Over the years, I’ve talked extensively about carbohydrates, fats, fiber, vitamins, minerals, and antioxidants — but not so much about protein. Then again, what’s to say about protein? Protein is protein, right? It’s the stuff in meat, chicken, fish, and soy. There may be different sources, but it’s all the same, isn’t it? It’s not like there are different kinds of protein. You can’t break dietary protein into subgroups like you can with fat — categorizing it as saturated, unsaturated, and trans fats. Or can you? As it turns out, protein is not so simple, and there are a number of questions that need to be addressed when you’re thinking about what protein to eat such as bioavailability, speed of uptake, the size of the protein molecule, allergies, etc. And since I’m currently involved in a project to develop the next generation of hypoallergenic protein, now seemed as good a time as any to address the issue. Let’s begin by covering the basics…then spiraling out in ever expanding detail.

What is protein and how does it relate to diet and health?

The simplest, least useful, definition is that proteins are long chain molecules made up of amino acids joined by peptide bonds. Next to water, protein is the most plentiful substance in your body and is the principal constituent of the protoplasm in every cell of your body. That said, there is not just one kind of protein, but many kinds in the human body, each with a different function. For example, different proteins can:

• Provide structure, as found in ligaments, fingernails, and hair
• Aid in digestion in the form of digestive enzymes
• Play a role in immunity in the form of immunoglobulins
• Aid in movement in the form of muscles
• Tell your body what to do and when as seen in peptide hormones
• Transport oxygen as hemoglobin
• And even play a role in our ability to see. The lens of the eye is pure crystallin protein.

Interestingly enough, your body does not actually utilize protein directly when you eat it. When you consume protein, for the most part, the body breaks it down into its constituent amino acids, absorbs those amino acids through the intestinal tract, and then using genetic instructions encoded in your body, reassembles them into the proteins it needs to perform all its functions. For example, it takes dairy protein you eat, breaks it down in the digestive tract into its constituent amino acids, absorbs those amino acids, and then reassembles them into muscle protein to help you become Arnold Schwarzenegger. Thus, milk protein from Elsie the Cow becomes the Governor of California. Whenever the body assembles a protein from amino acids, when it builds muscle for example, it needs a variety of amino acids to complete the process. Some of these amino acids may be produced in the body itself. Others may come from dietary sources. But nine amino acids can only come from dietary sources because your body cannot produce them no matter what you eat. These nine are considered essential, not because they’re more important, but again because your body cannot manufacture them and therefore they must be part of your diet on a regular basis. These include:

1. Phenylalanine
2. Valine
3. Threonine
4. Tryptophan
5. Isoleucine
6. Methionine
7. Leucine
8. Lysine
9. Histidine (your body can manufacture histidine, but usually not in sufficient amounts)

If your diet is chronically deficient in any one of the essential amino acids, the building of protein in the body stops, which brings us to a key point. Your ability to utilize protein is profoundly affected by the “limiting amino acid” in your diet — kind of a “you’re only as strong as your weakest link sort of thing.” For example, if you are vegetarian and rely on rice for your protein, rice tends to be low in lysine. Over time, the lack of lysine in your diet may become a limiting factor in the ability of your body to assemble proteins. Simply adding legumes, which are high in lysine, to the diet corrects the problem and allows your body to build all of the proteins that it needs. It is a good idea, therefore, to mix your protein sources so that deficiencies in any one source are corrected by another. In addition, this limits the loss of nitrogen in the liver where amino acids are broken down, thereby releasing ammonia and causing an increase in the production of uric acid. Bottom line: getting a good mix of amino acids in your protein sources increases your overall net protein utilization and reduces the chances of gout.

To summarize everything that we’ve covered so far, let’s just say that protein, as a category, is one of the essential nutrients along with carbohydrates, fats, vitamins, minerals, oxygen and water. In fact, the word protein comes from the Greek word “prota”, meaning “of primary importance.” Protein has a critical physiological function. It is primarily used in the body to build, maintain, and repair body tissues. In some cases, if protein intake is greater than that required by the body to perform its primary function, the excess protein may be converted to energy for immediate use (as happens with bodybuilders and performance athletes)  or it will be stored in the body as fat (as happens for the rest of us). Note: protein will only be used by the body as an energy source after other energy sources (i.e., carbohydrates and fats) are exhausted or unavailable.

And that concludes Protein 101. Now let’s move on to the more interesting stuff.

Structure of protein and how it’s digested and utilized

Protein bioavailability is not just a function of the amino acids that are present. It’s also dictated by the structure of the protein. Some proteins are more amenable to being broken down (digested) than others. For the purposes of this newsletter, we don’t really have to plumb the depths of biochemistry, or the nature of the peptide bonds that hold proteins together. However, it is necessary to discuss briefly how proteins are assembled from amino acids and the various shapes those proteins take.

There are some 20 different amino acids which are commonly identified. Each and every protein is made from these 20 amino acids put together in varying order and in varying amounts and combinations, thus providing the possibility of almost limitless combinations. That said, most proteins are large molecules that may contain several hundred to many thousand amino acids arranged in branches and chains.

The assembly of amino acids into proteins is actually determined and directed by information encoded in your genes. Each protein has its own unique amino acid sequence as specified by the gene encoding that particular protein. Protein synthesis takes place inside cellular cytoplasm and can actually reach a rate as high as the joining of up to 20 amino acids per second in a given cell. In fact, the assembly of amino acids is responsible for more than just the creation of protein. It is also responsible for the creation of peptides and polypeptides, which can be thought of as “short” or “incomplete” proteins. It should not be surprising then that the definitions of proteins, polypeptides, and peptides somewhat overlap. The protein designation, however, is generally used to refer to longer, complete biological molecules in a stable structure.

The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass. Some proteins may contain just a few hundred amino acids strung together, but the largest can contain close to 30,000 amino acids all chained together.

So how does a protein composed of a chain of 27,000 amino acids achieve stability? And the answer is through structure. These long chains fold in on themselves to form stable structures.

Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state — although proteins may shift between several related structures during the course of performing their biological functions.

There are many reasons biochemists try to determine the various structures of any given protein. Most notably, those structures give clues as to the function of the protein in the human body. But for our purposes, there’s one primary reason for being aware of protein structure. Protein structure plays a major role in determining how readily it can be broken down into its constituent amino acids during the digestive process. In other words, it plays a major role in determining protein bioavailability its propensity to stimulate allergic responses.

How what you eat with protein affects your health

When found in nature, protein never comes by itself. Whether from animal or vegetable sources, protein comes in the presence of various fats and carbohydrates. In most cases, their presence is a non issue. But in a small number of cases, these “extras” play a major factor in determining the digestibility of the protein. For example, some accompanying nutrients can inhibit proteolytic enzymes that would normally break down the protein, or can suppress the release of stomach acid necessary for the digestion of the protein, or simply cover the protein so that enzymes and stomach acid cannot reach it. For example, studies have shown that eating fruit pectin at the same time you eat protein may cover the protein with a hydrogel, which prevents the stomach enzyme pepsin from reaching the protein, thus inhibiting digestion of the protein.

This is not true for all proteins, and requires high pectin fruit to be an issue, but it certainly calls to mind the old food combining axiom not to eat proteins with carbohydrates. Interestingly enough, although such studies support the axiom, they do not necessarily support the theory behind it that the problem results from carbohydrates suppressing the release of gastric juices.

Determining protein bioavailability to optimize nutrition

Protein bioavailability is the sum total of the three factors we mentioned above:

1. The mix of amino acids in the protein — or in the combination of proteins eaten during the day. Remember, the shortage of an essential amino acid provides a limiting factor on how much of the overall protein can be utilized by the body.
2. The structure and size of the protein molecule. The larger and more tightly folded the molecule, the less able the body is to break it down. Large proteins that frequently undergo incomplete digestion include those found in wheat, corn, dairy, and soy. It is not coincidental that these foods are identified by the FDA as being highly allergenic. (We will discuss protein allergies more in our next newsletter.)
3. The other foods (or components in the protein source itself) that inhibit the breakdown of the protein.

Protein utilization can be measured

There are several tests for measuring protein utilization, or bioavailability, although they’re a bit like the story of the blind men describing an elephant — each one gives an incomplete picture. The blind man who feels the trunk says an elephant is like a snake. The one who feels its legs says an elephant is like a tree. The one who feels the ears says an elephant is like a giant fan. And the one who feels its body says an elephant is like a massive wall. Each one provides useful information; but each one also provides an incomplete picture.

The Kjeldahl method is the standard for measuring the total protein concentration in food. It provides the number that you normally see on nutrition labels on the side of food packages. Unfortunately, it tells you nothing about how much of that protein actually gets used by the body — which in some cases can be very little.

Biological value (BV) measures how much of the protein that you eat gets incorporated into your body tissue. It does so by measuring how much of the nitrogen in the protein you eat is absorbed by the body and then how much is excreted. The assumption is that the difference is what got incorporated into your body protein. Its weakness is that BV varies greatly depending on how food is prepared and according to what other foods were eaten in the recent diet that can alter nitrogen measurements. Although the following three methods all provide better measures of protein utilization, BV is still commonly used by nutritionists out of force of habit.

Net protein utilization (NPU) is the ratio of amino acids converted to proteins to the ratio of amino acids supplied in the protein source. Experimentally, this value is calculated by determining the amount of dietary protein you are consuming and then measuring how much nitrogen is excreted. It is significantly affected by the limiting amino acids (as discussed earlier) in the particular food.

Protein Efficiency Ratio (PER) is based on the weight gain of a test subject divided by its intake of a particular food protein during the test period. Theoretically, it is a biological assay of the quality of a particular protein, measured as the gain in weight of an animal per gram of a particular protein eaten. At one time, this was the industry standard, but unfortunately PER is based upon the amino acid requirements of growing rats, which differ noticeably from that of humans.

Protein digestibility corrected amino acid score (PDCAAS) evaluates protein quality based on the amino acid requirements of humans. This is now the preferred standard. Nevertheless, it too has holes.

• PDCAAS takes no account of where proteins have been digested and cannot account for proteins that are absorbed by bacteria in the digestive tract.
• PDCAAS is calculated solely on the basis of single protein consumption and therefore once again does not calculate the changes in protein utilization resulting from the intake of complementary protein sources.

Improving protein utilization for optimum health

Now let’s take what we’ve covered so far and see if we can extract some benefit from it that will help us improve our ability to improve the utilization of the protein we eat.

Consume more than one type of protein

As we’ve discussed, protein utilization is defined, to a large degree, by the limiting protein in the diet. Even complete proteins (those containing all of the essential amino acids) can still be out of balance so as to limit maximum utilization. Although dairy and egg tend to be well balanced and largely avoid this problem, they present other issues as we will see in subsequent parts of this series on protein. Meat, chicken, and fish, on the other hand, can benefit from the consumption of other proteins that help balance them out. And soy, most definitely.

Take supplemental digestive enzymes with your dietary protein

This can make a huge difference when it comes to facilitating your body’s ability to break down complex proteins and eliminating the byproducts of incompletely digested proteins from previous meals. We will discuss this more in the next part of the series when we talk about protein allergies.

• An overview of enzymes
• Digestive enzymes

Watch what you eat with your proteins

Some of the theories behind food combining may not be scientifically supported, but empirically the concept works.

And this is probably a good place to take a break and end this newsletter. When we continue our series on protein we will:

• Compare different protein sources
• Explore the nature of protein allergies
• Talk about how much protein you actually need
• Examine some “special conditions” related to the over-consumption of protein and the use of the wrong kinds of proteins
• And finish by looking at the ideal protein

Read More About Protein

• Comparing Protein, Part 2
• Problems with Protein, Part 3