sorry if my wording above wasn’t clear. denaturing isn’t what gets them past the stomach, the initial effect of the stomach is to release hcl which starts the denaturing process which activates many enzymes including pepsinogen into pepsin (triggered auto-catylization). Since pepsin is activated it can then catalyze other enzymes activating them, it will also break down enzyme inhibitors which activates yet other enzymes. enzyme inhibitors are designed to break down before enzymes so that enzymes are activated during the breakdown process. this is how they function. so this very process the stomach starts of breaking down proteins is actually what accomplishes the main ways that enzymes are activated, which in turn then catalyze and act upon their respective processes.
Even though this process starts in the stomach only 20% of free proteins are actually denatured in the stomach before the food slurry passes to the small intestines, that includes enzymes. Which means contrary to common outdated misconceptions, most protein is not broken down yet, again including enzymes. additionally the initial process of denaturing and breaking down is what converts many enzymes from their inactive to active forms, including our own digestive enzymes, so they start doing what we need them to do. this slurry created in the stomach is then passed to small intestines where the remaining pepsin from the stomach but mostly, trypsin and chymotrypsin from the pancreas, enzymes in the food itself, and intestinal epithelium actually break down the bulk of the proteins that will be broken down to amino acids during digestion rather then passed. The remainder of proteins that aren’t broken down in this stage are passed on. The enzymes that aren’t broken down which remain active the remainder of the process and play roles in the processes that the yeast/bacterial/enzyme processes in the large intestines and bile take over.
The model of:
- stomach breaks down protein to amino acids
- small intestines absorb all the amino acids
is an oversimplification base on a somewhat outdated and incomplete understanding of a much more complex system.
[quote]Protein digestion is primarily a result of the activity of enzymes secreted by the pancreas. Aminopeptidases associated with the intestinal epithelium further digest proteins. [1]
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both through catalyzation and through the breaking down of enzyme inhibitors.
it isn’t that all enzymes make it through each stage, but the ones that do are active and do precisely what they were originally created to do. our bodies continue to add enzymes at various stages to the digestive process, and the less enzymes at any stage equal a higher the load on the body to compensate with manufactured enzymes. which has two negative impacts, 1) the long term extra load on our enzyme systems takes a toll 2) we are only capable of making certain subset enzymes which limits which nutrients can be broken down or manufactured and results in nutritional deficiencies and imbalances.
humans also use cooking and heat to break down foods, and heat does a great job, but it also has the effects i mentioned in my initial comment, the enzyme thing was just ONE of the bullet points. The only reason it specifically blew up into was the total focus and write off of that one point upthread by another commenter, well that and the fact that it is probably the most misunderstood aspect. All the vitamin, antioxidants, and other phyto-nutrients destroyed by heating is a bigger deal, imho.
Enzymes and the metabolic processes of the liver are a much more fun conversation. 
