An atom is mostly empty space. At its centre is a tiny, dense nucleus that holds the protons and neutrons, so it carries all the positive charge and almost all the mass. The electrons move in shells in the space around it.
The proton number tells you which element the atom is. The nucleon number is protons plus neutrons. In a neutral atom, electrons equal protons. An ion has gained or lost electrons only.
The size of an atom or ion depends on how strongly the nucleus pulls on the outer electrons: more protons pull them in, more shells push them out.