The purpose of training is simple; to teach your body to adapt to certain stressors. By gradually increasing stress, our bodies are forced to recover and rebuild stronger than before. This concept holds true for all tissues and systems of the body.
It is important to train physiology just as you do your muscles. "The main goals of long runs are to improve our carbohydrate storage capacity and to become more efficient at using our fuel. The long run works by sending our bodies into crisis during those last few miles when our fuel supply is running low, which signals our bodies to adapt so that the next time we run long, our bodies are prepared to cope with that stress." (1)
One goal of long runs is to teach your body to burn more fat and less carbohydrates. Developing your fat burning engine will increase the amount of energy you can generate, reduce the amount of carbohydrates you use, and stretch out the glycogen supply during long runs. Added together, you have a more stable and enduring energy supply, better endurance, and faster finish times.
There are two main sources of fuel during exercise: carbohydrates and fat. Carbohydrates burn quickly. Think of them as the high octane fuel of a drag racing car. Whereas, fats burn slowly. If you filled your car engine with high octane fuel, you wouldn't get very far before you have to re-fuel. Same holds true with the body. This is fine for a 5K race, but for longer distances, this will have you chasing a bonk.
On the contrary, there is days worth of fuel sitting dormant in our body in the form of fat that is just waiting to be used (yes, even in those with very low body fat percents...there is still plenty). When you are burning fat during exercise, your carbohydrate stores are spared and can be saved for the kick at the end of the race. The one where you pass your competitor that has red-lined because he/she is out of fuel.
The body can be trained to burn fat more quickly and efficiently, or increase fat metabolism. The enzymes responsible for fat metabolism lie in the mitochondria (structures within muscle cells). Fats are transported into the mitochondria where, in the presence of oxygen, they are broken down to generate energy. More mitochondria means more fat metabolism, more ATP, and more energy.
The body can only store so much carbohydrate. When in excess, the body will generally choose to burn carbohydrates over fat. When we take in a carbohydrate drink or supplements during training, it prevents us from fully reaching the decreases in fuel stores that lead to the adaptation of fat burning. Therefore, it is important to regularly "push" the body beyond its comfort zone in terms of re-fueling during training. Of note, it is also very important to periodically practice your nutrition plan during training, so do not interpret the above sentence as a "never eat during exercise" message. Rather, plan a couple longer workouts (maybe 1 run and 1 bike) per week where you don't re-fuel and force your body to adapt.
Reference (1): Steve Magness. The Science of Running.


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