10.1 Nucleic Acid Chemistry, the Double Helix & Chromatin Organisation

10.1 Nucleic Acid Chemistry, the Double Helix & Chromatin Organisation

Deoxyribonucleic acid (DNA) serves as the universal repository of hereditary information across all cellular life forms. To function effectively, genomic DNA must balance physical stability against accessibility: it must remain chemically resilient across organismal lifespans while permitting rapid, sequence-specific unwinding during replication, repair, and transcription.

---

1. Nucleic Acid Chemistry and the Double Helix

Nitrogenous Bases: Purines vs. Pyrimidines

Nucleotides consist of three covalently linked components: an aromatic nitrogenous base, a five-carbon pentose sugar (2'-deoxyribose in DNA, ribose in RNA), and one to three phosphate groups esterified to the 5'-hydroxyl carbon. Nucleotides without phosphate moieties are termed nucleosides (base + pentose via a β-N-glycosidic bond to C1' of the sugar).

Nitrogenous bases fall into two structural categories:

• Purines: Double-ring aromatic heterocycles composed of a six-membered pyrimidine ring fused to a five-membered imidazole ring. The purines are Adenine (A) and Guanine (G) (Mnemonic: "PURe As Gold").
• Pyrimidines: Single six-membered unsaturated aromatic rings. The pyrimidines are Cytosine (C), Thymine (T) (exclusive to DNA), and Uracil (U) (replaces thymine in RNA) (Mnemonic: "CUT the PYe"). Thymine contains a 5-methyl group absent in uracil, a modification critical for distinguishing genuine genomic thymine from deaminated cytosine.

Purines (Two Rings)                  Pyrimidines (Single Ring)
   Adenine (6-amino)                    Cytosine (4-amino, 2-keto)
   Guanine (2-amino, 6-keto)            Thymine (2,4-diketo, 5-methyl) [DNA]
                                        Uracil (2,4-diketo) [RNA]

Watson-Crick Pairing and Chargaff's Rules

In 1953, James Watson and Francis Crick elucidated the secondary structure of double-stranded DNA (dsDNA). The two strands form a right-handed double helix stabilized by:

1. Complementary Base Pairing: Specific hydrogen bonding between purines and pyrimidines:
   • Adenine pairs with Thymine via two hydrogen bonds (A = T).
   • Guanine pairs with Cytosine via three hydrogen bonds (G ≡ C).
2. Base Stacking Interactions: Van der Waals forces and hydrophobic interactions between the flat, π-electron-rich aromatic rings stacked vertically along the helical axis contribute more free energy to duplex stability than the hydrogen bonds themselves.

Chargaff's Rules govern double-stranded DNA genomes:

• %A = %T
• %G = %C
• Total Purines = Total Pyrimidines: %(A + G) = %(C + T) = 50%
• The (A + T) / (G + C) ratio varies widely across species, but within any dsDNA duplex, the purine-to-pyrimidine ratio is strictly 1.0.

Quantitative MCAT Application: If a double-stranded viral DNA genome is determined to contain 32% cytosine, then guanine must also equal 32%, totaling 64% GC content. The remaining 36% is split equally between adenine (18%) and thymine (18%).

Thermodynamics of DNA Denaturation (Melting)

Thermal disruption of hydrogen bonding and base stacking separates dsDNA into single strands (denaturation or "melting"). The melting temperature (Tm) is defined as the temperature at which 50% of the double-stranded helical structure is converted into random-coil single strands, observable spectroscopically via the hyperchromic shift (increased ultraviolet absorbance at 260 nm due to unstacked, exposed aromatic rings):

• GC Content: Because G ≡ C base pairs share three hydrogen bonds and exhibit superior stacking thermodynamics compared to the two hydrogen bonds of A = T pairs, DNA with higher GC content has a proportionately higher Tm.
• Ionic Strength: Cations (such as Na+ and Mg2+) shield the repulsive negative charges of adjacent phosphodiester backbones, stabilizing the duplex and raising Tm.
• pH Extremes & Denaturants: Highly alkaline environments (pH > 11.5) deprotonate nitrogenous ring nitrogens, destroying hydrogen bonds without breaking covalent phosphodiester bonds. Chemical denaturants like urea and formamide destabilize hydrogen bonding, lowering Tm.

Antiparallel Polarity and Helical Conformations

The phosphodiester backbone possesses an invariant polarity: the 3'-hydroxyl group of one deoxyribose forms an ester bond with the 5'-phosphate group of the adjacent sugar. The two complementary strands run in antiparallel directions: one strand terminates in a free 5'-phosphate (5' end) and runs toward a free 3'-hydroxyl (3' end), while its partner strand runs 3' to 5'.

Under physiological aqueous conditions, dsDNA predominantly adopts the B-DNA conformation:

• Right-handed double helix.
• Diameter of approximately 2.0 nm.
• 10.0 to 10.5 base pairs per complete 360° turn, with a pitch of 3.4 nm (0.34 nm rise per base pair).
• Major groove (wide, deep) and minor groove (narrow, shallow). Sequence-specific DNA-binding proteins, such as transcription factors, predominantly insert α-helical recognition motifs into the major groove where hydrogen-bonding donors and acceptors uniquely identify base pairs without unwinding the helix.
• Alternative conformations include A-DNA (dehydrated, compact right-handed helix with 11 bp/turn, observed in DNA-RNA hybrids and double-stranded RNA) and Z-DNA (left-handed, elongated zigzag conformation with 12 bp/turn, observed in alternating purine-pyrimidine tracts such as poly(dG-dC) and associated with transcriptional torsional tension).

2. Higher-Order Chromatin Organization and Epigenetics

Human diploid somatic cells contain approximately 6.4 × 10^9 base pairs of nuclear DNA distributed across 46 chromosomes, totaling roughly 2 meters of linear polymer that must fit within a nucleus averaging only 5–10 µm in diameter. Achieving this >10,000-fold packaging requires multi-tiered structural compaction.

The Nucleosome Core Particle

The basic fundamental repeating structural unit of eukaryotic chromatin is the nucleosome:

• Histone Octamer Core: Formed by two copies each of four core histone proteins: H2A, H2B, H3, and H4. Core histones are small (11–15 kDa) proteins rich in positively charged, basic amino acids—specifically lysine and arginine (>20% of residues). These basic side chains form tight electrostatic salt bridges with the negatively charged polyanionic phosphodiester backbone of DNA.
• Wound DNA: Exactly 146–147 base pairs of B-DNA wind 1.65 turns in a left-handed superhelix around the octamer core.
• Linker DNA and Histone H1: Approximately 20–80 base pairs of "linker DNA" span adjacent nucleosomes, generating the classic 10-nm "beads-on-a-string" fiber. Linker Histone H1 binds outside the core octamer at the DNA entry and exit sites, clamping the DNA and directing compaction into higher-order 30-nm chromatin fibers (solenoid or zigzag architectures).

Linear DNA (2 nm) 
   --> Nucleosomes / Beads-on-a-String (10 nm) 
   --> Linker H1 Compaction (30 nm fiber) 
   --> Radial Loop Domains on Scaffold Matrix (300 nm) 
   --> Condensed Chromatids (700 nm) 
   --> Metaphase Chromosome (1400 nm)

Euchromatin vs. Heterochromatin

Chromatin exists in dynamic operational states governed by post-translational modifications of histone N-terminal "tails" and direct DNA modifications:

1. Euchromatin:

   • Structure: Decondensed, open conformation accessible to transcription machinery.
   • Staining: Lightly stained under light microscopy during interphase.
   • Replication: Replicates early in S phase.
   • Transcriptional Activity: High; contains actively expressed genes.
   • Epigenetic Marks: Characterized by high levels of histone acetylation (e.g., H3K9ac, H3K27ac) and histone H3 lysine 4 trimethylation (H3K4me3).

2. Heterochromatin:

   • Structure: Compact, densely aggregated conformation inaccessible to RNA polymerases.
   • Staining: Densely and darkly stained, often concentrated along the inner nuclear lamina and around the nucleolus.
   • Replication: Replicates late in S phase.
   • Transcriptional Activity: Silenced or repressed.
   • Subtypes:
     • Constitutive Heterochromatin: Permanently condensed across all developmental cell lineages (e.g., centromeres, telomeres, pericentromeric tandem satellite repeats).
     • Facultative Heterochromatin: Regions dynamically converted between euchromatin and heterochromatin depending on cell differentiation or hormonal cues (e.g., the inactive X chromosome in female mammalian somatic cells, termed the Barr body).
   • Epigenetic Marks: Marked by histone deacetylation, histone H3 lysine 9 trimethylation (H3K9me3), histone H3 lysine 27 trimethylation (H3K27me3), and DNA cytosine hypermethylation at CpG islands.

The Histone Code and Chromatin Modifying Enzymes

• Histone Acetyltransferases (HATs): Catalyze the transfer of an acetyl group from acetyl-CoA to the ε-amino group of lysine residues. Acetylation neutralizes the positive charge of lysine, eliminating electrostatic interactions with the negatively charged DNA backbone. The chromatin structure loosens, recruiting transcription factors and promoting gene activation.
• Histone Deacetylases (HDACs): Hydrolyze acetyl groups from lysine tails, restoring the positive charge. Strong electrostatic attraction between histones and DNA resumes, compressing chromatin into transcriptionally repressed heterochromatin.
• DNA Methyltransferases (DNMTs): Add methyl groups to the C5 position of cytosine residues within CpG islands (regions rich in cytosine-phospho-guanine dinucleotides located near gene promoters). DNA methylation sterically interferes with transcription factor binding and recruits methyl-CpG-binding domain proteins (MBDs), which in turn recruit HDACs and histone methyltransferases to establish long-term gene silencing.

---

DNA versus RNA

Passage figures often distinguish the two nucleic acids by a single structural feature, so keep the four differences separate from the many similarities.