first of all let's make sure you have atoms and elements straight
imagine a whole pile of atoms and you with a very tiny pair of tweezers and a very powerful magnifying glass and a couple of hundred mason jars. And you decide to sort that pile of atoms into those mason jars by the number of protons in their nucleus.
so you take the first jar and write on it with a sharpie.. "atoms with 1 proton".. and on the 2nd jar you write "atoms with 2 protons.. and so on and so on. After awhile you have all the jars labeled... "atoms with __ protons" and you start sorting
into the jar labeled "atoms with 1 proton".. go all the atoms you can find with exactly 1 proton. Into the jar labeled atoms with 92 protons go all the atoms you see with 92 protons... and so on and so on. When you're done sorting, you have some jars with lots of atoms, some jars with a few atoms, and some jars are empty.
Now that everything is sorted, you think to yourself.. "self.. I don't like these labels".. so you change the names. On the jar with atoms containing 1 proton, you write "hydrogen". On the jar of 2 proton atoms.. you write "helium"... etc
now you notice something funny. not all the atoms of a particular jar have the same mass. So you look closer and see they have different numbers of neutrons.
the mason jars (empty, full, or partially full) represent "elements"
the atoms... are grouped into elements by the number of protons in their nucleus.
"isotopes" are how we distinguish between atoms of the same element with different #'s of neutrons
All atoms have a region of electron density surrounding the nucleus. Since protons have a +1 charge and electrons have a -1 charge, the number of protons dictates the number of electrons in a neutral atom.
All chemical reactions involve reorganization of electrons around those atoms. So atoms from different elements have different electron densities and different chemical reactivities.
as to wood, oil, bones and clouds. some materials have large organic molecules formed by combinations of carbon, nitrogen, phosphorous and oxygen etc... some materials are formed by combinations of other materials like calcium and oxygen. others are combinations of hydrogen and oxygen. The number of elements found in nature is about 90+ and you can have a few or hundreds or thousands of atoms combined into substances, each with different physical and chemical properties. The larger the molecule, the less likely it is to be found in the vapor phase in nature... etc