This is a great question, and not one that has a simple answer. Let me shed some light on the subject, though...
First, the universe comes down to energy. Matter (mass) is energy, but in a different form (similar to water and ice). Think of it as though matter is energy that is captured in a sort of bubble. Once it is matter, it gets properties of gravity, electric charge, and inertia.
Protons stick together in the nucleus with help from neutrons. For each proton, an atom wants an electron to balance its charges. The geometry in an atom, balancing charges, electrical attractions and repulsions, etc. is very complicated, but it is generally defined first by the protons, then the electrons, and finally the bonds with other atoms (as in molecules). Factor in heat and it all goes wild.
The geometry of the electron shells really define the characteristics of the atom.
This is overly simple, but the point is that the protons define the charge of the nucleus, the charge wants to be neutralized by electrons, and the electrons repel each other while being attracted to the nucleus (that they cannot simply crash into). Everything floats, and electrons are shared among atoms. The electrons give the atoms color, magnetic properties, bonding strength, etc.
FYI - protons, neutrons, and (maybe) electrons are made of smaller parts, as well. And those parts may be made of smaller parts. We don't know it all. Yet...