Appearance
1.2 — The Molecules You Are Made Of
Weigh a seventy-kilogram adult man and take him apart by substance. About 42 kilograms of him is water. About 11 kilograms is protein. About 11 kilograms is fat. Around 4 kilograms is mineral, most of it calcium and phosphate locked into bone. And carbohydrate — the thing most people think of as the fuel of the body — comes to roughly half a kilogram, which is less than one percent.
Nearly everything you will ever read about health, nutrition, disease or medicine is about those five numbers and how they move. So this page builds the molecules behind them, starting with the one that is 60 percent of you.
Water, and why life could not have been built out of anything else
A water molecule is one oxygen atom with two hydrogen atoms attached. That is the whole formula, H₂O, and it explains none of the interesting behaviour. The interesting behaviour comes from two facts about its shape and its charge.
The molecule is bent, not straight. The two hydrogens sit at an angle of about 104.5° from each other rather than on opposite sides. Volume IV, Chapter 10.3 derives why — the oxygen has two pairs of electrons that are not in bonds, and they push the hydrogens closer together than a flat 120° arrangement would give.
The oxygen pulls the shared electrons toward itself. Oxygen is electronegative, meaning it holds electrons more tightly than hydrogen does. The word is worth keeping: it will describe half the chemistry in this volume. Because the electrons spend more of their time near the oxygen, the oxygen end of the molecule carries a slight negative charge and each hydrogen end carries a slight positive charge. Not full charges like an ion, just a lopsided distribution. A molecule with that lopsidedness is called polar, as in having poles.
Now combine the two. Because the molecule is bent, the two positive ends both point the same general way and do not cancel out. So water is not just made of polar bonds, it is a polar molecule overall — a tiny magnet-like thing with a negative side and a positive side.
The dashed lines in that figure are hydrogen bonds, and they are the single most important weak force in biology. A hydrogen bond is the attraction between a hydrogen that is already bonded to a very electronegative atom — oxygen, nitrogen or fluorine — and a lone pair of electrons on another such atom nearby. It is about a twentieth the strength of a real chemical bond, which is exactly what makes it useful: strong enough to hold a shape, weak enough to be undone by ordinary body-temperature jostling. Every protein shape in Chapter 1.3 and both strands of DNA in Chapter 2.1 are held together by these.
Four consequences follow, and each one shows up in a hospital.
Water dissolves anything charged or polar, and refuses anything that is not. Drop table salt into water and the polar water molecules crowd around each sodium and chloride ion, surrounding it with their oppositely charged ends until the crystal comes apart. This is why blood can carry sodium, potassium, calcium, glucose, amino acids and waste — all of them either charged or polar. Substances that dissolve in water are called hydrophilic, water-loving. Substances made of carbon and hydrogen with no charge separation — oils, fats, waxes — have nothing for water to grip, so water molecules stick to each other instead and squeeze them out. Those are hydrophobic, water-fearing. Hold on to that word. The entire architecture of the cell membrane in Chapter 1.4, and the folding of every protein in Chapter 1.3, comes from hydrophobic molecules being pushed together by water that would rather bond to itself.
Water takes a lot of energy to heat up. Raising one gram of water by one degree takes 4.18 joules, which is high — several times what it takes for most other liquids. The reason is that a good part of the energy goes into breaking hydrogen bonds rather than into making molecules move faster, and temperature only measures the movement. Because you are mostly water, this makes your body a thermal flywheel: a fever climbs slowly, a cold room cools you slowly, and there is time for the temperature control system to act before anything reaches a dangerous value.
Water takes an enormous amount of energy to evaporate, and this is how you survive summer. Turning one gram of water at skin temperature into vapour takes about 2.4 kilojoules. That energy has to come from somewhere, and it comes out of your skin. Sweating a litre of water and having it evaporate removes roughly 2,400 kilojoules — about 580 kilocalories — of heat from your body. This is the only cooling mechanism you have that still works when the air is hotter than you are. It is also why humidity is the dangerous variable rather than temperature: if the air is already saturated, the sweat does not evaporate, no heat leaves, and the sweat simply drips off having accomplished nothing. Chapter 23.10 covers heat stroke, which is what happens when that fails.
Ice floats. As water cools toward freezing, the hydrogen bonds lock the molecules into an open hexagonal lattice that holds them further apart than they were in the liquid. Solid water is therefore less dense than liquid water — 0.917 grams per cubic centimetre against 1.000 — and floats. Almost no other substance does this. It is why a frozen lake has liquid water and living fish under a lid of ice rather than being frozen solid from the bottom up, and therefore why life survives winters at all.
Carbon: the reason biology is possible
Every molecule in the rest of this page is built on a skeleton of carbon. There is a specific reason, and it is not mystical.
A carbon atom has four electrons in its outer shell and room for eight, so it forms four covalent bonds — the most of any small, common atom. Four is the number that makes complexity possible. With two bonds you can only make chains. With three you can make simple branches. With four you can make chains, branches, rings, and three-dimensional structures with a distinct left-handed and right-handed version, and you can do all of it while carbon–carbon bonds stay strong enough not to fall apart at body temperature.
Silicon sits directly below carbon in the periodic table and also forms four bonds, which is why science fiction keeps proposing silicon life. It does not work well in practice: silicon–silicon bonds are much weaker and come apart in water, and silicon's version of carbon dioxide is silicon dioxide — sand — which is a solid you cannot breathe out.
Functional groups: the handful of attachments that do all the work
A long carbon chain by itself is chemically boring; petrol is a good example. What makes a biological molecule do something is the small clusters of atoms hung off that chain. These are functional groups, and there are only about six worth memorising because they cover almost everything in this volume.
| Group | Written as | What it does | Where you meet it |
|---|---|---|---|
| Hydroxyl | —OH | Makes the molecule water-friendly | Sugars, alcohol |
| Carbonyl | —C=O | Reactive site for joining | Sugars, ketone bodies |
| Carboxyl | —COOH | Acidic — gives up an H⁺ | Fatty acids, amino acids |
| Amino | —NH₂ | Basic — accepts an H⁺ | Amino acids, DNA bases |
| Phosphate | —PO₄²⁻ | Carries energy, adds charge | ATP, DNA, membranes |
| Sulfhydryl | —SH | Forms bridges that lock shape | Cysteine, hair, insulin |
The two to watch are carboxyl and amino, because a molecule carrying one of each is an amino acid and that is what you are largely made of. And phosphate, because attaching or removing a phosphate is how the cell switches almost everything on and off.
One reaction pattern, used everywhere
Large biological molecules are almost all polymers: long chains built by joining many copies of a small unit called a monomer. Poly means many, mono means one, mer means part. Sugar monomers chain into starch; amino acid monomers chain into protein; nucleotide monomers chain into DNA.
Two reactions build and break every one of them, and they are the same reaction run backwards.
Condensation joins two monomers by removing a water molecule: an —OH is taken from one and an —H from the other, they leave together as H₂O, and the two monomers bond where the pieces were removed. Building anything therefore costs energy and produces water.
Hydrolysis is the reverse — hydro, water, lysis, splitting. A water molecule is added across the bond, its —OH going to one side and its —H to the other, and the chain breaks in two. Every digestive enzyme in your gut is doing hydrolysis: your saliva hydrolyses starch, your stomach and small intestine hydrolyse protein, your pancreatic lipase hydrolyses fat.
That is genuinely the whole pattern. Learn it once here and Chapters 9.1 through 9.5 on digestion become mostly bookkeeping.
Carbohydrates: the fast fuel
A carbohydrate is, in the simplest reading of the name, a hydrated carbon: the general formula is Cn(H₂O)n, one water's worth of hydrogen and oxygen per carbon. Glucose is C₆H₁₂O₆.
Monosaccharides are single sugar units. Mono, one; saccharide, sugar. Glucose is the one your body runs on and the one measured when a doctor checks your blood sugar. Fructose is the sugar in fruit; it has the same formula C₆H₁₂O₆ but the atoms are arranged differently, which makes it a different molecule with different behaviour — the liver has to convert it before the rest of the body can use it. Galactose is the third, and it arrives mostly as half of milk sugar.
Disaccharides are two units joined by condensation. Sucrose, ordinary table sugar, is glucose plus fructose. Lactose, milk sugar, is glucose plus galactose. Maltose, from digesting starch, is glucose plus glucose.
Lactose is worth a paragraph because it explains a symptom a large part of the world lives with. To absorb lactose you need an enzyme called lactase in the lining of your small intestine to hydrolyse it into its two halves. Every mammal makes lactase as an infant and almost every mammal switches the gene off after weaning, because no adult mammal in the wild drinks milk. In humans, some populations — mostly those with long histories of dairy farming in northern Europe, parts of Africa and parts of India — carry a mutation that keeps the gene switched on for life. This is called lactase persistence, and it is the minority condition worldwide. If you do not have it, undigested lactose travels on into your large intestine, where your gut bacteria ferment it, producing gas and drawing water into the bowel. The result is bloating, cramps and diarrhoea an hour or two after milk. It is not an allergy and it is not damaging your gut; it is an enzyme you stopped making, exactly as your species always did.
Polysaccharides are long chains, and here the same monomer gives radically different materials depending only on how the links are angled.
Starch is the plant's glucose store — a chain of glucose units linked in the alpha configuration, which curls the chain into a helix. Your enzymes hydrolyse alpha links, so you can digest starch.
Glycogen is your own glucose store, the animal version of starch, and much more heavily branched. Branching matters because enzymes chew from the ends of a chain, so more branches means more ends means faster release. You carry roughly 100 grams of glycogen in your liver and roughly 400 grams in your skeletal muscle. These two stores do different jobs and this distinction is clinical. Liver glycogen is public — the liver can release free glucose into the blood, and this is what keeps your blood sugar from crashing between meals and overnight. Muscle glycogen is private — muscle lacks the enzyme needed to release free glucose, so muscle glycogen can only be burned by that muscle itself. The total is enough for roughly a day of resting metabolism, or between 90 and 120 minutes of hard endurance exercise, which is precisely the "wall" that marathon runners hit.
Cellulose is the same glucose, linked in the beta configuration, which lays the chain out straight instead of curling it. Straight chains stack side by side and hydrogen-bond into fibres of enormous strength; this is wood, cotton and paper. No human enzyme can break a beta link. Cellulose therefore passes through you untouched, and we call it dietary fibre. It is not useless — it holds water, gives stool bulk, keeps things moving, and feeds the bacteria in your colon that produce short-chain fatty acids your gut lining lives on. Cows extract calories from grass not because they have a special enzyme but because they house bacteria that do, in a fermentation chamber called the rumen.
Chitin is a glucose chain with a nitrogen group added, and it makes insect shells and fungal cell walls.
Carbohydrates supply about 4 kilocalories per gram. Keep that number; the comparison in the next section is the point.
Lipids: the dense store, the barrier, and the signal
Lipid is a category defined by behaviour rather than structure: a lipid is any biological molecule that does not dissolve in water. That grouping covers three quite different things.
A fatty acid is a long hydrocarbon tail with a carboxyl group at one end. The tail is hydrophobic; the carboxyl head is hydrophilic. Whether the tail is straight or kinked is what separates the fats in your kitchen.
Saturated means every carbon in the tail holds as many hydrogens as it can — no double bonds. The tail is straight, so the molecules stack neatly and the fat is solid at room temperature. Butter, ghee, coconut oil, the fat on meat.
Unsaturated means the tail contains one or more carbon–carbon double bonds. In the natural form, called cis, the double bond puts a permanent kink in the chain. Kinked chains cannot pack tightly, so the fat is liquid at room temperature: olive oil, mustard oil, fish oil. Monounsaturated has one double bond, polyunsaturated has several.
Trans fats are the industrial exception and the reason this paragraph exists. If you take a liquid unsaturated oil and partially hydrogenate it to make it solid and shelf-stable, some of the remaining double bonds flip from the kinked cis shape to the straight trans shape. The result behaves like a saturated fat in your food and like nothing your body has an evolved answer for in your arteries. Trans fats raise LDL cholesterol and lower HDL simultaneously, which is a combination almost nothing else does, and the evidence linking them to heart disease was strong enough that the World Health Organization called for their global elimination in 2018. Many countries have now banned or capped them.
A triglyceride is three fatty acids joined to one glycerol molecule by condensation, and it is what body fat and dietary fat are made of. Its virtue is energy density: fat supplies about 9 kilocalories per gram against carbohydrate's 4, more than double. The reason is straightforward chemistry — the carbons in a fatty acid are almost fully surrounded by hydrogen and carry very little oxygen, so there is far more left to oxidise. Carbohydrate is already partly oxidised before you start.
That number decides how your body stores energy. Storing a day's reserve as glycogen would be impossible: glycogen also binds about three grams of water per gram, so it is heavy and bulky. A person carrying 12 kilograms of body fat is carrying roughly 108,000 kilocalories, enough for weeks of survival, in a form that weighs almost nothing extra because fat stores essentially dry. This is a very good design for an animal that could not count on eating tomorrow, and a poor one for an animal with a refrigerator.
Phospholipids replace one of the three fatty acids with a phosphate group. That single change creates a molecule with a water-loving head and two water-fearing tails, and that is the molecule the entire cell membrane is built from. Chapter 1.4 is about what happens when you drop a lot of them into water.
Steroids are a completely different shape: four carbon rings fused together. Cholesterol is the parent of the family, and it has a reputation it only half deserves. Your cells need it in their membranes to keep them at the right stiffness. Your body converts it into every steroid hormone you have — cortisol, aldosterone, testosterone, oestrogen, progesterone. It is the starting material for vitamin D when sunlight hits your skin, and for the bile acids that let you digest fat at all. Your liver makes most of what you carry; diet contributes less than most people assume. The problem with cholesterol is not its existence but what happens when the particles carrying it lodge in an artery wall, which is Chapter 18.1 in full.
Proteins: the machinery
An amino acid is named for what it carries: an amino group and an acid group, both on the same central carbon. The fourth attachment, the R group or side chain, is the entire source of variety. There are twenty standard amino acids in human proteins, differing only in what R is. Glycine's R is a single hydrogen. Tryptophan's is a double ring. Cysteine's ends in —SH, which lets two cysteines form a strong bridge that locks a protein's shape — and which, incidentally, is what a hairdresser is breaking and reforming when they give someone a permanent wave.
Two amino acids join by condensation: the carboxyl of one and the amino group of the next release a water molecule and bond directly. The link is called a peptide bond, a short chain is a peptide, and a long folded one is a protein.
Nine of the twenty are essential, meaning your body cannot build them and you must eat them: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. "Essential" here is a technical word that means only must come from the diet — the other eleven are just as necessary to your body, you can simply make them yourself. A protein source containing all nine in useful amounts is called complete: eggs, milk, meat, fish, soy and quinoa are. Most single plant foods are low in one or two, which is why rice and dal eaten together works well — rice is short on lysine and rich in methionine, dal is the reverse.
What proteins actually do is nearly everything. They are the enzymes that catalyse every reaction. They are the fibres that make tendon, skin and hair. They are the pumps and channels in every membrane. They are the antibodies of the immune system, the haemoglobin that carries your oxygen, the actin and myosin that contract your muscles, and the receptors that hormones bind to. Protein also supplies about 4 kilocalories per gram, but burning it for fuel is a last resort, because to do so the body has to strip the nitrogen off and dispose of it as urea — which is Chapter 10.2's problem.
Chapter 1.3 is entirely about how a chain of amino acids folds into a machine.
Nucleic acids: the instructions
The monomer is a nucleotide, and it has exactly three parts: a five-carbon sugar, a phosphate group, and a nitrogen-containing base. Chain them by joining the phosphate of one to the sugar of the next and you get a backbone with bases sticking out sideways.
DNA uses the sugar deoxyribose and the four bases adenine, thymine, guanine and cytosine. It is double-stranded, the two strands held together by hydrogen bonds between paired bases, and it stores the instructions.
RNA uses ribose — one oxygen more, which is what the "deoxy" in DNA refers to — and swaps thymine for uracil. It is usually single-stranded, and it carries instructions out to be used.
Nucleotides also do a second job that has nothing to do with heredity. ATP is a nucleotide: adenine, ribose, and three phosphates in a row. Breaking off the last phosphate releases usable energy, and that reaction powers essentially every process in your body. Chapter 1.6 is about where that energy comes from.
How this shows up in your own life
Everything above has a direct reading in ordinary experience.
The food label on any packet is these four families and nothing else. Carbohydrate at 4 kcal/g, protein at 4, fat at 9, plus water, fibre and ash. If a label's numbers do not add up when you multiply them out, it is wrong. Alcohol, which is none of the four, sits at 7 kcal/g, which is why drinks add up faster than people expect.
A blood test measures these molecules directly. Glucose is a monosaccharide. Triglycerides, LDL and HDL are lipids being carried around. Albumin and globulin are proteins. Urea and creatinine are what is left after protein has been burned. By the end of Chapter 16.5 you will be able to read your own report line by line.
And dehydration is a molecular problem, not a comfort problem. Losing water concentrates everything dissolved in it, and every one of the control loops above is calibrated for the normal concentration. Lose 2 percent of your body water and physical and mental performance measurably drop. Lose 10 percent and you are in serious clinical trouble. This is why oral rehydration solution — water with a precise ratio of salt and sugar — has been called one of the most important medical advances of the twentieth century, and it works for a reason you now have the pieces to understand. Chapter 1.4 explains why the sugar has to be in there.
What the next page fixes
This page said proteins are the machinery of the body and left it as an assertion. A chain of amino acids is not a machine — it is a piece of string. Chapter 1.3 shows how that string folds itself into a precise three-dimensional shape, why the shape is the function, and what happens to you when the shape is lost.