Paper, glass and iron are all made up of atoms. In fact, all the matter around us is made up of atoms. Whether we talk about an airplane or a laptop or rocks, it's all made of atoms. There are very few exceptions to this on earth and the commonly used examples are sub atomic particles such as electrons and protons. Similarly, outside the earth, we can think of neutron stars as not being made of atoms.
But for all the matter that we see daily, the atom is the basic ingredient. The atoms differ from each other based on the number of electrons and protons and that's what gives them different properties. We can also have compounds containing different atoms and get a different set of properties with each compound. This is why paper is so thin and glass is transparent.