Lots. They are fundamentally different classes of molecules.
Carbohydrates are heavily hydroxylated hydrocarbons (that is, lots of -OH groups. They often form small rings. Your body digests them for energy.
Proteins are fragile and complex structures formed from chains of amino acids (nitrogen-containing acids) which are then folded into a unique form so that they can serve specific functions in the body.
Fats are long oily acids (long-chain hydrocarbons with a small acid group on the end) which are bond to a glycerol molecule on one end.
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