In particle physics nothing has shape as you might think about it. Every particle is a point in space with a repulsion field around it. This repulsion force gets stronger the closer you get. In a sense it creates the shape of the particle, which is a perfect sphere.
Now if we zoom out a bit we can think about protons and neutrons. Each of these is actually created by 3 particles called quarks. So maybe we could think about these as 3 balls stuck together. However, particles are always moving, so the location of any particle can only be thought of as a sphere of possible locations. Effectively a proton or neuron is the combination of the quark particles, resulting in their own repulsive sphere.
Zoom out again and we have the nucleus of an atom made up of neutrons and protons. The fun bit now is that the above explanation applies again, and the nucleus is best thought of as a perfect sphere.
Zoom out again (a lot) and we have electrons. These are negatively charged and attracted to the positively charged protons. However they’re less attracted than the quarks are attracted to each other, so they can go a lot further away from the nucleus. Once again we can’t say exactly where a particle is, but this time the possible locations are much larger, forming this electron cloud everyone is talking about.
Electrons are a lot more tricky than the other particles. They get shared with neighbouring atoms, helping to create molecules, or even wandering off further creating electricity.
However getting back to your original question. Everything is a repulsion sphere, until we get to molecules which are collections of spheres. At which point the concept of shape starts to become relevant. We can observe molecules and see these shapes.
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