In an atom: the nucleus is made of electrons and protons. protons have positive charges. neutrons have negative charges. all of the above.

The nucleus of an atom contains protons and neutrons.
Protons have positive charges, neutrons have neutral charges (no charge), and electrons have negative charges.  That is why when you determine net charge of atom you only look at the proton to electron ratio since the neutrons don't matter when it comes to charge.

I hope this helps.  Let me know in the comments if anything is unclear.