The above methods provide schemes for determining protein quality based upon either animal growth or amino acid composition using scoring. A particular drawback with the scoring system is that it does not consider other factors inherent in the test protein or the effect of how the protein is prepared for consumption. How food is prepared may significantly affect the bioavailibility of individual amino acids. As discussed above, some plants contain protein inhibitors of proteolytic digestive enzymes. Although soy protein is limiting in terms of its methionine content (180), rats fed soy protein grow poorly because of trypsin inhibition (134). Heat processing of the soy protein inactivates these inhibitors and improves growth (180).
However, heat processing itself may damage amino acids. For example, heat treatment of protein in the presence of reducing sugars can promote reactions altering the lysine amino groups in the protein. This reaction, called the Maillard, or "browning," reaction, can be seen in milk processing in which lactose reacts with lysine at high temperatures. Oxidative or alkaline processing conditions may alter other essential and nonessential amino acids, inducing loss of methionine or formation of amino acid products that have toxic properties. Likewise, storage conditions may affect the nutritional quality of the protein. Thus, processing or "cooking" the protein source as well as storage conditions and other factors must be considered in evaluating the quality of the protein.
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