In A Nutshell
Atoms are the smallest pieces of matter; they are made of particles (protons and electrons). When atoms are grouped together, these groups are called molecules (the smallest pieces of compounds).
The Whole Bushel
You probably think of atoms, molecules, and particles as all being extremely small pieces of matter. This is not exactly accurate; while atoms are matter—the smallest pieces of matter you can find—molecules are the smallest bits of compounds. And particles aren’t matter, but the building blocks of it.
For example, copper is an element. A copper atom is the smallest piece of copper that exists. Hydrogen is also an element; two hydrogen atoms and one oxygen atom combine to form a molecule of water, which is a compound.
While atoms are the tiniest bits of matter, they are made of the sub-atomic building blocks of matter—protons and electrons—revolving around a nucleus. The “atomic number” of an element, as seen on a periodic chart, refers to the number of protons contained in one atom of that element.