Water for instance contains both Hydrogen and Oxygen. Hydrogen has one proton, and possibly one neutron, it depends. Oxygen however is quite different than hydrogen, the reason for that is the number of protons. For instance, Oxygen has eight protons. Protons and electrons are the reason why there are different structures. Atomic structures make up molecules and so they make up structures that are in different states of matter.
In a solid structure, the molecules are closer together and give this structure it's solid appearance. In a liquid structure, like water for instance, the molecules can allow for other structures to pass through it. In a gas structure, the molecules are far enough apart and are at a low enough concentration that the structure of a gas itself appears invisible to us. We know Oxygen is there when we run fast, jump or move around. Oxygen at room temperature is a gas and this allows us to breathe it.
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