Lego blocks are the building blocks of Lego sets but they are also made up of smaller things (plastics, dyes, etc). If you had all those things separately you wouldn’t necessarily be able to make the lego set, but using the blocks you can easily. Same with atoms, even if you had a bunch of protons, neutrons, or electrons it would be extremely difficult to make water, but if you had hydrogen and oxygen you could easily.
There are a couple of reasons for this. For one, it has become tradition. They used to be the smallest units we knew about. That being said, we know that’s not the case now, but it would kind of silly to introduce young students to subatomic stuff because it gets WEIRD. Subatomic science is tricky and lots of fancy math and doesn’t make any sense without at least bachelor’s degree level math. It’s not intuitive and puzzles most people. If someone says they really get quantum physics, they are lying. So they are the smallest sensible/useful thing to learn about in school
Atoms are the smallest parts of an element that are still that element. An oxygen atom is still oxygen, and a sodium atom is still sodium.
Not only that, but they are the smallest pieces that you can easily divide an object into. (The word “atom” itself comes from the Greek for “not cut”.) Breaking an atom into its component particles permanently requires a particle accelerator, whereas you can typically separate the atoms of a piece of an element from one another with an ordinary knife or even your hands.
You can think of atoms as being like Lego bricks and subatomic particles as the molecules of plastic that the bricks are made of. Dismantling a Lego model is much easier than breaking the blocks up into molecules.
So just as Lego bricks are the building blocks of Lego models, atoms are the building blocks of matter.
EDIT: grammar, clarification
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