Fate of helium moving toward a singularity On the molecular level, if an atom, consider helium, were to fall into a black hole, what would be the ultimate fate of its electrons, protons and neutrons?
I'll take the reference of an observer falling with the helium atom. At the Event horizon, the tidal force across a helium atom is still minute, $10^{-29}N$ much less than the Coulomb forces between the electrons and nucleus, still less than the strong forces inside the nucleus. So the atom will fall through the event horizon without damage. (The region around the black hole can be a pretty violent place, with lots of hard X rays from the superheated matter, which would likely have ionised the atom, but I'll suppose it somehow manages to avoid this)

As it falls past the event horizon it is doomed. Think of the singularity less of a place in the middle of the black hole, and more as a point in time. It is inevitable our He atom will reach that point. As it approaches it the tidal forces will grow larger, eventually sufficient pull the atom apart. To describe what happens now would require a good description of quantum gravity, which we don't have.

The is no physics that describes what happens "after" the singularity. Think of the singularity as a point in time, but for the atom it is also the end of time for the atom. It is possible that something beyond our current understanding prevents a singularity from forming, but that is speculation. 

This is explained diagramatically in a Penrose diagram