DNA Structure and Replication: Foundations of Genetic Inheritance

Chapter 7: DNA Structure and Replication

7.1 DNA Is the Hereditary Molecule of Life

DNA is the fundamental hereditary material in all living organisms. Before its role was established, scientists identified several essential characteristics that hereditary material must possess.

• Localized to the nucleus and a component of chromosomes.

• Present in a stable form in cells.

• Sufficiently complex to contain information needed for structure, function, development, and reproduction of an organism.

• Able to accurately replicate itself so that daughter cells contain the same information as parent cells.

• Mutable, undergoing a low rate of mutations that introduces genetic variation and serves as a foundation for evolutionary change.

Chromosomes Contain DNA

• In 1869, Friedrich Miescher isolated DNA from nuclei of white blood cells, calling it "nuclein."

• Microscopic studies soon identified the fusion of male and female nuclei during reproduction, and chromosomes were observed.

Early Evidence for DNA as Hereditary Material

• In 1895, Edmund Wilson suggested that nuclein (DNA) might be the hereditary material, noting that sperm and eggs contribute the same number of chromosomes during reproduction.

• He connected nuclein with the chromatin of chromosomes.

Rediscovery of Mendel and Chromosome Theory

• In 1900, Mendel’s hereditary principles were rediscovered.

• In 1903, Walter Sutton and Theodor Boveri described parallels between chromosome partitioning into gametes and inheritance of genes.

Focus on the Nucleus and Chromosomes

• By 1920, DNA was identified as the principal component of nuclein.

• DNA is a polynucleotide consisting of four repeating subunits: adenine (A), thymine (T), cytosine (C), and guanine (G), held together by covalent bonds.

DNA as the Candidate Hereditary Material

• By 1923, DNA was localized to chromosomes and considered a candidate for hereditary material.

• However, proteins and RNA were also present in chromosomes, and lipids and carbohydrates were considered as candidates.

The Transformation Factor Responsible for Heredity

• Frederick Griffith identified two strains of Pneumococcus: S (smooth, virulent) and R (rough, non-virulent).

• He showed that a single gene mutation could convert an S strain to an R strain of the same antigenic type.

Example: Griffith’s experiment demonstrated that heat-killed S strain bacteria could transfer hereditary material to live R strain bacteria, transforming them into virulent S type.

Griffith’s Experimental Results

• Mice infected with SIII developed pneumonia and died.

• Mice infected with RII or heat-killed SIII survived.

• Mice infected with heat-killed SIII and live RII died, and live SIII bacteria were recovered—indicating transformation.

Griffith’s Proposal

• He proposed a "transformation factor" carried hereditary information but could not identify the molecule.

• This process, now known as transformation, is used by bacteria to transfer DNA.

DNA Is the Transformation Factor

• Avery, MacLeod, and McCarty showed that only destruction of DNA prevented transformation, identifying DNA as the hereditary molecule.

DNA Is the Hereditary Molecule: Hershey-Chase Experiment

• Hershey and Chase (1952) used bacteriophages (viruses that infect bacteria) to show that DNA, not protein, is the genetic material.

• Phages inject DNA into bacteria, leaving the protein shell outside.

• Radioactive labeling of DNA and protein demonstrated that only DNA entered the bacterial cell and directed viral replication.

7.2 The DNA Double Helix Consists of Two Complementary and Antiparallel Strands

The secondary structure of DNA, identified by Franklin and modeled by Watson and Crick, is a double helix composed of two polynucleotide chains.

• Each chain is made of four types of nucleotides joined by covalent phosphodiester bonds.

• Despite its apparent simplicity, DNA is a complex informational molecule.

DNA Nucleotides

• A DNA nucleotide consists of a deoxyribose sugar, a nitrogenous base, and up to three phosphate groups.

• The sugar has five carbons (1', 2', 3', 4', 5').

• The base is attached to the 1' carbon, and the phosphate group is attached to the 5' carbon.

Types of DNA Bases

• Pyrimidines (thymine, cytosine): single ring structure.

• Purines (adenine, guanine): double ring structure.

• Deoxynucleotide monophosphates (dNMPs) are incorporated into DNA chains; deoxynucleotide triphosphates (dNTPs) are precursors not part of the chain.

Assembly of Polynucleotide Chains

• DNA polymerase catalyzes the formation of phosphodiester bonds between the 3' hydroxyl of one nucleotide and the 5' phosphate of the next.

• This forms a sugar-phosphate backbone with alternating sugars and phosphates.

The DNA Duplex: Complementarity and Antiparallel Structure

• Two polynucleotide chains form a stable double helix by two rules:

  • Complementary base pairing: A pairs with T, G pairs with C.

  • Antiparallel orientation: One strand runs 5' to 3', the other 3' to 5'.

Basis of Complementary Pairing

• Each base pair combines one purine with one pyrimidine.

• Hydrogen bonds stabilize the base pairs: two between A and T, three between G and C.

• The antiparallel arrangement is essential for stable hydrogen bonding.

The Twisting Double Helix

• Franklin’s research revealed two forms of DNA: A-form and B-form (B-form is most common).

• B-form DNA has a diameter of 20 Å (1 Å = $10^{-10}$ m), with each base pair contributing equally to the diameter.

Nucleotide Base Stacking

• Base pairs are spaced at intervals of 3.4 Å along the duplex.

• This tight packing leads to base stacking, offsetting adjacent base pairs and causing the helical twist.

Major and Minor Grooves

• Base-pair stacking creates major grooves (12 Å wide) and minor grooves (6 Å wide).

• These grooves are sites where DNA-binding proteins interact with the DNA.

The Three Forms of DNA

• B-form: Most common, right-handed helix.

• A-form: Right-handed, occasionally detected in cells, common in bacteriophage.

• Z-form: Left-handed, zigzag backbone, found near transcription start sites.

7.3 DNA Replication Is Semiconservative and Bidirectional

DNA replication ensures the accurate transmission of genetic information. The mechanism is highly conserved across all organisms.

• Each parental DNA strand remains intact during replication.

• Each parental strand serves as a template for a new, complementary daughter strand.

• Each daughter DNA duplex contains one parental and one daughter strand (semiconservative replication).

Models of DNA Replication

• Semiconservative: Each daughter duplex contains one parental and one daughter strand.

• Conservative: One duplex contains both parental strands, the other both daughter strands.

• Dispersive: Each duplex contains interspersed parental and daughter segments.

The Meselson-Stahl Experiment

• Used cesium chloride (CsCl) centrifugation to distinguish DNA molecules of different densities.

• Bacteria were grown in heavy nitrogen ($^{15}N$), then transferred to light nitrogen ($^{14}N$).

• After one replication, DNA had intermediate density; after two, half was light and half intermediate—supporting the semiconservative model.

Origin and Directionality of Replication

• Replication is bidirectional from a single origin in bacteria; eukaryotes have multiple origins.

• Replication bubbles and forks form as DNA is copied in both directions.

• Pulse-chase labeling and electron microscopy provided evidence for bidirectional replication and multiple origins in eukaryotes.

Key Concepts Table: DNA Structure and Replication

Feature	Description
Hereditary Material	DNA, localized in the nucleus, stable, complex, replicable, mutable
Nucleotide Structure	Deoxyribose sugar (5 carbons), base at 1', phosphate at 5'
Base Pairing	A-T (2 H bonds), G-C (3 H bonds), antiparallel strands
DNA Forms	B-form (common), A-form, Z-form (left-handed)
Replication Model	Semiconservative, bidirectional, multiple origins in eukaryotes

Sample Questions and Answers

Question	Answer
In a nucleotide, to which carbons are the phosphate and base attached?	Phosphate: 5' carbon; Base: 1' carbon
DNA replication in both bacteria and eukaryotes may be described as:	Bidirectional and semiconservative
What did the theta structures observed by Cairns indicate about DNA replication in E. coli?	Replication initiates from a single origin

Additional info: This summary integrates foundational experiments and structural details essential for understanding DNA as the hereditary material and the mechanism of its replication, as covered in a college-level genetics course.