Nucleic Acids and Chromosome Structure

Four Criteria Necessary for Genetic Material:
- Information: Must contain the information necessary to construct an entire organism.
- Replication: Must be accurately copied.
- Transmission: Can be passed from parent to offspring; must be passed from cell to cell.
- Variation: Must account for the known variation within each species and among different species.

Scientific Inquiry and Historical Context:
- In the 1910s, T. H. Morgan’s group demonstrated that genes are located on chromosomes.
- The two components of chromosomes, DNA and protein, became candidates for the genetic material.
- Until the 1940s, proteins were thought to be the stronger candidate.
- The role of DNA in heredity was understood through studies involving bacteria and their viruses.

Key Experiment by Frederick Griffith (1928):
- Studied Streptococcus pneumoniae with two strains:
- Pathogenic (Type S): Secretes a capsule, appears smooth (S), and causes fatal infections in mice.
- Harmless (Type R): Does not secrete a capsule, appears rough (R), and does not cause fatal infections in mice.
- Mechanism of Infection:
- The capsule shields bacteria from the immune system, allowing survival in the bloodstream.
- Key Findings:
- Mixing live R bacteria with heat-killed S bacteria resulted in the death of the mouse.
- Blood from the dead mouse contained living type S bacteria, showing that a transformation had occurred.
- This process was termed transformation.

Phenomenon Explained:
- Genetic material was transferred from heat-killed type S to live type R bacteria, giving them the ability to secrete capsules.
- Inheritance of the capsule-secreting trait was observed in offspring.
Hypothesis Formation:
- A purified macromolecule from type S that functions as genetic material can convert Type R bacteria to Type S.
- Key Materials:
- Type R and Type S strains of Streptococcus pneumoniae.

Purification of DNA:
- Break open cells and separate DNA through centrifugation.
- Mix DNA extract with Type R bacteria; replicate with DNase, RNase, or protease to digest respective nucleic acids.
- Control setup: do not add DNA extract to Type R cells.

DNA transformation results showed DNA is responsible for converting Type R cells to Type S.
Source: Avery, O.T., MacLeod, C.M., and McCarty, M. (1944). Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types.

Components:
- Nucleotides: Building blocks of DNA and RNA.
- Strand: Linear polymer of DNA or RNA.
- Double Helix: Two strands of DNA intertwined.
- Chromosomes: Complex structures of DNA associated with proteins.
- Genome: Complete genetic material of an organism.

Carbons are numbered clockwise starting from the ring oxygen.
- Carbons: Designated as 1’ to 5’ (read as “one prime”).
- Base is attached to 1' carbon, phosphate to 5' carbon, and hydroxyl group to 3' carbon on sugar.

Deoxyribonucleic Acid (DNA):
- Formed from nucleotides (A, G, C, T).
- Composed of three components:
- Phosphate Group
- Pentose Sugar: Deoxyribose (lacks oxygen in 2' position = H).
- Nitrogenous Base:
  - Purines: Adenine (A), Guanine (G).
  - Pyrimidines: Cytosine (C), Thymine (T).

Ribonucleic Acid (RNA):
- Formed from nucleotides (A, G, C, U).
- Composed of three components:
- Phosphate Group
- Pentose Sugar: Ribose (contains oxygen in 2' position = OH).
- Nitrogenous Base:
  - Purines: Adenine (A), Guanine (G).
  - Pyrimidines: Cytosine (C), Uracil (U).

Covalent Bonds: Nucleotides are covalently bonded via phosphodiester bonds where the phosphate links two sugars.
- Directionality: Written from 5' to 3' (e.g., 5' – TACG – 3').

X-ray Diffraction:
- Technique to study molecular structure by exposing DNA to X-rays and determining the pattern on photographic plates.
Contributions by Rosalind Franklin:
- Produced images allowing conclusions about DNA’s helical structure, with sugar-phosphate backbones on the exterior and bases on the inside.

Erwin Chargaff (1950):
- Demonstrated that the DNA base composition varies between species, supporting DNA as genetic material.
- Two findings known as Chargaff’s rules:
- Amount of adenine (A) = amount of thymine (T).
- Amount of cytosine (C) = amount of guanine (G).

Based on Franklin's images, Watson and Crick deduced that DNA was helical with two antiparallel strands forming a double helix, conforming to Chargaff's rules.
Base Pairing:
- A pairs with T, and G pairs with C, establishing specific pairing rules necessary for DNA replication.

Two DNA strands form a double helix structure, stabilized by hydrogen bonding.
- Major and minor grooves in the helix allow protein binding, affecting gene expression.

Chromosome Definition: Discrete units of genetic material consisting of chromatin (a DNA-protein complex), typically one linear double-stranded DNA molecule.
- Length of eukaryotic chromosomes can exceed one meter, yet must fit in cells 10 to 100 micrometers in diameter.

Nucleosomes: DNA wrapped around histone proteins, shortening its length sevenfold.
30-Nanometer Fiber Formation: Further shortening occurs in a zigzag structure involving nucleosome interactions.
Radial Loop Domains: Loop domains formed by protein interactions, ranging from 25,000 to 200,000 base pairs, further compacting DNA for cell division.

Compaction levels are not uniform; euchromatin is less compact compared to heterochromatin.
During cell division, chromosomes become even more compact, visible as metaphase chromosomes.

Semiconservative Model: Proposed by Watson and Crick, stating original strands serve as templates resulting in two new strands, each containing one parental and one daughter strand.
Experimental evidence from Meselson and Stahl confirmed the semiconservative nature of DNA replication through isotopic labeling in E. coli.

Proteins Involved:
- DNA helicase, topoisomerase, and single-strand binding proteins facilitate unwinding and stabilization of DNA strands.
- RNA primers synthesized by primase initiate new strand formation, executed by DNA polymerase.
Lagging vs. Leading Strands:
- Leading strand synthesized continuously; lagging strand synthesized in fragments (Okazaki fragments).

DNA polymerases proofread new DNA, correcting incorrect nucleotides to maintain fidelity.
Telomeres consist of repetitive sequences that do not code for genes; their shortening is implicated in cellular senescence, while telomerase can extend telomeres, often reactivated in cancer cells.