From what I understand, it's excreted. Or what's left after the intestinal flora and fauna get through with it is excreted, anyhow.
We had a discussion in another thread about excess protein 'stressing' kidney function, and I re-examined everything I had read previously about protein intake and the way our bodies process it. In a nutshell, the liver can deaminate more protein per hour (raising blood urea levels) than the kidneys can filter out the waste products. However, the intestines cannot absorb as much as the liver can process, so blood levels of urea don't reach damaging levels *unless* there is reduced kidney function.
As to the AAs that make it into the bloodstream, they are utilized as needed by most tissues, with excess being oxidized by the liver or being used for gluconeogenesis. However, protein uptake by muscle is strongly insulin dependent, and to make matters more complicated, one study indicated that a rise in protein levels promoted a greater amount of protein synthesis in muscle than an elevated steady-state level. i.e. protein synthesis increased upon initial transfusion of AAs, but then tapered off even though blood AA levels were kept constant under infusion. *That* bit of info knocked me for a loop, and changed the way I was thinking.
I also think I found the reasoning behind the 'no more than 30 grams in one sitting' bit of advice that keeps cropping up. If you combine protein absorption speeds with intestinal transit time and gastric emptying rates, you wind up with something around 30 grams of protein being able to be absorbed by the jejunum before the meal passes through to the ileum and large intestine.
All of the above is why I've come to the conclusion that 240-ish grams of protein a day is about the most anyone really *needs* to eat. And I think it's even less than that, because if you think about it.. muscle is about 25% protein. So in theory, 100 grams of protein should make 400 grams of muscle (more, once you figure in glycogen and IMTG). *Maybe* on extreme gear someone could gain a pound of muscle a day, but that's still only using 100 grams of protein, plus whatever else (maybe 60 grams) is needed for regular body maintenance.
And yeah, I think one reason whey is so damned anabolic is simply because using it increases the amount of protein that gets absorbed, compared to other, whole-food sources.
Granted, there are lots and lots of caveats due to the limited scope and focus of the studies available, namely no one has really tried to answer the question of just how much protein can one absorb in a day. Everything is inferred from studies based on smaller, single meal or bolus consumption's effect on blood AA levels, not a total nitrogen intake/excretion monitoring over a longer period of time.