DNA Structure and Replication

Nucleic acids allow for the transmission of diverse genetic information through various genes.
This genetic diversity leads to different cellular functions based on how genes are transcribed into proteins.
Key Concept: Mutation capacity of DNA
- Important for adaptation to environmental changes (e.g., global warming, new diseases).
- Balances replication accuracy with the ability to mutate, promoting evolution.

Main Cellular Components:
- Polysaccharides
- Lipids
- Proteins
- DNA
- RNA
Pre-1944 belief: Proteins were thought to be the genetic material due to:
- Greater variety (20 amino acids vs. 4 nucleotide bases: A, G, C, T).
- Perception of DNA as repetitive (junk DNA).
Quote Highlight: Nobel Prize winner's comment on DNA being a "stupid substance".
Shift to Understanding DNA as Genetic Material: Through significant experiments proving DNA's role.

Organism: Streptococcus pneumoniae (causes pneumonia).
Two bacterial strains:
- R Strain (rough): Avirulent (does not cause disease).
- S Strain (smooth): Virulent (causes disease).
Key Observations:
- Infected mice with:
- S strain => Death
- R strain => Survival
- Heat-killed S strain => Survival.
- Mixed heat-killed S strain with live R strain => Mice died; living S strain recovered from dead mice.
Conclusion: Nonliving heritable substance transformed R strain into virulent S strain.

Investigated what component was responsible for transformation in Griffith's experiment.
Methods included:
- Enzymatic degradation of components (polysaccharides, lipids, RNA, proteins, DNA).
Result:
- Destruction of DNA resulted in loss of transforming ability.
Conclusion: DNA must be the genetic material.

Components of a Nucleotide:
- Deoxyribose sugar
- Phosphate group (attached to the 5' end)
- Nitrogenous base (attached to the 1' end, can be A, T, C, G).
Deoxyribose Sugar: Differs from ribose by having a hydrogen at the 2' position instead of a hydroxyl group.
Importance of 3' and 5' positions for DNA replication.

Types of Bases:
- Purines: Adenine (A), Guanine (G) - two-ring structure.
- Pyrimidines: Cytosine (C), Thymine (T) - single-ring structure.
Mnemonic: Purines are larger than pyrimidines.

Study on Nucleotide Composition:
- Found that the number of adenines (A) equals thymines (T), and the number of guanines (G) equals cytosines (C).
Conclusions:
- Ratio: A = T; G = C.
- Sum of purines (A + G) equals sum of pyrimidines (C + T).
Example Calculation:
- If 20% A, then also 20% T, leaving 60% for C and G, thus 30% each.

Focused on bacteriophages (viruses affecting bacteria) to determine genetic material.
Used radioactive sulfur (protein) and phosphorus (DNA) labels.
Findings:
- Radioactive phosphorus found inside E. Coli, confirming DNA as genetic material.
- Quote: "DNA is the molecule, resulting in madness for those who study it."

Rosalind Franklin and Maurice Wilkins: X-ray crystallography leading to DNA structural insights.
- Results: DNA has a helical structure with a consistent width of 2 nm and a helical turn of 3.4 nm.
Watson and Crick (1953): Modeling DNA structure based on previous studies, defining base pairing rules (A-T, G-C) compatible with Chargaff's rules.

A pairs with T (two hydrogen bonds).
G pairs with C (three hydrogen bonds).
Importance: Pairing allows for easier separation at the AT-rich regions during replication. Hydrogen bonds vs phosphodiester bonds: Hydrogen bonds hold bases together, phosphodiester bonds hold the sugar-phosphate backbone.

Ways to Replicate DNA:
- Semi-conservative: Each DNA molecule is composed of one old and one new strand.
- Conservative: Original strands remain intact while new strands synthesize.
- Dispersive: New strands are mixed with old segments.

Experiment Steps:
- Labeled DNA of E. Coli with heavy (15N) and light (14N) nitrogen.
- Observed density separation patterns in centrifuged samples.
Findings: Confirmed semi-conservative replication through density shift observations.

Components: Origin of replication, helicase, primers, DNA polymerases, ligase.
Leading Strand: Continuous synthesis towards the replication fork with one RNA primer.
Lagging Strand: Built discontinuously through Okazaki fragments, requiring multiple RNA primers.

Helicase: Unwinds DNA.
DNA Polymerase:
- Polymerase I: Replaces RNA primers with DNA.
- Polymerase III: Responsible for synthesizing the bulk of DNA.
Primer: RNA sequence created by primase to initiate synthesis on template strand.
Ligase: Joins Okazaki fragments on lagging strand.

Eukaryotes have multiple linear chromosomes, necessitating multiple origins.
Coordination is crucial to ensure proper replication timing and prevention of mutations.

Telomeres: Repeated nucleotide sequences at chromosome ends to prevent shortness during replication (TTAGGG in humans).
Enzyme: Telomerase, an RNA-protein complex, adds telomeric sequences back to ends using reverse transcriptase.
Implications: Active in germ cells, critical for mitigating chromosomal shortening; associated with aging and cancer.

Lack of telomere maintenance can lead to premature aging syndromes (e.g., Werner syndrome).
Telomerase inhibitors hold potential for cancer therapies targeting overactive telomerase in cancer cells.
Effects: Maintains genetic material integrity while allowing for controlled cellular aging.