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We will start backwards. When we hike (or run) we move our limbs in desired motions and speeds. To get the desired movements, we need our muscles to contract. Muscles cannot contract without having energy available. So we need to get energy to the muscles.
Where does the energy come from, you say? Well, it depends on the energy demands of the muscle. Compare walking at 3 mph on a flat terrain to walking 3pmh on a steep trail and running 6 mph on a steep trail. Wouldn't you agree the energy demands are different? In the 6 mph case, there is a high energy demand and it is probable that this pace could not be kept up for long. High energy demand exercise is considered anaerobic exercise. This basically means that the energy for the muscles is produced without using oxygen. This means that the energy supply is quite limited, and may only last for a few minutes. But because the energy can be created without oxygen, a lot of it can be produced quickly, so fast movements that last 10 seconds - 3 minutes will rely on this source.
While still depending on fitness level, the two 3 mph cases are more likely to utilize aerobic energy. Because We can broadly classify exercise into 2 forms: 1) Anaerobic & 2) Aerobic exercise. "Aerobic" indicates that energy used for exercise requires oxygen, while anerobic exercise does not use oxygen. Now, you might be able to guess which one is going to be important in endurance exercise - aerobic. Energy derived from chemical reactions without oxygen will give you energy more rapidly - but cannot last very long.
We can break down energy stores to 4 sources:
1. ATP-CP - Anaerobic
ATP-CP uses creatine phosphate to produce energy (ATP). It is known as the "immediate" energy source, and will basically depleted after 6-10 seconds of the highest energy exertion. So activities such as sprinting 100 m will use mostly this energy pathway. You'll notice in an all-out effort that you quickly cannot go as fast as when you started. This is because after 10 seconds, you run out of this energy and have to utulize the other energy pathways which cannot give as high of an energy output.
In Hiking Terms
Ideally, you will not be focusing on this energy system when hiking, but it can happen. Take, for instance, a really steep, but short climb that you want to ascend as fast as possible. You may push as hard as possible to get to the top, and you will be using ATP-CP to do it. But obviously, you cannot do that for long, and if you are doing a long hike, you wouldn't want to try that and then wear yourself out.
This energy system will only be utilized during interval training. Intervals from 5 seconds to 5 minutes will at least partially tap the ATP-CP system, and for hiking you would only want to focuse on the longer duration intervals. As you will be hiking for several hours, you will want to train with longer intervals that also heavily utilize oxygen. More on this later.
2. Glycolysis - Anaerobic
Glycolysis is the generic term for the breaking down of glycogen. Glycogen is basically a storage of carbohydrates in the muscles. It can be broken anaerobically (without oxygen) or aerobically. Anerobically, the process cannot last as long as lactic acid is produced. This acid is the burning sensation you feel in muscles when doing high intensity exercise...and so the fact that this energy lasts from 30 seconds to a few minutes makes sense.
In Hiking Terms
An important system to consider when hiking - if only because when doing steady state hiking, its something you want to avoid. If you are planning on doing several hours of hiking, you do not want to feel the burn in your muscles at the beginning - unless you are doing it for training. You will be able to go further if avoiding this intensity of exercise (you can only do for a few minutes). So when the hikes get steep, trying to keep the same pace will require more energy for your muscles, and they'll start using anaerobic glycolysis. To avoid it, slow your pace down!
Very important. A major determinant of cardiovascular fitness is your aerobic/anaerobic threshold (AT). The level of intensity at the AT is when the body can flush out the lactic acid as quickly as it is created. At higher intensity, the body cannot remove it quickly enough. By training above this threshold, you can train your body to better flush out the lactic acid, and increase the intensity at which AT occurs.
Bouts of exercise from 30 seconds to 10 minutes will tax the anaerobic glycolysis system. Training in this range will be an important part to improve hiking performance, more on this later.
3. Glycolysis - Aerobic
The burning of glycogen using oxygen can last much longer, as lactic acid isn't produced. So this rate of energy can last much longer...but how long? Well, I'll have to do a better literature review to better estimate, but it's going to be directly related to how much glycogen you have stored in your muscles. So when you workout, you need to eat carbohydrates to replenish these storages. If you don't, you will feel fatigued, as your body can't produce energy at the rate you are used to. That's why you'll see people eating all sorts of sugary stuff when doing multi-hour endurance activities. Gatorade came to signficance partly due to showing that by giving carbohydrate calories to people during exercise, the participants could perform the exercise for longer.
In Hiking Terms
A main energy system to use when hiking. When you are breathing hard, you are using this pathway. Breathing hard = using a lot of oxygen! You'll use it all the time when doing moderate + hikes. The key, of course, is to make sure you don't deplete your glycogen stores before you finish the hike (or at least the hard part). This is done partly by bringing some carb-dense food, and partly by hiking at an intensity that also uses #4 below.
Again very important. You want to be able to take in a lot of oxygen for your body to use. Although it seems that you are limited by your lungs when working and breathing hard, it almost always comes down to the fitness of your heart and muscles. Training at intensities that you can only do for less than 1 hour will train your heart to pump strongly, and train your muscles to process oxygen for glycolysis more efficiently.
So training to get stronger at hiking is based around switching between aerobic and anerobic glycolysis. Mixing up intensities that you can hold between 5 and 20 minutes will sufficiently tax the cardiovascular system. It will help push the AT up higher, so you can hike at a higher intensity for longer - as long as you have the glycogen reserves!
4. Fatty Acid Metabolism - Aerobic
Uses oxygen and fatty acids to produce ATP. Burning fat will not give you as much energy / time as you need for strenuous exercise, so your body uses it more at lower intensities. I will not get into the discussion about thinking this means you should exercise at a lighter intensity to burn more fat, but basically it's not true. You want to burn the most calories to lose weight.
In Hiking Terms
You'll be using this energy pathway during hiking, especially for the longer ones. Unlike aerobic glycolysis, you won't run out of fat to use for energy. You just can't go as fast when relying on it. That's why when you are planning to go far, you have to go slow enough to use a good amount of your energy from fat. You'll plan on the rest coming from carbohydrates, but you may have only 1000 - 1500 kcal of glycogen available, so plan to spread it out over a few hours!
While some may argue specifically about improved ability to extract ATP from fat, this is not an important system to focus on when training. Basically, it's not intense enough. It's not pushing your heart to pump oxygen, nor pushing your muscles to use it. And it certainly isn't improving the AT threshold. You'll use it when doing high-intensity intervals - in the rest portion. Otherwise, don't expect to exercise at this intensity and gain significant improvements in fitness.