Organic Chemistry — The Chemistry of Living Things

Organic chemistry is the study of carbon-containing compounds. The name comes from the old (incorrect) belief that these compounds could only be made by living organisms. We now know they can be synthesised in labs — but it remains true that virtually every molecule in a living organism is an organic compound. Why is carbon the centre of life's chemistry? Carbon has 4 valence electrons — it can form 4 covalent bonds simultaneously, with other carbons, with hydrogen, oxygen, nitrogen, sulfur, and more. It forms single, double, and triple bonds. It can chain into long molecules, branch, or form rings. This versatility allows carbon to form millions of different stable molecules — no other element comes close. The four major classes of biological molecules — carbohydrates, lipids, proteins, and nucleic acids — are all organic compounds. Understanding their chemistry explains how your body stores energy, builds structure, runs reactions, and stores genetic information.

The carbon backbone of an organic molecule is relatively inert. Chemical reactivity comes from functional groups — specific clusters of atoms attached to the backbone that give the molecule its properties and reactions. Think of functional groups as the "business end" of a molecule. Two molecules with the same carbon backbone but different functional groups behave completely differently. Key functional groups in medicine: | Group | Structure | Properties | Example | |-------|-----------|------------|---------| | Hydroxyl | –OH | Polar, H-bonds with water, makes molecule soluble | Ethanol (C₂H₅OH), glucose | | Carboxyl | –COOH | Acidic (donates H⁺) | Amino acids, fatty acids, aspirin | | Amino | –NH₂ | Basic (accepts H⁺) | Amino acids, adrenaline | | Carbonyl | C=O | Reactive, polar | Glucose (aldehyde form) | | Phosphate | –PO₄ | Acidic, charged, transfers energy | ATP, DNA backbone | | Methyl | –CH₃ | Non-polar, hydrophobic | Epigenetic methylation of DNA | | Sulfhydryl | –SH | Forms disulfide bonds (–S–S–) | Protein folding (cysteine) | Medical relevance: Aspirin (acetylsalicylic acid) works by permanently transferring an acetyl group (–COCH₃) to COX enzymes — blocking their active site and preventing prostaglandin (inflammation molecule) synthesis. This is an example of a drug acting through its functional group.

Isomers are molecules with the same molecular formula but different arrangements of atoms. This seemingly subtle difference can have enormous biological consequences. Structural isomers: Different connectivity of atoms. Glucose (C₆H₁₂O₆) and fructose (C₆H₁₂O₆) are structural isomers — same formula, different structure, different properties. Glucose is the body's primary fuel; fructose is metabolised differently (primarily in the liver). Stereoisomers (chirality): Many biological molecules are chiral — they exist as two non-superimposable mirror images, like left and right hands. These mirror images are called enantiomers (L and D forms, or R and S forms). Biological systems are exquisitely sensitive to chirality because enzymes have precisely shaped active sites: - L-amino acids are used to build proteins (the "right" hand). D-amino acids are not incorporated (bacteria use some D-amino acids in cell walls — which is why antibiotics targeting those walls are harmless to human cells). - Ibuprofen: The S-enantiomer is the active painkiller; the R-enantiomer is inactive but converts slowly to the S form in the body. - Thalidomide (historical): One enantiomer treated morning sickness; the other caused severe birth defects. Tragically, they interconvert in the body, so separating them couldn't prevent harm. This disaster revolutionised drug safety testing. Chirality is one reason drug development is complex — you must test both enantiomers.

Carbohydrates (sugars and starches) Built from carbon, hydrogen, and oxygen in a 1:2:1 ratio (CH₂O)ₙ. Monosaccharides (glucose, fructose, galactose) are simple sugars. Disaccharides (sucrose, lactose, maltose) are two joined monosaccharides. Polysaccharides (starch, glycogen, cellulose) are long chains. Functions: primary energy source (glucose → ATP), energy storage (glycogen in liver and muscle), structural roles (cellulose in plant cell walls). In medicine: blood glucose monitoring, IV glucose in hypoglycaemia, lactose intolerance (inability to digest lactose). Lipids (fats, oils, steroids) Hydrophobic — mostly C and H, few O. Triglycerides (three fatty acid chains on a glycerol backbone) store energy — 9 kcal/g vs 4 kcal/g for carbohydrates. Phospholipids form cell membranes (hydrophilic head, hydrophobic tails). Steroids share a four-ring carbon structure — cholesterol, sex hormones (oestrogen, testosterone), cortisol, bile acids, and vitamin D are all steroids. Many drugs mimic or block steroid hormones. Proteins (amino acid chains) 20 amino acids, each with an amino group, carboxyl group, and a unique side chain (R-group). Joined by peptide bonds (carboxyl + amino → release water). Structure determines function: enzymes, antibodies, hormones (insulin), structural proteins (collagen, keratin), transport proteins (haemoglobin), receptors. Denaturation (by heat, acid, organic solvents) unfolds proteins — destroying their function. Cooking denatures proteins in food; fever can denature proteins in your body. Nucleic acids (DNA and RNA) Built from nucleotides (phosphate + sugar + base). DNA: double helix, deoxyribose, bases A/T/C/G, permanent genetic information. RNA: single strand, ribose, bases A/U/C/G, working copy of genetic information. The phosphate backbone is why DNA is acidic (hence "nucleic acid"). The negative charge helps DNA compact with positively charged histones in the nucleus.

Biological macromolecules are built by stringing together smaller units (monomers) — amino acids into proteins, nucleotides into DNA, glucose into glycogen. The reaction that joins them is always the same: Condensation (dehydration synthesis): Two monomers join, releasing a water molecule (H₂O). Requires energy (from ATP). This is how peptide bonds, glycosidic bonds, and ester bonds are all formed. Hydrolysis: A bond is broken by adding a water molecule. Releases the monomers. Often catalysed by specific enzymes. Digestion is entirely hydrolysis: proteases break peptide bonds in protein → amino acids; amylases break glycosidic bonds in starch → glucose; lipases break ester bonds in triglycerides → fatty acids + glycerol. Medical connections: - Aspirin irreversibly acetylates COX enzymes — a condensation reaction that permanently blocks them. That's why aspirin's antiplatelet effect lasts the lifetime of the platelet (~10 days) — platelets can't make new COX. - Penicillin inhibits the enzymes that build bacterial cell walls by condensation reactions — without cross-linking, the cell wall is weak → bacteria lyse (burst). - Angiotensin-converting enzyme (ACE) inhibitors — blood pressure drugs that block the enzyme that cleaves (hydrolyses) angiotensin I to the active angiotensin II. Blocking this hydrolysis → less vasoconstriction → lower blood pressure.