Chapter 14 – DNA Structure & Function

Discovery of DNA as Genetic Material

The identification of DNA as the molecule responsible for heredity was established through a series of landmark experiments.

• Griffith Experiment: Demonstrated the phenomenon of transformation in bacteria, showing that a 'transforming principle' could transfer genetic information from dead to living cells.

• Avery, MacLeod, McCarty Experiment: Identified DNA as the 'transforming principle' by systematically eliminating proteins, RNA, and DNA from bacterial extracts and showing only DNA could transform cells.

• Hershey & Chase Experiment: Used radioactive labeling of DNA and protein in bacteriophages to show that DNA, not protein, enters bacterial cells and directs viral replication.

Example: Hershey and Chase used 32P to label DNA and 35S to label protein, confirming DNA as the genetic material.

General Structure of DNA

DNA (deoxyribonucleic acid) is a double helix composed of two antiparallel strands of nucleotides.

• Nucleotide: Consists of a phosphate group, deoxyribose sugar, and a nitrogenous base (adenine, thymine, cytosine, guanine).

• Double Helix: The two strands are held together by hydrogen bonds between complementary bases.

Complementary Base Pairing

• Adenine (A) pairs with Thymine (T) via two hydrogen bonds.

• Cytosine (C) pairs with Guanine (G) via three hydrogen bonds.

Models of DNA Replication

Three models were proposed for DNA replication:

• Conservative: Parental DNA remains intact; new DNA is entirely new.

• Semiconservative: Each new DNA molecule consists of one parental and one new strand.

• Dispersive: Parental and new DNA are interspersed in both strands.

Correct Model: The semiconservative model is correct.

Meselson-Stahl Experiment: Used isotopic labeling of nitrogen to demonstrate semiconservative replication.

Enzymes and Proteins in DNA Replication

• DNA Polymerase: Synthesizes new DNA strands by adding nucleotides to the 3' end.

• DNA Polymerase I: Removes RNA primers and replaces them with DNA.

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

• Primase: Synthesizes short RNA primers to initiate DNA synthesis.

• Ligase: Joins Okazaki fragments on the lagging strand by forming phosphodiester bonds.

• Helicase: Unwinds the DNA double helix at the replication fork.

• Topoisomerase: Relieves supercoiling ahead of the replication fork.

• Single-Strand DNA Binding Proteins (SSBPs): Stabilize unwound DNA strands and prevent reannealing.

• Sliding Clamp: Holds DNA polymerase in place during strand extension.

Replication Fork and DNA Synthesis

• Replication Fork: The Y-shaped region where DNA is unwound and new strands are synthesized.

• Direction of Synthesis: DNA nucleotides are always added to the 3' end of the growing strand.

Leading vs. Lagging Strand

• Leading Strand: Synthesized continuously in the direction of the replication fork.

• Lagging Strand: Synthesized discontinuously in short segments (Okazaki fragments) away from the fork.

Okazaki Fragments: Short DNA fragments synthesized on the lagging strand, later joined by DNA ligase.

Telomerase and DNA Repair Mechanisms

• Telomerase: Enzyme that extends telomeres (repetitive DNA at chromosome ends) to prevent loss of genetic information during replication.

• Nucleotide Excision Repair: Removes bulky DNA lesions (e.g., thymine dimers) by excising a short single-stranded DNA segment and filling the gap.

• Mismatch Repair: Corrects errors missed by DNA polymerase proofreading by removing and replacing mismatched bases.

Types of Mutations

• Silent Mutation: Alters a codon but does not change the amino acid sequence.

• Missense Mutation: Changes a codon, resulting in a different amino acid.

• Nonsense Mutation: Converts a codon into a stop codon, leading to premature termination.

• Frameshift Mutation: Insertion or deletion of nucleotides that shifts the reading frame, altering downstream amino acids.

Chapter 9 – Cell Communication

Cell Signaling Overview

Cell signaling is the process by which cells detect and respond to external or internal signals, coordinating cellular activities.

Types of Cell Signaling

• Autocrine Signaling: Cells respond to signals they themselves produce.

• Paracrine Signaling: Signals are released to affect nearby cells.

• Juxtacrine Signaling: Direct contact between neighboring cells via membrane-bound molecules.

• Endocrine Signaling: Hormones are released into the bloodstream to affect distant target cells.

Local vs. Long-Distance Signaling: Local signaling (autocrine, paracrine, juxtacrine) affects nearby cells, while long-distance signaling (endocrine) involves hormones traveling through the circulatory system.

Stages of Cell Signaling

• Reception: Signal molecule (ligand) binds to a receptor protein.

• Transduction: Signal is relayed and amplified through a cascade of molecular events.

• Response: The cell carries out a specific activity, such as gene expression or metabolic change.

Short-Term vs. Long-Term Responses

• Short-Term Responses: Rapid, temporary changes such as enzyme activation or ion channel opening.

• Long-Term Responses: Changes in gene expression, cell growth, or differentiation that persist over time.

Ligands

• Ligand: A molecule that binds specifically to a receptor, triggering a cellular response. Examples include hormones, neurotransmitters, and growth factors.