Write An Essay On The Chemistry Of Protein


by Dr. Lawrence Wilson

© December 2015, L.D. Wilson Consultants, Inc.

All information in this article is for educational purposes only.  It is not for the diagnosis, treatment, prescription or cure of any disease or health condition.


Protein is a critical food group for everyone.  Most adults need about 10 to 11 ounces of a protein food each day.  The best way to eat this is to have two portions daily of 4 to 5 ounces each of a protein food.

Also, women can have up to 6 eggs per week.  Men can have up to 8 eggs per week, and no more.

Proteins need to be cooked, but not overcooked.

Avoid all pig products, although they are nutritious.  Most can contain parasite cysts or eggs, even when well-cooked.

Too much protein causes toxicity of the liver and kidneys, and excess production of proteinaceous toxins in the colon, evidenced by foul-smelling stools.  Too little protein in the diet can cause weight gain or loss, and severe malnutrition.



Definition. Proteins are one of the most amazing group of molecules in the human body.  They are complex combinations of smaller chemical compounds called amino acids.  These are like the bricks or building blocks of a building.

There are about 22 amino acids.  Some can be made in the body from other amino acids, or in other ways.  However, at least 8 or 10 of them must be obtained from our diet.  All of the amino acids contain oxygen, hydrogen, carbon and nitrogen.  Many also contain sulfur. 

Like building blocks, millions of these amino acids are chained together, stuck together, and folded over each other to form complicated shapes and structures to create millions of critical body components.

              Metaphorical definition.  Proteins are associated with motion, the basic quality of animal life.  While plant life is more concerned with sugars and carbohydrates, animal life is more concerned with proteins.  (However, all life contains both proteins and carbohydrates.) 



The quick answer is they are used to make most everything in our bodies.  Here are a few of their main uses.

Hormones.  Many of the hormones such as insulin and progesterone are proteins.

Oxygen transport.  Hemoglobin, a blood protein, carries oxygen to the cells. 

Cellular repair.  Heat shock proteins help rebuild our cells after stress. 

Binding and transport of nutrients.  Transferrin, metallothionine, ceruloplasmin and other transport proteins bind to minerals and other things, and carry them throughout the body. 

Movement.  Muscle protein (such as myoglobin) is responsible for our ability to move.

Holding genetic information.  Proteins such as RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) in the nuclei of our cells are responsible for the genetic code.

Structural proteins. Proteins are also essential for the body structure.  Bone consists of a protein matrix that fills with calcium and other minerals.  Other structural proteins include collagen, cartilage, elastin and keratin that form the skin and other structures.

Enzymes.  All enzymes are proteins.  Thousands of enzymes facilitate every chemical reaction in the body.

Conversion to fuel. Proteins may also be converted to sugar or fat to be used as fuel for the body.  This is not ideal, but it does occur in some people.


            The main source of protein is our diet.  We eat proteins from animals and plants.  Our bodies can synthesize some of the amino acids, but many of them must be obtained from the diet. 

When we eat protein from plant or animal foods, we must break it down into its simpler amino acid components.  This is called protein digestion.  This is like taking apart a building and sorting out all the bricks to be used to build a new building.

Then our bodies reassemble the amino acids into our body proteins.  This is called protein synthesis or biosynthesis.  It is like taking the bricks and building a new building.

We also have some capacity to change one amino acid into another, to give us more types of “building blocks” with which to make our body proteins.


Protein-containing foods can be roughly divided into three groups depending on how much protein they contain:

1. High protein foods include red meats, poultry, fish, eggs, nuts, seeds, cheese, yogurt and beans.  Others are wheat germ, brewer’s yeast, nutritional yeast and some algae such as spirulina.  These foods contain about 20% protein or more.  I do not recommend spirulina or algae as they are difficult on the liver due to some of their contents.  They are often found in some “green superfood” powders, food bars and drinks.

I find that everyone needs to eat some high-protein foods today.  However, eating too much of them, especially too much eggs, (more than about 10 eggs per week) is not ideal and causes intestinal auto-intoxication.  This just means that the body cannot digest all that protein and so some of the protein putrefies or rots in the intestinal tract, giving rise to poisonous substances, and often some gas and bloating or smelly stools.

2. Medium-protein foods include grains such as rice, wheat, oats, millet and barley.  These contain 6 to 14% protein and are considered incomplete proteins.  This means they should be combined with other protein foods to provide complete protein.  Unfortunately, modern hybrid grains often contain much less protein than the grains that were grown 100 years ago or earlier.  Wheat, for example, used to have 12-14% protein and now contains six percent in many instances.  Even organically grown grains today are hybrids.

3. Low-protein foods include fruits, vegetables and juices.  These contain less than 5% protein.  Living on a low protein diet of mainly fruit, for example, does not work well for human beings, in my experience.


            In addition to the sources above, some people like to use protein supplements.  These include 1) protein powders, 2) protein bars, 3) meal replacements, 4) hydrolyzed or pre-digested protein and 5) amino acid supplements.  Let us discuss these products in more detail. 

            Powders versus whole foods.   Protein powders and supplements are made from a variety of sources.  Some are better than others.  The best is probably egg protein powder.  However, I never recommend protein powders and meal replacements for the following reasons:

1. Too yin.  Smoothies and shakes usually contain powders, which are all yin, combined with a sweetener, which is yin, and water, which is yin.  All of this is bad for health and difficult to digest properly for most people.  

2. Much less nourishing.  You will get far more nutrition from an egg than from egg protein powder, or from peas rather than pea protein powders, etc.  The powders are all refined and many nutrients have been stripped away.

3. Bad food combinations.  Combining powders with water with fruit, often and other things is usually a terrible food combination.

4. Must drink too much liquid with the drink.  It is best not have much liquid with meals.  this is not possible with a drink or smoothie.  The liquid dilutes the stomach acid and impairs proper digestion of the food.

Whey protein.  This product is extremely popular, especially among body builders and it is highly recommended by many holistic doctors.  It contains a decent balance of the amino acids and other minerals and substances. 

However, recent research I have done indicates it contains toxic forms of nickel and copper.  In addition, it is very yin when taken in a smoothie or a shake, and forms bad food combinations in these drinks with too much liquid with the food.  Therefore, I cannot recommend it at all.  Its toxic components cause it to be stimulating, so a lot of people love it.

Whey protein is reputed to help people quit smoking, and I would agree that using some whey protein is better than smoking cigarettes, but that is its only advantage.  Once you have quit cigarettes, then move on and stop the whey protein powder in favor of whole food proteins such as eggs, meats and raw cheeses.

Soy protein.  The most popular protein drinks and bars are often made from soy.  The label may say made from soy protein isolate or just soy or soybean protein.  However, often it just says textured vegetable protein and this also means soy in most all cases.  Thousands of products are made of this, such as Hamburger Helper, vegetarian burgers and many other products.

Soy problems.  Soy protein powders and foods made with it are probably the worst ones and are best avoided altogether.  Soy is not a particularly high quality source of protein, although it is technically a complete protein.

However, the soy is always processed and must be.  This renders it less desirable as processing damages the protein structure a lot.  In fact, it is usually a leftover byproduct of the manufacture of soybean oil.  Chemicals such as acetone may be used to extract the oil, leaving a residue of chemicals in the soy protein.

Soy has other drawbacks such as containing too much copper, low zinc, enzyme inhibitors, thyroid inhibitors and other toxic residues.  Its main benefit is its low cost, which is very important to food manufacturers.

Egg.  Egg protein powder is also often labeled as albumin.  This is generally a much better form of protein powder, drink or bar than soy or most others.  However, I still suggest eating whole foods, not protein powders of any kind.

Milk Sources.  The two powders made of milk protein are whey powder and casein.  Whey is a little better, but I don’t suggest either of them.

Others.  Protein powders may also be made from rice, peas, yeast or fish.  I do not recommend any of them, in general.

            Hydrolyzed protein. Some protein supplements such as Bragg’s Liquid Aminos contain pre-digested protein.  This means the protein has been broken down into its amino acids by a chemical process so it requires much less digestion.

The source is often soy, however.  This is a definite disadvantage.  Also, unfortunately, hydrolyzed protein always contains some monosodium glutamate or MSG, a harmful food chemical.  It occurs naturally as part of the processing of hydrolysis.

Pure grown amino acids.  A more expensive type of protein supplement is pure amino acids that are made by fungal organism in a laboratory.  These usually come in capsules and are called free-form amino acids.

These can be useful for some cancer patients or others who cannot digest protein well at all.  I do not recommend them for most people, however, because they are 1) very yin, a type of toxicity, and 2) made from fungus, which can cause allergic reactions in some individuals.

              Meal replacements. Meal replacements are usually protein powders mixed in with extra vitamins and minerals, and usually a sweetener.  They are usually terrible food combinations, contain too much sugar, too much water, and are hard on the digestion.  Most are also nutritionally incomplete, and much too yin.  They may be needed for parenteral nutrition, or tube feeding, if a person cannot eat regular food.  Otherwise, I do not recommend them at all. 

Even if a person must be fed through a tube, I think it is better to make fresh purees from cooked vegetables and some meats, rather than use most meal replacement powders and liquids.


Sugary protein drinks, powders and bars.  Beware of protein bars, powders and meal replacements that are high in sugars.  This is often the case because otherwise the product would not taste good. 

The label may say sugar, corn syrup, fructose, glucose, lactose, liquid sugar, honey, agave nectar, rice syrup, barley malt or fruit juices.

I also suggest avoiding ALL PRODUCTS containing Nutrasweet or Equal that are often used instead and in “low calorie” bars and powdered drink mixes.  To sweeten a protein drink, Stevia, xylitol, mnanitol or sorbitol are more healthful sweeteners.  Even better, stay with protein foods since all sweet-tasting foods and drinks tend to keep the sweet taste alive and the artificial sweeteners and the others can deceive your body to some degree and are thus less healthful.

            Other Additives.  Also beware that most protein powders, bars and drinks contain natural or artificial colors and flavors, preservatives and perhaps a dozen other chemicals.  This is yet another reason to eat whole foods rather than chemical concoctions of protein powders, liquids, pills or bars. 

Also remember that while protein supplements may be helpful at times, they are never a substitute for food. Whole, natural, minimally cooked and processed proteins are essential for our life and our health and there is no substitute for them.



            Complete protein foods.  Meats, poultry, fish, eggs, cheese, yogurt, soy and peanuts are considered ‘complete proteins’.  This is a useful but not absolutely true concept that means that these proteins contain a good balance of all of the essential amino acids that our bodies need. 

Our bodies require at least 22 amino acids for health and well-being.  Of these, 10 or so are called ‘essential’.  This means we need to ingest them in our diet.  We don’t need to eat the other 12 or so, because we can convert the essential ones into them inside our bodies.

Incomplete protein foods. These include grains, beans, nuts, seeds and even some forms of meats such as rabbit.  They are commonly eaten as stapes in poorer nations and by strict vegetarians, also called vegans.

If a person does not eat complete protein foods, one must eat a variety of less complete protein foods in order to obtain all the required amino acids.  Otherwise deficiency symptoms, some irreversible, will begin to appear.

In our experience, eating a lot of incomplete proteins or lower quality protein foods is never advisable unless one is very ill with cancer or some other extreme situation.  They just do not nourish the body as well.

Biological quality.Some protein foods contain a much better balance of the essential amino acids than others.  A food with a good balance has a higher rating of biological quality.  Egg protein (albumin) rates highest in biological quality.  Meat protein has the second best biological quality.

Other quality factors.  These include freshness, how the food was grown or raised and how it is prepared.  Other quality factors include the breed of chicken or other animal, the soil the food is grown on and many other subtle qualities.  Even the altitude at which a food is grown or raised can influence its nutritional qualities, for example.

Raw protein foods.  Some people prefer all raw diets and I am aware of this.  However, we have not found this a beneficial system for most people, especially those with low vitality.  Read about the concept of Vitality on this website.  Raw foods can contain parasites, bacteria, viruses fungi and other harmful microorganisms that are mainly killed by cooking.

Cooking protein.  Too much cooking denatures or damages protein, which is why an egg becomes harder with cooking.  For this reason, protein foods should be cooked lightly for the best nutrition. 

I don’t recommend overcooking meat, eggs (as in hard boiling or deep frying) because this ruins the protein structure and makes them much harder to digest.  Read more about this subject in the article on this site entitled Raw Foods.



            Proteins must be broken down into their amino acids to be used in our bodies.  If they are not properly broken down, they rot or putrefy.  This is a very toxic process that literally poisons the body and causes foul-smelling bowel movements and gas.  This is how you know some putrefaction is going on. 

Pepsin and hydrochloric acid in the stomach and trypsin and chymotrypsin from the pancreas are among the important protein-digesting enzymes.  One must have enough of these enzymes to digest the amount of protein one eats or putrefaction will occur to some degree.  Most people do not have enough of these, which is why we supplement everyone with a protein digesting enzyme such as GB-3 or betaine hydrochloride and pepsin.


Digestion depends on general nutrition.  Our bodies convert sodium chloride to hydrochloric acid in the stomach to help break down protein.  Enzyme production also requires zinc, which is deficient in most people due to our depleted soils and refined food diets.  For example, vegetarian diets, for example, are lower in zinc.  Today, many children are born low in zinc due to their mother's zinc deficiency.

Other minerals and many vitamins are also needed to make digestive enzymes.  Thus one’s entire nutritional state is important for proper utilization of protein and its digestion into simple amino acids.  Then these must be recombined to make our proteins.  This is discussed later.

            Food habits and protein digestion.  For good protein digestion, eat slowly and chew thoroughly.  Relaxed, enjoyable, sit down meals help maximize digestive enzyme production.  Avoid overeating and relax after meals for at least 10 minutes to facilitate digestion.  

Take digestive enzymes if you are unsure whether you are digesting protein properly.  My favorite digestive enzymes are pancreatin and ox bile.  Hydrochloric acid and pepsin is another common protein-digesting product.


1. High levels of toxic metals.  These interfere with zinc and other vital minerals.

2. Stress keeps the sympathetic nervous system active and interferes a lot with digestion, a parasympathetic activity.

3. Fatigue does the same as stress and it weakens the digestion tremendously.  Always rest before meals if tired, even if it is just for a few minutes.

4. Nutritionally depletion, as explained above, impairs digestion a lot.

5. Infections in the intestines, which are quite common.  These include parasites, yeasts, bacteria and more.

6. Illnesses affecting the intestines such as colitis, ulcers, cancer and others.

7. Some pharmaceutical drugs and over-the-counter product interfere a lot with digestion.  Among the worst are anti-inflammatory drugs like Aspirin, Tylenol, Aleve, Excedrin and other anti-inflammatory drugs that irritate the stomach and can even cause ulcers.

Beta blockers, proton pump inhibitors and calcium supplements are others that interfere with digestion.  Some of the common names are propanolol, Inderal, Protonix, Prevacid, Prilosec, Tums, Choos, OsCal and many others in the same classes of drugs.

In fact, any toxic substance, even food additives will interfere with digestion, which is quite a delicate process.  This is just another reason to eat well and rest after meals as Mexicans and Europeans often do with a siesta after the large meal of the day.  This is a wise idea for everyone, even if it is a 10-minute rest.

8. An alkaline stomach due to drugs or nutritional or other imbalances interferes a lot with protein digestion.  The wrong acid in the stomach is another issue related to this one.  This is why the pH of the stomach is not enough.  It must be the correct acid as well, and why supplements are so helpful in many cases.

9. Improper bowel flora is another common cause of digestive problems.  Although this is most common in the large intestine, it can occur in the small intestine as well.  It is responsible for bloating, often, in the stomach due to gas formation.

10. Constipation and/or low fiber in the diet may also interfere with proper digestion.

11. Complex food combinations.  The simpler a meal, the easier it tends to be to digest.  This is why I suggest meals be constructed with cooked vegetables and either one protein or one starch only.  Also, monomeals (one type of food per meal) are also excellent.


              Digestive problems.  Hair mineral analysis reveals digestive problems in most everyone today.  This is due to the volume of toxic chemicals we ingest with our food and drinks, added to the stress of modern living and the use of pharmaceuticals and over-the-counter drugs that interfere with digestion.  Low vitality also plays a part.

            Indicators for impaired digestion on a hair test may include:

1. A sodium/potassium ratio less than about 2.5:1.  The lower the ratio, often the worse the digestive strength or vitality.  For this reason, the ratio is called the vitality ratio.

2. A hair potassium level of 4 mg% or less.  This is called Sympathetic Dominance and implies that the sympathetic nervous system is overused.  This, in turn, usually impairs digestion a lot, even if there are no recognizable symptoms.

3. A hair zinc level less than about 12 mg%.  Zinc is needed to make most of the digestive enzymes.  A low hair zinc level is often associated with inadequate digestive enzyme production.

4. An elevated level of any of the toxic metals or poor eliminator patterns.  The presence of excessive toxic metals often interferes with proper digestion.  Many compete with zinc, for example, which is a critical element in the production of digestive enzymes.

Other possible indicators of impaired protein digestion and utilization are:

1. A phosphorus level of 12.  This is not the case, however, if a pubic hair sample is used as this may cause elevated phosphorus readings.

2. A copper level above 2.5 or a hidden copper toxicity pattern.  Read Copper Toxicity Syndrome for more information about hidden copper toxicity.

            I would say most if not all the clients who come for nutritional guidance have one or more of these digestive indicators.  This is why I suggest that all adults take a powerful digestive enzyme containing ox bile and pancreatin to assist with protein digestion.


Vicious cycles are what destroy our bodies.  Impaired protein digestion causes nutrient deficiencies and often bowel toxicity.  This further impairs protein digestion, which in turn worsens nutritional status and the cycle continues until death occurs. 

For this reason, I make a point of recommending only high quality protein in adequate quantity.  Also, it is why I suggest avoiding all drugs and food additives, if possible, and to have excellent eating habits.  It is also why I suggest plenty of rest, with some rest before and after meals as well.

All of this is often necessary to break the vicious cycle of poor protein digestion, a very essential body function.


            Digesting proteins, which is breaking them down into their respective amino acids, is only half the battle in the proper utilization of proteins.  The other half is rebuilding the amino acids into the thousands of hormones, enzymes, tissues and organs of our bodies.

            Here another vicious cycle needs to be stopped.  This is that poor nutrition in general impairs synthesis of proteins that are needed to digest and synthesize more proteins.  If this cycle persists for any length of time, chronic disease and death will ensue.

            Thus, improving the overall state of nutrition is paramount to assist proper protein synthesis.  This includes virtually all the minerals and vitamins.  Equally important is to rid the body of toxic substances such as cadmium, arsenic, lead and hundreds of toxic chemicals that interfere with proper protein synthesis.

The mineral zinc must be singled out as particularly important for protein synthesis.  It is required for the enzyme RNA transferase, a key step in protein synthesis.  However, in fact, many minerals and vitamins and other nutrients are required for this complex process of DNA synthesis.

Once again, most people are deficient in zinc, selenium, chromium, bioavailable manganese and other nutrients, so their synthesis of protein is quite impaired.  This slows all healing and all rebuilding of body tissue.

Protein and wound healing.  I am often amazed how quickly and easily people with wounds or surgical scars that won’t heal complete their healing when they follow a complete nutritional balancing program to improve their overall health.  This has a lot to do with protein digestion and protein synthesis.  Anyone with wounds, scars or other areas of the body that will not heal properly probably has problems with adequate protein synthesis.


            Meats.  In my clinical experience of more than 30 years, I find that quality meats are excellent foods for human beings.  Vegetarian diets are all deficient, and I have not found a way around it.  They will sustain a person for a while, and one may feel better on a vegetarian regimen that eliminates junk foods and allergic foods.  However, serious deficiencies will soon occur that always shorten life.

Meats can be an important source of zinc, B-vitamins, amino acids, taurine, carnitine, alpha-lipoic acid and many other nutrients provided the meat is eaten in moderation, and in the correct food combinations.  Naturally raised meats are best.  Grass-fed and free range animals are often an excellent source of omega-3 fatty acids.

Meats from animals raised without hormones and antibiotics are higher quality and to be preferred.  Lamb is one of the best and can be eaten several times a week.  Most lamb is naturally raised, by the way.  I do not think it is necessary to buy “organically raised” lamb.  Chicken, turkey and wild game are also excellent protein foods, along with up to 10 eggs per week.

Beef is okay if raised naturally, but less recommended simply because most of it is quite hybridized.  This means it is not the same animal as it was 50 years ago.  This is somewhat a problem with all our livestock, but beef most of all.  Beef has become quite a bit more irritating to the body, as a result, and some people are quite sensitive or intolerant of it.  This does not seem to occur with lamb or wild game, however.

Pork, ham, bacon and all pig products should be totally avoided in any form, as they may contain trichina cysts and other parasites, even when supposedly properly cooked.

Also avoid all processed meats, in general, as they contain many additives such as nitrites and nitrates that are quite toxic for some people.  A little should be okay if it is all natural, such as natural hot dogs, for example, although these are made from beef, which is not the best.

Fresh meats are best.  Frozen chicken and turkey is okay.  Canned meats are usually loaded with additives to preserve them.  Dried “jerky” is not bad unless it is full of additives, as it usually is.  Smoked meats and fish are not quite as healthful, but may be eaten at times.

            Eggs.   The most maligned protein food is the egg.  Eggs contain excellent quality protein as well as lecithin, vitamin A and many other nutrients. 

The famous Framingham, Massachusetts heart disease study examined the question of egg consumption.  The study found those who regularly consumed eggs lived longer than those who ate eggs only occasionally.  Especially for those who prefer to eat less meat, eggs are an essential source of high-quality protein. 

How many eggs?  Women can have up to six eggs per week, and no more.  Men can have up to eight eggs per week, but not more.  Eating more than this causes some liver toxicity.

Preferably rotate them (and all foods) by having them no more than every other day.  Fresh is always best with eggs.  Right from the chicken is wonderful, and not too difficult in some places if you ask people who has chickens.

Eggs and meats should not be overcooked.  Eggs must be cooked, but the yolks should be runny.  They can be soft boiled, poached, lightly fried or mushy scrambled.  Do not eat hard-cooked eggs, as they are much harder to digest.

            Avoid processed eggs like Egg Beaters and others.  These may contain oxidized cholesterol, which is toxic.  To learn more about eggs and cholesterol, read Cholesterolphobia.

            Milk and Cheese.  Milk is a high-quality protein food.  However, most people are allergic to the milk from hybrid cows.  Organic milk is better in most cases, although hybridized milking cows are still used. 

Goat and sheep milks are excellent, and often better than cows milk.  Many goats and sheep are healthier than some cows, and are less hybridized than cows.  Organically raised is best.  Limit milk and all dairy intake to about 4 ounces daily for adults and a little less for children.  This is important, in part because milk is very yin in macrobiotic terms.  It is also not a particularly mineral-rich food.  It is best taken alone, and not as part of a meal, because of its watery nature. 

Natural, organic and preferably raw cheese can be a quality product unless one is sensitive to it.

Plain or vanilla yogurt or kefir is also excellent unless one is sensitive to it.  However, only have about 4 ounces daily, please.  Avoid sugary yogurt or kefir products.

If a person follows a complete nutritional balancing program, sensitivities to dairy and other quality foods tend to disappear as the gut rebuilds, although this will often take several years.

The common property of all proteins is that they consist of long chains of α-amino (alpha amino) acids. The general structure of α-amino acids is shown in . The α-amino acids are so called because the α-carbon atom in the molecule carries an amino group (−NH2); the α-carbon atom also carries a carboxyl group (−COOH).

In acidic solutions, when the pH is less than 4, the −COO groups combine with hydrogen ions (H+) and are thus converted into the uncharged form (−COOH). In alkaline solutions, at pH above 9, the ammonium groups (−NH+3) lose a hydrogen ion and are converted into amino groups (−NH2). In the pH range between 4 and 8, amino acids carry both a positive and a negative charge and therefore do not migrate in an electrical field. Such structures have been designated as dipolar ions, or zwitterions (i.e., hybrid ions).

Although more than 100 amino acids occur in nature, particularly in plants, only 20 types are commonly found in most proteins. In protein molecules the α-amino acids are linked to each other by peptidebonds between the amino group of one amino acid and the carboxyl group of its neighbour.

The condensation (joining) of three amino acids yields the tripeptide.

It is customary to write the structure of peptides in such a way that the free α-amino group (also called the N terminus of the peptide) is at the left side and the free carboxyl group (the C terminus) at the right side. Proteins are macromolecular polypeptides—i.e., very large molecules composed of many peptide-bonded amino acids. Most of the common ones contain more than 100 amino acids linked to each other in a long peptide chain. The average molecular weight (based on the weight of a hydrogen atom as 1) of each amino acid is approximately 100 to 125; thus, the molecular weights of proteins are usually in the range of 10,000 to 100,000 daltons (one dalton is the weight of one hydrogen atom). The species-specificity and organ-specificity of proteins result from differences in the number and sequences of amino acids. Twenty different amino acids in a chain 100 amino acids long can be arranged in far more than 10100 ways (10100 is the number one followed by 100 zeroes).

Structures of common amino acids

The amino acids present in proteins differ from each other in the structure of their side (R) chains. The simplest amino acid is glycine, in which R is a hydrogen atom. In a number of amino acids, R represents straight or branched carbon chains. One of these amino acids is alanine, in which R is the methyl group (−CH3). Valine, leucine, and isoleucine, with longer R groups, complete the alkyl side-chain series. The alkyl side chains (R groups) of these amino acids are nonpolar; this means that they have no affinity for water but some affinity for each other. Although plants can form all of the alkyl amino acids, animals can synthesize only alanine and glycine; thus valine, leucine, and isoleucine must be supplied in the diet.

Two amino acids, each containing three carbon atoms, are derived from alanine; they are serine and cysteine. Serine contains an alcohol group (−CH2OH) instead of the methyl group of alanine, and cysteine contains a mercapto group (−CH2SH). Animals can synthesize serine but not cysteine or cystine. Cysteine occurs in proteins predominantly in its oxidized form (oxidation in this sense meaning the removal of hydrogen atoms), called cystine. Cystine consists of two cysteine molecules linked by the disulfide bond (−S−S−) that results when a hydrogen atom is removed from the mercapto group of each of the cysteines. Disulfide bonds are important in protein structure because they allow the linkage of two different parts of a protein molecule to—and thus the formation of loops in—the otherwise straight chains. Some proteins contain small amounts of cysteine with free sulfhydryl (−SH) groups.

Four amino acids, each consisting of four carbon atoms, occur in proteins; they are aspartic acid, asparagine, threonine, and methionine. Aspartic acid and asparagine, which occur in large amounts, can be synthesized by animals. Threonine and methionine cannot be synthesized and thus are essential amino acids; i.e., they must be supplied in the diet. Most proteins contain only small amounts of methionine.

Proteins also contain an amino acid with five carbon atoms (glutamic acid) and a secondary amine (in proline), which is a structure with the amino group (−NH2) bonded to the alkyl side chain, forming a ring. Glutamic acid and aspartic acid are dicarboxylic acids; that is, they have two carboxyl groups (−COOH).

Glutamine is similar to asparagine in that both are the amides of their corresponding dicarboxylic acid forms; i.e., they have an amide group (−CONH2) in place of the carboxyl (−COOH) of the side chain. Glutamic acid and glutamine are abundant in most proteins; e.g., in plant proteins they sometimes comprise more than one-third of the amino acids present. Both glutamic acid and glutamine can be synthesized by animals.

Amino acid content of some proteins
aspartic acid**
glutamic acid**153.1311.0144.976.299.0155
total839 765 883 1,058 863 832
average residual weight119 131 113 95 117 120

The amino acids proline and hydroxyproline occur in large amounts in collagen, the protein of the connective tissue of animals. Proline and hydroxyproline lack free amino (−NH2) groups because the amino group is enclosed in a ring structure with the side chain; they thus cannot exist in a zwitterion form. Although the nitrogen-containing group (>NH) of these amino acids can form a peptide bond with the carboxyl group of another amino acid, the bond so formed gives rise to a kink in the peptide chain; i.e., the ring structure alters the regular bond angle of normal peptide bonds.

Proteins usually are almost neutral molecules; that is, they have neither acidic nor basic properties. This means that the acidic carboxyl ( −COO) groups of aspartic and glutamic acid are about equal in number to the amino acids with basic side chains. Three such basic amino acids, each containing six carbon atoms, occur in proteins. The one with the simplest structure, lysine, is synthesized by plants but not by animals. Even some plants have a low lysine content. Arginine is found in all proteins; it occurs in particularly high amounts in the strongly basic protamines (simple proteins composed of relatively few amino acids) of fish sperm. The third basic amino acid is histidine. Both arginine and histidine can be synthesized by animals. Histidine is a weaker base than either lysine or arginine. The imidazole ring, a five-membered ring structure containing two nitrogen atoms in the side chain of histidine, acts as a buffer (i.e., a stabilizer of hydrogen ion concentration) by binding hydrogen ions (H+) to the nitrogen atoms of the imidazole ring.

The remaining amino acids—phenylalanine, tyrosine, and tryptophan—have in common an aromatic structure; i.e., a benzene ring is present. These three amino acids are essential, and, while animals cannot synthesize the benzene ring itself, they can convert phenylalanine to tyrosine.

Because these amino acids contain benzene rings, they can absorb ultraviolet light at wavelengths between 270 and 290 nanometres (nm; 1 nanometre = 10−9 metre = 10 angstrom units). Phenylalanine absorbs very little ultraviolet light; tyrosine and tryptophan, however, absorb it strongly and are responsible for the absorption band most proteins exhibit at 280–290 nanometres. This absorption is often used to determine the quantity of protein present in protein samples.

Most proteins contain only the amino acids described above; however, other amino acids occur in proteins in small amounts. For example, the collagen found in connective tissue contains, in addition to hydroxyproline, small amounts of hydroxylysine. Other proteins contain some monomethyl-, dimethyl-, or trimethyllysine—i.e., lysine derivatives containing one, two, or three methyl groups (−CH3). The amount of these unusual amino acids in proteins, however, rarely exceeds 1 or 2 percent of the total amino acids.

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