Which Amino Acids Get Burned During Endurance Exercise?
Last week, we talked about amino acid oxidation - something most endurance athletes don’t think about. You’re not just burning fats and carbs during your workouts.
You’re also burning protein – roughly 5–10 grams per hour – which raises a very important question: where is that protein coming from, and more specifically:
Which amino acids are actually being used as fuel?
Not All Amino Acids Behave the Same
Protein isn’t a single substance - it’s made up of individual amino acids, each with different roles in the body. There are actually 20 standard amino acids – these 20 encompass the main pieces encoded directly by your individual genetic code (cool, right?) and are then used by your body to build proteins. Of the standard 20 (Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Proline, Serine, and Tyrosine – which I’m sure everyone remembers from high school chemistry), 9 are essential, meaning we must get them from food, and 11 are non-essential (meaning our body produces them).
And when it comes to exercise metabolism, they don’t all act equally.
Three stand out from that list:
- Leucine
- Isoleucine
- Valine
These are known as branched-chain amino acids (BCAAs).
What makes them unique is simple: Your muscles can use them directly for fuel during exercise.
BCAAs - How do they differ from Other Amino Acids?
Most amino acids are first processed in the liver before they can be used for energy, but BCAAs are the exception.
They bypass the liver and can be taken up directly by skeletal muscle, exactly where energy demand is the highest during exercise. That makes them uniquely suited to contribute to fuel production, especially as training stress rises and other fuel sources start to run low.
Leucine's "One-Way Door" Into Energy
Inside nearly all cells in your body, mitochondria are responsible for producing energy. The BCAA, Leucine, has a built-in pathway that sends it directly into these mitochondria, and once it enters, it’s committed to becoming a source of fuel within that cell’s metaphorical assembly line of energy production. There’s no turning back toward muscle building or repair in that moment — it becomes fuel. A true metabolic one-way door – all instigated by leucine.
At rest, amino acid oxidation (the topic we discussed in-depth in last week’s Science Wednesday) is relatively low. But during endurance exercise, that changes.
As training duration increases and glycogen stores begin to decline, your body starts pulling from additional fuel sources, including amino acids — especially leucine. Research shows leucine oxidation rises as sessions get longer, glycogen becomes limited, and overall physiological stress increases. In simple terms, the longer and harder you go, the more leucine enters the fuel mix.
This creates an interesting paradox.
Leucine plays two distinct roles in your physiology: during exercise, it can be burned for energy, but after exercise, it’s one of the key signals that drives muscle repair and adaptation. The same molecule that helps you recover is also one your body is actively using up during training. A sort of “catch-22” with leucine and the array of abilities it has in our body!
For endurance athletes, this has incredibly important implications and simply matters. Training doesn’t just rely on carbohydrates and fat — it also draws from amino acids like leucine.
That has real implications for nutrition. If you’re consistently oxidizing amino acids during training, your protein needs aren’t just about recovery anymore, but also about replacing what’s being used during the work itself. This helps explain why endurance athletes often require more protein than they realize and can dig themselves into huge stress and workload holes in training by not consuming an adequate amount.
Leucine – Fuel and Catalyst?
And this is where the story shifts.
Leucine isn’t just another amino acid — it’s also the key signal that turns muscle repair on. Over the next few Science Wednesdays, we’ll discover the sources of where that leucine comes from, break down how leucine activates recovery pathways like mTOR, why there’s a threshold effect, and why not all protein sources deliver enough leucine to fully maximize adaptation.
References
Wagenmakers AJ. Muscle amino acid metabolism at rest and during exercise: role in human physiology and metabolism. Exerc Sport Sci Rev. 1998;26:287-314. PMID: 9696993.
Lamont LS, McCullough AJ, Kalhan SC. Relationship between leucine oxidation and oxygen consumption during steady-state exercise. Med Sci Sports Exerc. 2001 Feb;33(2):237-41. doi: 10.1097/00005768-200102000-00011. PMID: 11224812.
Tarnopolsky M. Protein requirements for endurance athletes. Nutrition. 2004 Jul-Aug;20(7-8):662-8. doi: 10.1016/j.nut.2004.04.008. PMID: 15212749.
