7. DNA Structure and Replication

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Chapter 7: DNA Structure and Replication

7.1 DNA Is the Hereditary Molecule of Life

DNA is recognized as the fundamental hereditary molecule, possessing several essential characteristics that enable it to serve as the genetic material in all living organisms.

Localization: DNA is found in the nucleus and is a component of chromosomes.
Stability: DNA exists in a stable form within cells, ensuring reliable transmission of genetic information.
Complexity: DNA is sufficiently complex to encode all the information required for the structure, function, development, and reproduction of an organism.
Replication: DNA can accurately replicate itself, allowing daughter cells to inherit identical genetic information from parent cells.
Mutability: DNA undergoes mutations at a low rate, introducing genetic variation that underpins evolutionary change.

Chromosomes Contain DNA

The discovery of DNA dates back to 1869, when Friedrich Miescher isolated it from the nuclei of white blood cells, naming it "nuclein." Subsequent microscopic studies revealed the fusion of male and female nuclei during reproduction, and chromosomes were soon identified as carriers of hereditary material.

Early Suggestion That DNA Was the Hereditary Material

In 1895, Edmund Wilson proposed that DNA might be the hereditary material, noting that sperm and eggs contribute equal numbers of chromosomes during reproduction. He connected Miescher's nuclein to chromatin in chromosomes.

Rediscovery of Mendel

Mendel's principles of heredity were rediscovered in 1900. In 1903, Walter Sutton and Theodor Boveri independently described the parallels between chromosome partitioning into gametes and the inheritance of genes, reinforcing the chromosomal theory of inheritance.

Focus on the Nucleus and Chromosomes

By 1920, DNA was identified as the principal component of nuclein. Its basic chemistry was deciphered, revealing that DNA is a polynucleotide composed of four repeating subunits: adenine (A), thymine (T), cytosine (C), and guanine (G), held together by covalent bonds.

DNA as the Candidate Hereditary Material

In 1923, DNA was localized to chromosomes and considered a candidate for hereditary material. However, proteins, RNA, lipids, and carbohydrates were also considered possible candidates due to their presence in chromosomes.

The Transformation Factor Responsible for Heredity

Frederick Griffith's experiments with Pneumococcus bacteria identified two strains: S (smooth, virulent) and R (rough, non-virulent). He demonstrated that a single gene mutation could convert an S strain to an R strain of the same antigenic type.

Example: Griffith's Experiment

Mice infected with SIII strain developed pneumonia and died.
Mice infected with RII strain or heat-killed SIII survived.
Mice infected with heat-killed SIII and live RII developed pneumonia and died; live SIII bacteria were recovered, indicating transformation.

Griffith’s Proposal

Griffith proposed the existence of a "transformation factor" that could transfer hereditary information, but he could not identify the molecule. He described the process of transformation, now known as the uptake of DNA by bacteria.

DNA Is the Transformation Factor

Avery, MacLeod, and McCarty demonstrated that DNA is the transformation factor by showing that only destruction of DNA prevented transformation in their experiments with heat-killed SIII and live RII bacteria.

DNA Is the Hereditary Molecule

Hershey and Chase (1952) confirmed that DNA is responsible for bacteriophage infection of bacterial cells. Bacteriophages are viruses that infect bacteria, consisting of a protein shell and a DNA-containing head.

Hershey and Chase Experiments

Proteins contain sulfur, DNA contains phosphorus.
Phages were labeled with radioactive 35S (protein) or 32P (DNA).
After infection and agitation, radioactivity was found in the empty phage particles (protein label) or inside bacteria (DNA label), proving DNA is the genetic material.

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

Structure of DNA

Rosalind Franklin identified the secondary structure of DNA, which was modeled by Watson and Crick. DNA consists of four nucleotides joined by covalent phosphodiester bonds, forming two polynucleotide chains that create a double helix.

DNA Nucleotides

A DNA nucleotide is composed of a sugar (deoxyribose), a nitrogenous base, and up to three phosphate groups.
The base attaches to the 1' carbon, a hydroxyl group to the 3' carbon, and phosphates to the 5' carbon.

Types of DNA Bases

Pyrimidines: Thymine and cytosine (single ring).
Purines: Adenine and guanine (double ring).
dNMPs: Deoxynucleotide monophosphates, part of polynucleotide chains.
dNTPs: Deoxynucleotide triphosphates, not part of chains.

Assembly of Polynucleotide Chains

DNA polymerase catalyzes the formation of phosphodiester bonds between nucleotides.
Each chain has a sugar-phosphate backbone of alternating sugar and phosphate groups.

The DNA Duplex

Complementary base pairing: A pairs with T, G pairs with C.
Antiparallel strands: The two strands run in opposite directions (5' to 3' and 3' to 5').

Basis of Complementary Pairing

One purine pairs with one pyrimidine.
Stable hydrogen bonds form: two between A and T, three between G and C.
Antiparallel arrangement is essential for stable hydrogen bonding.

The Twisting Double Helix

Franklin's research revealed A-form and B-form DNA; B-form is most common.
B-form DNA has a diameter of 20 Å ( m).
Each purine-pyrimidine base pair yields the same dimension.

Nucleotide Base Stacking

Base pairs are spaced at intervals of 3.4 Å.
Base stacking: Offset of adjacent base pairs so their planes are parallel, leading to the helical twist.

Major and Minor Grooves

Base-pair stacking creates gaps (grooves) in the sugar-phosphate backbone.
Major groove: ~12 Å wide; Minor groove: ~6 Å wide.
Grooves are sites for DNA-binding proteins to interact with nucleotides.

Three Forms of DNA

Form	Helical Twist	Rotation per Base Pair	Base-Pair Spacing	Base Pairs per Turn	Helix Diameter
A-Form	Right-handed	32.7°	2.6 Å	11	23 Å
B-Form	Right-handed	34.3°	3.4 Å	10.5	20 Å
Z-Form	Left-handed	60.2°	3.7 Å	12	18 Å

Additional info:

Z-form DNA is commonly found near transcription start sites and has a zigzag backbone due to its left-handed twist.