After your protein powder shake or protein meal has digested and passed through the walls of the small intestine (as described in Protein Digestion and Metabolism Part 1) almost all of it ends up in the liver.
The liver then processes most of these amino acids and peptides, with about 20% (mainly BCAAs) moved on directly back into the blood stream to be used by other cells in the body. Those remaining in the liver, are synthesised into other amino acids, enzymes, hormones and other types of protein that the body needs. In this way, your diet doesn’t need to match the exact mix of amino acids that your body needs. There only needs to be adequate amounts of the essential amino acids (these can’t be synthesised in the body) and then liver takes care of the rest. The human body cannot store large quantities of amino acids with only about 100g in the blood plasma pool and a small amount in other body tissues. If there is too much protein in the diet, the liver also deals with this by breaking down the excess so that the nitrogen containing part is converted to urea for excretion. The remaining carbon containing part can be broken down to provide energy or it can be converted to carbohydrate or fat for storage. If there is insufficient protein in the diet for the bodies requirements, it will start breaking down its own protein.
This means that as the muscles contain large amounts of protein this is where it starts. The body will catabolise or breakdown the protein in muscle cells and ultimately other organs of the body to get the amino acids it needs. In a healthy person, there should be a balance between the input of nitrogen to the body and its output. The input is mostly from protein, though some other foods may contain small quantities of nitrogen too. The output of nitrogen is mainly in urine although a little is lost from other sources. Without any protein in the diet an 80kg person would lose about 27g of protein per day. However, for good health the recommended minimum protein intake is 0.8g per kg of body weight. During intense training protein needs may rise to between 1.4 to 2.0 g per kg bodyweight and, similarly, during low carbohydrate or low calorie diets. Injury or infection might also increase the bodies protein needs.