Everything in the universe follows fixed, discoverable, unchangeable laws and nothing can operate outside these laws, right?
I don't know. Nor do I see how anyone could.
Everything in existence is made out of atoms, what is the atom made of? Atoms are made of protons, neutrons and electrons.
That is not really very accurate either. Even from a strictly scientific perspective, not everything is made of atoms. There are ions, eletrons, various forms of energy and of subatomic particles. Lighting bolts, for instance, are not made of atoms.
The core of the atom is the nucleus, which is made of protons and neutrons, electrons orbit the nucleus; my question is why it is that way?
I think that what you actually mean to ask is "who made it so". I happen to believe that the answer is "no one", but it is a fairly open question.
Now, about gravity, gravity will always pull the planets into an orbit around the sun in the milky way or else each planet will move in a straight line away from the sun; why?
Not always. Only when the circunstances allow it. Our sun is expected to swallow our planet at some point far away in the future, for instance.
And again, your suggestion that there must be a purpose behind those circunstances does not have to be agreed with.
Gravity is what holds us on the ground and prevents everything from flying into Earth's orbit; why?
Not sure what you mean here. Why is gravity gravity? It just is, I suppose.
If you combine two hydrogen atoms with one oxygen atom you will always get water, why is that? why it won't come out as a rock or glass?
Not always, actually. It takes certain conditions for that to be possible, albeit fairly easy to find ones. And of course, a single molecule of water and water proper are not quite the same thing.
As for why chemistry is not fully random... why should it be?
If you mix red, green and blue in a certain proportion you will get white. You will never get black, why not?
Because it doesn't work that way (although, again, you are making some perhaps excessive assumptions).
Now let's move closer to your evolution theory.
Very slightly closer... we have got a long distance to go before even approaching biology.
Before it all started you need a very well balanced environment with gravity, solid ground, air and water, minerals for food and a very well balanced temperature . Not too cold that it will freeze the cell and not too hot that it will cook or even kill the cell.
Not really. Evolution did not begin with cells proper, and the first few living beings probably did not require "solid ground" or air, at the very least.
You also need light but the sun emits harmful radiation and the sun is about 150 millions kilometers away from us.
It is difficult to reach meaningful conclusions when you are making so many hurried assumptions. For instance, the sun is hardly the only source of light in existence, and even today it is not necessarily needed by any and all lifeforms.
As for the distance, what is your point? Sunlight travels for long distances, yes. So?
Maybe your evolution started there after which it came into the earth's orbit and made the ozone layer so it won't die from the harmful sun radiation.
Uh? "My" evolution? Maybe it is best if you come back after thinking this a bit more.