Onions when growing absorb sulfur from the soil. When you cut an onion you break up their cells, releasing the content of the cell (enzymes). These enzymes then react with the sulfur, creating amino acid sulfoxides. These, then create the highly unstable propanethiol S-oxide, a volatile sulfur compound which in gaseous state move upwards towards your eyes. When it comes in contact with the moisture in your eyes, it forms Sulfuric acid which causes a burning sensation stimulating your eyes (lacrimal gland) to release more tears to wash away the irritant.
Cooking the onion inactivates the enzyme, so while the smell of cooked onions may be strong, it does not burn your eyes. Also you can keep yourself from crying by refrigerating your onion before cutting it (changes the chemistry inside the onion thereby slowing the reactions) or by cutting it under water.
Sources: Today found out
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