Protons and Neutrons are composed of quarks that can be further identified as up or down. An electron does not break down into anything and is referred to as a type of Lepton. There are six types of quarks that vary in size and are considered the smallest unit of matter.
It is widely believed that electrons and quarks are actually vibrating filaments of energy and their movements cannot be predicted unless they are being observed, then they move along a path, but that path is also unpredictable.
Somehow, gravity holds all of this together along with the other forces of Physics.
As different atoms combine, different types of molecules are formed which gives rise to the various types of matter than we see around us., like a tree, a bird, a human, or a rock.
What is interesting about atoms is that they are always composed of a nucleus that contains protons and neutrons, with an electron flying around it as if in orbit all of its own.
We can break atoms apart or we can fuse atoms together, using what is called the weak/strong nuclear force, to create different type of matter. But no one really knows from where all these subatomic particles originated. Although and again, it is widely believed that the creation of the universe caused them to appear.
Now, the obvious question is, did these subatomic particles just start randomly connecting with each other? If so, then their random combinations are rather remarkable to say the least. The odds are against them randomly forming and yet that is exactly what they did.
Physics is not based on the appearances of random events and random combinations of subatomic particles... and yet, there is no other explanation, except speculation and conjecture.