All of the same atoms make up elements. It's the arrangement of these atoms that really matters. Your answer is true, an atom that makes up gold will indeed be the same atom that makes up silver.
Atoms are just mostly empty space, in fact about 99.99 infinitely percent of an atom is just empty space. We don't actually touch anything, not really. You never make solid contact with an object, but in fact what you're touching is that objects electrostatic field, or otherwise known as it's electron shell. You don't simply pass through an object because like charges repel eachother, the shell and your atoms, which creates the illusion that you're actually touching the object, when in fact your just touching it's invisible electrostatic shell.
If an atom gains an electron, it will have a NEGATIVE charge. Protons are positive charges, neutrons are neutral charges, electrons are negative charges. Add an electron that out-weighs the net-charge, which is 0, then you'll have an anion, or a negative charge.
The nucleus of an atom is indeed the center of an atom, the most dense area. This carries all of the weight (practically). The nucleus is indeed made up of positive and neutral charges, with an outer shell of negative charges. This is true.