The atom is the most basic piece of matter; every physical thing is made up of millions of atoms. The atom itself consists of three main particles: electrons, protons and neutrons. The numbers of these particles in an atom designate what the atom is, whether carbon, gold or oxygen. The protons and neutrons are found together at the center of the atom in a part called the nucleus. Surrounding this nucleus are the electrons. In a normal atom there are an equal number of the negatively charged electrons and the positively charged protons, meaning that atoms have a neutral charge.
Molecules are the next step up, in that they are a collection of atoms connected together. Everything on earth, whether organic or inorganic, is made up of molecules, which can consist of just two atoms or millions. The combinations and way the atoms connect in molecules decide what the molecule will be. For example, when two hydrogen atoms combine with one oxygen atom, a water molecule is made. Other molecules include fats, alcohols, proteins and fibers.
An ion is an atom or molecule in which the normally neutral charge has been made positive or negative. When the charge is not neutral it causes individual atoms to be attracted to other atoms that possess the opposite charge. The charge in an atom is changed when electrons are either added or removed to cause the ratio between electrons and protons to become uneven. When electrons are removed, the atom becomes positively charged; when they are added, it becomes negative.
Molecules and compounds are essentially the same thing in that they are both made from atoms that are bonded together. The only difference is that a molecule can be made of a single type of element such as oxygen, hydrogen or nitrogen. To be a compound there must be more than one type of atom in the molecule -- for example, water, which has hydrogen and oxygen, or carbon dioxide, which has carbon and oxygen.