If you looked at an onion under a microscope you would see it consists of lots of little sacs similar to an orange or a lemon. When you cut through it, these little sacs burst, spraying juice about and releasing fumes which affect some people worse than others. When you slice through an onion, you break open a number of onion cells. Some of these cells have enzymes inside of them, and when they are sliced open, the enzymes escape. The enzymes then decompose some of the other substances that have escaped from sliced cells. Some of these substances, amino acid sulfoxides, form sulfenic acids, which then quickly rearrange themselves into a volatile gas.
The gas reaches your eyes and reacts with the water that keeps them moist. This changes the chemical's form again, producing, among other things, a mild sulfuric acid, which irritates the eyes. The nerve endings in your eyes are very sensitive and so they pick up on this irritation (this is why our eyes sting when we slice onions). The brain reacts by telling your tear ducts to produce more water, to dilute the irritating acid so the eyes are protected. Your other reaction is probably to rub your eyes, but this will actually make the irritation a lot worse, of course, if you have onion juices all over your hands.
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