Amino acids are nitrogen-containing molecules that are the building blocks of all proteins in food and in the body. They can be used as energy, yielding about 4 calories per gram, but their primary purpose is the synthesis and maintenance of body proteins including, but not limited to, muscle mass.
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Amino Acids as Energy
During normal protein metabolism, a certain number of amino acids are pushed aside each day. When these amino acids are disproportionate to other amino acids for the synthesis of new protein, your liver and kidneys dispose of the nitrogen as urea, and the rest of the molecule is used as energy in a variety of ways. Then certain amino acids -- minus their nitrogen -- can enter the citric acid cycle -- the biochemical pathway that converts food into energy. Others can be converted to glucose or fat. This process may be enhanced when you take in more protein than you need.
Glucose for Energy
Your body relies on a continuous supply of glucose and fatty acids for energy for physical activity and cellular needs during rest. When you exercise, your body relies still more on glucose because fat is slower to metabolize. The higher your exercise intensity is, the more your body requires quicker-burning glucose. Some glucose is stored as glycogen in the liver and muscles and can be recruited when blood glucose is used up. When glycogen becomes depleted, the process of gluconeogenesis can take over -- the creation of new glucose from another source. The usual source for gluconeogenesis is amino acids.
From Amino Acid to Fatty Acid
Healthy people store adequate body fat to cover their energy needs. Although certain amino acids can be converted to fatty acids, there should be no need for this to occur in order to supply energy. But if a very high protein intake adds substantially more calories, theoretically those extra converted amino acids could add to body fat stores. A study published in the Journal of the International Society of Sports Nutrition in 2014 refutes this theory, indicating that very high protein intakes did not add body fat, at least in athletes.
Ideally, dietary protein is reserved for the maintenance and synthesis of body proteins and is not a preferred energy source. Traditional dietary guidelines advise that adequate carbohydrate intake spares muscle mass by preventing the need for gluconeogenesis from amino acids. However, a review published in the journal Nutrition and Metabolism in 2006 provides some evidence that the body adapts to low glucose intake, and there is no resultant loss in muscle mass, at least in people who exercise. Consult a qualified sports nutritionist to help you determine your optimal nutrient composition, especially if you are active.