🧬 Molecular Basis of Inheritance

Deoxyribonucleic acid (DNA) is the molecular blueprint of life. The informational content of living systems is encoded in discrete nucleotide sequences, replicated with sub-error proofreading fidelity, and translated through a universal triplet genetic code.

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1. 🧪 DNA Architecture & Chargaff's Equivalence Rules

Watson and Crick (1953) proposed the double-helical model of B-DNA based on Rosalind Franklin & Maurice Wilkins' X-ray diffraction data:

1. Two polynucleotide chains wound in a right-handed antiparallel orientation ($5^{\prime }\to 3^{\prime }$ and $3^{\prime }\to 5^{\prime }$).
2. Pitch of Helix: $3.4\text{nm}$ ($34\text{AA}$) containing $\text{a}\approx 10\text{base pairs (bp)}$ per turn; distance between adjacent base pairs = $0.34\text{nm}$ ($3.4\text{AA}$).
3. Hydrogen Bonding: Adenine pairs with Thymine ($A=T$, two H-bonds); Guanine pairs with Cytosine ($G\equiv C$, three H-bonds).

$$\text{Chargaff}\acute{\text{s}}\text{ Rules (For dsDNA Only):}\mathbf{[}\mathbf{A}\mathbf{]}\mathbf{=}\mathbf{[}\mathbf{T}\mathbf{]},\mathbf{[}\mathbf{G}\mathbf{]}\mathbf{=}\mathbf{[}\mathbf{C}\mathbf{]},\frac{\mathbf{[}\mathbf{A}\mathbf{]}\mathbf{+}\mathbf{[}\mathbf{G}\mathbf{]}}{\mathbf{[}\mathbf{T}\mathbf{]}\mathbf{+}\mathbf{[}\mathbf{C}\mathbf{]}}\mathbf{=}\mathbf{1.0}$$

Chargaff Rule Applicability

Chargaff's rules apply strictly to double-stranded DNA. If $\frac{A+G}{T+C}\ne 1.0$ or $A\ne T$, the genetic material is single-stranded DNA (ssDNA) (e.g., $\varphi \times 174$ bacteriophage).

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2. 🔬 Experimental Proof: DNA as the Genetic Material & Semiconservative Replication

                                  LANDMARK EXPERIMENTS
                                           │
         ┌─────────────────────────────────┼─────────────────────────────────┐
         ▼                                 ▼                                 ▼
   [GRIFFITH (1928)]             [AVERY, MacLEOD, McCARTY (1944)]    [HERSHEY & CHASE (1952)]
   ├── Streptococcus pneumoniae   ├── Biochemical purification        ├── Bacteriophage T2
   ├── S-strain (Virulent)        ├── Protease/RNase -> Transform     ├── 35S (Proteins) in supernatant
   └── Transforming Principle     └── DNase -> BLOCKS transformation  └── 32P (DNA) in pellet -> PROOF

2.1 The Meselson & Stahl Experiment (1958)

Grew E. coli in ${}^{15}N{H}_{4}Cl$ (heavy nitrogen) medium, then transferred to ${}^{14}N{H}_{4}Cl$ (light nitrogen):

• Generation 0: $100\text{\%}$ Heavy (${}^{15}N{-}^{15}N$) density band at CsCl equilibrium.
• Generation 1 (20 min): $100\text{\%}$ Intermediate / Hybrid (${}^{15}N{-}^{14}N$) density band $⟹$ Ruled out Conservative model!
• Generation 2 (40 min): $50\text{\%}$ Hybrid (${}^{15}N{-}^{14}N$) and $50\text{\%}$ Light (${}^{14}N{-}^{14}N$) $⟹$ Conclusively proved Semiconservative Replication.

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3. ⚙️ DNA Replication Machinery

Replication in E. coli proceeds bidirectionally from the oriC locus at a catalytic rate of $\text{a}\approx 2000\text{bp/sec}$:

  5' ────────────────────────► 3'  Leading Strand (Continuous synthesis towards fork)
  3' ◄──────────────────────── 5'  Template Strand

  5' ───►  ───►  ───►  ───►   3'  Lagging Strand (Discontinuous Okazaki fragments away from fork)

Enzyme / Factor	Core Biochemical Function
Helicase ($DnaB$)	Unwinds parent dsDNA by breaking H-bonds using ATP hydrolysis.
SSB Proteins	Prevent re-annealing and hairpin formation of single-stranded templates.
Topoisomerase / DNA Gyrase	Relieves positive supercoiling strain ahead of the advancing replication fork.
Primase ($DnaG$)	Synthesizes short complementary RNA primers ($10-12\text{nt}$) with a free $3^{\prime }-OH$.
DNA Polymerase III	Main catalytic replicating enzyme; synthesizes DNA strictly in $5^{\prime }\to 3^{\prime }$ direction with $3^{\prime }\to 5^{\prime }$ proofreading exonuclease activity.
DNA Polymerase I (Kornberg)	Removes RNA primers ($5^{\prime }\to 3^{\prime }$ exonuclease) and fills gaps with dNTPs.
DNA Ligase	Seals single-strand nicks by catalyzing phosphodiester bond formation between $3^{\prime }-OH$ and $5^{\prime }-P$.

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4. 📜 Transcription & Post-Transcriptional Processing

Transcription is the enzymatic synthesis of RNA from a DNA template directed by RNA Polymerase.

$$\text{Transcription Unit: }\text{Promoter (5}\acute{\text{)}}⟶\text{Structural Gene}⟶\text{Terminator (3}\acute{\text{)}}$$

4.1 Eukaryotic RNA Polymerases

• RNA Polymerase I: Synthesizes $28S,18S,5.8S$ rRNAs.
• RNA Polymerase II: Synthesizes hnRNA (Precursor to mRNA).
• RNA Polymerase III: Synthesizes tRNA, $5S$ rRNA, and snRNA.

4.2 Post-Transcriptional hnRNA Processing in Eukaryotes

1. Splicing: Removal of non-coding introns and ligation of coding exons catalyzed by the spliceosome (snRNPs).
2. Capping: Addition of 7-methylguanosine triphosphate ($m^{7}Gppp$) to the $5^{\prime }$-end.
3. Tailing (Polyadenylation): Addition of $200-300$ adenylate residues ($Poly-A$) to the $3^{\prime }$-end in a template-independent manner.

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5. 🎛️ Regulation of Gene Expression: The Lac Operon

Elucidated by François Jacob & Jacques Monod (1961) in E. coli:

  pI ── [ i-Gene ] ── pO ── [ Operator ] ── [ z-Gene ] ── [ y-Gene ] ── [ a-Gene ]
             │                                   │             │             │
             ▼                                   ▼             ▼             ▼
       Repressor Monomer                 β-Galactosidase   Permease     Transacetylase

1. Repressor Gene ($i$): Synthesizes active Lac Repressor Protein constitutively.
2. Operator ($O$): In absence of inducer (allolactose), repressor binds to operator, physically blocking RNA Polymerase $⟹$ Operon is OFF (Negative regulation).
3. Inducer Present: Allolactose binds the repressor, causing conformational inactivation; repressor detaches from operator $⟹$ RNA Polymerase transcribes polycistronic mRNA $⟹$ Operon is ON.
4. Structural Gene Enzymes:
   • $z$-gene: $\beta$-Galactosidase (Hydrolyzes lactose into Glucose + Galactose).
   • $y$-gene: Permease (Increases membrane permeability to $\beta$-galactosides).
   • $a$-gene: Transacetylase (Transfers acetyl group from Acetyl-CoA to $\beta$-galactosides).