The Science Behind Perfect Amino & Amino Acid Utilization

by Dr Minkoff May 02, 2023 16 min read

The Science Behind Perfect Amino & Amino Acid Utilization

If you’re reading this page, it’s likely that you’ve seen our claims for PerfectAmino Essential Amino Acids; and that you may have a few questions about them.

The first claim is that not all proteins are equal. That different proteins, once digested and absorbed, provide our bodies with different amounts of usable protein, gram for gram. 

For example, if you consume 1 gram of protein from whey, the body does not receive the same amount of usable protein to build new muscle, bone, etc. as it does from 1 gram of protein from whole eggs. 

The second claim is that the idea that we receive 4 calories for every gram of protein we consume is a misconception. And that it indicates a broader lack of understanding of what calories are outside of the scientific community, and what they have to do with muscle gain, energy, and body fat. 

A calorie is not a thing, but a measurement of energy production: How much energy is produced when a gram of carbohydrate, protein or fat is broken down and burned as fuel to create energy. 

When we consume carbohydrates, the majority of them are broken down and used to produce energy now. Or, they're used to make glycogen or body fat — stores of energy for the future. 

Not so with proteins or even fats. A significant portion of the fats we consume are used to make new cells or hormones. Only some of it is connected up with sugar molecules and stored as body fat.

And obviously, not all of the protein you consume is used as fuel. Some is used to build or repair muscle, cells, hormones, bone, skin, etc. There is no energy production here, hence, no calories, which are just measurements of energy production. 

So, if a gram of carbohydrate, protein, or fat was fully used for energy production we would get 4 calories, 4 calories, or 9 calories, respectively. If they were fully used for energy production.

Beyond this, not only are less than 4 calories of energy produced from any gram of protein, but we actually produce a different amount of energy, measured in calories, depending on which protein source we consume: eggs, soy, meat, fish, whey, pea, collagen, etc. Each one provides our body with a different amount of energy measured in calories. 

And the third claim is that PerfectAmino provides a source of pure essential amino acids that is 99% used to synthesize new protein in the human body, and thus provides almost no actual calories — less than one calorie for every five grams.

We’ll do our best to answer those claims here.

But to do this, first we need to look at what protein actually is and what happens with it when it enters our body:


Proteins are not just “proteins”. A protein is a molecule made up of smaller molecules called amino acids. (1,8,13)

Proteins are nothing but amino acids held together by peptide bonds. (Also note, collagen is just a type of protein. It isn’t something else, specific unto itself.)

There are about 500 different amino acids known, but only about 20 are used in the human body to make protein. (14)

To make, or “synthesize” a protein, these amino acids are bonded together into long chains of hundreds or thousands of different amino acids. Then the chains are coiled up, with new bonds holding the coils in place. These look much like a rope coiled up. (1,15)

But these proteins can contain any type or amount of different amino acids.

And, each protein with different amounts of any of the different amino acids are different and distinct from one another. These differences are necessary as they each have a different function inside the body. (3)

Amino acid composition and sequence determine the native structure, functionality, and nutritional quality of a protein in a set environment.” (16)

There are actually about 20,000 different exact and distinct proteins in the human body, each one a different variation in type and amount of amino acids. (2, 8)

And the amino acids a specific protein contains are, together, known as its amino acid profile.


One large misunderstanding is that when we consume proteins, they are broken down into “protein molecules” and then sent to where protein is needed.

This isn’t the case. By the time protein has been digested and absorbed and used in your body, it is in a completely different form than what it was when it came in. It’s been fully broken down, and fully rebuilt, into whatever the body needs at that time. (19)

You don’t have egg protein molecules or whey protein molecules in your muscle, and you don’t have powdered collagen molecules in your skin or bone. 

When you consume protein it goes through a very exact sequence of actions.

First, your stomach breaks it down. 

Between your stomach acid and digestive enzymes, the proteins you ate are pulled apart from each other and then the individual chains are uncoiled and broken apart. (20)

They aren’t broken into individual amino acids here, but into much smaller, uncoiled chains of about 20-40 amino acids in length. 

From your stomach they then go into your small intestine, where new enzymes are released. 

These new enzymes break the smaller chains of amino acids down further, until all bonds holding the amino acids together have been fully dissolved, and each amino acid is free-floating, unconnected to any other amino acid. (21)

So now, from complex proteins joined together in the form of meat or eggs or soy or collagen, we’ve completely broken these down into tens or hundreds of thousands of individual, unconnected amino acids.

At this point, these amino acids can be made into any of the twenty thousand plus forms of protein your body requires. (21)

These individual amino acids are then absorbed through the walls of your small intestine, pass through your liver, and are released into the bloodstream where they can be absorbed by individual cells throughout the body and joined together (synthesized) into new proteins of the exact type or types needed by that cell. (22)

And this is where calories, and how much of the protein we eat is actually used, comes in.

Because these cells don't need just any type or amount of amino acids to make new proteins. They have very exact needs. 


There are two main types of amino acids: Essential Amino Acids and Non-Essential Amino Acids. (These are also known as Indispensable Amino Acids and Dispensable Amino Acids.)

Non-Essential Amino Acids, or Dispensable Amino Acids, are amino acids the human body can make (synthesize) on its own, and so does not require from outside protein sources in your diet. (8)

Essential Amino Acids (EAAs), or Indispensable Amino Acids, are amino acids the body can not produce on its own, so we must acquire them from an outside protein source. (8)

But the trick here is that the non-essential amino acids are made by using the essential amino acids.

You need the essential amino acids to make all the non-essential amino acids that you need. 

But even more, you need all of the essential amino acids to make any protein that your body needs.

Your body cannot make proteins without all of the essential amino acids. 

If it’s missing even one, it cannot make new protein. (7, 10)

This missing amino acid is known as the “limiting” amino acid as, when it’s missing, or to the degree that it’s missing, it limits the amounts of the other essential amino acids that can be used to synthesize new protein. (7, 9)

“…the biological value of the dietary proteins depends on its constituent amino acids and show that if the eight essential amino acids are not available simultaneously at the time of the protein synthesis, the intracellular deficit, even though of only one amino acid, would limit the protein synthesis of the body.” (11)

This is why BCAAs, three of the essential amino acids known as Branched-Chain Amino Acids and touted as building new protein, do not in fact build new protein. (10)

It’s physically impossible for them to do so.

Your body requires each one of the essential amino acids to build new protein. And if it’s missing even one, no new proteins can be built. (7)

Also, it doesn’t need extra non-essential amino acids for this. It makes non-essential amino acids as it needs to for the proteins it needs to make.

But it goes even deeper than this. 

It doesn’t just need each of the essential amino acids. It needs each in an exact ratio one to another. 

This ratio is something scientists have been investigating for decades.

Normal growth and maintenance of health in humans requires all amino acids (IDAA [Indispensable Amino Acids], conditionally IDAA and dispensable amino acids) to be provided in appropriate quantity and form that is biologically utilizable (Pencharz and Young 2006). This aspect commonly referred to as availability or bioavailability, is very important to know because food proteins vary greatly in both the concentration and bioavailability of the IDAA and conditionally IDAA.” (6)

It’s not one of each. It’s two of this one, three of that, one of this, and ten of that one, etc.

If your body receives all of the essential amino acids, but is low on certain of them, then it won’t be able to use each of the others fully. 

This is known as the limiting amino acid. If all but one essential amino acid are present and in the correct ratio to make ten grams of new protein, but the quantity of one of them is only enough to make three grams of new protein along with the others, then no matter how many of the other EAAs you have, you can only make three grams of protein. (11)

For example, if you were building a table from Ikea, you need one table top and four legs to build one table. 

If you had two table tops and 7 legs, you could still only build one table, as you’re missing a leg.

While there are more than two EAAs, it’s the same principle. Your body can only build as much new protein as it has each of the essential amino acids in proper ratio to one another. If you want ten times the protein synthesis, then you need to 10x each individual EAA according to its ratio number. (10)

If you only increase one or two of them, then the amount increased is in fact an excess, and cannot be used by the body to make new protein. 

And this is where different types of proteins come in. 

Because while whey, pea, soy, meats, eggs, etc. may contain all of the EAAs, the essential amino acid ratios each contain is different. 

How much new protein your body can synthesize from the EAAs in a specific protein source comes down to how much of each essential amino acid exists in the correct ratio within that protein source. (6)

“The nutritional quality of a food protein depends on the absolute content of essential amino acids, the relative proportions of essential amino acids, and their ratios to nonessential amino acids." (16)

If a protein source, such as whey, consists of only 18% EAAs in the correct ratio to make new protein, with the other 82% being individual EAAs in excess of the correct ratio, or of other non-essential amino acids, then only 18% of the whey you are consuming can be used inside the body to make new protein. 

The other 82% of the protein (essential and non-essential amino acids) is excess, and therefore cannot be used to make new protein on its own.

And this is where calories come in. 

Because this excess isn’t stored or saved for later, and your body has to do something with it. 


When your body has excess sugar (carbohydrates) that it doesn’t need, it has a way to save it for later. 

It connects each individual sugar molecule together into chains. These chains of sugar are called glycogen, and they’re stored in your muscles and liver. (17)

When your cells need more energy, and there is no more sugar in your bloodstream, your body breaks these glycogen chains back down into individual sugars and releases them into the bloodstream for your cells to use. 

And if your body has so much excess sugar that it has filled all of the body’s glycogen stores and still has more, then it connects these sugars to fatty acids, forming triglycerides, and stores them in our fat cells as body fat. (18)

This is also how the extra fat we consume is stored. If the body has more fatty acids than it can use for energy or cellular structure, then it connects the fatty acids up to sugars and stores this as body fat in our fat cells.

Your body has no such storage ability for amino acids. They are synthesized into new proteins or cannot be used. (4,5,10)

When we consume proteins, and they’re fully broken down into amino acids, these amino acids are released into our blood stream for the cells to use. 

But these amino acids only stay in our blood stream for a few hours on average. If they’re not used in that time, because they’re in excess of what is needed, your body has to do something with them.

Amino acids are molecules that can themselves be broken down. And when they can’t be used to synthesize new proteins, that’s what happens.

If amino acids exist in excess, the body has no capacity or mechanism for their storage; thus, they are converted into glucose or ketones, or they are decomposed.” (5)

An amino acid molecule contains an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid.

“Most of the carbons from amino acid degradation are converted to pyruvate, intermediates of the TCA cycle or acetyl CoA. During fasting, these carbons are converted to glucose in the liver and kidney, or to ketone bodies in the liver. In the well fed state, they may be used for lipogenesis [the metabolic formation of fat].” (4)

This is where “protein has calories” comes in. Calories measure how much energy could potentially be produced by the breakdown of the amino acids in a protein, or the breakdown of a carbohydrate or fat.

But that’s potential.

Calories are the amount of energy released when your body breaks down (digests and absorbs) food.

If the amino acids were used to build new protein, then they were not broken down and no energy was released. 

It’s only the excess amino acids, the ones that could not be used to build new proteins, that then go through gluconeogenesis and are broken down, releasing glucose (sugar) and ketones, or which are directly oxidized as fuel — the energy measured in terms of calories.

But if you’re eating protein, and building muscle, then obviously at least some of the amino acids in the protein you’re consuming are being converted to new protein instead of being used as energy.


The key elements of an amino acid are carbon, hydrogen, oxygen and nitrogen.

Amino acid decomposition results in hydrocarbons and nitrogenous waste. However, high concentrations of nitrogen are toxic, as they produce ammonium ions. The urea cycle processes nitrogen and facilitates its excretion from the body.” (5)

This element of nitrogen as a component of an amino acid is key.

When an amino acid is deaminated, this nitrogen is released. This is measurable largely through urine, and to a lesser degree through fecal matter and sweat, and is what allows for the precise measurement of amino acid utilization within the human body.

When amino acids follow the anabolic pathway (protein synthesis) there is no release of nitrogen as it is still a constituent part of the amino acid which has now been utilized as part of a protein in the structure of the body.

But when amino acids are in excess, they follow the catabolic pathway (amino acid degradation or deamination), where they are broken down. This releases this nitrogen that was a component of the amino acid. 

The weight of nitrogen in an amino acid is known and can be measured. 

Very precisely, the molecular weight of an amino acid is 110Da, and nitrogen accounts for 16% of an amino acid. (13)

Therefore, we can measure the total nitrogen of a protein source prior to consumption, and then measure the nitrogen output in the proceeding period, allowing us to see the exact amount of the protein consumed that was anabolized (synthesized into new proteins) vs how much was catabolized (broken down into its constituent parts).

If anabolized, the amino acid is now part of the protein structure of the body and has caused no energy output. And we will see no nitrogen released from it.

If catabolized, the amino acid has been deaminated with resultant energy output and release of its nitrogen constituent, which can now be removed via urine and, to a lesser degree, through sweat and fecal matter.

“For most common proteins, 50–80 g of glucose can be derived from 100 g of ingested protein.” (12)

For example: If we take 10 grams of protein, and if nitrogen comprises 16% of each of the amino acids making up this protein, then we know there is 1.6 grams of nitrogen in 10 grams of protein. 

If we then find that half of that 1.6 grams of nitrogen was released through urine, feces, and sweat (0.8 grams), then we know that only half of the amino acids in the 10 grams of protein were used to synthesize new protein, while the other half was deaminated and used as an energy source — calories.

So, from 10 grams of protein consumed, we get only 5 grams the body has actually used for building new protein. And we also now know that 5 grams were converted to energy — calories — and so from those 5 grams we get 20 calories, as each gram of protein has the potential energy of 4 calories.

That’s a simple example. 

With the advent of PerfectAmino, and backed by multiple studies both singularly, and comparing PerfectAmino, whey, and whole hen eggs in triple-blind crossover studies, where the urine and feces of each participant was collected, and the nitrogen quantities measured, we now know the precise ratio of essential amino acids the body requires to synthesize new protein with near zero excess — .04 calories per serving of 5 grams of PerfectAmino.

Comparing this proprietary formula of PerfectAmino EAAs to the amino acid profiles of other protein sources, we are able to calculate the exact amount of amino acids each protein contains that will be used for protein synthesis vs. what will be deaminated and converted to energy  calories.

When we look at the amino acid profiles of whole hen eggs, we see that 48% of the essential amino acids exist in the correct ratio to be synthesized into new proteins in the human body, and 52% of the amino acids are in excess. 

This means that nearly half of the protein in a whole egg is used to build new protein in the body, and just over half is converted to energy, giving whole eggs an effective caloric measurement of 2.08 per gram. This is the highest ratio found in foods in nature.

In whey, we see that EAAs in the correct ratio to synthesize new protein constitute 18% of the amino acid profile, resulting in 82% excess amino acids that must be deaminated. This gives an effective caloric measurement of 3.28 calories per gram of whey. 

And in BCAAs (Branched Chain Amino Acids), which are only three of the essential amino acids and so cannot be used on their own to synthesize new protein, we find they are fully excess amino acids and subject to deamination.

“An extensive search of the literature has revealed no studies in human subjects in which the response of muscle protein synthesis to orally-ingested BCAAs alone was quantified, and only two studies in which the effect of intravenously infused BCAAs alone was assessed. Both of these intravenous infusion studies found that BCAAs decreased muscle protein synthesis as well as protein breakdown, meaning a decrease in muscle protein turnover. The catabolic state in which the rate of muscle protein breakdown exceeded the rate of muscle protein synthesis persisted during BCAA infusion.” (10) 


Not all proteins are equal. 

Proteins consist of amino acids, which are divided between the essential amino acids, those we must get from food sources, and non-essential amino acids, those our bodies can make on their own. 

To make new protein, our bodies require each of the essential amino acids. 

If we are missing even one, our bodies cannot make new protein. 

The essential amino acids must also be in an exact ratio one to another. 

Any quantity of amino acid above this level, singularly, results in an excess that cannot be used on its own. 

When we consume protein, our bodies break it down into the individual amino acids it’s composed of and then remove from these the essential amino acids that exist in the correct ratio one to another. 

With these our bodies make new proteins. 

Any excess essential or non-essential amino acids are converted to glucose (sugar), ketones, or oxidized as fuel directly. 

Calories measure the energy released when a food source is broken down (catabolized) and used as energy. 

The excess amino acids in a protein source, which could not be used to build new proteins, are the actual source of any calories in a protein source. And the amount of excess amino acids in a protein source differs from protein to protein based on those protein's exact amino acid profiles.

There is an exact, correct ratio of amino acids that is 99% used by the body to synthesize new protein, resulting in nearly zero excess amino acids. 

Thus, this ratio allows for nearly zero calories. 

Any alteration from this ratio results in excess amino acids which are then converted to energy, which is measured in calories.

Other protein sources differ from this ratio to varying degrees of 48% utilization for whole eggs, down to 18% utilization for whey and 16% utilization for soy. 

Thus, the amount of energy they produce upon breakdown of their excess amino acids, differs as well, with 52% of whole egg protein being deaminated and converted to energy, measured in calories, 82% of whey being deaminated, and 84% of soy being deaminated.

This excess energy comes mainly in the forms of sugar (glucose) and fat, after the amino acids have gone through the process of gluconeogenesis. 

These findings can be measured through the nitrogen output of any given protein source. 

Amino acids each have an exact amount of nitrogen. 

When excess amino acids are deaminated, this nitrogen is released and can be exactly measured. 

The measured amount of nitrogen output, compared to the amount of protein consumed, equates to the percent of unused, excess amino acids that were converted to sugar or fat.

This then shows us the percent of amino acids that were utilized to build new protein, and individual protein sources can be measured.


Only one protein source provides the exact ratio of essential amino acids needed by the human body to synthesize new protein and collagen without excess amino acids: PerfectAmino.

Its proprietary amino acid profile is composed of essential amino acids in a ratio that is 99% utilized by the body to synthesize new protein. 

With less than 1% excess amino acids to be deaminated, it provides only .04 calories for every five grams consumed.

PerfectAmino is the perfect source of protein.

Try it for yourself and find out the truth.


  2. The Size of The Human Proteome: The Width and Depth
  3. Protein — Which Is Best? International Society of Sports Nutrition Symposium, June 18-19, 2005
  6. Amino acid requirements in humans: with a special emphasis on the metabolic availability of amino acids
  7. Indicator amino acid oxidation: concept and application
  8. Biochemistry, Essential Amino Acids
  9. Nutritional Consequences of Excess Amino Acid Intake
  10. Branched-chain amino acids and muscle protein synthesis in humans: myth or reality?
  11. Block RJ, Mitchell HH. The correlation of the amino-acid composition of protein with their nutritive value. Nutr. Abstr. Rev. 1946; 16:249-278.
  12. Dietary Protein and Blood Glucose Concentration
  13. Protein and Amino Acids, National Library of Medicine
  14. Nonproteinogenic Amino Acid Building Blocks for Nonribosomal Peptide and Hybrid Polyketide Scaffolds
  15. Amino Acids, National Human Genome Research Institute
  16. Encyclopedia of Food Sciences and Nutrition
  17. The Role of Skeletal Muscle Glycogen Breakdown for Regulation of Insulin Sensitivity by Exercise
  18. From Sugar to Fat, National Library of Medicine
  19. Protein Digestion and Amino Acid Absorption
  20. Features of The Gastrointestinal Tract, Protein, Encyclopedia Brittanica
  21. Gut amino acid absorption in humans: Concepts and relevance for postprandial metabolism
  22. How much protein can the body use in a single meal for muscle-building? Implications for daily protein distribution

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