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As a matter of fact, it does. Moderate cooking % improves the biological value of protein, and excessive cooking reduces it. That's
why the best advice is medium rare for meats and "firm" (not overcooked) for eggs. And it's also why we recommend poaching foods.
Excessive cooking can destroy amino acids, and charring the surface of meats creates carcinogenic byproducts. A blackened steak has had many of its amino acids rendered useless. Similarly, the protein quality of bacon will have been reduced by the time it's crispy. Because amino acids are not brown, foods with a charred appearance will generally have less biological value.
Moderate cooking, though, often improves biological value and has a number of other benefits. Cooking reduces the risk of ingesting a harmful microorganism such as salmonella, which is usually transmitted through raw egg, as well as meat, fish or poultry. Cooking can also reduce the risk of Eschericia coli infection, a concern with undercooked meat. In addition, cooking can also neutralize certain toxins, including the one that causes botulism, while heat-resistant bacteria are destroyed by cooking at high temperature and pressure. Cooking will generally destroy any parasites as well, including the sushi worm.
Some raw foods contain ingredients that interfere with absorption or digestion. For example, raw soybean products have a chemical that inhibits protein digestion. Because cooking destroys the inhibitor, the protein in cooked soy products has a higher biological value than that in raw soy. Along the same lines, heat is useful for deactivating a protein called avidin found in egg whites that can reduce absorption of the vitamin biotin.
Overall, maximum protein bioavailability is best achieved by poaching (cooking in water at near boiling temperature). In this method, all amino acids are preserved because the cooking temperature stays at or below the boiling point, in contrast to barbecuing, frying or baking, in which the temperature can get above 400 degrees Fahrenheit. Besides improving protein quality slightly, poaching is more penetrating and can cook the interior of a chicken breast more quickly than would be possible in an oven. To make use of poached chicken breast, let it cool in the fridge, chop it into strips and add it to a salad or stir-fry. For a crispy brown outside, cover the poached breast with egg white and flour, then sear it in a frying pan.