Primer on Amino Acids

4. Primer on Amino Acids in Protein Synthesis Related to Evolutionary Theory
& Natural Selection
George A. Scheele, M.D.
December 15, 2015



Dr. Scheele has discovered new relationships between (i) Evolution, (ii) Natural Selection and (iii) Metabolic Health. The new discoveries are compatible with the theories of Evolution, Natural Selection through survival of the fittest, and the importance of essential amino acids in fitness, metabolic health and longevity. This innovative effort establishes a new field of dietary genomics and proteomics capable of defining a new field of nutritional pathology, which we intend to call the “Nutritional Pathosome.”


In the human body amino acids form peptides, polypeptide chains and proteins used by the body for a number of structures and functions. Out of the 20 amino acids necessary for protein synthesis, only five are made in the body and therefore are non-essential in the diet. Among the 15 that are essential in the diet, 6 are conditionally essential, meaning that their synthesis in the body is compromised by poor nutritional conditions. The rest (n=9) are wholly essential, meaning they must, under all circumstances, be obtained from the diet.

These three groups of amino acids are summarized in the Table below.

Essential (EAA)
The human body cannot make these amino acids
Semi-Essential (SEAA)
The ability to make these amino acids is compromised under conditions of poor
nutritious diets
Non-Essential (NEAA)
The human body can make these amino acids
Leucine Tyrosine Asparagine
Isoleucine Glycine Aspartate
Valine Cysteine Glutamate
Lysine Proline Alanine
Threonine Glutamine Serine
Methionine Arginine
  • Plants, bacteria and yeast make all 20 amino acids.
  • Arginine is considered “essential” for some infants, but not for adults.

While most of the amino acids are hydrophobic, four are considered hydrophilic. Two of these, Aspartate and Glutamate are negatively charged and two, Lysine and Arginine, are positively charged under physiological conditions. The nomenclature for these charged amino acids are shown below according to their full name, three-letter code and one-letter code:

Full Name 3-Letter Code 1-Letter Code Charge
Lysine Lys K Positive
Arginine Arg R Positive
Aspartate Asp D Negative
Glutamate Glu E Negative

Proteins derive their function from their folded structures which act as structural components or enzymes. The charged amino acids are found on the surface of these folded structures, which allows them to remain soluble in aqueous solutions. In addition to their specific binding functions to other molecules, proteins may bind electrostatically through charge interactions between positive and negative elements in the human body.

When proteins are separated by Two-Dimensional Gel Electrophoresis they are separated in the first dimension according to their charge and in the second dimension according to their size. The charge of individual proteins is expressed in their isoelectric point (pI) according to a summation of all charged amino acid residues within the protein. Thus anionic proteins with a preponderance of negative charged amino acids (D+E > K+R) show isoelectric points between 3.0 and 7.0. And cationic proteins with a preponderance of positive-charged amino acids (K+R > D+E) show isoelectric points between 7.0 and 11.5.


Whereas plants, bacteria and yeast synthesize all 20 of the amino acids required for protein synthesis, higher forms of life (vertebrates, mammals and humans) cannot synthesize 9 amino acids (essential amino acids) and have difficulty in synthesizing 6 amino acids (conditionally essential amino acids) but do synthesize the remaining 5 amino acids.

The restrictions in synthesis of amino acids in higher life forms have several natural correlations that have not been previously recognized in evolutionary thought or theory. In its simplest form, we not only have species that are slowly evolving to promote food intake and procreation which are prime forces sensitive to natural selection and species survival, but the necessity of finding foods rich in R & K means that natural selection occurs at the level of amino acid composition between individual proteins in higher organisms

These considerations may explain most of the chronic degenerative diseases (metabolic diseases) present in both animals and humans. See Evolutionary Theory and the Biology of Chronic Degenerative Disease and Aging (Article Number 3)


Based on his 5 year voyage on the Beagle from 1831 to 1836, Charles Darwin published “The Origen of Species” in 1859. From Darwin’s extensive observations on biological variations within and among species during his trip around South America, he deduced that the number of species on earth was not a fixed number, but that biological variation and speciation were a continuing phenomenon throughout biology. He further deduced that variations in traits observed in nature is a dynamic process that continues as a function of evolutionary time. When submitted to Natural Selection, Sexual Selection and even Group Selection, these variations aggregate in groups that form distinct species isolated by restrictions in sexual reproduction. Thus the development of new species occurs according to variations in traits followed by natural selection, a chance process, rather than by purposeful design.

Later scientific work, notably Mendel’s Genetics and the elucidation of the structure of DNA, RNA and proteins, as well as sequencing the human genome in 2000, provided much of the physical basis of Darwin’s theories on natural selection and evolution among species. But in the 19th century Darwin did not understand the structural features of proteins or the amino acids that give rise to protein structures, including the infinity of shapes that allow proteins to recognize one-another by “lock & key” mechanisms as well as other building blocks in nature such as molecular forms of carbohydrates and fat.

In the area of nutrition Darwin did not understand that 20 amino acids are required for the great diversity of life forms on planet earth. He did not understand that while plants, bacteria and yeast produce (synthesize) all 20 forms of nutritional amino acids, higher animals (vertebrates, mammals and humans) only make 5 of these amino acids. Higher animals can conditionally make another 6 amino acids (semi-essential amino acids) and under no circumstances can they make nine of the necessary amino acids (essential amino acids). To this day no one has explained why higher animals, including humans cannot make, under all conditions, 15 of the amino acids that it needs to remain healthy every minute of the day and night.

Dr. Scheele was the first to propose that the evolutionary development of advanced muscular-skeletal systems which conferred the advantages of advanced mobilities and predatory behaviors, necessitated the development of strong hunger and satiety signals, tethered to the absence and presence of essential amino acids, respectively, in the blood stream. In order to amplify these hunger signals during the long process in the evolution of higher animals they lost the ability to make (synthesize) essential amino acids but made up for this loss by gaining the advantage of increasing the acquisition of amino acids from the environment through predator capabilities that moved large amounts of essential amino acids up the food chain. These reciprocal evolutionary developments eventually allowed higher animals, including humans to advance far beyond other life forms on earth.

These predatory behaviors included foraging for primitive vegetables, grains and oils to obtain carbohydrates, fat and protein but involved the killing of animals, fish and birds to obtain adequate quantities of amino acids to build advanced protein structures. Hence food chain signals lead to hunger and satiety and, over longer periods of time, hunger and satiety correspond with sickness and health, respectively.

Dr. Scheele has also proposed that chronic degenerative diseases may be due, in large part, to the loss of positive-charged proteins in the organism (Selective Protein Deficiency Syndrome) due to an insufficient supply of positive-charged and essential amino acids in the diet. The acquisition of all 9 of the essential amino acids and all 6 of the semi-essential amino acids is not only required for health but is essential for procreation, including copulation, fertilization, pregnancy, breast feeding, and child development. At later stages in life, the acquisition of these essential and semi-essential amino acids is further necessary to optimize human productivity, achievement and longevity.

According to Dr. Scheele, the Origen of Species as well as the Origen of Health in all these developmental stages depend primarily on the acquisition of all 20 amino acids, including the essential amino acids that are not made in the body.

Today, in the great Halls of Medicine around the world, there is little if any appreciation of these basic nutritional facts, which include an appreciation of the fact that during evolution the development of muscles that provide movement and predatory behaviors in higher animals required that higher animals lose the ability to make essential amino acids that signal satiety and hunger to the organism. In this case satiety is signaled by an abundance of essential amino and hunger is signaled by an absence of essential amino acids in the food chain. The presence and absence of essential amino acids in the food chain signals satiety and hunger, respectively, to the Appetite Center of the brain, known as the Arcuate Nucleus found in the Hypothalamus.

Dr. Scheele’s work which correlates the absence and presence of positive-charged proteins with hunger and satiety and sickness and health (see Evolution Theory and the Biology of Chronic Degenerative Disease and Aging, Article Number 3) is an enormous breakthrough in understanding the evolution of nutrition in defining health and disease.

Footnotes: Other aspects of evolutionary theory have correlated the massive increase in the size of the human brain with eating meat, the invention of fire and an increase in carbohydrate intake as follows. Roughly seven million years ago our ancestors split off from apes. About 5 million years ago Hominins started eating meat and campfires appeared about 1.8 million years ago. About 800,000 years ago the fossil records show a drastic acceleration in the size of the Hominin brain. Between 28,000 and 10,000 years ago, the agricultural revolution allowed humans to harvest large amounts of grain for the benefit of human evolution.

It appears that the invention of fire, which allowed for cooking of meat, increased the flow of essential amino acids up the human food chain. However, along the way gene duplication events also increased the number of Amylase gene copies from 2 in apes to 18 in humans. Amylase is the enzyme that digests carbohydrate to sugar, which is essential for optimal brain activity. Today our outsized brains use up to a quarter of the calories we burn throughout the body. In summary, it appears that an increase in amino acid levels as well as sugar levels in the human food chain allowed for the enormous expansion of human brain capacity and the higher intelligence quotients observed in human beings. On the downside, the increase in copies of the Amylase gene have led to a predisposition toward high sugar levels and type-2 diabetes under conditions where carbohydrates and sugars dominate the diet.

Still other aspects of evolutionary theory have correlated the evolutionary appearance of digits after our first four-legged ancestors came out of the sea some 350 million years ago with man’s ability to build hunting tools and societal structures. The appearance of digits (fingers and toes) on each of the limbs and particularly the appearance of the opposable thumb in Hominins allowed humans to build the impressive societies that we live in today. Yet these societies must always pay attention to the flow of essential amino acids in the human food chain to optimize the preservation of the great societies that human beings have built.

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