Although they exist near the ultimately small end of the scale of matter, atoms and molecules are actually matter themselves and are made up of other particles. Molecules consist of two or more atoms, but what are atoms made up of?

Let's take a look at a conventional atom. At the center of the atom is a positively charged nucleus. Orbiting this nucleus are negatively charged electrons. Normally, these opposing electric charges keep the electrons and nucleus in a push-pull relationship. The nucleus is a heavy component, accounting for most of the weight of the atom. It is made up of protons, which are positively charged, and neutrons, which carry no positive or negative charge. The neutrons serve to bind the positively charged protons together, preventing the repulsion of like positive charges from causing protons to scatter.

Hydrogen atoms, among the simplest of all atoms, have only one proton and one electron, with no neutron. The more complex an atom is, however, the more protons and neutrons it possesses. The result is a heavier nucleus and more electrons. The orbits of electrons are governed by special rules, and the maximum number of electrons occupying the same orbit is fixed. Atoms also react in various ways with other atoms, including by binding with them through exchanging electrons in the outermost orbit.
When there is no space left in the outermost orbit, however, it is difficult for the atom concerned to react with other matter.

There are other structural elements within atoms, but by and large, this is the way atoms work.