Kidneys When you digest a protein, the body breaks down the protein into amino acids which the body then uses to build new proteins. But if there is an excess of amino acids, the body isn't capable of storing those excess amino acids for future use. So the body breaks down the amino acids into glucose, ketones, hydrocarbons and nitrogenous waste. The nitrogenous wastes are then converted to urea by the liver and the urea is extracted from the blood stream by the kidneys and expelled from the body.