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How Protein Digestion Affects Muscle Building, Fat Loss, Hormone Levels, Inflammation & Overall Health

by Dr. David Minkoff May 06, 2021 6 min read 0 Comments

How Protein Digestion Affects Muscle Building, Fat Loss, Hormone Levels, Inflammation & Overall Health

The ability to fully digest and absorb protein means the difference between killing or maximizing your muscle gains and fat loss, as well as your overall hormonal balances and your levels of energy, inflammation, and health. So understanding exactly how it works, and how to keep it working, or get it working, properly is very important.

When you consume food, you chew it and it goes down into your stomach. Here we see mostly protein digestion, with fats and carbs mainly being digested in the small intestine. 

When protein comes in, your stomach releases two main things: hydrochloric acid, or stomach acid, and an enzyme called pepsin.

This stomach acid does a few things: it helps break down proteins, breaks down minerals necessary for later protein synthesis in the body, and kills bacteria, fungi, parasites, and viruses coming in with your food and water. 

Each of these proteins you ate are made of hundreds or thousands of individual amino acids, all bonded together in long chains and then coiled up, with the coils also bonded together to form a complete “protein”. 

Breaking proteins down into more usable forms – Your stomach’s job

First, the stomach acid breaks the bonds holding the individual coils together. Then the pepsin starts breaking the bonds that hold the overall chain together. It doesn’t break all of them, but it breaks a lot. So by the end of this, instead of each protein molecule being a long chain of hundreds or thousands of amino acids all coiled up, it’s now broken up into many, much smaller chains of maybe 20 to 40 amino acids each. 

While this is happening, the level of stomach acid has been rising, which in turn is lowering the level of ph in the stomach. By the time these amino acid chains are broken up, the stomach acid should have reached a ph of about 1 or 2 (ph is just a measurement of how acidic something is or isn’t, with 1 being most acidic, 7 being neutral, and 14 being most alkaline). The stomach can handle this level of acid because of a mucous lining on your stomach’s walls. 

There is a valve between your stomach and small intestine keeping your stomach acid and food in the stomach while it does its job. A healthy stomach needs to reach a ph of 1 or 2 to trigger this valve between the stomach and small intestine to open and let the food through. If the stomach acid didn’t get this acidic, then the food would stay in the stomach much longer and go rancid. This causes the acid to bubble up and burn the esophagus, which isn’t made to handle this acid. Contrary to popular belief, the result is heartburn and acid reflux because there’s not enough stomach acid — not when there’s too much. 

So we want that stomach acid acidic, at a very low ph. If it’s not, then you get heartburn. But also, you get proteins that aren’t broken down enough. And they need to be as you’ll see. 

The finer details of digestion – The small intestine’s job

From here the food moves into the small intestine where more enzymes come in, further breaking these short amino acid chains up until they’re just free-floating individual amino acids — no more chains. This is what we want.

Other enzymes also start breaking down fats and carbohydrates and all of these broken-down pieces start moving through the intestinal wall into blood vessels that take them to the liver. The liver then filters all of this, looking for any toxins, and then releases it all out into the bloodstream. 

Let’s focus on this protein breakdown as it is important here. You see, the amino acid chains must be fully broken down into individual amino acids for a few reasons. 

First, if they are fully broken down, then the body can use them to build new proteins and collagen in the forms that it needs for muscle, bone, hormones, enzymes, etc. 

But if they’re not fully broken down — the body can’t use them. 

These partial chains of amino acids then either continue down the digestive path and leave as waste, or… they’re absorbed through the intestinal wall and get into the bloodstream and cause inflammation in the body. 

Remember those bacteria, fungi, parasites, and viruses I mentioned earlier? When proteins are not fully broken down and absorbed into the bloodstream, they carry these nasty little guys with them, henceforth to be known as foreign invaders — because they are your enemy. 

Also remember, a healthy stomach with high levels of stomach acid can kill these foreign invaders. Unfortunately, many still get past the gates and into your small intestine, but not to worry, your body has a last line of defense.

Call in the guards! – Your immune system’s job

There are three walls around your small intestine. The first is an inner lining only about one cell in thickness which sees the broken down nutrients and lets them through. The third wall is all the blood vessels surrounding the intestine which take these nutrients to the liver. But the second wall, between these two, is made of immune tissue. Lymph tissue to be exact. 

This is why you’ve heard that about 80% of your immune system is in your gut. This is it. 

When food comes into the small intestine, this lymph tissue sends out immune cells to check for any foreign invaders. And when the immune cells find some, they send antibodies to surround them and destroy them. This is an immune response. And there’s always some inflammation during an immune response. So if there were a lot of bacteria, like salmonella poisoning, you might get a belly ache. 

The way they recognize these bacteria, parasites, and fungi is by their shell, or outside coating, which is made out of protein. They know that any protein the body needs is already broken down into individual amino acids. So these whole protein structures must be foreign invaders. 

At this point, one of two things happens. Either they’re destroyed onsite or they make it down the path and are distributed via the bloodstream somewhere in the body, in which case the immune cells go there to kill them. This causes inflammation throughout the body. 

The immune cells also remember the exact protein structure of these invaders so they know them in the future. They have to so they don’t mistake the body’s protein structures for harmful bacteria and attack them (that’s what an auto-immune disease is, the body mistaking itself for harmful invaders and attacking itself).

How poor digestion of proteins causes inflammation throughout the body

Now consider this… if your digestive system didn’t fully break down all your protein into individual amino acids, and some of the partial amino acid chains got out into the bloodstream, then, when the immune system sees these, it knows they aren’t individual aminos or bodily protein structures. So it assumes… they must be harmful bacteria. 

So it launches an immune response. And immune responses create inflammation. Then, if this begins to happen daily because you have low stomach acid, inflammation is created continually in the body wherever these partial proteins land. This means a continual extra load on your immune system which is needed for muscle building and overall health . And it also means a continual source of stress for the body, which means a continual releasing of cortisol, the stress hormone that both breaks down muscle and instructs the body to store fat. Your body can handle a little at a time, but after years of this happening, and along with other causes, it really adds up.

The causes happen at a trickle and you may not even notice this happening, but eventually it may show up as fibromyalgia, lethargy, rheumatoid arthritis when these land at the joints, or just, “my body hurts.” Either way, this doesn’t work for building muscle or losing fat. 

If we have low stomach acid levels here, and more harmful bacteria make their way into the small intestine without being killed in the stomach, they can take root in the intestine and grow. It’s not acidic there. It’s dark and it’s warm. They love it! 

And they can start to consume some of the food that you ate. What do they give you in return? Gas and bloating. 

They’re not good tenants. 

But now, not only are you losing some of the protein you ate from it not being fully broken down, but you’re also losing it to these bacteria who eat some of it, and to cortisol released due to inflammation, which breaks down muscle and increases fat storage. 

This may seem small. 

It’s not. 

It affects our hormones, our energy levels, our cravings, and our ability to gain and lose muscle and fat.

We need these proteins fully broken down. 

Two workarounds for avoiding partial breakdown of proteins, improving digestion in the stomach, and reducing inflammatory invaders.

This is one reason PerfectAmino is so effective. It’s already fully broken down so that, no matter the state of your digestive tract, you’re getting all of that protein. And most people have some degree of lowered digestive acid these days, causing plenty of trouble in their bodies. 

So if you experience indigestion, heartburn, GERD or gas and bloating, I highly recommend you take PerfectAmino to ensure your body is getting the protein it needs, but also our Full Spectrum Digestive Support to ensure your body is fully breaking down proteins, killing harmful bacteria, and giving your body what it needs to function and thrive. 


*This website, including products, articles, and educational content are not intended to diagnose, cure, or prevent any disease. The statements on this website have not been evaluated by the food and drug administration. This website does not provide medical advice. The information contained in this website is for general information purposes only.

Dr. David Minkoff
Dr. David Minkoff

Dr. David Minkoff graduated from the University of Wisconsin Medical School in 1974 and was elected to the “Phi Beta Kappa” of medical schools, the prestigious Alpha Omega Alpha Honors Medical Fraternity for very high academic achievement. He then completed both a Pediatric Residency and Fellowship in Infectious Disease at the University of California at San Diego.

He worked at the University of California and Children’s Hospitals in San Diego as an attending physician in infectious disease while conducting original research on Ribaviron, a broad spectrum anti-viral agent to fight disease. He also co-directed a neo-natal intensive care unit and worked in emergency medicine.

In 1992, Dr Minkoff’s wife Sue, a Registered Nurse, became interested in nutrition and health and began to go to lectures from some of the experts in the field. At the time, Dr Minkoff was pretty fixed in his view of traditional medicine and it took a lot of convincing to get him to come to one of these lectures. After hearing Dr Jeffrey Bland speak, Dr Minkoff had a eureka moment and began pursuing the alternative field with a vengeance. Based on this new knowledge Dr Minkoff and his wife set up a small clinic in 1997 to help some friends with their medical problems. What began as an experiment blossomed into Lifeworks Wellness Center, one of the most successful clinics for complementary medicine in the United States. In the process, he gained expertise in Biological medicine, integrative oncology, heavy metal detoxification, anti-aging medicine, hormone replacement therapy, functional medicine, energy medicine, neural and prolotherapy, homeopathy and optimum nutrition. He studied under the masters in each of these disciplines until he became an expert in his own right. Dr Minkoff is one of the most in demand speakers in the field and wrote an Amazon best selling book called The Search For The Perfect Protein.

The demand for the products and protocols he discovered became a catalyst for founding BodyHealth.Com, a nutrition company that now manufactures and distributes cutting-edge nutritional solutions for the many health problems of today. Dr. Minkoff writes two free online newsletters, “The Optimum Health Report” and ”The BodyHealth Fitness Newsletter”, to help others learn about optimum health and fitness.

Dr. Minkoff is an avid athlete himself and has completed 44 Ironman Triathlons. To keep his fitness maximal, he lives the lifestyle he teachers to others and tries to set an example for others, so they can enjoy a life free of pain and full of energy.



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