Barriers to Protein Digestion and Absorption

by Dr Minkoff March 13, 2022 16 min read

Barriers to Protein Digestion and Absorption

by Dr. David Minkoff March 10, 2022 16 min read

The following is adapted from The Search for the Perfect Protein, chapter 4.

As we’ve already discussed, access to clean protein sources is only one part of the problem; it must also be properly digested. This is a complicated process that requires a healthy gastrointestinal (GI) tract, which, unfortunately, many people lack.

You must absorb enough essential amino acids per pound or kilogram of body weight because the protein we need is made from aminos. Like it or not, animal proteins are the best natural source of essential amino acids for our bodies to function optimally. Vegetable proteins, on the other hand, have mixes of essential amino acids, but they are lacking in one or two—they don’t nourish as well as animal protein. In other words, the level of amino acid utilization is poor. The bottom line is that our body is an animal body, and it needs proteins from animal foods to maintain its lean body mass.


In Chapter One, we discussed how protein is digested by the body. Now, we’ll take it a step further and talk about the role of stomach acid in this process. Ideally, protein digestion begins in the mouth—the process of chewing breaks the contents into a liquid so that stomach acids can chemically break down the fibers. (For the elderly, or for people who are missing teeth, this step is not completed and that can create a barrier to adequate protein digestion).

Once food reaches the stomach, the true digestion process commences. Stomach hydrochloric acid (HCl) is added to the liquid mixture of food, and the acids cause the protein’s coiled structures to open up or uncoil. The HCl also activates the pepsinogen enzyme to its active form, which is called pepsin. Pepsin starts to separate the protein amino acid chains into smaller units. If a muscle fiber has 6100 amino acids per chain of myosin, then those chains are “chopped up” into much shorter ones. For this process to occur, the acid levels in the stomach must be at the pH level of 1 to 2, which is very acidic.

We measure acidity and alkalinity by using the pH scale. The scale goes from 1 to 14. The lower the number the stronger the acid. In the middle is water which has a pH of about 7. This is considered neutral. Above 7 and up to 14 is alkaline. For the proteins to uncoil sufficiently and for the pepsinogen to be activated requires a pH of 1-2. Due to aging or nutritional deficiencies, most people over the age of forty have a stomach pH that is higher than the one-to-two range. Since digestion is compromised at higher pH levels, they won’t digest protein as well as a twenty-year-old will. 

For example, a strand of steak or halibut is a long muscle protein made up of thousands of amino acids per strand, and it must be broken down into smaller pieces until it hits the digestion endpoint in the small intestine, where all amino acids are either single or in much shorter chains in order for them to be absorbed in the small intestine.

Stomach Acid The Seven Major Functions Infographic
Signs that you have low stomach acid



Causes of Low Stomach Acid Infographic

That said, there are roughly twenty-four million prescriptions written every month in the United States,with fifteen million for Nexium alone.[1]  This number doesn’t include all of the purchases of drugs that block stomach acid to relieve heartburn and acid reflux—billion-dollar brands like Zantac and Pepcid are available over-the-counter. These drugs poison the parietal cells in the stomach (the ones that make hydrochloric acid), so they will stop producing acid, which is detrimental to protein digestion among other things.

If the pH of the stomach reaches a level of seven, it fully compromises digestion and impairs mineral absorption— we often find that individuals with a high stomach pH also have zinc, selenium, iron, iodine, and magnesium deficiencies. (Refer to the chart for more information).

Stomach pH also influences digestive system functionality. There is a valve between the esophagus and stomach called the gastroesophageal sphincterwhich is triggered to close when stomach acidity is high. If the pH is 1 or 2, the valve works as it should: it closes, and you won’t get reflux. If you have a pH of 4 or 5, you’re still acidic, but not enough to trigger the valve to close. This pH level causes acids to bubble up into your lower esophagus, which can cause burning in the throat, heartburn, and pain. (This is the typical mechanism of action in gastroesophageal reflux disease or GERD).

If the cause of heartburn is lowered amounts of stomach acid, we give patients hydrochloric acid tablets to take with meals, which will lower the pH and close the valve— these tablets eliminate heartburn without the need for stomach acid-blocking drugs. If you suspect that you have this condition, you can work with your nutritional-oriented health care practitioner to monitor you for healing and the best results.


The food we eat is not sterile, and we certainly don’t make a habit of boiling everything before we eat it. We eat raw fruits and vegetables all the time, and some people even eat raw fish or meat! Our food is always contaminated with various bacteria, parasites, and sometimes fungi. Stomach acid is the body’s main protection to stop those contaminants from reaching the small intestine—these foreign organisms are “boiled in acid” so to speak, so our body can defend against them. 

When people take medications to deal with heartburn or GERD, this can put them at risk for bacteria, parasites, and fungi. Without adequate stomach acid, these organisms can survive in the stomach and pass along to the small intestine where they can take up residence—this is known as small intestinal bacterial overgrowthor SIBO.Once they are there, they can cause inflammation of the small intestinal wall, which can compromise mineral and protein absorption. These foreign invaders can also ferment the food coming through the small and large intestines, which can lead to the production of methane and other gases, causing bloating and abdominal discomfort. In addition, these organisms produce their own waste that contains harmful chemicals—these are absorbed back into our bodies, causing other problems.

The following chart shows the organic acid urine test result of a patient with toxic bacteria and yeast overgrowth in their intestines. The high levels of organic acids demonstrate that these bacteria make toxic chemicals that are absorbed into the blood, processed by the liver, and then excreted through the kidneys. This is an example of the body being poisoned internally by abnormal microbes in the gut, which is often a consequence of antibiotic use: good bacteria are killed off, and resistive, toxic bacteria and yeasts overgrow and survive.

Compounds of Bacterial or Yeast / Fungal Origin infographic


Healthy vs damaged Duodenum Ileum infographic

Food sensitivity, intolerances, prescription medication, and unclean food (chemically saturated food), herbicides. SIBO, and toxic colonic bacteria, and yeast can damage the intestine’s delicate membrane lining, which can cause secondary malabsorption of partially digested proteins.

Once the partially digested proteins reach the small intestine, they undergo further breakdown by pancreatic enzymes and the enzymes in the villi of the small intestine. 

The process of protein digestion is very complex, and if there are blocks at any point along the way, digestion may not occur. This leaves a person with inadequate amounts of essential amino acids to build or repair the body.

Additionally, all of the enzymes needed for the job are, of course, proteins, and one can get into the catch-22 that I mentioned earlier: They won’t digest or absorb enough amino acids, and then won’t have enough to even manufacture the enzymes to do the digesting. This happens more often than you think—it’s not a rare occurrence. Refer to the chart for enzymes and their specific actions.

Proteolytic Enzymes and Their Actions infographic

In our clinic, we routinely measure levels of amino acids in the blood. This indicates whether or not a patient’s diet and digestion result in normal blood amino acid levels. The following chart is the typical lab result we see from people who don’t eat enough proteins, don’t properly digest and absorb them. The levels of most of the essential amino acids are very low, which underlies many common health problems.


Genova Diagnostics infographic

To solve these problems, you must handle the glitches along the way. One of the ways we bypass many of the barriers to digestion is by giving the patient PerfectAmino—the amino acids are already in a digested form, so we don’t have to worry about the body taking care of this process.

In the formulation of supplemental amino acids, they come together with an L and R orientation, but the body can’t use the right—the left form fits the structure, and the right simply doesn’t fit. It’s like putting a right-handed person in a row of left-handed people who are all trying to write a paper: the right-handed person will bump someone’s arm because they don’t fit the form.

Furthermore, since amino acids come in two forms: an L form, which is left; and an R form, which is right, many companies sell amino acids which are 50:50 of each. However, in human biology, only the L form can be used. Perfect Amino is ideal because it contains only the L form, and is of pharmaceutical-grade purity. Taken on an empty stomach with a glass of water or a sports drink, the amino acids are in the bloodstream within twenty-three minutes, even if you have impaired digestion in the stomach or small intestine.

Taking Perfect Amino is a powerful way to bypass the major system barriers our bodies have acquired due to our lifestyles and the plethora of drugs available today, prescribed or otherwise. When proteins are properly digested and absorbed, single amino acids are taken in by the small intestinal cells, put into the bloodstream, and sent to the cells of the body. Once they are there, they are reassembled into body proteins.

How Your Body Uses Amino Acids as Building Blocks Infographic


There is a wide range of complexity and amino acid combinations in body proteins. The most abundant proteins in the body are collagen (it’s about 30 percent of all the proteins, which makes up the framework of the body), hemoglobin (the protein in red blood cells that carries oxygen and carbon dioxide), and muscle tissue. Among the estimated, 20-50,000 other proteins are growth hormone, insulin, neurotransmitters, and many different enzymes.


Enzymes are required for digestion. They are the proteins that catalyze chemical reactions in a cell, and it’s likely they were the first proteins synthesized in the ocean before biological life even existed. During the first few billion years of the earth’s formation, there was ample nitrogen gas in the atmosphere, but very little oxygen; somehow, the nitrogen was incorporated into mixtures of carbon, hydrogen, and oxygen and the first amino acids were formed. Then, these amino acids combined into proteins that acted as facilitators for chemical reactions to occur more easily. These proteins are known as enzymes.

Proteins in the Body infographic

To illustrate how enzymes work, imagine that a muscle cell has to manufacture more fibers. There are amino acids strewn all over the place within the cell. Now, the size of an amino acid in relation to the cell is like a piece of dust on planet earth—it’s tiny. Suppose you want to manufacture the muscle protein actinthat contains 6100 amino acids in its chain. How are you going to get all of those amino acids lined up in the right order—and they have to be exactlyright—so the structure is perfect?

Think of it this way: amino acids float all over the place, and you need to get them into a specific order. The enzyme acts like a docking station (a slot that each amino acid can fall into), and they must fall into them in the right sequence, so they can bond. Now as enzymes are proteins, they have to be made in the same way! Only God knows how this ever got worked out. To make a protein, you have to get one amino acid next to another, and then next to another. They won’t line up automatically if they just float around in the big space of a cell. The enzyme docking station provides a magnetic or chemical attraction so they move together and bond, and then manufacture a protein.


Enzymes don’t just build—they can also take things apart. Digestive enzymes can cleave bonds between amino acids. Since all processes that relate to manufacturing and modifying require energy, enzymes also burn the fuel of a cell and capture the energy released when it occurs. They also play a key role in detoxifying the body of poisonous waste matter and chemicals.

If you recall from Chapter One, enzymes from the pancreas like trypsin and chymotrypsin are able to pull apart long protein chains from milk, meat, beans, and nuts into individual amino acids—if you’re already lacking in protein or essential amino acids, you can also have low digestive enzyme levels. We can measure a patient’s chymotrypsin levels by testing their stool to see if they are making enough of it to digest food. We’ve found that many people age thirty-five and older have low chymotrypsin levels, most likely due to a lack of dietary essential amino acids.

When this is the case, the individual is stuck in a vicious cycle: Proteins arrive at the small intestine, but there is a lack of chymotrypsin to digest them; they don’t absorb enough amino acids to make more chymotrypsin, and unfortunately, the cycle continues.


Heartburn commercials are no strangers in the world of television advertising. The makers of Pepcid confidently tell us we can eat a hoagie with sausage and peppers and not feel any heartburn. It’s the wrong message, and it indoctrinates the public so heavily that they believe the answer to their problem is another drug. “I’ll just take this, and I’ll be fine.” Food allergies or intolerances can actually be the root cause of reflux for some people, but they think the solution is found in a pill. There is hard evidence that taking stomach acid blocking drugs are linked to higher early death risk and increases risks for cancer and other debilitative diseases.[2]  Taking heartburn medication on a regular basis is comparable to numbing your hand with an anesthetic and then putting your hand on a hot stove. You won’t feel the pain, but you’ll smell the burning flesh, and you know that it isn’t good for you. But since it doesn’t hurt, you don’t remove your hand.

Another large trend in the medical industry is the release of new antibiotic drugs to treat SIBO, but the drugs kill off all of the beneficial organisms—the person is often left in a worse state than before they started taking the drug! The three-drug combination for the bacterial infection H Pylorican produce the same result, and this puts patients at risk for potentially deadly bacteria, like C. Diff. However, when there’s good acid in the stomach, these bacteria cannot live either. If modern medicine appreciated the intelligent design of the human body and worked withit to restore its natural functionality, most of the health care being administered in the U.S. would be unnecessary.


Enzymes are the key to health. They are needed for energy production, detoxification, protein and DNA synthesis, tissue repair, and every function of the body. If someone is lacking essential amino acids, it means that they also have an enzyme deficiency. Without adequate enzymes in the various tissues of the body, it cannot perform at peak efficiency.


I pity the poor people who go to the doctor because of heartburn or an ulcer—let’s hope the gastroenterologist doesn’t find H. pylorion an endoscopy. The patient will be prescribed a month or two of three different antibiotics that not only kill the bad bacteria, but also kill the good, natural flora in the intestine. Not only that, they will also breed overgrowth of yeasts and toxic bacteria that are notantibiotic-sensitive. It’s unfortunate that people get into endless cycles and distort their normal physiology due to incorrect interventions, when there are better ways to restore normal function that won’t lead to these issues.

Simple actions like restoring stomach acid with supplemental hydrochloric acid, adding pancreatic digestive enzymes, using probiotics to restore normal flora, and taking Perfect Amino to give the body the essential amino acids blend into a scenario that restores health—without the use of compromising drug therapies. These interventions usually work, and they are always worth a try if the practitioner is up to snuff.


In most people, the small intestine is about twenty-five feet long, folded over itself numerous times. If you unfolded it, closed one end, and pumped air in, its surface area would be about the same as that of two tennis courts. Despite its huge area, it’s very compact, and every little fold has another fold; there are villi and microvilli to maximize the area and absorb nutrients, and there are enzymes on the surface to aid in digestion activation.

The villi and microvilli greatly increase surface area available for absorption of nutrients.

The inner lining of the small intestine is only one cell layer thick. In addition to the villi, there is a “glue” that holds these cells together. Let’s say someone eats a steak and it enters the body as the big, long chain of about 6100 amino acids per fiber. The pepsin in the stomach will cut them down to five hundred amino acid chains. When the partially digested proteins reach the small intestine, the pancreatic enzymes cut them down to single amino acids, or into short chains of a few amino acids. If the chains are longer than that, they will not be absorbed by the microvilli—they will be too big.

If the tight junctions between the small intestinal cells are too permeable due to local injury (see the chart for causes), the longer chains can pass through the tight junctions into the bloodstream—this is known as leaky gut. It’s “leaky” because substances that should never be allowed to enter the body do so through a “leak” in the intestinal wall barrier. The junction that was once tight is now open.

Gastrointestinal-Wall infographic

Our immune system considers most of these substances to be “foreign”—these are proteins that come from cows, pigs, bacteria, or parasites. As a safeguard, nature put three-fourths of our immune system within the wall of our small intestine as a shield against such invasions. This is known as the Gut Associated Lymphoid Tissue (GALT). When these foreign proteins pass through, an immune response is generated to target these invaders, and this process underlies most autoimmune diseases, like Rheumatoid Arthritis and Lupus. The immune system becomes so agitated from the load of foreign proteins that it begins to attack similar proteins in its own body, thus the autoimmune reaction. The system turns against its own tissue, and much like what happens in a war with friendly fire, an airplane drops a bomb on its own troops by mistake. 

The protein that modulates the permeability of the tight junctions between the cells is called zonulin.If there is injury to the tight junction, the level of zonulin in the stool and bloodstream can increase and is considered to be an indicator of leaky gut.

When the tight junctions are open, then bacteria and parasites can come across, also—these can be commonly identified in blood samples if they are viewed with certain microscopes. Please refer to the graphic.

Lyme Parasite due to leaky gut

If there has been a great deal of damage to the small intestine due to drugs, bacteria, infection, and the like, the leak can be large and many foreign proteins can enter. The immune system then goes into a state of hyper action and hypervigilance—it sees “infidels” climbing over the wall, and it shoots anything that moves. This can result in severe, inflammatory autoimmune diseases, such as rheumatoid arthritis, lupus, and even multiple sclerosis.


Development of Leaky Gut And Top Causes of Increased Zonulin infographic

The unfortunate side effect of leaky gut is that we now have an epidemic of autoimmune disease—our immune system creates antibodies, mostly due to leaky gut and invading foreign particles.

As proteins, cow muscle and cartilage look a lot like human protein, and since the foreign proteins resemble our own, the system begins to attack its own joints and cell nuclei. 

We see autoimmune disease in the form of rheumatoid arthritis, where the immune system attacks joints, or in lupus, where it attacks cell nuclei; or in multiple sclerosis, where it attacks myelin, the coating around nerve cells.

We see patient after patient at the clinic with these diseases, and through detailed testing, we discover that they have high amounts of environmental toxins, such as glyphosate, in their bodies. We also find that they have low levels of stomach acid, have yeast and parasites in their small intestine; a lack of normal bacterial flora in their colons; low levels of digestive enzymes from their pancreas; and low levels of amino acids in their blood. When we document these toxicities, infections, and deficiencies, we can begin the process to properly repair their physiology and restore their health without the use of drugs. Their leaky gut will seal, the auto-immune process ceases, and the disease will abate.

We’ve discussed the barriers to protein digestion and ways to overcome them, but not everyone will seek out these natural remedies. Since poor protein digestion leads to deficiency and this is still a common issue, we’ll move into talking about the consequences to the body if this problem is allowed to continue.


One of our patients was a sixty-three-year-old female who’d had rheumatoid arthritis for ten years. The pain and swelling in her joints had been getting worse before she came to us. Her previous doctor put her on three strong anti-inflammatory drugs: plaquenil, prednisone, and methyltrexate. These were supposed to block her immune system so it could no longer attack her body, but they were not working. The doctor was prepared to put her on the “ultimate” new drug, Embril—one that carried grave warnings about causing cancer or tuberculosis (TB). The drug claimed to be effective, but it was dangerous.

The patient was afraid to take this drug, so she asked for our help. We did a stool test and discovered that she had two parasites, did not have enough good bacteria, and that her system was heavily colonized with yeast overgrowth. She also had severe deficiencies in amino acids, minerals, vitamins, and essential fatty acids. Once we identified her systemic issues, we targeted them so her body could heal. We began a program to restore her intestinal flora, kill the pathogens with natural herbal remedies, and rehabilitate the integrity of her intestinal membrane—she took a lot of Perfect Amino, along with many other supplements and intravenous fluids. Within five months, her joint pain was gone and the swelling had lessened considerably. She felt really good and said she “felt like a new gal.”

Before she started our treatment program, she had been tested by her rheumatologist due to the worsening of her condition. Her initial tests were positive for antinuclear antibody (ANA), rheumatoid factor, and an elevated sedimentation rate (which was an indicator of inflammation in the body). We retested her after she had followed our recommended protocols, and her antinuclear antibody and rheumatoid factor had both gone negative. Her sedimentation rate also dropped from sixty to a normal reading of fifteen.

During our treatment process, she was able to wean off the prednisone and methyltrexate. She asked me if she had to go back to the rheumatologist, and I told her that she didn’t—handling her disease process our way had worked very well, and she should continue to remain healthy in the future. “But,” I added, “If you could go back just one more time, for me, and show him your results, I’d appreciate it. If he asks what you’ve done to see these improvements, show him your lab work and tell him you went to the natural doctor. If he needs assistance with any of his other patients, I’d be happy to help.”


Want to learn more? Click HERE to get your copy of Dr. Minkoff's book, "The Search for the Perfect Protein" today!



  1. Science News, “Popular heartburn drugs linked to higher early death risk,” Science Daily, July 5, 2017,
  2. Science News, “Popular heartburn drugs linked to higher early death risk,” Science Daily, July 5, 2017,

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