protons and electrons I am a novice in physics and a few things are not clear to me in electromagnetism:
Consider the experiment of giving a piece of metal positive charge (which I assume consists of protons), by keeping a piece of rod with negative charge close to the metal and touching by your finger the farther side of it from the rod. 
Assuming that the electrons and protons are parts of the atoms, does this mean that the rod is 
actually taking the electrons away from the atoms? Is the magnetic repulsion of a rod enough to do so?
If this is the case my second question is, if this happens then it means that the atoms of the metal do not have the same (say chemical) structure as before, since they have their electrons and protons taken away from them. but Apparently this has not happened to the metal. Can you explain this experiment with regards to actually what is happening to the structure of atoms of the metal? 
 A: Metals consist of a lattice of positively charged atoms in a sea of electrons that can move around freely. You can almost think of a metal as a vessel for a charged liquid made from electrons. Just like with other vessels, one can take part of that liquid out and put it in another similar vessel. That's what happens when we are moving charges around. 
So when you are charging a piece of metal positively, you are simply taking electrons out of its electron sea, which leaves it with more positively charged atoms than electrons. This does indeed change the chemical structure of the metal, but only very, very little, because there are many electrons in a macroscopic piece of metal, and one can only take very few of them away. For the same reason, a negatively charged piece of metal has a few more electrons in its electron sea, than there are positively charged atoms in the lattice. 
None of this has anything to do with magnetism. These are strictly electrostatic phenomena. The atomic explanation of how metals form these seas of electrons and what happens chemically when you take some of them away are unfortunately complex and I won't bother you with them. 
A: In this experiment, the metal gains a positive charge due to electrons leaving the metal via your finger.  The number of electrons (and protons) on the rod stays the same.  And the electrons in the metal don't leave the metal due to a magnetic repulsion, but rather due to an electrostatic repulsion between the excess of electrons in the rod, and the electrons in the metal.
The chemical structure of the metal isn't affected significantly by the loss of some electrons onto your finger, because in a metal, certain electrons, called the electrons in the "conduction band" aren't closely associated with any one atomic nucleus.  Instead, those electrons form a "sea of electrons" that flow freely throughout the metal.  So the loss of a few electrons out of that sea of electrons onto your finger has a negligible effect on any one atom in the metal.
