Biomolecules & Enzymes — Full Coverage Summary

Living systems are defined by the chemistry of four major classes of biomolecules: carbohydrates, proteins, lipids, and nucleic acids. Each class has a distinct molecular architecture that underpins its biological function. Enzymes — primarily protein-based catalysts — govern the vast majority of metabolic reactions in all living organisms with exceptional efficiency and specificity.

Carbohydrates follow the empirical formula ($CH_{2}O$)n and are classified by their degree of polymerization. Monosaccharides are the irreducible monomers: hexoses such as glucose ($C_{6}H_{12}O_{6}$) and fructose are the primary energy substrates of cells, while pentoses — ribose and deoxyribose — form the structural backbone of RNA and DNA respectively. When two monosaccharides condense via dehydration synthesis, a glycosidic bond forms, creating a disaccharide. The three nutritionally important disaccharides are sucrose (glucose + fructose, the primary transport sugar in plants), lactose (galactose + glucose, found in milk and hydrolysed by lactase), and maltose (glucose + glucose, produced during starch digestion). Polysaccharides result from extensive polymerization and serve either storage or structural roles. The critical distinction lies in the stereochemistry of the glycosidic bond: alpha-glycosidic bonds (as in starch amylose, amylopectin, and glycogen) produce coiled, digestible storage molecules, while beta-glycosidic bonds (as in cellulose and chitin) create straight, rigid, indigestible structural polymers. Humans possess alpha-amylase but not cellulase, making cellulose nutritionally indigestible (dietary fibre). Glycogen, the animal counterpart of starch, is more highly branched than amylopectin — branching every 8-12 glucose units versus 24-30 in amylopectin — providing more free non-reducing ends for rapid glucose mobilisation during metabolic demand.

Proteins are polymers of 20 different amino acids joined by peptide bonds, formed by dehydration synthesis between the carboxyl group of one amino acid and the amino group of the next. Their structure is organised hierarchically across four levels, each characterised by distinct stabilising forces. Primary structure is the linear amino acid sequence maintained by covalent peptide bonds. Secondary structure consists of regular, local structural patterns — the alpha-helix (exemplified by keratin in hair and nails) and the beta-pleated sheet (exemplified by silk fibroin) — stabilised by backbone hydrogen bonds between carbonyl oxygens and amide hydrogens. Tertiary structure is the global three-dimensional folding of a single polypeptide chain, maintained by R-group interactions: covalent disulphide bonds between cysteine residues, hydrophobic clustering of non-polar side chains, ionic bonds (salt bridges) between oppositely charged groups, and additional hydrogen bonds between polar side chains. Quaternary structure, as exemplified by haemoglobin, arises when two or more individually folded polypeptide subunits associate through similar interactions. Haemoglobin consists of four subunits (2 alpha and 2 beta chains), each carrying a haem prosthetic group capable of binding one oxygen molecule. Protein structural integrity is critical for function: denaturation — irreversible disruption of secondary and tertiary structure by heat or extreme pH — abolishes biological activity without breaking peptide bonds.

Lipids are hydrophobic molecules constituting the third major biomolecule class. Triglycerides (glycerol esterified to three fatty acids) serve as the primary long-term energy reserves in animals, storing over twice the energy per gram of carbohydrates (9 kcal/g versus 4 kcal/g). The physical state of triglycerides is determined by the degree of fatty acid unsaturation: saturated fatty acids (no C=C double bonds) pack tightly and are solid at room temperature (animal fats), while unsaturated fatty acids (one or more C=C double bonds) have kinked chains that prevent close packing and remain liquid at room temperature (plant oils). Phospholipids differ fundamentally: substituting one fatty acid for a charged phosphate head group creates an amphipathic molecule with a hydrophilic head and hydrophobic tails, driving spontaneous bilayer formation in aqueous environments. This phospholipid bilayer is the structural foundation of all biological membranes. Cholesterol, a steroid lipid derived from the four-ring carbon skeleton, moderates membrane fluidity by preventing both excessive rigidity at low temperatures and excessive fluidity at high temperatures, functioning as a membrane fluidity buffer. Other steroids — cortisol (stress response), testosterone and oestrogen (reproductive function) — are lipid-soluble signalling molecules derived from cholesterol.

Nucleic acids — DNA and RNA — are polymers of nucleotides, each comprising a pentose sugar, a nitrogenous base, and one or more phosphate groups. DNA's double helical structure, with its complementary base pairing (adenine-thymine via 2 hydrogen bonds; guanine-cytosine via 3 hydrogen bonds), provides stable, antiparallel double-stranded storage of genetic information. The greater number of hydrogen bonds in G-C pairs makes high GC-content DNA more thermally stable. RNA, using ribose (with a 2'-OH) and uracil in place of thymine, is generally single-stranded and serves transient functional roles: mRNA carries genetic information from DNA to ribosomes; tRNA acts as the adapter molecule that brings specific amino acids to the ribosome; rRNA provides the structural and catalytic framework of ribosomes.

Enzymes are biological catalysts that dramatically accelerate metabolic reactions. Their defining property is specificity — each enzyme acts on a particular substrate complementary to its active site. The lock-and-key model (Fischer, 1894) proposed a rigid active site; the induced fit model (Koshland, 1958), now more widely accepted, describes a flexible active site that reshapes upon substrate binding. Fundamentally, enzymes lower the activation energy of reactions without altering the equilibrium, the direction, or the net free energy change ($\Delta G$) — they are purely kinetic agents. The six enzyme classes are: oxidoreductases (redox reactions), transferases (group transfer), hydrolases (hydrolysis using water), lyases (non-hydrolytic bond cleavage), isomerases (molecular rearrangements), and ligases (bond formation using ATP). Enzyme activity is tunable by temperature (optimum approximately 37°C for human enzymes; denaturation above this), pH (pepsin optimum pH 2; trypsin optimum pH 8), and substrate concentration (described by Michaelis-Menten kinetics). Competitive inhibitors occupy the active site, increasing apparent Km while leaving Vmax unchanged; they are displaced by excess substrate. Non-competitive inhibitors bind allosteric sites, decreasing Vmax while leaving Km unchanged; they cannot be overcome by substrate. Cofactors essential to enzyme function include coenzymes (loosely bound organic molecules such as N$AD^{+}$ from niacin and FAD from riboflavin), prosthetic groups (tightly bound non-protein components such as haem), and metal ions ($Zn^{2+}$, $Mn^{2+}$). The protein portion alone (apoenzyme) is inactive; only the complete holoenzyme (apoenzyme + cofactor) is catalytically functional. Crucially, ribozymes — RNA molecules with catalytic activity, discovered by Cech and Altman (Nobel Prize 1989) — demonstrate that not all enzymes are proteins.