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When you consume food, it must pass through the stomach and into the intestines before it is absorbed into the body. The process of muscle contractions that push food along the esophagus and into the stomach and then through the intestines is called 'peristalsis'. Its speed can vary.
Food ingested loses its form in the acid bath known as the stomach, and turns into an indistinguishable mass called 'chyme'. Chyme is pushed through the intestines by peristalsis, and the outer layer gets 'eaten' (or taken up) by the walls of the intestine into the body. This is the process of nutrient absorption.
So basically, there may not be much difference between your breakfast and your morning snack, as the morning snack could just meet up with and fuse with the hunk of chyme that your breakfast has become. The chyme does not stay in the intestines for a set time - it varies.
Getting amino acids into the intestines
Transportation into the intestines
Dietary protein (or amino acids) that lay around in the gut will be absorbed into the intestines, and later into the body, by amino acid transporters.
There are many different transporters that take up amino acids. The most common are sodium (Na) dependent transporters that can take up neutral or charged amino acids and then there are some chloride (Cl) dependent transports as well. The general idea is that some transports are assisted by ions and are catered to different amino acids. Some transporters also exist for small di-(two) or tri-(three)peptides, which are groups of amino acids, usually by a transport known as PEPT-1. Collectively, the assortment of transporters in the intestines determines the bulk amount of amino acids that can be transported into the intestines and is the rate-limiting step.
The overall amount of absorption can be determined by measuring fecal amino acids (if not absorbed, nitrogen's only other significant route is rectal excretion). The oro-ileal digestibility (a measure of overall protein usage) tends to be around 91-95% depending on source and assuming a reasonable acute dose (10-50g at once), with animal sources a bit higher than plant.
The rate of uptake on an hourly basis fluctuates between 5-10g per hour, depending on source.
Can I eat too much at once?
Amino acids and some peptides are able to self-regulate their time in the intestines. An example of this is the digestive hormone CCK which, in addition to regulating appetite and satiety in response to food can also slow down intestinal contractions and speed in response to protein. CCK is released when dietary protein is present, and demonstrates a way in which the body can slow down digestion in order to absorb all present protein.
Protein storage and release
Small intestines be saving my muscles?
The small intestines are also an organ, and they need nutrients to survive as well. The small intestines will absorb a lot of amino acids, but may eat some to survive and proliferate. Almost half of eaten amino acids are used by the gut and related tissues, with the gut consuming more of the amino acids found normally in animal products. Specifically Glutamate, Glutamine, Branched Chain Amino Acids, Threonine, Cysteine, and Arginine.
Due to this high demand, the small intestines are able to absorb and hold onto a large amount of amino acids; waiting to release them until the body needs them, and can recycle some amino acids.
Free amino acid pool?
Due to the aforementioned ability of the small intestines to 'hold' onto protein, they are considered a 'free amino acid pool' that the body can draw amino acids from on an as-needed basis. Its not wholly an 'out' storage though, as the intestines may partake in some 'recycling' and bring up amino acids to turn into glutamine (their main fuel source).
During periods of protein deprivation, the gut may reduce its need to use amino acids as fuel though.
Putting it All Together
If we assume the final goal is health, you can consume a fair amount per sitting as the gut will tend to slow down absorption and feast happily on the amino acids. No study has looked at the 'maximal' amount that can be consumed though, as 'health' is hard to define accurately.
The same notion applies to building muscle and losing fat, which want amino acids floating around in the blood (systemic circulation) rather than hopping between the intestines and liver (portal circulation). The body will tend to slow down absorption in response to how much you eat, as the presence of amino acids can self-regulate their own digestion.
The body likes to adapt in response to stresses, and is pretty good at it. There isn't a single number which is the answer here, as the body tends to try and preserve all amino acids. How effective it is at this is individual.
In a study done on women, consumption of more than 54g of protein in a single meal versus across four meals resulted in no differences. As these women had on average 90 lb of lean mass, it is highly plausible that more protein could be efficiently processed. The same researchers found that a single high protein meal was actually more effective in a population of elderly women.
Research done on Intermittent Fasting supports the theory that your body can cope with far more protein than most people think, with two studies showing that the consumption of an average of 80-100g of protein in 4 hours yielded no differences in lean mass
That being said, since fecal losses of protein and short-chain peptides tend to smell incredibly bad one can use a 'sniff-test' after bowel movements to assess if protein is being lost in the feces and thus not taken up by either the intestines or the muscle.
30g of protein?
You may have heard that you can’t digest more than 30 grams of protein in one sitting. This notion of a “protein intake ceiling” derives partly from early studies that observed increased nitrogen losses in the urine with increased protein intakes. This was thought to mean that the extra protein was wasted.
We now know that things aren’t so simple. When you eat protein, your body doesn’t use it directly; instead, it breaks it down into its constituent amino acids and uses those to make its own proteins. When you eat more protein, your body can afford to replace more of its damaged or oxidized proteins, so that your protein synthesis and breakdown are both increased.
In other words, eating more protein increases your body’s protein turnover. The raised levels of urinary nitrogen then reflect, not a waste of eaten protein, but an increase in the breakdown of your body’s damaged or oxidized proteins.
(Note that elevated levels of urinary nitrogen can also indicate health issues, such as problems with kidney function.)
The notion of a “protein intake ceiling” derives also from studies on the body’s muscle protein synthesis (MPS) response to different intakes of protein.
One study in healthy young men found that eating more than 20 grams of whole-egg protein didn’t further increase MPS.
Another study in younger and older people found that 90 grams of protein from 90% lean beef didn’t increase MPS more than did 30 grams.
However, your body doesn't use dietary protein only to make muscle, or even only to make other proteins. It also uses the nitrogen from the dietary protein’s amino acids to synthesize important non-protein molecules, such as purines and pyrimidines, the building blocks for nucleic acids such as DNA and RNA.
Moreover, your small intestines are able to absorb and store a large amount of amino acids, ready to be used when your body needs them. (Note, also, that higher protein intakes increase satiety, which is particularly helpful if you’re trying to cut calories as part of a weight-loss diet.)
In short, the idea that eating more than 30 grams of protein results in wasted protein is incorrect. Your body will break down and use all the protein you eat, sooner or later, one way or another.