Microwaves have some significant effects on foods -- they can denature proteins, decrease vitamin content and destroy enzymes. However, none of these effects are unique to microwave ovens. Conventional cooking has identical effects, notes Dr. D. Zhang and colleagues in a 2004 study in "Food Chemistry," as these are all effects of heating, rather than effects unique to microwave radiation.
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A microwave oven cooks food by causing the molecules that make up the food -- specifically water molecules -- to vibrate rapidly. As they vibrate, these molecules rub against each other, which generates heat through friction. If you rub your hands together rapidly, you'll feel your palms get warm -- this is similar to the way in which a microwave generates heat through friction. Given enough vibration, the food generates enough heat to cook it.
You may have heard that the radiation a microwave depends on damages your food or has a negative effect upon it. This is not true. Despite the fact that the words sound similar, "radiation" and "radioactive" are not the same thing. Microwave radiation is much more similar to heat wave radiation than it is to nuclear radiation; it can't "kill" your food or make it dangerous or radioactive. In fact, the only effects that a microwave can have on food are those that stem from heating -- just as conventional cooking can affect food through heating it.
Effects of Heating
When you heat food, you affect the proteins in it. Heat makes proteins change shape, which is called "denaturing" the proteins. While this causes them to lose function, it doesn't affect the nutrient value. In fact, you don't use any of the proteins in your food for their function. When you consume protein, your stomach acid denatures the protein -- just as heat does -- and you break the protein down into its constituent parts, explain Drs. Mary Campbell and Shawn Farrell in their book "Biochemistry." Enzymes are proteins, and you don't use the enzymes in your food. As such, though microwaving, like conventional cooking, destroys enzymes, this is of no concern, because the enzymes your body depends on are produced by the cells of the digestive tract.
Another effect of microwaving on food is that it slightly reduces the vitamin content. Again, however, this is an effect of heat, and is true in the case of conventional cooking as well. Dr. D. Zhang and colleagues note that any cooking method decreases vitamin content, with more destruction occurring the longer food is cooked. Since microwaves cook food more quickly, they actually result in less destruction of vitamins than conventional cooking methods.