Why does amount of protons define how matter is? My question might sound convoluted but my mind is twisting right now so my apologies in advanced. 
Why is it that when I have one proton and one electron it is Hydrogen a clear flammable gas, and when I have say, twelve, it is carbon the driving force of life as we know it and then we end up with 239 and we have uranium a radioactive element. 
How does the amount of protons affect what matter will be? Why does the amount of these particle things magically make one thing air and another cyanide?
If I have one pebble it is a pebble, if I have 13 its just more of the same pebbles. What makes protons different?
Sorry this is so convoluted, 
any reply is appreciated
 A: Your day to day experience of the material world is governed by chemistry.  This is at some level the science of atoms and groups of atoms.
Things like hardness, colour, toxicity and others are all largely determined by the interaction of atoms.  In particular the outer coating of atoms, the electrons.  Obviously the details of why element or compound A is harder or softer than compound B is incredibly diverse and complicated.
Typically the number of electrons is equal to the number of protons (but not always!)  as atoms like to be electrically neutral and so for each positive proton, one negative electron will stick to the atom.  So from this we can see that the number of protons indirectly affects the behaviour of an atom via the number of electrons...
A: Long answer: Any Chemistry textbook. 
Short answer: The number of electrons of an atom is the same as the number of protons in the nucleus. This number of electrons (Identical to the position number in PSE!) defines all the chemistry of that atom. 
A: The proton is, in some sense, a red herring. Only the total charge of the nucleus (which happens to be the number of protons in certain units) is important to keep the atom electrically neutral. The detailed structure inside the nucleus (like the fact that it consists of protons and neutrons) is not relevant for chemistry. You should be asking to the number of electrons instead.
A: Heavy and light analogues of hydrogen probe the limits of quantum chemistry

To make the ultra-light isotope, scientists swapped the proton with a positively charged muon, which has just 11% of the mass of a proton. And to make ultra-heavy hydrogen, they replaced one of the electrons in a helium atom with a negative muon.
The researchers tested the behaviour of these new atoms in a chemical reaction called a hydrogen exchange, in which a lone hydrogen atom plucks another from a two-atom hydrogen molecule — just about the simplest chemical reaction conceivable. In a paper in Science1, they report that both the weedy and the bloated hydrogen atoms behave just as quantum theory predicts they should.

