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As I recall from my biology classes, proteins are denatured, not destroyed, through heating. When food's consistency is transformed through cooking, for example -- meat and fish can became firmer or, if overcooked, even plastic-like or rubbery -- denaturation is at work. (See the wikipedia link below.)
Denatured protein is a current fitness fad. Because it's a fad, I'm inclined to listen to the claims but also to be very skeptical. (See the fitday.com link below.)
In general terms, cooking actually makes it easier for enzymes to digest proteins, not harder, and denatures the proteins in harmful bacteria to the point of destroying that bacteria's ability to survive. (See the elmhurst.edu link.)
Cooking (heating) tends to coagulate proteins from food. The exception is made by egg white. Coagulation is making proteins less digestible.
Some sensitive amines are altered by heat, while other proteins are destroyed.
Both, cystine and cysteine, are so distorted by the presence of heat and water, they become unusable for nutritional purposes.
The most important of all components of the proteins, lysine, is destroyed by heat. Glutamine is also essential and it is destroyed by heat.
Other proteins are transformed and thus become unusable for nutrition.
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