double-stranded helical molecule with specific base pairing and structural properties.

• Double Helix: Two antiparallel strands twisted into a helix.

• Antiparallel Strands: The two DNA strands run in opposite directions (5' to 3' and 3' to 5').

• Complementary Base Pairing: Adenine pairs with thymine, and guanine pairs with cytosine via hydrogen bonds.

• Supercoiling: DNA can be further twisted to fit within the cell.

• Denaturation/Renaturation: DNA strands can separate (denature) and rejoin (renature) under certain conditions.

DNA Packaging and Chromatin Structure

DNA is organized and compacted within the cell nucleus through association with proteins.

• Chromatin: DNA-protein complex that forms chromosomes.

• Histones: Proteins that DNA wraps around to form nucleosomes.

• Nucleosomes: Fundamental units of chromatin, consisting of DNA wrapped around histone octamers.

• Loops and Heterochromatin: Higher-order structures that further compact DNA.

• Plasmids: Small, circular DNA molecules found in bacteria.

Chapter 17: Cell Cycle, DNA Replication, Mutation, and Repair

M-Phase, Interphase, and Cell Cycle Checkpoints

The cell cycle consists of distinct phases and regulatory checkpoints to ensure proper cell division.

• M-Phase: Mitotic phase where cell division occurs.

• Interphase: Period of cell growth and DNA replication (G1, S, G2 phases).

• Cell Cycle Checkpoints: Control mechanisms that ensure the fidelity of cell division.

DNA Replication Mechanisms

DNA replication is a semiconservative process involving multiple enzymes and steps.

• Meselson-Stahl Experiment: Demonstrated semiconservative replication, where each daughter DNA contains one parental and one new strand.

• Origin of Replication: Specific DNA sequence where replication begins.

• Replication Fork: Y-shaped region where DNA is unwound and replicated.

• Single-Stranded Binding Proteins (SSB): Stabilize unwound DNA strands.

• Topoisomerases (Gyrase): Relieve supercoiling tension ahead of the replication fork.

• DNA Helicase: Unwinds the DNA double helix.

• Primase: Synthesizes RNA primers to initiate DNA synthesis.

• RNA Primers: Short RNA sequences required for DNA polymerase to begin synthesis.

• DNA Polymerase III (Bacteria): Main enzyme for DNA synthesis in prokaryotes.

• DNA Polymerase I (Bacteria): Removes RNA primers and fills in gaps.

• DNA Ligase: Seals nicks in the DNA backbone.

• Polymerase Chain Reaction (PCR): Laboratory technique to amplify DNA sequences.

Equation for DNA synthesis:

$\text{(dNMP)}_n + dNTP \rightarrow \text{(dNMP)}_{n+1} + PP_i$

End Replication Problem and Telomeres

Linear chromosomes face challenges in replicating their ends, which is solved by telomeres and the enzyme telomerase.

• Telomeres: Repetitive DNA sequences at chromosome ends that protect genetic information.

• Telomerase: Enzyme that extends telomeres, preventing loss of DNA during replication.

DNA Mutation and Repair Mechanisms

Cells possess multiple mechanisms to repair DNA damage and maintain genetic integrity.

• Mutagens: Physical (e.g., radiation) and chemical agents that cause DNA mutations.

• Base Excision Repair: Removes and replaces damaged bases.

• Nucleotide Excision Repair: Removes bulky DNA lesions, such as thymine dimers.

• Homologous Recombination: Repairs double-strand breaks using a homologous template.

• Non-homologous End Joining: Directly ligates broken DNA ends without a template.

Comparison of DNA Repair Mechanisms

Repair Mechanism	Main Function	Template Required?
Base Excision Repair	Removes single damaged bases	No
Nucleotide Excision Repair	Removes bulky lesions	No
Homologous Recombination	Repairs double-strand breaks	Yes
Non-homologous End Joining	Repairs double-strand breaks	No

Additional info: The notes have been expanded to include definitions, mechanisms, and examples for each listed topic to provide a comprehensive study guide for cell biology students.