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To understand what protein denaturing is, you have to understand the biochemistry of what proteins are.
A protein is a molecule. It’s a bunch of atoms bonded together. But the atoms that are bonded together aren’t random; proteins are specifically made out of repeating units, called amino acids.
You can think of a protein like a long chain, except that most of the links in the chain have something “extra” attached on to them. These “extra” bits then bind together to create a stable structure, and some of them also help perform the protein’s functions.
(And the vast majority of things that your body does, are done by proteins. Muscle contraction is one example, but your body’s biochemistry and thinking and such are all also done by proteins.)
Denaturing the protein means that you disrupted the way that all those “extra” bits are bound together. Denaturing does (typically) make the protein non-functional.
But the thing is, when we eat protein, it’s food: when we digest and absorb protein, we already break it apart and break it down anyway. To digest proteins, we break them down all the way into the individual links, the amino acids. And then we absorb those, and use them to construct our body’s own proteins.
Since your body already breaks the protein apart into the individual amino acids, in order to digest and absorb it, it doesn’t really matter whether the structure of the extra bits gets broken down early.
The problem that would lower the protein content would be if the amino acids themselves started to break down, if the links themselves got broken.
The protein in eggs denatures when they are cooked. This is why it changes from liquid to solid. It has no effect on your metabolism of the protein. Protein denatures in your stomach acid; it’s still protein, and will be absorbed by your gut.