The answer is that the enzymes do not get cooked or killed by the acids in the stomach. They are just "not active" in that environment. In the small intestine, however, they are once again activated because of the more alkaline pH.

Also, a lot of digestion goes on before the stomach pH gets lowered. Dr. Edward Howell did a lot of work on the subject. One of his books is called Enzyme Nutrition. He found over and over again that the pancreases of cooked food eaters was much larger than the pancreases of raw food eaters. He concluded from this that the pancreas had to produce many more enzymes when the food was cooked as demonstrated by its increased size. The organ had to increase in size to provide more surface area for producing more of the secretions that it produces. This has been corrobarated by other researchers in enzymes such as Howard Loomis, Jr. who has written many books on the subject. Also, nothing ever gets cooked in the body. The body temperature is 98.6° F and cooking does not start until between 105° F and 118° F, depending on the type of food.

The following is from my book Hooked on Raw:

"A food, which contains carbohydrate, protein and fat, is chewed and mixed with enzymes that are secreted into the mouth by the salivary glands. Here the process of digestion begins. The Ptyalin (salivary amylase) secreted by the parotid glands work on the carbohydrates (starch). Protease, released by the submandibular glands, work on protein; and lipase, released by the sublingual glands. work on fat. In addition, Cellulase, which digests the soluble parts of cellulose, is released from raw fibrous foods by thorough chewing. (Cellulase is not produced by the body.) Then the food moves into the upper stomach,* where enzymes from the raw food, as well as salivary enzymes, continue their work. The food stays in the upper stomach for approximately 30-60 minutes. Up to 60% of the carbohydrate (starch), 30% of the protein and 10% of the fat is digested even before the food moves to the lower stomach area. When the stomach secretes enough hydrochloric acid to lower the pH to below 3, the food moves into the lower stomach, where pepsin is activated and works upon the protein. Finally the food moves into the first part of the small intestine where 'enzymes delivered to the duodenum in pancreatic juice continue the digestion of starch and protein. In addition, pancreatic lipase is responsible for the digestion of most of the dietary fat'.

Hope this has helped.

Many blessings to you,