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An atom is the smallest amount of an element. Elements are pure substances with no contaminants. Although an atom is made of smaller subatomic particles, i.e. Protons,neutrons, and electrons. If an atom is split or any of those particles are removed, it ceases to be that elemental substance. A molecule is the smallest part of any aggregate substance. For instance, splitting water molecules into hydrogen (element) and oxygen (also an element). A cell is made of hundreds of thousands of molecules. RNA, DNA, Rhizomes, the cell wall etc. Are all made up of molecules not atoms. Some molecules are simple like water, others such as biological molecules such as neurotransmitters can be very large structures comparatively. You can see Cells with a normal microscope, but atomic and molecular structures can only be seen with an electron microscope.

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