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DNA Structure and Packaging: Key Experiments and Molecular Details

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DNA Structure and Packaging

Introduction

DNA (deoxyribonucleic acid) is the hereditary material in almost all living organisms. Understanding its structure and the experiments that revealed its role as the genetic material is foundational in cell biology. This section summarizes the historical experiments, molecular composition, and structural features of DNA.

Experiments on the Nature of DNA

Griffith's Experiment (1928)

  • Objective: To determine how certain bacteria cause disease.

  • Method: Mice were injected with different combinations of Streptococcus pneumoniae (smooth/virulent and rough/non-virulent forms).

  • Findings: Mice injected with a mixture of heat-killed virulent (smooth) bacteria and live non-virulent (rough) bacteria died, indicating that a 'transforming principle' from the dead bacteria converted the non-virulent bacteria into a virulent form.

  • Conclusion: The ability to cause disease (virulence) was transferred via a molecule, later identified as DNA. This process is called transformation.

  • Example: Transformation is now a standard technique in molecular biology for introducing new genetic material into cells.

Avery, MacLeod, and McCarty (1944)

  • Objective: To identify the 'transforming principle' responsible for transferring genetic information.

  • Method: Repeated Griffith's experiment, systematically removing proteins, RNA, and lipids from the heat-killed smooth bacteria.

  • Findings: Only when DNA was degraded did transformation not occur, indicating DNA was the information-carrying molecule.

  • Conclusion: DNA, not protein or RNA, is the genetic material.

Hershey and Chase (1952)

  • Objective: To provide definitive evidence that DNA is the genetic material.

  • Method: Used bacteriophages (viruses that infect bacteria) labeled with radioactive isotopes: 32P for DNA and 35S for protein. After infection, they separated the viral protein coats from the bacteria.

  • Findings: Only radioactive DNA entered the bacterial cells and directed viral replication, not the protein.

  • Conclusion: DNA is the molecule responsible for heredity in viruses as well.

Discovery and Chemical Composition of DNA

Miescher (1869)

  • Discovery: Identified a substance in the nucleus with high nitrogen (N) and phosphorus (P) content, which he named nucleic acids.

  • Properties: Acidic, associated with the nucleus.

Biomolecular Composition of DNA

  • Nucleotide: The basic unit of DNA, consisting of a nucleoside (sugar + base) and a phosphate group.

  • Sugar: Deoxyribose (a five-carbon sugar).

  • Phosphate: Attached to the 5' carbon of the sugar.

  • Nitrogenous Bases: Attached to the 1' carbon of the sugar. The bases are:

    • Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA)

    • Purines: Adenine (A), Guanine (G)

  • Directionality: DNA strands have a 5' phosphate end and a 3' hydroxyl end. New nucleotides are added to the 3' end.

Theories and Rules on Base Composition

Levene's Tetranucleotide Theory (1910–1938)

  • Proposed that DNA was composed of repeating units of four nucleotides in a fixed sequence. This theory was later disproven.

Chargaff's Rules

  • Found that the amount of adenine (A) equals thymine (T), and guanine (G) equals cytosine (C) in DNA from various organisms.

  • This base pairing regularity suggested a specific pairing mechanism in DNA structure.

DNA Source

Adenine

Thymine

Guanine

Cytosine

Calf

1.7

1.6

1.2

1.0

Yeast

1.8

1.9

1.0

1.0

Bacteria

1.1

1.0

2.6

2.4

Determining DNA Structure

Franklin and Wilkins

  • Used X-ray diffraction to show that DNA is a helical molecule and measured its dimensions.

Watson and Crick (1953)

  • Proposed the double-helix model of DNA based on X-ray data and Chargaff's rules.

  • Key features of the model:

    • Phosphate groups are on the outside of the helix; bases are on the inside.

    • DNA is a double helix held together by hydrogen bonds between bases.

    • The two strands are antiparallel (run in opposite directions).

    • Base pairing explains Chargaff's rules: A pairs with T, G pairs with C.

Structural Details

  • One complete turn of the helix is 3.4 nm in height and contains 10 base pairs, so the distance between bases is 0.34 nm.

Hydrogen Bonding in DNA

  • Base Pairing: Purines (A, G) pair with pyrimidines (T, C) via hydrogen bonds.

  • Specificity: A pairs with T via two hydrogen bonds; G pairs with C via three hydrogen bonds.

  • Stability: While individual hydrogen bonds are weak, the large number of bonds in the DNA molecule provides overall stability.

Rule: Hydrogen bonds form between a hydrogen atom bound to nitrogen on one base and oxygen or nitrogen on the other base.

Summary Table: Base Pairing

Base Pair

Number of Hydrogen Bonds

Adenine–Thymine (A–T)

2

Guanine–Cytosine (G–C)

3

Key Equations and Concepts

  • Nucleotide Structure:

    • Nucleotide = Nucleoside + Phosphate

    • Nucleoside = Sugar + Base

  • Base Pairing:

Additional info: The discovery of DNA's structure paved the way for understanding genetic replication, gene expression, and modern biotechnology techniques.

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