The Chemical Basis of Life's Extraordinary Symphony
Level: GCSE foundations, A-level and introductory university extension. This lesson is about the chemistry underneath all of biology: the handful of elements life is made from, the bonds that hold them together, and the one molecule — water — that makes the whole thing work.
Ask a simple question and most textbooks dodge it: what is a cell actually made of? One list of percentages gives proteins 15–25%, lipids 20–30% and water 70–80% — and those numbers add up to more than 100%. That is not because cells are mysterious. It is because the list mixes up two different kinds of figures: percentages of wet weight and percentages of dry weight. This lesson starts from the numbers that do add up, and builds the chemistry from there.
What a cell is actually made of
Take a single E. coli bacterium and dry it out completely. What is left, by dry weight, is roughly this:
| Component | Share of dry weight (approx.) |
|---|---|
| Protein | ~55% |
| RNA | ~20% |
| DNA | ~3% |
| Lipid | ~9% |
| Polysaccharide | ~5% |
| Other small molecules | ~8% |
Those figures add up to about 100% — as they should. And the water that was dried away? About 70% of the living cell's wet weight. A typical mammalian cell is similar in shape: water about 70%, protein about 15–20%, lipid only about 2–5% (not 20–30% — that figure belongs to fat-storing adipose cells, not to a typical cell), carbohydrate about 1–3%, and nucleic acids about 1–2%. Two things jump out of that table. First, water is by far the biggest ingredient, which is why this lesson spends so much time on it. Second, RNA is far more abundant than DNA in a growing bacterium — about 20% against 3%. RNA is the higher one, because a growing cell is busy making protein, and protein synthesis runs on RNA.
Six elements do almost all the work
Living things are built from a strikingly short shopping list. Six elements — carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur, remembered as CHNOPS — make up about 96% of the mass of living matter. Oxygen is the biggest share (about 65%), then carbon (about 18%), hydrogen (about 10%) and nitrogen (about 3%). The rest of the periodic table shows up only in traces: calcium in bones and shells, iron in haemoglobin, magnesium at the centre of chlorophyll, iodine in thyroid hormones. The pattern is the first thing to notice: life does not use exotic elements. It uses the lightest, most common ones — and it uses them cleverly.
Carbon is the clever part. A carbon atom has four electrons in its outer shell and needs four more to fill it, so it forms four covalent bonds. Four bonds mean chains, branches and rings — and chains, branches and rings mean an almost endless variety of molecules from one element. Carbon can bond to itself, to hydrogen, to oxygen and to nitrogen, and the same atoms rearranged give different molecules. Glucose and fructose both have the formula C6H12O6, yet one is the sugar in blood and the other is the sugar in fruit: same formula, different structure, different molecule. Molecules like that are called isomers, and carbon's talent for making them is the reason living things are so varied.
Three kinds of bond
Everything in this lesson comes back to three ways atoms stick together. A covalent bond shares electrons: two atoms each contribute to a shared pair, and the pair holds them together. A polar covalent bond shares unequally — oxygen pulls the shared electrons towards itself, so one end of the bond is slightly negative and the other slightly positive. An ionic bond transfers an electron outright: sodium gives one to chlorine, and the resulting Na+ and Cl− ions attract. A hydrogen bond is different from both: it is the weak pull between a hydrogen atom on one polar molecule and an oxygen or nitrogen atom on another. One hydrogen bond is feeble — about 20 kJ/mol against about 460 kJ/mol for the covalent bond inside a water molecule — but millions of them together hold DNA's two strands together and keep water liquid.
Two confusions to clear up, because examiners set questions on exactly these. First, a hydrogen bond is not the bond inside a water molecule — the O–H links inside H2O are polar covalent bonds. Hydrogen bonds form between water molecules. Second, ionic bonds are strong in a crystal but fall apart in water: polar water molecules surround each ion and pull it away, which is why salt dissolves.
Water: the molecule that makes life possible
Water looks simple — H2O, three atoms — and it behaves like nothing else. The reason is shape. Oxygen pulls the shared electrons towards itself, so the oxygen end of the molecule carries a slight negative charge (δ−) and each hydrogen a slight positive charge (δ+). And the molecule is bent, at an angle of 104.5°, so the two partial charges never cancel out. That bent, lopsided molecule is polar, and polarity explains nearly everything water does.
Because each water molecule carries partial charges, it hydrogen-bonds to its neighbours — up to four of them at once. That network of weak bonds, constantly breaking and reforming, gives water four properties that life depends on. First, cohesion: water sticks to itself, so it can be pulled up a plant in an unbroken column. Second, adhesion: water sticks to other surfaces, which helps it climb narrow tubes. Third, a high specific heat: water absorbs a lot of heat (4.18 joules per gram per degree) with only a small temperature change, so a body that is mostly water does not swing wildly in temperature. Fourth, a high heat of vaporisation: turning water into vapour takes so much heat that sweating cools the body — the heat leaves with the water. And there is a fifth, stranger one: ice floats. In ice, hydrogen bonds lock water molecules into an open lattice that takes up more room than liquid water, so ice is less dense (0.917 g/cm³ against 1.00 g/cm³) and floats — which is why lakes freeze from the top down and the life underneath survives winter.
Water is also the great solvent. Salts and sugars dissolve because polar water molecules surround their charged parts; oil does not, because oil molecules are non-polar and cannot form hydrogen bonds with water. That split — substances that mix with water (hydrophilic) and substances that avoid it (hydrophobic) — shapes every cell: membranes are built from it, with their water-loving heads facing out and their water-fearing tails tucked inside.
pH: a small scale with big consequences
Acidity is measured on the pH scale, and the scale is logarithmic: pH = −log[H+], where [H+] is the hydrogen ion concentration. That minus sign and that log are the whole trick. A solution with [H+] = 1 × 10−4 mol/L has pH 4. Raise the hydrogen ions tenfold, to 10−3, and the pH falls by exactly one unit, to 3. Two solutions two pH units apart differ a hundredfold in hydrogen ions — which is why a pH of 3 is not "a little more acidic" than a pH of 6, but a thousand times more acidic.
Living things guard their pH fiercely. Human blood is held between pH 7.35 and 7.45 by buffers — substances that soak up added acid or base and resist pH change. Blood's main buffer is the bicarbonate system. Outside that narrow band, enzymes change shape and stop working, which is why a blood pH of 7.0 is a medical emergency, not a rounding error. The same logic runs through the body: stomach acid sits near pH 2 because pepsin needs it, and the small intestine is brought back towards neutral before digestion continues.
Functional groups: the working parts
Most of a biomolecule is a carbon skeleton, but what the molecule does is decided by the small groups of atoms stuck onto that skeleton — the functional groups. Six of them do most of the work in biology. The hydroxyl group (—OH) makes molecules polar and soluble, as in sugars and alcohols. The carbonyl group (C=O) marks aldehydes and ketones, including sugars. The carboxyl group (—COOH) makes a molecule acidic — it is one of the two defining groups of every amino acid and the head of every fatty acid. The amino group (—NH2) acts as a base and is the other defining group of amino acids. The phosphate group (—OPO32−) carries energy in ATP and links the backbone of DNA and RNA. The sulfhydryl group (—SH) forms disulfide links that pin a protein's folded shape. Learn the six by structure and by job, not just by name: an exam question will show you a structure and ask what it can do.
From small molecules to macromolecules
Life builds big molecules from small ones, and the pattern is the same every time: monomers join into polymers by dehydration synthesis, and polymers are split back into monomers by hydrolysis. Dehydration synthesis removes a water molecule to make a bond; hydrolysis adds one back to break it.
| Macromolecule | Monomer | Bond | Example |
|---|---|---|---|
| Carbohydrate | Monosaccharide (glucose) | Glycosidic | Starch, cellulose |
| Protein | Amino acid (20 types) | Peptide | Enzymes, haemoglobin |
| Nucleic acid | Nucleotide | Phosphodiester | DNA, RNA |
| Lipid | Not a true polymer | Ester | Triglyceride, phospholipid |
Lipids are the odd one out: a fat is one glycerol plus three fatty acids, a small assembly rather than a long chain of repeating monomers, so lipids are not true polymers. That is a favourite exam trap, and it is worth remembering as a sentence: carbohydrates, proteins and nucleic acids are polymers; lipids are not.
Worked example: counting the joins
The figures below are practice figures, invented for this lesson — not measurements from any experiment. Five glucose molecules are joined into a short chain by dehydration synthesis. Each join releases one water molecule. Five monomers need four joins, so four water molecules are released. The same arithmetic runs backwards: breaking that chain apart by hydrolysis needs four water molecules added back. Count the joins, not the monomers — that is the step students most often miss.
Metabolism: breaking down and building up
Metabolism is the sum of all chemical reactions in a cell, and it runs in two directions. Catabolism breaks large molecules into smaller ones and releases energy — respiration is the example everyone knows. Anabolism builds large molecules from smaller ones — photosynthesis, protein synthesis — and it needs energy input. The two are coupled by ATP: catabolism charges ATP up, anabolism spends it. ATP carries its energy in its phosphate groups, and removing the terminal phosphate by hydrolysis (ATP → ADP + inorganic phosphate) releases about 30 kJ per mole under standard conditions.
That direction matters. Anabolic reactions do not release energy. Building a molecule costs energy; breaking one down pays for it. If anabolism released energy, cells would get energy for free every time they built a protein, and the whole energy economy of life would run backwards. It is exactly the kind of error that costs marks.
Five mistakes that sound like chemistry
1. "Hydrogen bonds are strong." One hydrogen bond is weak — about 20 kJ/mol. They matter because there are millions of them, not because any single one is strong.
2. "Water has no charge, so it must be non-polar." Water is electrically neutral overall, but its charges are unevenly spread: slightly negative on oxygen, slightly positive on the hydrogens. That unevenness is what polar means.
3. "pH 6 is twice as acidic as pH 3." The scale is logarithmic, not linear. pH 3 has a thousand times more hydrogen ions than pH 6.
4. "Anabolism releases energy." It needs energy input. Catabolism releases it. (See the correction above.)
5. "All four macromolecules are polymers." Three are. Lipids are not true polymers — a fat is one glycerol plus three fatty acids.
How to answer an exam question on this topic
Use the sequence structure → property → consequence. Name the structure, say what property it gives, then state what follows from it in the living thing.
Here is the pattern applied, in one paragraph. Water is polar because oxygen pulls the shared electrons towards itself and the molecule is bent — structure. That polarity lets water molecules hydrogen-bond to each other and to charged solutes — property. So water is an excellent solvent, has a high specific heat that steadies body temperature, and forms ice that floats and insulates the water below — consequence. The limits are that the same polarity that makes water a good solvent also means it cannot dissolve non-polar substances, and that hydrogen bonds are weak individually, so their effects depend on numbers. That paragraph names a structure, a property, three consequences and a limit — which is what the marks are for.
Frequently asked questions
Why is carbon so special, and not silicon?
Silicon also forms four bonds, but its bonds are longer and weaker, and silicon dioxide is a solid rock (sand), not a gas a plant could take in. Carbon's small size lets it form strong double bonds and long chains, and carbon dioxide is a gas that dissolves in water.
Why does water have such a high boiling point for such a small molecule?
Because of hydrogen bonding. Each water molecule is held to its neighbours by up to four hydrogen bonds, and a lot of heat is needed to break them all. A similar-sized molecule without hydrogen bonds, like methane, boils at −161°C.
Can pH be below 0 or above 14?
In concentrated laboratory acids and bases, yes — the 0–14 scale is the everyday range, not a hard limit. In living things, pH stays roughly between 1 and 9.
Why is blood pH controlled so tightly?
Because enzymes work only in a narrow pH range. A shift of even half a unit changes the charges on amino acid side chains, alters enzyme shape, and can stop reactions altogether.
Are all biomolecules polymers?
No. Carbohydrates, proteins and nucleic acids are. Lipids are not true polymers.
What is the difference between cohesion and adhesion?
Cohesion is water molecules attracting each other, through hydrogen bonds. Adhesion is water molecules attracting other surfaces, such as the walls of a xylem vessel. Both help water rise in plants.
Continue learning
- Biological Method — the method behind the chemistry in this lesson: how experiments, not opinions, settle what a molecule does.
- Microscopy and Cell Size — the scale of the cells whose chemistry this lesson describes, and why viruses need an electron microscope.
- Decoding Bacterial World: Size, Shape, and Arrangement — the bacterium whose dry-weight composition opens this lesson, and how to read its shape under a microscope.
- Navigating the World of Viruses — the other kind of biological particle: nucleic acid and protein, and nothing else.
- Carbohydrates — the first macromolecule family in detail: monosaccharides, disaccharides and polysaccharides.
Sources and further reading
These notes were written from the sources below and from the site's own linked lessons. The worked figures in the practice examples are invented for teaching and are labelled as such.
- OpenStax, Biology 2e, Chapter 2: The Chemical Foundation of Life — elements, bonds, water, pH and functional groups.
- Khan Academy, Biology: Water, acids, and bases — polarity, hydrogen bonding and the pH scale.
- BBC Bitesize, GCSE Biology: Biological Molecules — carbohydrates, proteins, lipids and their tests.
- Biology LibreTexts, Introductory Biology: The Building Blocks of Molecules — functional groups and macromolecules.
- Alberts et al., Molecular Biology of the Cell — the dry-weight composition of E. coli used in the opening table.
20 Explained MCQs — answers hidden until opened
Open each question to reveal its answer and explanation. The interactive quiz below uses a different set of questions.
1. Which four elements make up about 96% of the mass of living things?
A. Carbon, calcium, iron and sodium B. Hydrogen, helium, carbon and oxygen C. Oxygen, silicon, aluminium and iron D. Carbon, hydrogen, oxygen and nitrogen
Answer: D. Carbon, hydrogen, oxygen and nitrogen dominate living matter; phosphorus and sulfur — the P and S of CHNOPS — make up most of the rest.
2. Why is carbon the backbone of life's molecules?
A. It is the lightest element B. It can form four covalent bonds, building chains, branches and rings C. It carries a positive charge D. It dissolves easily in water
Answer: B. Carbon's four bonds let it build long chains, branches and rings — the skeletons of proteins, DNA and carbohydrates.
3. Glucose and fructose both have the formula C6H12O6 but different structures. What are they?
A. Isomers B. Isotopes C. Ions D. Polymers
Answer: A. Same molecular formula, different arrangement of atoms — that is the definition of isomers.
4. A covalent bond forms when:
A. an electron is transferred from one atom to another B. a hydrogen atom is attracted to oxygen C. two atoms share a pair of electrons D. two ions attract each other
Answer: C. Covalent means shared: two atoms share one or more pairs of electrons, and the shared pair holds them together.
5. In a polar covalent bond, the electrons are:
A. transferred completely B. shared equally C. shared unequally — pulled towards the more electronegative atom D. not involved at all
Answer: C. Oxygen pulls shared electrons towards itself, so the bond has a slightly negative end and a slightly positive end.
6. Table salt (NaCl) is held together by:
A. metallic bonds B. hydrogen bonds C. covalent bonds D. ionic bonds — attraction between Na+ and Cl−
Answer: D. Sodium gives an electron to chlorine, and the resulting opposite charges — Na+ and Cl− — attract.
7. A hydrogen bond is:
A. a strong bond inside a water molecule B. a bond formed by sharing electrons C. a weak attraction between a hydrogen on one polar molecule and oxygen or nitrogen on another D. the bond that holds NaCl together
Answer: C. A hydrogen bond is not a bond inside a molecule at all — it is the weak pull between two separate polar molecules.
8. Why is a water molecule polar?
A. Its hydrogen atoms are larger than oxygen B. It is a straight molecule C. Oxygen pulls the shared electrons towards itself and the molecule is bent D. It has an extra electron
Answer: C. Oxygen is more electronegative than hydrogen, and the bent shape stops the two partial charges cancelling out.
9. In liquid water, one water molecule can hydrogen-bond to at most:
A. eight neighbours B. four neighbours C. one neighbour D. two neighbours
Answer: B. Two lone pairs on oxygen accept two hydrogen bonds, and its two hydrogens donate two more — four in total.
10. Why does ice float on water?
A. Water is heavier when cold B. Hydrogen bonds hold the molecules in an open lattice, so ice is less dense than liquid water C. Ice contains air bubbles D. Ice is warmer than water
Answer: B. In ice, hydrogen bonds lock water molecules into an open, spaced-out lattice. That lattice takes up more room than liquid water, so ice is less dense and floats.
11. Water's high specific heat (4.18 J/g/°C) means that:
A. water boils at a low temperature B. a large amount of heat changes water temperature only slightly, so living things stay stable C. water cannot absorb heat D. water heats up very quickly
Answer: B. A high specific heat means water resists temperature change — which is why a body that is mostly water does not swing wildly in temperature.
12. Oil does not dissolve in water because:
A. oil is heavier than water B. water repels all liquids C. oil molecules are too large to fit between water molecules D. oil molecules are non-polar and cannot form hydrogen bonds with water
Answer: D. Water molecules would rather hydrogen-bond to each other than make room for non-polar oil, so the oil is pushed together instead.
13. Practice figures: a solution has a hydrogen ion concentration of 1 × 10^-4 mol/L. What is its pH?
A. pH 4 B. pH 3 C. pH 10 D. pH 14
Answer: A. pH = −log[H+]. The negative log of 10^-4 is 4, so the solution has pH 4.
14. Practice figures: the hydrogen ion concentration of a solution rises tenfold. What happens to its pH?
A. It does not change B. It falls by 1 unit C. It rises by 1 unit D. It rises by 10 units
Answer: B. The pH scale is logarithmic: a tenfold rise in hydrogen ions lowers the pH by exactly one unit.
15. The pH of human blood is normally kept between:
A. 8.0 and 8.5 B. 5.5 and 6.0 C. 6.0 and 6.5 D. 7.35 and 7.45
Answer: D. Blood pH is held in a narrow band, 7.35–7.45, by buffers. Outside that band, enzymes stop working properly.
16. The functional group —COOH is called the:
A. hydroxyl group B. carboxyl group C. phosphate group D. amino group
Answer: B. —COOH is the carboxyl group: a carbon double-bonded to one oxygen and single-bonded to a hydroxyl group. It makes a molecule acidic.
17. The group that stores and transfers chemical energy in ATP is the:
A. hydroxyl group B. sulfhydryl group C. carbonyl group D. phosphate group
Answer: D. ATP carries its energy in its phosphate groups; removing the terminal phosphate releases the energy the cell uses.
18. Every amino acid carries which two functional groups?
A. Amino and carboxyl B. Methyl and amino C. Hydroxyl and carbonyl D. Phosphate and sulfhydryl
Answer: A. An amino acid is defined by having both an amino group (—NH2) and a carboxyl group (—COOH) on the same carbon.
19. Practice figures: five glucose molecules are joined into a short chain by dehydration synthesis. How many water molecules are released?
A. 1 B. 10 C. 4 D. 5
Answer: C. Five monomers need four joins, and each join releases one water molecule — so four waters are released.
20. Which statement about metabolism is correct?
A. Catabolism breaks molecules down and releases energy; anabolism builds molecules up and needs energy input B. Both catabolism and anabolism release energy C. Anabolism needs no energy at all D. Anabolism releases energy and catabolism uses it
Answer: A. Building molecules costs energy; breaking them down pays for it. A common error is to think anabolism releases energy. It does not.
Separate Interactive Quiz — 20 different questions
These quiz questions are different from the MCQs above. Select an answer for each question. You will not see whether an answer is correct until you submit all 20 questions. Use Reset to try again.
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