DNA & RNA

Each nucleotide monomer has: (1) a pentose sugar — ribose in RNA (–OH at C2') or 2-deoxyribose in DNA (–H at C2'); (2) a nitrogenous base attached to C1' of the sugar via an N-glycosidic bond; (3) a phosphate group esterified to the C5' –OH of the sugar. The phosphate (pKa ≈ 1 and ≈ 6) carries a negative charge at physiological pH, making nucleic acids highly polar, water-soluble molecules. Nucleoside triphosphates (NTPs such as ATP, GTP, CTP, UTP) are the activated monomers used during polymerization, providing the energy for bond formation through hydrolysis of pyrophosphate.

Nucleotides are joined by phosphodiester bonds: the 3'-hydroxyl group of one nucleotide attacks the α-phosphate of an incoming nucleoside triphosphate in a nucleophilic substitution reaction, releasing inorganic pyrophosphate (PPi). The resulting bond connects the 3' carbon of one sugar to the 5' carbon of the next via a phosphate bridge — hence 'phosphodiester.' The backbone of every strand therefore reads: –sugar–phosphate–sugar–phosphate– with bases projecting outward. Each strand has a free 5'-phosphate end and a free 3'-hydroxyl end, giving it chemical directionality. By convention, sequences are always written 5' → 3' (e.g., 5'-ATGCGT-3').

In double-stranded DNA, two antiparallel strands wind around a common axis, forming a right-handed helix (B-form DNA, the most common physiological form). The hydrophobic bases stack in the interior (~3.4 Å apart), providing significant stabilization through π–π stacking interactions. Complementary base pairs form in the interior via hydrogen bonds: A···T (two H-bonds, N–H···N and N–H···O) and G···C (three H-bonds). The helix completes one full turn every ~10.5 base pairs (~34 Å rise per turn). The exterior sugar-phosphate backbone, negatively charged due to ionized phosphate groups, faces the aqueous environment. Major and minor grooves alternate around the helix, providing sites for protein binding and regulation.

RNA is predominantly single-stranded, though it can fold back on itself to form local double-helical regions (hairpin loops). Three major types of RNA operate in protein synthesis: (1) Messenger RNA (mRNA) — carries the genetic code transcribed from DNA as codons (triplets of bases) to the ribosome; (2) Transfer RNA (tRNA) — small cloverleaf-shaped adaptor molecules (~76–90 nucleotides) that carry amino acids and have an anticodon loop that base-pairs with mRNA codons during translation; (3) Ribosomal RNA (rRNA) — the structural and catalytic component of ribosomes (in prokaryotes: 16S, 23S, 5S; in eukaryotes: 18S, 28S, 5.8S, 5S). Additional classes include small nuclear RNA (snRNA) involved in splicing, microRNA (miRNA) and small interfering RNA (siRNA) involved in gene regulation, and ribozymes — catalytic RNA molecules that can cleave phosphodiester bonds.

DNA is more chemically stable than RNA due to the absence of the 2'-OH group. In RNA, the 2'-OH can act as an intramolecular nucleophile, attacking the adjacent phosphodiester bond and leading to hydrolysis under alkaline conditions — a reaction that does not occur in DNA. This is why DNA serves as a stable long-term storage molecule, while RNA is suited for transient informational roles. Additionally, DNA uses thymine (5-methyluracil) where RNA uses uracil; the methyl group on thymine helps prevent deamination-derived mutations by allowing DNA repair enzymes to distinguish thymine from uracil (the deamination product of cytosine).

• \text{NMP}_n — Growing polynucleotide chain (n residues) (—): The existing nucleic acid strand with a free 3'-OH group at its terminus.
• \text{NTP} — Nucleoside triphosphate (—): Activated monomer (e.g., dATP, GTP) supplying both the new nucleotide unit and the energy for bond formation via its α-β pyrophosphate bond.
• \text{NMP}_{n+1} — Extended polynucleotide chain (—): The chain elongated by one nucleotide via a new 3'–5' phosphodiester bond.
• \text{PP}_i — Inorganic pyrophosphate (—): Released byproduct (P2O7^4−); its subsequent hydrolysis to 2 Pi by pyrophosphatase makes the overall reaction thermodynamically favorable (ΔG° ≈ −30 kJ/mol).

Problem. A double-stranded DNA molecule has the base composition: 32% adenine. (a) What percentage of the bases are cytosine? (b) How many hydrogen bonds per 100 base pairs does this molecule contain?

Answer. %C = 18%; Total hydrogen bonds per 100 base pairs = 118

• Proteins and Amino Acids — Like nucleic acids, proteins are biological polymers whose monomers (amino acids) are linked by covalent bonds (peptide bonds) and whose sequence determines three-dimensional structure and function. Understanding both classes of macromolecules is essential for molecular biology.
• ATP and Biological Energy Transfer — ATP (adenosine triphosphate) is a nucleoside triphosphate — a nucleotide — that powers the polymerization reaction forming phosphodiester bonds. The hydrolysis of pyrophosphate during DNA/RNA synthesis drives the reaction forward thermodynamically.
• Hydrogen Bonding and Intermolecular Forces — Complementary base pairing in DNA is mediated by hydrogen bonds (N–H···O and N–H···N). Understanding the geometry and energy of hydrogen bonds explains base-pair specificity, helix stability, and DNA melting temperature.
• Nucleophilic Substitution Reactions — Phosphodiester bond formation during DNA synthesis involves a nucleophilic attack by the 3'-OH group of the growing chain on the α-phosphate of an incoming NTP — a classic SN2-type mechanism at phosphorus.