Molecules are groups of atoms held together by chemical forces. They are the smallest particles of a substance retains all of the physical and chemical properties of that substance. Molecules are made of two or more atoms. For example, an oxygen molecule has two oxygen atoms, a water molecule has two hydrogen atoms and one oxygen atom, and biological molecules, such as proteins and DNA, can be made up of many thousands of atoms. A molecule is the smallest unit of a compound that can exist by itself.