Secondary metabolites are organic compounds produced by organisms that are not directly involved in normal growth, development or reproduction. They provide ecological advantages (defence, competition, attraction). Alkaloids: nitrogen-containing secondary metabolites from plants. Generally bitter taste, pharmacological activity. Examples and sources: Morphine (Papaver somniferum — opium poppy): narcotic analgesic, pain relief. Codeine (Papaver somniferum): cough suppressant. Quinine (Cinchona tree bark): antimalarial. Caffeine (Coffee, tea): CNS stimulant. Nicotine (Tobacco, Nicotiana tabacum): CNS stimulant, insecticide. Cocaine (Coca leaves, Erythroxylum coca): local anaesthetic, CNS stimulant. Atropine (Datura, Atropa belladonna): anticholinergic, eye drops. Colchicine (Colchicum autumnale, autumn crocus): inhibits tubulin polymerisation, used in gout. Reserpine (Rauwolfia serpentina): antihypertensive.

Enzymes: biological catalysts, almost all are proteins (exception: ribozymes — catalytic RNA). Properties: specific, lower activation energy, not consumed in reaction, sensitive to pH and temperature, require cofactors. Trypsin: serine protease. Cleaves peptide bonds after positively charged amino acids (Arg, Lys). Present as inactive trypsinogen in pancreatic juice → activated by enterokinase (from duodenal brush border cells). Digests dietary proteins in small intestine. Part of a cascade: trypsin also activates chymotrypsinogen → chymotrypsin, and proelastase → elastase. Classification by reaction type: Oxidoreductases (oxidation-reduction), Transferases (group transfer), Hydrolases (hydrolysis — trypsin), Lyases (addition/removal without hydrolysis), Isomerases (isomeric change), Ligases (joining with ATP). Trypsin: Hydrolase > Peptide hydrolase (peptidase) > Endopeptidase (serine protease).

Lectins: proteins that specifically recognise and bind to particular carbohydrate (sugar) sequences. NOT enzymes (don't catalyse reactions). Found in: plants (concanavalin A, phytohaemagglutinin), animals (selectins, galectins), microbes. Concanavalin A (Con A): isolated from seeds of jack bean (Canavalia ensiformis). Binds specifically to α-D-mannose and α-D-glucose residues. Requires Ca²⁺ and Mn²⁺ for binding. Uses: T-lymphocyte mitogen (stimulates T-cell proliferation → used in immunology research). Haemagglutinin (clumps red blood cells). Cell biology research — detects mannose-containing glycoproteins. Phytohaemagglutinin (PHA): from kidney bean (Phaseolus vulgaris). B and T cell mitogen. Wheat germ agglutinin (WGA): binds GlcNAc and sialic acid. Animal lectins: selectins (cell adhesion — leukocyte rolling on endothelium). Galectins (β-galactosides). Important in: cell-cell recognition, immunity, cancer metastasis.

Collagen: most abundant protein in the human body (~25-35% of total protein). Fibrous, structural protein. Found in: skin, tendons, ligaments, cartilage, bone matrix, blood vessels, cornea. Structure: triple helix — three polypeptide chains (α-chains) wound around each other. Characteristic repeat: Gly-X-Y (every third amino acid = glycine; X often = proline; Y often = hydroxyproline). Hydroxyproline is unique to collagen — absent from most other proteins. Formed by post-translational modification of proline → hydroxylation requires vitamin C (ascorbic acid). Scurvy: vitamin C deficiency → insufficient hydroxyproline → unstable collagen → blood vessel fragility, wound healing failure, gum disease. 28 types of collagen (Type I most abundant — skin, tendon, bone. Type II — cartilage. Type III — blood vessels. Type IV — basement membrane). Extracellular matrix: collagen fibrils + proteoglycans (ground substance). Also includes fibronectin, laminin, elastin.

Terpenoids (terpenes): largest class of secondary metabolites. Derived from isoprene units. Examples: menthol (from mint), camphor, rubber (polyterpene), carotenoids, essential oils. Phenolics: phenolic OH group. Examples: Lignin (plant cell wall), tannins (astringency in tea, bark), flavonoids, anthocyanins (flower pigments), salicylic acid. Glycosides: sugar + non-sugar (aglycone). Examples: cardiac glycosides (digitalis from Digitalis purpurea — used for heart failure), cyanogenic glycosides (in cassava — toxic HCN), glucosinolates (in mustard). Fatty acid derivatives: waxes (beeswax, carnauba), cutin (leaf cuticle), suberin (waterproofing in cork, Casparian strip). Nitrogenous compounds (other than alkaloids): betaines, amino acids (unusual ones like canavanine in legumes — insect toxin), polyamines, purines, betalains.

Many enzymes require non-protein components for activity. Cofactors: inorganic metal ions. Zn²⁺: carbonic anhydrase, carboxypeptidase, alcohol dehydrogenase. Fe²⁺/Fe³⁺: cytochromes, catalase, peroxidase, haemoglobin (not enzyme). Cu²⁺: cytochrome oxidase. Mg²⁺: hexokinase, many kinases, chlorophyll. Mn²⁺: arginase. Coenzymes: organic cofactors, often vitamins. NAD⁺ (from niacin/B₃): oxidation-reduction in glycolysis, Krebs. FAD (from riboflavin/B₂): succinate dehydrogenase in Krebs. CoA (from pantothenic acid/B₅): acetyl group transfer. Pyridoxal phosphate (PLP, from B₆): transamination, amino acid metabolism. Thiamine pyrophosphate (TPP, from B₁): pyruvate decarboxylase, α-ketoglutarate dehydrogenase. Biotin (B₇): CO₂ fixation (pyruvate carboxylase, acetyl-CoA carboxylase). Tetrahydrofolate (from folate/B₉): one-carbon transfer. Cobalamin (B₁₂): methionine synthase, methylmalonyl-CoA mutase. Prosthetic groups: tightly bound coenzymes (e.g., haem in cytochrome, biotin in pyruvate carboxylase).

ECM (extracellular matrix) = the non-cellular component surrounding cells in tissue. Provides: structural support, physical scaffolding, biochemical signals, regulates cell behaviour. Components: Fibrous proteins: collagen (structural support, tensile strength), elastin (elasticity — found in arteries, lungs, skin), fibronectin (cell adhesion, wound healing), laminin (basement membrane). Ground substance: proteoglycans (core protein + glycosaminoglycan chains — hyaluronic acid, chondroitin sulfate, heparan sulfate, keratan sulfate, dermatan sulfate). Highly hydrated → gives tissue turgor, allows nutrient diffusion. Hyaluronic acid: synovial joint fluid (lubricant), vitreous humor of eye, skin moisturisation → target for cosmetic fillers. Diseases of ECM: Marfan syndrome (fibrillin mutation → weak elastic fibres → aortic aneurysm, lens dislocation). Osteogenesis imperfecta (collagen type I mutation → brittle bones). Ehlers-Danlos syndrome (various collagen mutations → hyperflexible joints, fragile skin).

Structural proteins: collagen (connective tissue), keratin (hair, nails, skin), actin/myosin (muscle contraction), tubulin (microtubules). Transport proteins: haemoglobin (O₂), transferrin (iron), albumin (lipids, drugs), LDL/HDL (cholesterol). Enzymes: all biological catalysts (amylase, lipase, trypsin, DNA polymerase, ATP synthase). Hormones: insulin, glucagon, growth hormone, ADH, oxytocin (all peptide hormones). Regulatory proteins: transcription factors, histones, p53, Rb. Antibodies/Immunoglobulins: IgG, IgM, IgA, IgE, IgD — immune defence. Storage proteins: ferritin (iron storage), casein (milk protein → amino acids for infant), ovalbumin (egg protein). Receptor proteins: ion channels (nicotinic ACh receptor), GPCRs (G-protein coupled receptors), enzyme-linked receptors (receptor tyrosine kinases → insulin receptor). Contractile: actin, myosin, troponin, tropomyosin. Toxins: ricin (from castor bean), botulinum toxin, snake venom phospholipase.