Atoms and elements are the smallest units of chemistry, atoms are made of protons, electrons, and neutrons (protons and neutrons are made of quarks), which give atoms certain physical and chemical properties.
Elements are different types of atoms, different elements have different numbers of protons and different numbers of neutrons and electrons. For example, hydrogen has one proton, helium two, lithium three.
Molecules are formed when two or more atoms are chemically bonded (like carbon monoxide, a single carbon and a single oxygen that share electrons).