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The smallest unit of matter that can enter into a chemical reaction is an atom. This is the smallest unit of chemical matter.

The smallest unit of matter in all is believed to be a fermion.

Matter is made up of molecules, which are made up of various atoms. Atoms are made of neutrons, protons and electrons. Protons and neutrons are made up of both quarks and gluon (think of gluon as the "glue" that holds together quarks). Electrons are made from leptons. Both leptons and quarks are types of fermions.

There are some even smaller, theorized, units such as the tachyon-- and the smallest unit of matter might not be a unit at all, but rather a vibration.

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