The number of protons in an atom determines the kind of material:
Hydrogen 1 proton
Helium 2 protons
Lithium 3 protons
Beryllium 4 protons
etc Copper 29 protons
etc Uranium 92 protons
The number of protons is referred to a the atomic number, thus the atomic number of copper is 29.
The neutron simply adds to the weight of the nucleus and hence the atom. There is no simple rule for determining the number of neutrons in any atom. In fact atoms of the same kind can contain different numbers of neutrons. For example chlorine may contain 18 - 20 neutrons in its nucleus.
The atoms are chemically indistinguishable and are called isotopes. The weight of an atom is due to the protons and neutrons (the electrons are negligible in weight), thus the atomic weight is virtually equal to the sum of the protons and the neutrons.
The electron orbits define the size or volume occupied by the atom. The electrons travel in orbits which are many times the diameter of the nucleus and hence the space occupied by an atom is virtually empty! The electrical properties of the atom are determined by how tightly the electrons are bound by electrical attraction to the nucleus.
A neutral atom contains an equal number of positive charges (protons) and negative charges (electrons). It is possible for an atom to gain or loose an electron.
An atom (or possibly a group of atoms) which loses an electron has lost one of its negative charges and is therefore left with an excess of one positive charge; it is called a positive ion. An atom that gains an electron has an excess of negative charge and is called a negative ion.