Biochemistry basics

A living cell is a tiny but very complex chemical factory: thousands of reactions per second run at just 37 °C, in a neutral medium, amazingly fast thanks to enzymes. In this lesson we apply earlier topics — thermodynamics, kinetics, acid–base equilibria and bonding — to biomolecules.

Carbohydrates

Monosaccharides — glucose (an aldohexose) and fructose (a ketohexose), both C₆H₁₂O₆ — exist in water mostly as rings. Two monosaccharides condense into a disaccharide through a glycosidic bond: C₆H₁₂O₆ + C₆H₁₂O₆ → C₁₂H₂₂O₁₁ + H₂O. Sucrose = glucose + fructose, maltose = 2 glucose, lactose = glucose + galactose. Polysaccharides (C₆H₁₀O₅)ₙ: starch (plant storage, α-1,4 and α-1,6 links), the more branched glycogen (animal storage) and cellulose (β-1,4 links, a structural material; humans lack an enzyme to break it down).

Lipids

Triglycerides are esters of glycerol with three fatty acids. Saturated acids (stearic C₁₇H₃₅COOH, palmitic C₁₅H₃₁COOH) have straight chains that pack tightly — animal fats are solid. In unsaturated acids (oleic C₁₇H₃₃COOH) a cis C=C bond kinks the chain — plant oils are liquid. Hydrogenation saturates the double bonds: C₁₇H₃₃COOH + H₂ → C₁₇H₃₅COOH (this is how margarine is made). Phospholipids have a hydrophilic “head” and two hydrophobic “tails”: in water they form the bilayer at the heart of cell membranes. Fats are the densest energy store: ≈ 9 kcal/g (≈ 37 kJ/g), against ≈ 4 kcal/g for carbohydrates and proteins.

Proteins and enzymes

Proteins are built from amino acids joined by peptide bonds and have four levels of structure. They transport (haemoglobin), build (collagen, keratin), defend (antibodies) and regulate (insulin), and most importantly act as enzymes. An enzyme binds its substrate at the active site (lock-and-key or induced-fit model) and lowers the activation energy. Every enzyme has an optimum temperature and pH: pepsin in the stomach works best at pH ≈ 2, trypsin in the intestine at pH ≈ 8.

Deriving the Michaelis–Menten equation. In E + S ⇌ ES → E + P, the concentration of the ES complex quickly becomes steady: k₁[E][S] = (k₋₁ + k₂)[ES]. Substituting [E]₀ = [E] + [ES] and v = k₂[ES] gives the formula below, with Vmax = k₂[E]₀ and Km = (k₋₁ + k₂) / k₁.

Nucleic acids

A nucleotide consists of a nitrogenous base, a pentose (deoxyribose in DNA, ribose in RNA) and a phosphate group. The two antiparallel strands of DNA are held together by complementary base pairs: A–T (2 hydrogen bonds) and G–C (3 hydrogen bonds). Hence Chargaff's rule: A = T and G = C. RNA has uracil (U) instead of thymine. Genetic information flows DNA → RNA → protein; each amino acid is encoded by a codon of three nucleotides (64 codons, 20 amino acids).

ATP — the cell's energy currency

ATP consists of adenine, ribose and three phosphate groups. Its hydrolysis releases energy: ATP + H₂O → ADP + Pᵢ, ΔG°′ ≈ −30.5 kJ/mol (more negative, about −50 kJ/mol, under cell conditions). A non-spontaneous reaction is coupled to ATP hydrolysis: the Gibbs energies add up and the total becomes negative. In respiration one glucose molecule yields about 30–32 ATP (older textbooks say 36–38), so roughly a third of the oxidation energy is stored in ATP.