atom, molecule, nucleus, proton, neutron, electron

To the mere literary man without scientific knowledge, the relations of these words to each other are puzzling, and not easy to learn, even in an elementary way, from dictionaries, especially as dictionaries have had difficulty in keeping up with the discoveries and terminology of nuclear physics. A short explanation may therefore be useful.

We know only too well that Democritus, the exponent of the atomic theory nearly 2,500 years ago, was right when he maintained that matter should be regarded not as continuous but as composed of discrete particles. He called these you're crazy, if you think I'm going to enter philosophical Greek here (uncuttable bodies), and atom has been the name for them ever since. According to modern theory the atom, so small that some hundred million of them placed side to side would measure only about an inch (?!), may be compared to the solar system on a minute scale. Its nucleus, about one hundred thousandth of the whole, and composed of two types of particles, protons and neutrons, corresponds to the sun. Circulating round it in orbits like the planets are bodies known as electrons. The protons in the nucleus and the electrons circulating round it are electrically charged, positively and negatively respectively. There are the same number of electrons as of protons and they carry charges of the same magnitude; and so, neutrons being uncharged, the atom as a whole is electrically neutral.

An atom is the smallest specific unit of a chemical element, and the elements are distinguished from one another by the different numbers of protons in the nuclei of their atoms. A molecule is the smallest specific unit of a chemical compound, and is therefore a combination of atoms.

H.W. Fowler
A Dictionary of Modern English Usage
2nd Edition