Discovery of DNA's structure and function Knowledge-Based Study

Study notes

1. Historical Experiments Identifying DNA

   Prior to the mid-twentieth century, many scientists presumed proteins were the carriers of genetic information due to their structural complexity and composition of 20 amino acids, compared to only four nucleotides in DNA. A series of landmark experiments proved that DNA is the true genetic material:

   • Frederick Griffith (1928): Demonstrated the phenomenon of transformation using two strains of Streptococcus pneumoniae. Living non-virulent R strain bacteria absorbed a hereditary factor from heat-killed virulent S strain bacteria and transformed into live, virulent S strain organisms.
   • Avery, MacLeod, and McCarty (1944): Systematically treated heat-killed S strain extracts with digestive enzymes (proteases, RNases, and DNases). Transformation was prevented only when DNase degraded the DNA, demonstrating that DNA is the transforming agent.
   • Hershey and Chase (1952): Used bacteriophage T2 labeled with radioactive isotopes to determine whether protein or DNA entered bacterial host cells during infection. Phage protein coats were labeled with sulfur-35 ($^{35}\text{S}$) and viral DNA was labeled with phosphorus-32 ($^{32}\text{P}$). Agitation in a blender and subsequent centrifugation showed that only $^{32}\text{P}$ entered the bacterial cells and directed the production of new viral particles, definitively establishing DNA as the genetic material.

   The Chemical Basis of Nucleotides

   A DNA molecule is a polymer of nucleotides. Each nucleotide consists of three structural components:

   1. A five-carbon pentose sugar (deoxyribose)
   2. A negatively charged phosphate group attached to the 5' carbon
   3. A nitrogenous base attached to the 1' carbon

   Nitrogenous bases are classified into two groups:

   • Purines: Double-ring bases, adenine (A) and guanine (G).
   • Pyrimidines: Single-ring bases, cytosine (C) and thymine (T).

   Chargaff's Discovery

   In 1950, biochemist Erwin Chargaff analyzed the base composition of DNA extracted from various organisms and established two essential empirical rules:

   • The base composition of DNA varies across different species, demonstrating molecular diversity.
   • Within a given species, the percentage of adenine equals thymine ($\text{A} = \text{T}$), and the percentage of guanine equals cytosine ($\text{G} = \text{C}$). Consequently, the total amount of purines equals the total amount of pyrimidines ($\text{A} + \text{G} = \text{T} + \text{C}$).

   X-Ray Crystallography and Structural Modeling

   In the early 1950s, physical evidence was integrated with chemical data to decipher the three-dimensional geometry of DNA:

   • Rosalind Franklin and Maurice Wilkins: Franklin utilized X-ray diffraction techniques to produce high-resolution diffraction patterns of crystallized DNA fibers. Her famous Photo 51 revealed distinct structural features: an X-shaped diffraction pattern characteristic of a helix, a uniform diameter of 2.0 nanometers, a distance of 0.34 nanometers between adjacent base pairs, and a full helical repeat period of 3.4 nanometers (comprising 10 base pairs per turn).
   • James Watson and Francis Crick (1953): By combining Franklin's crystallographic measurements with Chargaff's base-pairing ratios, Watson and Crick constructed the double-helical model of DNA.

   Key Features of the Double Helix

   • Two antiparallel strands: The two polynucleotide chains run in opposite orientations; one strand runs in the 5' to 3' direction, while the complementary strand runs 3' to 5'.
   • Sugar-phosphate backbone: Located on the exterior of the helix, joined by strong covalent phosphodiester bonds.
   • Complementary base pairing: Located on the interior of the helix. Specific purines pair exclusively with specific pyrimidines: adenine forms two hydrogen bonds with thymine ($\text{A}=\text{T}$), and guanine forms three hydrogen bonds with cytosine ($\text{G}\equiv\text{C}$). This specific pairing accounts for the consistent 2.0 nanometer width of the helix.

   Connecting Molecular Structure to Genetic Function

   The discovery of the double helix immediately clarified how DNA fulfills its biological roles:

   • Information Storage: Genetic instructions are encoded linearly within the sequence of nitrogenous bases along the strand. Because nucleotide sequences can vary infinitely, DNA can store vast amounts of developmental and metabolic instructions.
   • Mechanism for Replication: Watson and Crick famously noted that the specific pairing of bases immediately suggested a copying mechanism. Because each strand is complementary to the other, each individual strand serves as a template during replication. This directly pointed to a semiconservative mode of replication, which was later experimentally confirmed by Meselson and Stahl in 1958.
   • Chemical Stability: The internal arrangement of hydrophobic nitrogenous bases, supported by horizontal hydrogen bonds and vertical base-stacking interactions, protects the genetic code from chemical alteration, while the exposed hydrophilic sugar-phosphate backbone provides structural stability in an aqueous cellular environment.