Start here: why biology begins with chemistry#
A leaf, a muscle and a strand of DNA look nothing alike. Underneath, they are made of the same few kinds of atom, joined together in the same few ways. That is why this module comes before cells, before energy and before genes: every later module leans on it.
You do not need a chemistry class first. Every word is explained the first time it appears, and the only maths is counting and multiplying by ten.
The short videos for Module 02 are in production. This page is the written version, complete on its own, and each video will be added here as it is published.
Atoms and elements: what you are made of#
An atom is the smallest piece of an element that still has that element's chemical properties. Picture a heavy centre, the nucleus, surrounded by a cloud of much lighter particles.
| Particle | Where it is | Charge | What it decides |
|---|---|---|---|
| Proton | In the nucleus | Positive (+1) | Which element the atom is |
| Neutron | In the nucleus | None (0) | Which version, or isotope, of the element |
| Electron | Around the nucleus | Negative (−1) | How the atom bonds to others |
An element is a kind of atom, defined by its number of protons. Every atom with 6 protons is carbon. Every atom with 8 is oxygen. Change the number of protons and you have a different element.
Neutrons can vary without changing the element. Oxygen-16 and oxygen-18 are both oxygen; the second just has two extra neutrons and is a little heavier. Those versions are called isotopes, and biologists use them as labels. That is exactly how, in 1941, researchers showed that the oxygen released in photosynthesis comes from water (Module 07 tells that story).
Living things use only a small part of the periodic table. Four elements, oxygen, carbon, hydrogen and nitrogen, make up about 96% of the mass of a human body. Most of the rest is a few others such as calcium, phosphorus, potassium and sulfur.
Ions: atoms with a charge#
A normal atom has as many electrons as protons, so the plus and minus charges cancel out. Some atoms hold on to their outer electrons loosely and give one or more away. Others grab one or more extra. Either way, the charges no longer cancel, and the atom becomes an ion: an atom (or a small group of atoms) with an overall charge.
- Sodium tends to lose one electron. That leaves it with one more proton than electrons, so it carries one positive charge: Na+.
- Chlorine tends to gain one electron: Cl−.
Ions matter in your body every second. Your nerves send signals by letting sodium and potassium ions rush across a membrane, and your muscles contract when calcium ions are released inside them.
Losing an electron makes an atom positive, not negative. Electrons carry the negative charge, so taking one away leaves the positive protons in the majority.
Three ways atoms hold on to each other#
Atoms are rarely alone. They join together, and the way they join decides almost everything about what the result can do. Biology relies mainly on three kinds of attraction. There are even weaker pulls too, which later modules bring in when they are needed.
| Covalent bond | Ionic attraction | Hydrogen bond | |
|---|---|---|---|
| What happens | Two atoms share one or more pairs of electrons | A positive ion and a negative ion pull on each other | A hydrogen already bonded to oxygen or nitrogen, and so slightly positive, is drawn to a slightly negative oxygen or nitrogen nearby |
| Strength | Strong | Strong in a dry crystal, weak in water; weaker than covalent | Weak on its own, strong in large numbers |
| Example | The O–H bonds inside one water molecule | Na+ and Cl− in a grain of salt | Between neighbouring water molecules; between the two strands of DNA |
A molecule is a group of atoms held together by covalent bonds, like water, H2O. Covalent bonds are the skeleton of every molecule in your body. They are strong enough that they do not fall apart at body temperature.
Hydrogen bonds are the opposite kind of useful. Each one is weak, so they break and re-form easily, which lets enzymes unzip the two strands of DNA and copy them. But there are so many of them that together they hold structures firmly in shape.
A hydrogen bond is not the bond inside a water molecule. Inside H2O, oxygen and hydrogen share electrons: that is a covalent bond. A hydrogen bond is the weaker pull between one water molecule and the next.
Why water is polar, and why that matters#
In a water molecule, the oxygen atom and the two hydrogen atoms share electrons, but not fairly. Oxygen pulls the shared electrons towards itself, like a bigger child holding most of a blanket. So the oxygen end of the molecule is slightly negative and the hydrogen ends are slightly positive. The molecule is also bent, not straight, so those charges do not cancel out.
A molecule with a slightly negative end and a slightly positive end is called polar. Water's polarity is the single fact behind almost everything that makes it special:
- Cohesion. Water molecules stick to each other through hydrogen bonds. Cohesion causes surface tension, and it keeps the column of water inside a tree unbroken as evaporation from the leaves pulls it up from the roots.
- Adhesion. Water also sticks to other polar surfaces, such as the walls of a narrow glass tube. Together with cohesion, that lets water creep up narrow spaces, which is called capillary action.
- A good solvent. The partly charged ends of water molecules cluster around ions and polar molecules and separate them from each other, which is why salt and sugar dissolve. Salt splits into Na+ and Cl− ions; sugar molecules stay whole but spread out through the water. Oils are not polar, so they do not mix with water.
- Steady temperature. Water has a high specific heat: it takes a lot of heat to warm up, because much of the energy goes into breaking hydrogen bonds instead of speeding the molecules up. Lakes, oceans and bodies change temperature slowly.
- Ice floats. When water freezes, hydrogen bonds lock the molecules into an open pattern that takes up more space, so ice is less dense than liquid water. Ponds freeze from the top down, and the floating ice insulates the water underneath so it usually stays liquid.
Oxygen hogs the electrons. Water is polar because its oxygen pulls the shared electrons towards itself, and cohesion, adhesion, dissolving, steady temperature and floating ice all follow from that one fact.
pH: counting hydrogen ions#
A tiny fraction of water molecules split into hydrogen ions (H+) and hydroxide ions (OH−). The pH scale measures how concentrated hydrogen ions are in a solution: how many there are in a given amount of liquid. It usually runs from 0 to 14.
- pH 7 is neutral, like pure water at room temperature.
- Below 7 is acidic: more hydrogen ions than pure water. Stomach acid is around pH 2.
- Above 7 is basic, also called alkaline: fewer hydrogen ions than pure water.
The scale counts in powers of ten. Each step down means ten times as many hydrogen ions. So pH 4 is not a little more acidic than pH 5. It has ten times the hydrogen ions of pH 5, and pH 3 has a hundred times as many as pH 5.
Living things are fussy about pH because the shape of a protein depends on it, and a protein's shape decides its job. Human blood stays between about 7.35 and 7.45. Chemicals called buffers, such as the bicarbonate system in blood, keep it there by soaking up extra hydrogen ions or releasing them when there are too few.
A lower pH means more hydrogen ions, not fewer. The number goes down as the acidity goes up.
Why carbon is special#
Carbon has four electrons available for bonding, so each carbon atom can form four covalent bonds. Think of it as a building block with four connectors. It can link to other carbon atoms in long chains, branch, close into rings, and form double bonds, while still holding on to hydrogen, oxygen and nitrogen.
No other element found in living things is that versatile. Even silicon, which can also form four bonds, cannot build such stable, varied chains. That is why the large molecules of life (carbohydrates, lipids, proteins and nucleic acids such as DNA) all have carbon skeletons. Molecules built on a carbon skeleton, usually with hydrogen attached, are called organic molecules. Those large molecules are the subject of the next module.
The short videos in this module#
Module 02 breaks into short videos, each answering one question. They are planned in this order and will appear on this page as they are published.
- Planned02.1 · What is an atom?
- Planned02.2 · What makes one element different from another?
- Planned02.3 · Protons, neutrons and electrons: what does each one do?
- Planned02.4 · What is an ion?
- Planned02.5 · What is a covalent bond?
- Planned02.6 · What holds salt together?
- Planned02.7 · What is a hydrogen bond?
- Planned02.8 · Why is water polar?
- Planned02.9 · Why does water stick to itself?
- Planned02.10 · What does pH measure?
- Planned02.11 · Why is carbon special?
Key terms#
- Atom
- The smallest piece of an element that keeps that element's chemical properties.
- Element
- A kind of atom, defined by its number of protons.
- Isotope
- A version of an element with a different number of neutrons.
- Ion
- An atom, or small group of atoms, that has gained or lost electrons, so it carries a charge.
- Covalent bond
- Two atoms sharing one or more pairs of electrons; strong.
- Ionic attraction
- The pull between a positive ion and a negative ion.
- Hydrogen bond
- A weak pull between a hydrogen that is bonded to oxygen or nitrogen, and so slightly positive, and a slightly negative oxygen or nitrogen nearby.
- Polar
- Having a slightly negative end and a slightly positive end, as water does.
- Cohesion
- Water molecules sticking to each other.
- Adhesion
- Water sticking to other polar or charged surfaces.
- Specific heat
- How much heat it takes to warm a substance up; water's is high.
- pH
- A measure of how concentrated hydrogen ions are in a solution; lower means more acidic.
- Buffer
- A chemical that keeps pH steady by taking up or releasing hydrogen ions.
Check yourself#
Answer each one out loud before you open it. Reading the answer without trying first feels like learning and is not.
1. An atom has 8 protons and 10 neutrons. Which element is it, and what is unusual about it?
Oxygen, because it has 8 protons. Most oxygen atoms have 8 neutrons, so this one is the heavier isotope oxygen-18.
2. A sodium atom gives away one electron. What is its charge now, and why?
Plus one. It still has 11 positive protons but only 10 negative electrons, so one positive charge is left over.
3. What is the difference between the bond inside a water molecule and a hydrogen bond?
Inside the molecule, oxygen and hydrogen share electrons: a strong covalent bond. A hydrogen bond is the weaker pull between the slightly positive hydrogen of one molecule and the slightly negative oxygen of another.
4. Why does ice float on liquid water?
Hydrogen bonds lock frozen water into an open pattern that takes up more space, so ice is less dense than the liquid around it.
5. Solution A has pH 3 and solution B has pH 5. How do their hydrogen ion levels compare?
A has a hundred times as many hydrogen ions as B. Each step on the pH scale is a factor of ten, and two steps is ten times ten.
Frequently asked questions#
Which elements are living things mostly made of? Oxygen, carbon, hydrogen and nitrogen, which together make up about 96% of the mass of a human body.
Why is water polar? Its oxygen pulls shared electrons towards itself, making the oxygen end slightly negative and the hydrogen ends slightly positive, and the molecule's bent shape keeps those charges from cancelling.
What is the difference between cohesion and adhesion? Cohesion is water sticking to water. Adhesion is water sticking to other polar or charged surfaces, such as the wall of a glass tube.
Why is carbon the basis of life? Each carbon atom can form four covalent bonds, so carbon can build the long chains, branches and rings that large biological molecules need.
What does a pH of 7 mean? Neutral: the same as pure water at room temperature. Lower is acidic and higher is basic.
Practise this module
72 practice questions on the chemistry of life, from atoms, isotopes and ions to bonds, water, pH and carbon, with an explanation for every answer. Free, offline, no account.
Open the biology practice app →Sources#
Clark, M. A., Douglas, M. and Choi, J. (2018). Biology 2e, Chapter 2: The Chemical Foundation of Life. OpenStax, Rice University. Open-access textbook treatment of atoms, bonds, water and carbon.
Ruben, S., Randall, M., Kamen, M. and Hyde, J. L. (1941). Heavy oxygen (O18) as a tracer in the study of photosynthesis. Journal of the American Chemical Society, 63(3), 877–879. The isotope-labelling experiment mentioned under isotopes.