ISSA SN Chapter 4: Protein and Amino Acids: Muscle Builders and More

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Chapter Goals:

  • Describe and define the main terms relating to amino acids and proteins.
  • Know the different types of amino acids and proteins and their major functions.
  • Find the nonessential and the essential amino acids.
  • Know how proteins and amino acids affect athletic performance and health. 


Proteins and their building blocks, amino acids, will be discussed in great detail throughout this chapter. Protein is a vital part of the diet and has many bodily roles. The roles are mostly structural, but the body may also use the protein as energy during intensive exercise to meet the metabolic needs when the nutrition is inadequate. When this happens, the body breaks down the muscle tissue to use its proteins. This is a big setback for athletes training to make gains in muscle. 

If we take in too much protein in the diet, we will store this as fat, just as we normally do with the excess carbs. This allows for increases in ammonia and uric acid. They are both waste products. 

Athletes aim to keep their protein intake at the right level based on their body weight, activity level, and the muscle fibers’ composition. Endurance athletes will usually need more protein due to the higher amount of slow twitch fibers, but this is only when compared to the general population. Strength athletes have larger muscles and more fast twitch fibers, meaning they need the greatest amount of fibers. 

What is Protein?

Protein is one of our macronutrients, perhaps the most important. It is a polypeptide which is a compound that has 10 – 100 amino acids making it up. The amino acids are held together with a peptide bond, which is a form of a special chemical bond. 

Significance of proteins and amino acids for athletes:

  • Protein is the source of amino acids.
  • Athletes will need a higher protein intake than the general population.
  • Amino acids are known as the building blocks for the recovery, growth, and production of many bodily proteins.
  • Branched chain amino acids are special amino acids used for energy and are needed in greater amounts.
  • Single amino acids will elicit certain effects like increased growth hormone, IGF, testosterone, and nitric oxide production. 
  • Collagen is a special protein. It is a connective tissue making up a third of the protein in our bodies.

Protein is required for the repairing of cells, their growth, and for maintenance. Another use is the production of enzymes, hormones, and DNA. Protein is found in many shapes and sizes and put into two main categories, conjugated and simple proteins. Protein makes up the vast majority of the dry weight of the body cells. Some of the major properties of the proteins are transportation, contractile roles, hormone production and use, structural roles, receptor roles, and enzymes. 

The Amino Acids

The amino acids are classified based on their need in the diet by the body. We have three different categories we use. Indispensable amino acids are the ones that the body can’t synthesize, and they are needed in the diet. Conditionally indispensable amino acids are the ones that require a source when the rate of synthesis of the body can’t meet metabolic needs. Dispensable amino acids are the last category, and these are the amino acids that can be made in sufficient levels if they need to be. These are the US terminologies. 

The Canadian terminologies place the amino acids into two different groups. The first is the essential amino acids. We must take these amino acids into the body through diet since they cannot be made. Then we have the nonessential amino acids, which we are actually able to produce in our bodies in some form with the use of other amino acids. 

Proteins/Amino Acids and Energy

It functions the same as fats and carbs when it needs to. This only really happens in times of starvation and in times of severe restriction of calories. The body releases amino acids and proteins from the muscle tissues for use as energy or in the energy cycles if needed. This protein catabolism sometimes happens in times of high intensity exercise. 

Even when an athlete has a good diet, the body will still use some amino acids as fuel in big bouts of exercise. The muscles use branched chain amino acids to supply limited energy in the hard exercise bouts. These three amino acids alone can be used over the use of other proteins when needed. Leucine is used more so than the other two BCAAs. 

Rating the Quality of Proteins

Just like carbs, we see differences in the proteins we take in. Not all protein is equal. 

Complete Versus Incomplete Proteins

The competing proteins will be those with essential or indispensable amino acids in the levels that are good enough for normal growth and boy weight maintenance. Indispensable amino acids, again, are the ones we cannot produce. 

Incomplete proteins will be proteins that do not have at least one of the indispensable amino acids. This deficiency creates a limiting condition, adversely affecting growth and development rates.

Protein Efficiency Ratio

This is another way to find the quality of some proteins. The PER is calculated with lab animals. It refers t the weight gained and the amount of protein taken in. an example is casein protein. Here we see a PER of 2.86, showing that for every 2.86 grams of weight taken on, it only takes 1 gram of the casein protein. 

The main criticism of this PER method is that it looks at testing on animals and not humans, so it must be somewhat off. 

Net Protein Utilization

This is a way we can find how digestible the proteins are. It is done by measuring how much nitrogen is taken in from the amino acids in a protein. The more nitrogen we see absorb, the more digestible the protein is. 

This is calculated by measuring someone’s nitrogen intake from amino acids, comparing the nitrogen put out by the body, and seeing how much is needed to balance those two levels. 

Biological Value

These have not been entirely standardized, but there is one method that scientists prefer most. The general formula is nitrogen retained divided by the absorbed nitrogen and then multiplied by 100. This gets you the BV. 

It does not actually show the fat of the amino acids on the body, just using nitrogen and nothing else. So, it is not a favorite for assessing proteins and amino acids. 

Amino Acids Score

This came about in response to the other testing being limited in that they look at specific things that might matter less. This method relies on assessing the score of proteins based on the amino acids they contain. 

Protein Quality for Athletes

Ingesting the highest quality proteins based on those rating systems will be needed. Protein and amino acid supplements will be used for fortifying diets to help the total need for proteins and specific amino acid needs. Along with the basic needs of proteins, there is an increased ingestion of certain amino acids for boosting metabolism processes.

Nitrogen Balance

The balancing of nitrogen has been looked at quite a bit in research. Nitrogen makes the amino acids different and distinguishes protein from the other macronutrients. The nitrogen balance means that the same amount of nitrogen is entering the body as the amount that is leaving the body. A negative balance could show the cannibalization of the muscle tissues. All athletes should aim to balance this. 

Designing Protein and Amino Acid Products

Amino acid profiles are put as one of the main things to look for when making a product. Most products will have a wide variety of amino acids. 

Another major factor to look at for products is going to be the rate of absorption of the proteins and amino acids. The faster the absorption rate, the quicker it can get through the body. 

The main point regarding the quality of proteins is that some sources have naturally greater quality than others. By combining or adding amino acids, the quality of the diet can be improved significantly. 

Free Form and Peptide Bonded Amino Acids

When looking at the content of amino acids for food and supplements, we use the terms peptide bonded and free form. 

The free form amino acids are those in a free state or simply alone. When the protein is taken in and digested, some amino acids will be put into free forms for transporting easily around the body. Di-peptides will be when there are two linked amino acids together. Tri-peptides are the three linked amino acids; anything more than that will be called polypeptides. 

Hydrolyzed proteins are a protein that is broken down by enzymes and mixed with the free form, di-peptide, and tri-peptides. 

Digestion of Protein and Amino Acids

The actual mechanical digestion starts, as always, in the mouth when we are chewing our food. From there, it goes to the stomach, where pepsin is an enzyme that joins in to break the proteins into smaller segments. They will then go into the intestines, where they will be absorbed in forms as big as tri-peptide, but usually smaller than that. The enzymes will continually digest the polypeptides into smaller forms as they travel down the intestines.

When the amino acids enter the bloodstream, they will be moved to the liver and a few things happen then. They are possibly going to be made into other amino acids or proteins. They might be used for further breakdown and or used as energy. Another option is for them to enter the circulation system and be used by a cell elsewhere in the body. 

The proteins leave the stomach in 2 – 3 hours or more, depending on the amount of fat or food taken in. This means it is often a good idea to limit the fat in your food when you are trying to maximize your body’s use of protein.

Amino Acid Review

Alanine and Beta-Alanine

Alanine is indispensable and found in a high quantity within the muscle tissues along with the dispensable amino acids due to the ability to manufacture them. Alanine plays an important role in biochemical processes during times of training. 

Beta-alanine is a new part of the sports supplements we see on the market. It has gained popularity due to much clinical research that shows it as a benefit and promoter of performance benefits for athletes. 


This is a conditionally indispensable amino acid that plays a critical role in many metabolic factors that are extremely important for athletes. Arginine is more popular for the role of stimulating growth hormone for humans and IGF levels. It is shown to increase these levels of hormones.


This amino acid is dispensable and made in the body from aspartic acid. It involves things such as the nervous system functioning, preventing nervousness, and extreme calmness. 

Aspartic Acid

This is a dispensable amino acid that reduces the ammonia level in the blood following times of exercise. It is naturally found in plants and animals. 

Branched Chain Amino Acids

These are the three amino acids of Leucine, Isoleucine, and Valine. 

These three indispensable amino acids comprise around 35% of the content of amino acids within muscle tissues. Leucine has been viewed as the most important of the three by far. It is two times more often found than isoleucine and valine. 

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Some benefits relating to exercise and the BCAA supplements are:

  • Increases in endurance for the individual.
  • Reduction in the amount of fatigue experienced. 
  • Mental performance has been shown to go up along with increases in the level of energy.
  • Protein synthesis is stimulated.
  • We see improvements in the balance of nitrogen. 
  • We see improvements in the function of our immune system due to the role of those three amino acids.
  • We see increases in the amount of lean body tissue and an associated increase in strength.

Leucine, a Key BCAA. 

Leucine has been seen as one of the most crucial BCAAs and this is due to the effect had on energy production and the major role of the synthesis of proteins. These are vastly important in exercising for obvious reasons. 

BCAAs Help to Increase Training Strength, Endurance, and Muscle Mass

Many studies have involved bodybuilders of varying ages, and they have found that the groups experienced increases in body weight and, of course, more so in all of the groups using the BCAAs. This was mainly in the increases in lean body mass. Strength gains were made along with this, as it often happens when we gain lean body mass. 


This is a dispensable amino acid with a main role in the urea cycle to remove the ammonia found within our blood. The research is evolving quite a bit and has not been perfectly discovered yet. 


This is a conditionally dispensable amino acid based on sulfur. The body makes this from both methionine and serine. It is important for producing hair, proteins, connective tissue, insulin, and taurine. 


This is another conditionally dispensable amino acid like cysteine. It is made from two molecules of cysteine. 

Glutamic Acid

This is also known as glutamate, and it is a dispensable amino acid that is found in protein. It is part of the Krebs cycle and is important for carbs’ metabolism.


This is a conditionally dispensable amino acid found in our diet proteins and is manufactured in the body when needed. It is one of the more plentiful amino acids found in the body. 


This is a conditionally dispensable amino acid that is made from serine. Folate acts as the coenzyme. It is a good precursor for many bodily substances.


This is an indispensable amino acid that is important for the repair and growth of our tissues. 


This is one of the popular and useful BCAAs and is needed for hemoglobin. 


This is another indispensable amino acid that we find in large amounts in the muscle tissues around the body. We need it for the proper growth and development of our bones. It also helps us with the absorption of calcium.


This is another indispensable amino acid that bears sulfur. It plays a role in transmethylation, which is the metabolic process by which an amino acid gives a methyl group to some other compound. 


This is a dispensable amino acid that is not found in proteins. The main role here will be through the urea cycle, making it vital to remove ammonia from the blood.


This is an indispensable amino acid and a precursor for tyrosine, which is not an essential amino acid. 


This is an amino acid that is conditionally dispensable. It is found in great amounts within the collagen in the body. It is made from and also potentially changed into glutamic acid. 


This amino acid is dispensable and found in proteins and may also come from glycine, another amino acid. This amino acid’s metabolism forms vital substances like choline and some phospholipids. Those are both essential for forming neurotransmitters and are used to stabilize the cell membranes.


This is a dispensable amino acid and sulfur bearing. It works plays a big role in our brain tissues and the function of the nervous system. It regulates blood pressure and transports the body’s electrolytes into cell membranes. 


This is an amino acid that is indispensable and found in proteins. It is important for our tooth enamel, other proteins, elastic tissues, and for collagen. 


This amino acid is indispensable and needed when producing vitamin B3 and serotonin. Both are important in the body.


This is an indispensable amino acid made from phenylalanine, another essential amino acid. 


This is the last amino acid. It is indispensable and a member of the branched chain amino acids we discussed before. 

Special Protein and Amino Acid Needs of the Athlete

Simply having a fixed goal amount of protein is not enough when you are an athlete looking for the best results. We must look at the roles that all amino acids play and the food quality we take. 

We can use the protein guidelines as a baseline, but it does not stop there. Another thing to consider is the need for more protein when we are kids and developing. 

Depending on the sport of choice for the athlete, there are requirements found to be about 1.5 – 2.5 grams per kg of body weight for adult athletes. Even then, a bodybuilder might even require as much as 3 grams per kilogram, which is significantly more than the RDA. And excess protein is not going to be converted into muscle tissue. Instead, it will be used for energy or fat storage. So, we cannot simply take in a crazy amount of protein without having some problems. 

Food and Supplement Sources of Protein

These proteins are, of course, found in both plants and animals, and in the case of animal protein, this usually implies the intake of fat with it. Most of the plant sources are less beneficial and will usually be more incomplete proteins than their animal counterparts.

Whey Protein Gets Results, Too

This is the most expensive main protein in protein products and has some distinct advantages over others. It enhances the amount of glutathione production. It has a high amount of important BCAAs. It also contains a significant amount of essential and nonessential amino acids. It is one of the complete proteins we use in powder form. 

Estimating Daily Protein Requirements

The usual charts and calculations use a dynamic approach to find what someone’s needs are. This is based on their lean body mass and their activity level. 

Summary of Proteins and Athletes’ Relationship

Athletes require around 2 – 3 times the DRIs for protein.

Ideally, the requirements must be calculated based on the person’s lean body weight. 

The highest quality proteins possible should be a large part of the diet.

Protein supplements and tablets of amino acids need to be used to fortify dietary proteins from food sources.

Protein should be taken with each meal, but not before events.

BCAAs can be taken to fortify food proteins and during exercise to possibly spare the muscle tissue from being used as energy. Protein powders can also be used.

Calcium and vitamin B6 need to be increased for athletes with diets high in protein and need to be a part of the formulations of amino acids for growing muscles and recovering from work. 

Amino acids should be combined to release hormones, detoxify from ammonia, relax, and stimulate. 

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Tyler Read - Certified Personal Trainer with PTPioneer

Tyler Read

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