amino acid

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Concept

Amino acids are organic compounds made of carbon, hydrogen, oxygen, nitrogen, and (in some cases) sulfur bonded in characteristic formations. Strings of amino acids make up proteins, of which there are countless varieties. Of the 20 amino acids required for manufacturing the proteins the human body needs, the body itself produces only 12, meaning that we have to meet our requirements for the other eight through nutrition. This is just one example of the importance of amino acids in the functioning of life. Another cautionary illustration of amino acids' power is the gamut of diseases (most notably, sickle cell anemia) that impair or claim the lives of those whose amino acids are out of sequence or malfunctioning. Once used in dating objects from the distant past, amino acids have existed on Earth for at least three billion years—long before the appearance of the first true organisms.

How It Works

A "map" of Amino Acids

Amino acids are organic compounds, meaning that they contain carbon and hydrogen bonded to each other. In addition to those two elements, they include nitrogen, oxygen, and, in a few cases, sulfur. The basic structure of an amino-acid molecule consists of a carbon atom bonded to an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and a fourth group that differs from one amino acid to another and often is referred to as the-R group or the side chain. The-R group, which can vary widely, is responsible for the differences in chemical properties.

This explanation sounds a bit technical and requires a background in chemistry that is beyond the scope of this essay, but let us simplify it somewhat. Imagine that the amino-acid molecule is like the face of a compass, with a carbon atom at the center. Raying out from the center, in the four directions of the compass, are lines representing chemical bonds to other atoms or groups of atoms. These directions are based on models that typically are used to represent amino-acid molecules, though north, south, east, and west, as used in the following illustration, are simply terms to make the molecule easier to visualize.

To the south of the carbon atom (C) is a hydrogen atom (H), which, like all the other atoms or groups, is joined to the carbon center by a chemical bond. To the north of the carbon center is what is known as an amino group (-NH₂). The hyphen at the beginning indicates that such a group does not usually stand alone but normally is attached to some other atom or group. To the east is a carboxyl group, represented as-COOH. In the amino group, two hydrogen atoms are bonded to each other and then to nitrogen, whereas the carboxyl group has two separate oxygen atoms strung between a carbon atom and a hydrogen atom. Hence, they are not represented as O₂.

Finally, off to the west is the R-group, which can vary widely. It is as though the other portions of the amino acid together formed a standard suffix in the English language, such as -tion. To the front of that suffix can be attached all sorts of terms drawn from root words, such as educate or satisfy or revolt—hence, education, satisfaction, and revolution. The variation in the terms attached to the front end is extremely broad, yet the tail end, -tion, is a single formation. Likewise the carbon, hydrogen, amino group, and carboxyl group in an amino acid are more or less constant.

A Few Additional Points

The name amino acid, in fact, comes from the amino group and the acid group, which are the most chemically reactive parts of the molecule. Each of the common amino acids has, in addition to its chemical name, a more familiar name and a three-letter abbreviation that frequently is used to identify it. In the present context, we are not concerned with these abbreviations. Amino-acid molecules, which contain an amino group and a carboxyl group, do not behave like typical molecules. Instead of melting at temperatures hotter than 392°F (200°C), they simply decompose. They are quite soluble, or capable of being dissolved, in water but are insoluble in nonpolar solvents (oil-and all oil-based products), such as benzene or ether.

Right-Hand and Left-Hand Versions

All of the amino acids in the human body, except glycine, are either right-hand or left-hand versions of the same molecule, meaning that in some amino acids the positions of the carboxyl group and the R-group are switched. Interestingly, nearly all of the amino acids occurring in nature are the left-hand versions of the molecules, or the L-forms. (There-fore, the model we have described is actually the left-hand model, though the distinctions between "right" and "left"—which involve the direction in which light is polarized—are too complex to discuss here.)

Right-hand versions (D-forms) are not found in the proteins of higher organisms, but they are present in some lower forms of life, such as in the cell walls of bacteria. They also are found in some antibiotics, among them, streptomycin, actinomycin, bacitracin, and tetracycline. These antibiotics, several of which are well known to the public at large, can kill bacterial cells by interfering with the formation of proteins necessary for maintaining life and for reproducing.

Amino Acids and Proteins

A chemical reaction that is characteristic of amino acids involves the formation of a bond, called a peptide linkage, between the carboxyl group of one amino acid and the amino group of a second amino acid. Very long chains of amino acids can bond together in this way to form proteins, which are the basic building blocks of all living things. The specific properties of each kind of protein are largely dependent on the kind and sequence of the amino acids in it. Other aspects of the chemical behavior of protein molecules are due to interactions between the amino and the carboxyl groups or between the various R-groups along the long chains of amino acids in the molecule.

Numbers and Combinations

Amino acids function as monomers, or individual units, that join together to form large, chainlike molecules called polymers, which may contain as few as two or as many as 3,000 amino-acid units. Groups of only two amino acids are called dipeptides, whereas three amino acids bonded together are called tripeptides. If there are more than 10 in a chain, they are termed polypeptides, and if there are 50 or more, these are known as proteins.

All the millions of different proteins in living things are formed by the bonding of only 20 amino acids to make up long polymer chains. Like the 26 letters of the alphabet that join together to form different words, depending on which letters are used and in which sequence, the 20 amino acids can join together in different combinations and series to form proteins. But whereas words usually have only about 10 or fewer letters, proteins typically are made from as few as 50 to as many as 3,000 amino acids. Because each amino acid can be used many times along the chain and because there are no restrictions on the length of the chain, the number of possible combinations for the formation of proteins is truly enormous. There are about two quadrillion different proteins that can exist if each of the 20 amino acids present in humans is used only once. Just as not all sequences of letters make sense, however, not all sequences of amino acids produce functioning proteins. Some other sequences can function and yet cause undesirable effects, as we shall see.

Real-Life Applications

DNA (deoxyribonucleic acid), a molecule in all cells that contains genetic codes for inheritance, creates encoded instructions for the synthesis of amino acids. In 1986, American medical scientist Thaddeus R. Dryja (1940-) used amino-acid sequences to identify and isolate the gene for a type of cancer known as retinoblastoma, a fact that illustrates the importance of amino acids in the body.

Amino acids are also present in hormones, chemicals that are essential to life. Among these hormones is insulin, which regulates sugar levels in the blood and without which a person would die. Another is adrenaline, which controls blood pressure and gives animals a sudden jolt of energy needed in a high-stress situation—running from a predator in the grasslands or (to a use a human example) facing a mugger in an alley or a bully on a playground. Biochemical studies of amino-acid sequences in hormones have made it possible for scientists to isolate and produce artificially these and other hormones, including the human growth hormone.

Amino Acids and Nutrition

Just as proteins form when amino acids bond together in long chains, they can be broken down by a reaction called hydrolysis, the reverse of the formation of the peptide bond. That is exactly what happens in the process of digestion, when special digestive enzymes in the stomach enable the breaking down of the peptide linkage. (Enzymes are a type of protein—see Enzymes.) The amino acids, separated once again, are released into the small intestine, from whence they pass into the bloodstream and are carried throughout the organism. Each individual cell of the organism then can use these amino acids to assemble the new and different proteins required for its specific functions. Life thus is an ongoing cycle in which proteins are broken into individual amino-acid units, and new proteins are built up from these amino acids.

Essential Amino Acids

Out of the many thousands of possible amino acids, humans require only 20 different kinds. Two others appear in the bodies of some animal species, and approximately 100 others can be found in plants. Considering the vast numbers of amino acids and possible combinations that exist in nature, the number of amino acids essential to life is extremely small. Yet of the 20 amino acids required by humans for making protein, only 12 can be produced within the body, whereas the other eight—isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine—must be obtained from the diet. (In addition, adults are capable of synthesizing arginine and histidine, but these amino acids are believed to be essential to growing children, meaning that children cannot produce them on their own.)

A complete protein is one that contains all of the essential amino acids in quantities sufficient for growth and repair of body tissue. Most proteins from animal sources, gelatin being the only exception, contain all the essential amino acids and are therefore considered complete proteins. On the other hand, many plant proteins do not contain all of the essential amino acids. For example, lysine is absent from corn, rice, and wheat, whereas corn also lacks tryptophan and rice lacks threonine. Soybeans are lacking in methionine. Vegans, or vegetarians who consume no animal proteins in their diets (i.e., no eggs, dairy products, or the like) are at risk of malnutrition, because they may fail to assimilate one or more essential amino acid.

Amino Acids, Health, and Disease

Amino acids can be used as treatments for all sorts of medical conditions. For example, tyrosine may be employed in the treatment of Alzheimer's disease, a condition characterized by the onset of dementia, or mental deterioration, as well as for alcohol-withdrawal symptoms. Taurine is administered to control epileptic seizures, treat high blood pressure and diabetes, and support the functioning of the liver. Numerous other amino acids are used in treating a wide array of other diseases. Sometimes the disease itself involves a problem with amino-acid production or functioning. In the essay Vitamins, there is a discussion of pellagra, a disease resulting from a deficiency of the B-group vitamin known as niacin. Pellagra results from a diet heavy in corn, which, as we have noted, lacks lysine and tryptophan. Its symptoms often are described as the "three Ds": diarrhea, dermatitis (or skin inflammation), and dementia. Thanks to a greater understanding of nutrition and health, pellagra has been largely eradicated, but there still exists a condition with almost identical symptoms: Hartnup disease, a genetic disorder named for a British family in the late 1950s who suffered from it.

Hartnup disease is characterized by an inability to transport amino acids from the kidneys to the rest of the body. The symptoms at first seemed to suggest to physicians that the disease, which is present in one of about 26,000 live births, was pellagra. Tests showed that sufferers did not have inadequate tryptophan levels, however, as would have been the case with pellagra. On the other hand, some 14 amino acids have been found in excess within the urine of Hartnup disease sufferers, indicating that rather than properly transporting amino acids, their bodies are simply excreting them. This is a potentially very serious condition, but it can be treated with the B vitamin nicotinamide, also used to treat pellagra. Supplementation of tryptophan in the diet also has shown positive results with some patients.

Sickle Cell Anemia

It is also possible for small mistakes to occur in the amino-acid sequence within the body. While these mistakes sometimes can be tolerated in nature without serious problems, at other times a single misplaced amino acid in the polymer chain can bring about an extremely serious condition of protein malfunctioning. An example of this is sickle cell anemia, a fatal disease ultimately caused by a single mistake in the amino acid sequence. In the bodies of sickle cell anemia sufferers, who are typically natives of sub-Saharan Africa or their descendants in the United States or elsewhere, glutamic acid is replaced by valine at the sixth position from the end of the protein chain in the hemoglobin molecule. (Hemoglobin is an iron-containing pigment in red blood cells that is responsible for transporting oxygen to the tissues and removing carbon dioxide from them.) This small difference makes sickle cell hemoglobin molecules extremely sensitive to oxygen deficiencies. As a result, when the red blood cells release their oxygen to the tissues, as all red blood cells do, they fail to re-oxygenate in a normal fashion and instead twist into the shape that gives sickle cell anemia its name. This causes obstruction of the blood vessels. Before the development of a treatment with the drug hydroxyurea in the mid-1990s, the average life expectancy of a person with sickle cell anemia was about 45 years.

Amino Acids and the Distant Past

The Evolution essay discusses several types of dating, a term referring to scientific efforts directed toward finding the age of a particular item or phenomenon. Methods of dating are either relative (i.e., comparative and usually based on rock strata, or layers) or absolute. Whereas relative dating does not involve actual estimates of age in years, absolute dating does. One of the first types of absolute-dating techniques developed was amino-acid racimization, introduced in the 1960s. As noted earlier, there are "left-hand" L-forms and "right-hand" D-forms of all amino acids. Virtually all living organisms (except some microbes) incorporate only the L-forms, but once the organism dies, the L-amino acids gradually convert to the mirror-image D-amino acids.

Numerous factors influence the rate of conversion, and though amino-acid racimization was popular as a form of dating in the 1970s, there are problems with it. For instance, the process occurs at different rates for different amino acids, and the rates are further affected by such factors as moisture and temperature. Because of the uncertainties with amino-acid racimization, it has been largely replaced by other absolute-dating methods, such as the use of radioactive isotopes.

Certainly, amino acids themselves have offered important keys to understanding the planet's distant past. The discovery, in 1967 and 1968, of sedimentary rocks bearing traces of amino acids as much as three billion years old had an enormous impact on the study of Earth's biological history. Here, for the first time, was concrete evidence of life—at least, in a very simple chemical form—existing billions of years before the first true organism. The discovery of these amino-acid samples greatly influenced scientists' thinking about evolution, particularly the very early stages in which the chemical foundations of life were established.

Where to Learn More

"Amino Acids." Institute of Chemistry, Department of Biology, Chemistry, and Pharmacy, Freie Universität, Berlin (Web site). <http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids_en.html>.

Goodsell, David S. Our Molecular Nature: The Body's Motors, Machines, and Messages. New York: Copernicus, 1996.

"Introduction to Amino Acids." Department of Crystallography, Birbeck College (Web site). <http://www.cryst.bbk.ac.uk/education/AminoAcid/overview.html>.

Michal, Gerhard. Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology. New York: John Wiley and Sons, 1999.

Newstrom, Harvey. Nutrients Catalog: Vitamins, Minerals, Amino Acids, Macronutrients—Beneficial Use, Helpers, Inhibitors, Food Sources, Intake Recommendations, and Symptoms of Over or Under Use. Jefferson, NC: McFarland and Company, 1993.

Ornstein, Robert E., and Charles Swencionis. The Healing Brain: A Scientific Reader. New York: Guilford Press, 1990.

Reference Guide for Amino Acids (Web site). <http://www.realtime.net/anr/aminoacd.html#tryptophn>.

Silverstein, Alvin, Virginia B. Silverstein, and Robert A. Silverstein. Proteins. Illus. Anne Canevari Green. Brookfield, CT: Millbrook Press, 1992.

Springer Link: Amino Acids (Web site). <http://link.springer.de/link/service/journals/00726/>.

Organic compounds possessing one or more basic amino groups and one or more acidic carboxyl groups. Of the more than 80 amino acids which have been found in living organisms, about 20 serve as the building blocks for the proteins.

All the amino acids of proteins, and most of the others which occur naturally, are α-amino acids, meaning that an amino group (NH₂) and a carboxyl group (COOH) are attached to the same carbon atom. This carbon (the α carbon, being adjacent to the carboxyl group) also carries a hydrogen atom; its fourth valence is satisfied by any of a wide variety of substitutent groups, represented by the letter R in the structural formula below.

In the simplest amino acid, glycine, R is a hydrogen atom. In all other amino acids, R is an organic radical; for example, in alanine it is a methyl group (CH₃), while in glutamic acid it is an aliphatic chain terminating in a second carboxyl group (CH₂CHCOOH). Chemically, the amino acids can be considered as falling roughly into nine categories based on the nature of R (see table).

*See articles on the individual amino acids listed in the table.

Occurrence

Amino acids occur in living tissues principally in the conjugated form. Most conjugated amino acids are peptides, in which the amino group of one amino acid is linked to the carboxyl group of another. Amino acids are capable of linking together to form chains of various lengths, called polypeptides. Proteins are polypeptides ranging in size from about 50 to many thousand amino acid residues. Although most of the conjugated amino acids in nature are proteins, numerous smaller conjugates occur naturally, many with important biological activity. The line between large peptides and small proteins is difficult to draw, with insulin (molecular weight = 7000; 50 amino acids) usually being considered a small protein and adrenocorticotropic hormone (molecular weight = 5000; 39 amino acids) being considered a large peptide.

Free amino acids are found in living cells, as well as the body fluids of higher animals, in amounts which vary according to the tissue and to the amino acid. The amino acids which play key roles in the incorporation and transfer of ammonia, such as glutamic acid, aspartic acid, and their amides, are often present in relatively high amounts, but the concentrations of the other amino acids of proteins are extremely low, ranging from a fraction of a milligram to several milligrams per 100 g wet weight of tissue. The presence of free amino acids in only trace amounts points to the existence of extraordinarily efficient regulation mechanisms. Each amino acid is ordinarily synthesized at precisely the rate needed for protein synthesis.

General properties

The amino acids are characterized physically by the following: (1) the pK₁, or the dissociation constant of the various titratable groups; (2) the isoelectric point, or pH at which a dipolar ion does not migrate in an electric field; (3) the optical rotation, or the rotation imparted to a beam of plane-polarized light (frequently the D line of the sodium spectrum) passing through 1 decimeter of a solution of 100 grams in 100 milliliters; and (4) solubility. See also Ionic equilibrium; Isoelectric point; Optical activity.

Since all of the amino acids except glycine possess a center of asymmetry at the α carbon atom, they can exist in either of two optically active, mirror-image forms, or enantiomorphs. All of the common amino acids of proteins appear to have the same configuration about the α carbon; this configuration is symbolized by the prefix L-. The opposite, generally unnatural, form is given the prefix D-. Some amino acids, such as isoleucine, threonine, and hydroxyproline, have a second center of asymmetry and can exist in four stereoisomeric forms. See also Stereochemistry.

At ordinary temperatures, the amino acids are white crystalline solids; when heated to high temperatures, they decompose rather than melt. They are stable in aqueous solution, and with few exceptions can be heated as high as 120°C (248°F) for short periods without decomposition, even in acid or alkaline solution. Thus, the hydrolysis of proteins can be carried out under such conditions with the complete recovery of most of the constituent free amino acids.

Biosynthesis

Since amino acids, as precursors of proteins, are essential to all organisms, all cells must be able to synthesize those they cannot obtain from their environment. The selective advantage of being able rapidly to shift from endogenous to exogenous sources of these compounds has led to the evolution of very complex and precise methods of adjusting the rate of synthesis to the available level of the compound. An immediately effective control is that of feedback inhibition. The biosynthesis of amino acids usually requires at least three enzymatic steps. In most cases so far examined, the amino acid end product of the biosynthetic pathway inhibits the first enzyme to catalyze a reaction specific to the biosynthesis of that amino acid. This inhibition is extremely specific; the enzymes involved have special sites for binding the inhibitor. This inhibition functions to shut off the pathway in the presence of transient high levels of the product, thus saving both carbon and energy for other biosynthetic reactions. When the level of the product decreases, the pathway begins to function once more.

The metabolic pathways by which amino acids are synthesized generally are found to be the same in all living cells investigated, whether microbial or animal. Biosynthetic mechanisms thus appear to have developed soon after the origin of life and to have remained unchanged through the divergent evolution of modern organisms.

Biosynthetic pathway diagrams reveal only one quantitatively important reaction by which organic nitrogen enters the amino groups of amino acids: the reductive amination of α-ketoglutaric acid to glutamic acid by the enzyme glutamic acid dehydrogenase. All other amino acids are formed either by transamination (transfer of an amino group, ultimately from glutamic acid) or by a modification of an existing amino acid. An example of the former is the formation of valine by transfer of the amino group from glutamic acid to α-ketoisovaleric acid; an example of the latter is the reduction and cyclization of glutamic acid to form proline.

Importance in nutrition

The nutritional requirement for the amino acids of protein can vary from zero, in the case of an organism which synthesizes them all, to the complete list, in the case of an organism in which all the biosynthetic pathways are blocked. There are 8 or 10 amino acids required by certain mammals; most plants synthesize all of their amino acids, while microorganisms vary from types which synthesize all, to others (such as certain lactic acid bacteria) which require as many as 18 different amino acids.

Amino acids are the building blocks of proteins. They are so named because all have a basic amino group (-NH₂) and an acidic carboxyl group (-COOH). Peptides, polypeptides, and proteins are formed from strings of amino acids joined together by the formation of peptide bonds. All proteins are formed from combinations of only 20 different amino acids, whether the proteins derive from bacteria or from man.

Amino acids are described as essential or non-essential. The non-essential ones can be synthesized in the body but the essential amino acids are those which must be present in the diet (phenylalanine, valine, tryptophan, threonine, lysine, leucine, isoleucine, and methionine). If any one of these amino acids is missing from the diet then many proteins which include this essential component cannot be synthesized. Consequently many other amino acids cannot then be used; they are broken down (deaminated) and the nitrogen is excreted as urea and creatinine, leading to a negative nitrogen balance, as more nitrogen is excreted than is taken in as dietary protein.

The adult body cannot absorb whole proteins from the gut, although young babies are able to absorb antibodies, which are proteins, from mother's milk; this provides passive immunity for the first year or so of life. The digestive processes break down dietary protein to amino acids and small peptides (two or more linked amino acids). Carriers, specific for a single amino acid or a group of similar amino acids, are present in the cells lining the intestine and are responsible for the specific uptake into these cells. Some dipeptides (and maybe tripeptides) also have specialized carrier molecules for uptake in the intestine, and the final stage of their digestion to amino acids takes place in these epithelial cells themselves. Thence they move into the circulating blood; thus amino acids from the diet enter the body's amino acid pool, mixing with other amino acids derived from the breakdown of body proteins in the continual turnover associated with growth, repair, and renewal of tissues. Cells of the different tissues take up selectively from the blood whichever amino acids they need for synthesis of their own proteins. The circulating amino acids gained from digestion are in no great danger of excretion via the kidneys: they are filtered at the glomeruli but are mostly reabsorbed into the blood as they pass down the kidney tubules.

Finally, how is the dietary intake of protein linked to the need for amino acids, particularly the essential ones? The linkage need not be a strong one, as connections exist between the metabolism of amino acids and the metabolism of fats and carbohydrates. Further, there can be conversion of one amino acid to another, at least for the non-essential amino acids. These transamination reactions are common in tissues that have been damaged, as repair and resynthesis take place. Thus after a myocardial infarction the level of the relevant enzymes — transaminases — rises in the blood, and this measurement is used for diagnostic purposes. Excess amino acids are subject to oxidative deamination: the amino group is removed and excreted as nitrogen products and the residue converted either to a ketone body, called acetoacetic acid (one of the products also of fat metabolism), or to products readily converted to glucose. Amino acids are there-fore divided into ketogenic or gluconeogenic (conversion to glucose) types.

Nitrogen losses in the urine may be greater than the nitrogen intake in the diet (negative nitrogen balance) not only when the essential amino acids are missing, but also when the calorie intake is adequate but the overall protein content of the diet is too low; this occurs in kwashiorkor, common in poorly nourished children. If the diet is inadequate in calories as well as deficient in protein, body proteins are broken down to form glucose for energy. This can be prevented by giving glucose, which is thus said to be ‘protein-sparing’.

— Alan W. Cuthbert

See also peptides; proteins.

The basic units from which proteins are made. Chemically compounds with an amino group (-NH₂) and a carboxyl group (-COOH) attached to the same carbon atom.

Eleven of the amino acids involved in proteins can be synthesized in the body, and so are called non-essential or dispensable amino acids, since they do not have to be provided in the diet. They are alanine, arginine, aspartic acid, asparagine, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine.

Nine amino acids cannot be synthesized in the body at all and so must be provided in the diet; they are called the essential or indispensable amino acids—histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. In addition, arginine may be essential for infants, since their requirement is greater than their ability to synthesize it. Two of the non-essential amino acids are made in the body from essential amino acids: cysteine (and cystine) from methionine, and tyrosine from phenylalanine.

The limiting amino acid of a protein is that essential amino acid present in least amount relative to the requirement for that amino acid. The ratio between the amount of the limiting amino acid in a protein and the requirement for that amino acid provides a chemical estimation of the nutritional value (protein quality) of that protein, termed chemical score. Most cereal proteins are limited by lysine, and most animal and other vegetable proteins by the sum of methionine + cysteine (the sulphur amino acids). In whole diets it is usually the sulphur amino acids that are limiting.

A number of other amino acids also occur in proteins, including hydroxyproline, hydroxylysine, γ-carboxyglutamate and methylhistidine, but are nutritionally unimportant since they cannot be re-utilized for protein synthesis. Other amino acids occur as intermediates in metabolic pathways, but are not required for protein synthesis, and are nutritionally unimportant, although they may occur in foods. These include homocysteine, citrulline, and ornithine.

The amino acids can be classified by the chemical nature of the side-chain. Two are acidic: glutamic acid (glutamate) and aspartic acid (aspartate), with a carboxylic acid (—COOH) group in the side-chain. Three, lysine, arginine, and histidine, have basic side-chains. Three, phenylalanine, tyrosine, and tryptophan, have aromatic side-chains. Three, leucine, isoleucine, and valine, have a branched side-chain. These three have very similar metabolism, and a rare genetic disease affecting their metabolism results in maple syrup urine disease. Two, methionine and cysteine, contain sulphur in the side-chain; although cysteine is not an essential amino acid, it can only be synthesized from methionine, and it is conventional to consider the sum of methionine plus cysteine (the sulphur amino acids) in respect to protein quality.

An alternative classification of the amino acids is by their metabolic fate; whether they can be utilized for glucose synthesis or not. Those that can give rise to glucose are termed glucogenic (or sometimes antiketogenic); those that give rise to ketones or acetate when they are metabolized are termed ketogenic. Only leucine and lysine are purely ketogenic; isoleucine, phenylalanine, tyrosine, and tryptophan give rise to both ketogenic and glucogenic fragments; the remainder are purely glucogenic.

These are the chemicals which form the building blocks of protein. There are about 80 naturally occurring amino acids, but only about 20 are used in proteins. Some amino acids, the essential or indispensable amino acids, can be obtained only from the diet. The other amino acids can be synthesized in the body provided that the total intake of protein is adequate. Amino acids may be used as an energy source during endurance activities, but they probably supply no more than 10 per cent of the body's demands. Some amino acids (such as gamma-aminobutyric acid and glutamate) function as neurotransmitters, acting as chemical intermediaries during the transmission of nerve impulses.

ESSENTIAL AMINO ACIDS
• histidine
• isoleucine
• leucine
• lysine
• methionine
• phenylalanine
• threonine
• tryptophan
• valine

NON-ESSENTIAL AMINO ACIDS
• alanine
• arginine
• aspartic acid
• cysteine (made only from methionine)
• cystine (made only from methionine)
• glutamic acid
• glutamine
• glycine
• hydroxyproline
• ornithine
• proline
• serine
• tyrosine (made only from phenylalanine)

An organic acid in which one of the CH hydrogen atoms has been replaced by NH₂. Amino acids are the building blocks of proteins.

Description

Amino acids are known as the building blocks of protein, and are defined as the group of nitrogen-containing organic compounds composing the structure of proteins. They are essential to human metabolism, and to making the human body function properly for good health. Of the 28 amino acids known to exist, eight of them are considered "essential," defined as those that can be obtained only through food. These essential amino acids are tryptophan, lysine, methionine, phenylalaine, threonine, valine, leucine, and isoleucine. The "non–essential" amino acids include arginine, tyrosine, glycine, serine, glutmamic acid, aspartic acid, taurine, cycstine, histidine, proline, alanine, and creatine, which is a combination of arginine, glycine, and methionine.

The human body, minus water, is 75% amino acids. All of the neurotransmitters (proteins) but one are composed of amino acids; and 95% of hormones are amino acids. Amino acids are key to every human bodily function with every chemical reaction that occurs.

Amino acids occur naturally in certain foods, such as dairy products, meats, fish, poultry, nuts, legumes, and eggs. Those sources are considered more complete than vegetable protein, such as beans, peas, and grains, also considered a good—even if not complete—source of amino acids.

Amino acids became popular as dietary supplements by the end of the twentieth century for various uses, including fitness training, weight loss, and certain chronic diseases. Claims exist in holistic medicine that indicate amino acid supplements taken in the proper dosage can aid also in fighting depression, allergies, heart disease, gastrointestinal problems, high cholesterol, muscle weakness, blood sugar problems, arthritis, insomnia, bipolar illness, epilepsy, chronic fatigue syndrome, autism, attention-deficit hyperactivity disorder (ADHD), and mental exhaustion.

Description

Amino acid therapy as a supplemental aid to a healthy diet joined the fitness craze in the United States by the end of the 1990s. According to author Brenda Adderly in Better Nutrition, in September of 1999, "The creation of new protein from amino acids and the breaking down of existing protein into amino acids are ongoing processes in our bodies. If, for example, you are working out and developing certain muscles, amino acids come to the rescue with new protein to build muscle cells," Adderly noted. "Similarly, when you eat a complete protein, such as meat or beans and rice, the body breaks down the amino acids in that food for later use." Understanding the balance of amino acids in the body can be often the first clue to understanding why a person suffers many ailments, ranging from depression to upset stomach to obesity. Deficiencies in the proper balance of amino acids is likely to occur in those with poor diets. Because stress, age, infection, and various other factors including the amount of exercise a person does, can also affect the levels of amino acids, people with healthy, nutritious diets could also find that they also suffer deficiencies. Adderly adds that, "Not only are the symptoms of amino acid deficiencies wide ranging, but there are no RDAs (recommended daily allowances) or other guidelines, to help us tell if we are least covering all the bases. Add to that the complicated matter of keeping track of all 28 some with names most of us have never even heard and the situation begins to seem overwhelming."

Essential Amino Acids

The amino acids, which are derived only from food and that the body cannot manufacture, perform various functions.

• Tryptophan. This is considered a natural relaxant, helps alleviate insomnia; helps in the treatment of migraine headaches; helps reduce the risk of artery and heart spasms; and works with lysine to reduce cholesterol levels.
• Lysine. Aids in proper absorption of calcium; helps form collagen for bone cartilage and connective tissues; aids in production of antibodies, hormones, and enzymes. Research has indicated it also might be effective against herpes by creating the balance of nutrients that slows the growth of the virus causing it. A deficiency could result in fatigue, lack of concentration, irritability, bloodshot eyes, retarded growth, hair loss, anemia, and reproductive problems.
• Methionine. Properties include providing the primary source of sulfur that can prevent disorders of the hair, skin, and nails; lowers cholesterol by increasing the liver's production of lecithin; reduces liver fat; protects kidneys; and promotes hair growth.
• Phenylalaine. This serves the brain by producing norepinephrine, the chemical that is responsible for transmitting the signals between the nerve cells and the brain; can maintain alertness; reduces hunger pains; acts as an antidepressant; and improves memory.
• Threonine. Makes up a substantial portion of the collagen, elastin, and enamel protein; serves the liver by preventing buildup; aids the digestive and intestinal tracts to function better; and acts as a trigger for metabolism.
• Valine. Promotes mental energy; helps with muscle coordination; and serves as a natural tranquilizer.
• Leucine. Works with isoleucine to provide for the manufacture of essential biochemical processes in the body that are used for energy, increasing the stimulants to the upper brain for greater mental alertness.

Roles of Certain Non–essential Amino Acids

• Glycine. Facilitates the release of oxygen for the cell–making process; key role in manufacturing of hormones and health of immune system.
• Serine. Source of glucose storage by the liver and muscles; provides antibodies for immune system; synthesizes fatty acid sheath around nerve fibers.
• Glutamic acid. Nature's "brain food" that increases mental prowess; helps speed the healing of ulcers; aids in combatting fatigue.

Creatine in the Spotlight

One of the most discussed amino acid supplements available on the market is creatine monohydrate. The body produces small amounts of creatine in the kidneys, liver, and pancreas, making it a non-essential acid. With most diets that include red meat or fish, also come a few grams of creatine. It is stored in muscle cells and is used in activities, such as weight lifting and sprinting, providing the necessary thrust of energy for such activities. But the natural supply of creatine produced by the body is quickly depleted. After approximately 10 seconds, when muscle fatigue becomes apparent, the daily production is used.

According to Timothy Gower, writing for Esquire in February of 1998, "Scientists identified creatine 160– odd years ago, but only in the 1980s did they figure out that muscle cells can be 'loaded' with up to 30% more of the compound than they normally carry. Since then, several studies have shown that weight lifters primed on the supplement tire less easily, allowing them to work out longer." Gower also noted that creatine users find that the weight they add on is fat-free, whether that is lean tissue or some is water weight, no one has yet determined, since muscle cells do fill with water during creatine loading. Additionally, while it can add to the burst of the energy a sprinter needs to perform well, creatine does not do anything for the marathon runner going for several hours.

Commercially available since 1993, the long-term effects still remain unknown. One 2002 study did show that creatine use improved rehabilitation for injured athletes and another has shown that using the supplement does not increase risk of injury. It should be noted that some 20–30% of people researched showed no improvement using creatine. One early report indicated that creatine could be beneficial for some people in spurring metabolism, burning calories and helping in weight loss. Those reports were as yet inconclusive.

General Use

Amino acid supplements to a healthy diet are used for various purposes. The most common uses include: sustaining strength in weight training to build muscles; improving heart and circulatory problems or diseases, particularly in the aging; the treatment of chronic fatigue syndrome; treating depression and anxiety; treating eating disorders, such as bulimia and/or anorexia, along with overeating; increasing memory; building up and sustaining the body's immune system in fighting bacteria and viruses. It is important to note that, while the necessity and role of all amino acids has been verified in the maintenance of optimum health, research is not extensive enough to provide indisputable verification of the touted benefits of such supplements over the long term.

Nonetheless, some members of the scientific medical community would seem to confirm what amino acid proponents have long believed to be true. One such study from the Journal of the American College of Cardiology brought good news for the millions suffering from chronic heart failure. Dr. Rainer Hambrecht and colleagues from the University of Leipzig, (Germany) tested the amino acid L-arginine on 38 heart-failure patients. Knowing that the human body converted it into nitric oxide, a chemical that relaxes blood vessels, the researchers gave one group 8 g of it daily for four weeks; another group simply did forearm exercises; and a third group combined the supplement with the exercise. The people who took the supplement alone increased their blood-vessel dilation by a factor of four, as did the exercise group. Those who took both the supplement and performed the exercise increased it by six. More recent studies on arginine in 2002 found that the supplement may help reduce risk of postoperative infections. Further, arginine may enhance women's sexual function.

Supplements are recommended by alternative medical practitioners particularly for those who are not getting a proper diet, especially vegetarians who might not be getting a balance of complete protein, as well as athletes, anyone under severe stress, and anyone whose alcohol intake level is moderate to high.

Preparations

Supplements of various amino acids are available primarily in capsule, tablet, or powder form. A common way of taking amino acids is in a "multiple" amino acid gel cap. These contain sources of protein from gelatin, soy, and whey. The market for supplements in wholesale, retail, and internet sales was estimated to reach into the millions of dollars, with literally hundreds available. Internet sales were a fast-growing area particularly with the use of such supplements as creatine powder publicized by well-known Olympic stars and professional athletes. Daily usage of creatine as evident from research indicated that usage should be leveled at 5 g of powder in a glass of orange juice, and could be taken up to four times a day during peak athletic training. Maintenance dosages were recommended at 5 g once a day.

Side Effects

Because amino acids are naturally produced substances both in the human body and in the protein derived from animal and dairy products, as well as being present in food combinations such as beans and rice, such supplements are not regulated by the United States Food and Drug Administration (FDA), nor are there any specified daily requirements, and they also do not show up in either drug or urine tests. Amino acid supplements might be classified as having no affect at all. Long-term effects were not yet evident, however, due to the relatively recent phenomenon of use.

Interactions

Interactions of amino acids with drugs has not been sufficiently studied to determine yet if any adverse effects result from using amino acids with medications.

Resources

Periodicals

Adderly, Brenda. "Amino Acids." Better Nutrition (September 1999). Available from http://web2.infotrac.galegroup.com.

"Amino acid screening." Everything You Need to Know about Medical Tests, Annual. Springhouse Corporation: 1996. Available from http://web2.infotrac.com.

Antinoro, Linda. "Food and Herbs That Keep Blood Moving, Prevent Circulatory Problems." Environmental Nutrition (February 2000).

"Arginine Seems to Benefit Both Immune and Sexual Response." RN (February 2002): 22.

Austin Nutritional Research. "Amino acids." Reference Guide for Amino Acids. 2000. Available from http://www.realtime.net/anr/aminoacid.html.

Body Trends Fitness Products. "Amino acids." bodytrends.com commercial website. (2000). Available from http://wwwbodytrends.com.

"Creatine Supplementation Speeds Rehabilitation." Health and Medicine Week (January 21, 2002): 6.

Davidson, Tish. "Amino acid disorders screening." Gale Encyclopedia of Medicine. Edition 1. Detroit: 1999. Available from http://web2.infotrac.galegroup.com.

Dolby, Victoria. "Anxiety? Send herbs, 5–HTP, and amino acids to the rescue!" Better Nutrition (June 1998). Available from http://web2.infotrac.galegroup.com.

Gersten, Dennis J., M.D. "Amino Acids: Building Blocks of Life, Building Blocks of Healing." The Gersten Institute for Integrative Medicine. (2000). Available from http://www.imagery.com.

Gower, Timothy. "Eat Powder! Build Muscle! Burn Calories!" Esquire (February 1998). Available from http://www.brittannica.com.

Moyano, D.; Vilaseca, M.AA.; Artuch, R.; and, Lambruschini, N. "Plasma Amino Acids in Anorexia Nervosa." Nutrition Research Newsletter (November 1998). Available from http://web2.infotrac.com.

"Studies Say Creatine is OK." Obesity, Fitness & Wellness Week (January 12, 2002): 12.

Toews, Victoria Dolby. "6 Amino Acids Unleash the Energy." Better Nutrition (June 1999). Available from http://web2.infotrac.com.

Totheroh, Gailon. "Amino Acid Therapy Pays Off." Christian Broadcasting Network (10 May 1999). Available from http://www.cbn.com.

Tuttle, Dave. "Muscle's little helper." Men's Fitness (December 1998). Available from http://web2.infotrac.com.

Wernerman, Jan. "Documentation of clinical benefit of specific amino acid nutrients." The Lancet (5 September 1998). Available from http://web2.infotrac.galegroup.com/itw.

Williams, Stephen. "Passing the Acid Test." Newsweek (27 March 2000).

[Article by: Jane Spehar; Teresa G. Odle]

The building blocks of protein. They have an amine group (-NH₂) and a carboxyl group (-COOH ). There are about 80 naturally occurring amino acids, but only about 20 are used in proteins. Some of the amino acids can be obtained only from the diet: these are called essential amino acids and are used to manufacture the others. Amino acids may be used as an energy source during endurance activities, but they probably supply no more than 10% of the body's demands. Some amino acids, such as gamma-aminobutyric acid and glutamate function as neurotransmitters, acting as chemical intermediaries during the transmission of nerve impulses. The essential amino acids are histidine (essential for children only), isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The non-essential amino acids are alanine, arginine, aspartic acid, cysteine, cystine, glutamic acid, glutamine, glycine, hydroxyproline, ornithine, proline, serine, and tyrosine.

Amino acid

Basic organic molecules that combine to form proteins. Amino acids are made up of hydrogen, carbon, oxygen, and nitrogen. Some examples of amino acids are lysine, phenylalanine, and tryptophan.

Any one of a class of organic compounds containing the amino (NH₂) and the carboxyl (COOH) group, occurring naturally in plant and animal tissues and forming the chief constituents of protein.
In certain inherited or acquired disorders of metabolism, specific amino acids accumulate in the blood (aminoacidemia) or are excreted in excess in the urine (aminoaciduria). Urinary amino acid levels are increased in liver disease, muscular dystrophies, phenylketonuria (PKU), lead poisoning and folic acid deficiency.

• acidic a. a's — those containing carboxylic acids in their side chains, e.g. aspartate and glutamate.
• basic a. a's — amino acids containing side chains that accept protons at physiological pH, e.g. lysine, arginine, and histidine.
• branched-chain a. a's — methyl branched amino acids.
• a. a. dehydratase — an enzyme which contributes significantly to the total production of ammonia in the body.
• essential a. a's — the amino acids which animals must ingest with their diets and which vary between species and physiological status. The commonly accepted list of essential amino acids includes arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Birds also require glycine and cats require taurine in their diets.
• free a. a's — amino acids free in the blood, providing an available source for all tissues for catabolism.
• glucogenic a. a. — an amino acid which yields either pyruvate or oxaloacetate and glucose synthesis can occur.
• ketogenic a. a. — an amino acid whose carbon skeleton yields ketone bodies; leucine is an example.
• a. a. nutritional deficiency — the effects may be the same as a deficiency of total protein, reduced growth and production, reduced food intake, loss of body weight, but deficiencies of individual amino acids may have specific effects, e.g. taurine in cats. See also methionine, lysine, arginine.
• a. a. poisoning — methionine has caused growth retardation and cervical paralysis in turkey poults.
• a. a. ratio — a decreased ratio of branched chain to aromatic amino acids in plasma can be used to detect chronic liver disease or portacaval shunts in dogs.
• a. a. sequencer — automatic machine for determining the amino acid sequence of a protein.
• sulfur a. a's — essential amino acids containing sulfur, cysteine, cystine and methionine.
• a. a. transamidation — see transamidation.
• a. a. transamination — see transamination.
• urinary a. a's — analysis may be used to detect inherited disorders of metabolism, such as cystinuria, tyrosinemia and citrullinemia.

This article is about the class of chemicals. For the structures and properties of the standard proteinogenic amino acids, see Proteinogenic amino acid.

The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right

Amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H₂NCHRCOOH, where R is an organic substituent.^[1] In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon atom, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. These side chains can vary in size from just a hydrogen atom in glycine, to a methyl group in alanine, through to a large heterocyclic group in tryptophan.

Amino acids are critical to life, and their most important function is their variety of roles in metabolism. One particularly important function is as the building blocks of proteins, which are linear chains of amino acids. Every protein is chemically defined by this primary structure, its unique sequence of amino acid residues, which in turn define the three-dimensional structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked together in varying sequences to form a vast variety of proteins.^[2] Amino acids are also important in many other biological molecules, such as forming parts of coenzymes, as in S-adenosylmethionine, or as precursors for the biosynthesis of molecules such as heme. Due to this central role in biochemistry, amino acids are very important in nutrition. Amino acids are commonly used in food technology and industry. For example, monosodium glutamate is a common flavor enhancer that gives foods the taste called umami. They are also used in industry. Applications include the production of biodegradable plastics, drugs and chiral catalysts.

Contents 1 History 2 General structure 2.1 Isomerism 2.2 Zwitterions 3 Occurrence and functions in biochemistry 3.1 Standard amino acids 3.2 Non-standard amino acids 3.3 In human nutrition 3.4 Non-protein functions 4 Uses in technology 4.1 Chemical building blocks 4.2 Biodegradable plastics 5 Reactions 5.1 Chemical synthesis 5.2 Peptide bond formation 5.3 Biosynthesis and catabolism 6 Hydrophilic and hydrophobic amino acids 7 Table of standard amino acid abbreviations and side chain properties 8 See also 9 References and notes 10 Further reading 11 External links

History

The first two amino acids were discovered in the early 1800s. In 1806, the French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that proved to be asparagine, the first amino acid to be discovered.^[3][4] Another amino acid that was discovered in the early 19th century was cystine, in 1810,^[5] although its monomer, cysteine, was discovered much later, in 1884.^[6][4] Glycine and leucine were also discovered around this time, in 1820.^[7]

General structure

Further information: Proteinogenic amino acid

Lysine with the carbon atoms in the side chain labeled

In the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the carbonyl group is called the α–carbon and amino acids with a side chain bonded to this carbon are referred to as alpha amino acids. These are the most common form found in nature. In the alpha amino acids, the α–carbon is a chiral carbon atom, with the exception of glycine.^[8] In amino acids that have a carbon chain attached to the α–carbon (such as lysine, shown to the right) the carbons are labeled in order as α, β, γ, δ, and so on.^[9] In some amino acids, the amine group is attached to the β or γ-carbon, and these are therefore referred to as beta or gamma amino acids.

Amino acids are usually classified by the properties of their side chain into four groups. The side chain can make an amino acid a weak acid or a weak base, and a hydrophile if the side chain is polar or a hydrophobe if it is nonpolar.^[8] The chemical structures of the twenty-two standard amino acids, along with their chemical properties, are described more fully in the article on these proteinogenic amino acids.

The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side chains that are non-linear; these are leucine, isoleucine, and valine. Proline is the only proteinogenic amino acid whose side group links to the α-amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position.^[8] Chemically, proline is therefore an imino acid since it lacks a primary amino group,^[10] although it is still classed as an amino acid in the current biochemical nomenclature,^[11] and may also be called an "N-alkylated alpha-amino acid".^[12]

The two optical isomers of alanine, D-Alanine and L-Alanine

Isomerism

Of the standard α-amino acids, all but glycine can exist in either of two optical isomers, called L or D amino acids, which are mirror images of each other (see also Chirality). While L-amino acids represent the vast majority of amino acids found in proteins, D-amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails.^[13] They are also abundant components of the peptidoglycan cell walls of bacteria.^[14] and D-serine may act as a neurotransmitter in the brain.^[15] The L and D convention for amino acid configuration refers not to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde from which that amino acid can theoretically be synthesized (D-glyceraldehyde is dextrorotary; L-glyceraldehyde is levorotary). Alternatively, the (S) and (R) designators are used to indicate the absolute stereochemistry. Almost all of the amino acids in proteins are (S) at the α carbon, with cysteine being (R) and glycine non-chiral.^[16] Cysteine is unusual since it has a sulfur atom at the first position in its side-chain, which has a larger atomic mass than the groups attached to the α-carbon in the other standard amino acids, thus the (R) instead of (S).

An amino acid in its (1) unionized and (2) zwitterionic forms

Zwitterions

Amino acids have both amine and carboxylic acid functional groups and are therefore both an acid and a base at the same time.^[8] At a certain pH known as the isoelectric point an amino acid has no overall charge, since the number of protonated ammonium groups (positive charges) and deprotonated carboxylate groups (negative charges) are equal.^[17] The amino acids all have different isoelectric points. The ions produced at the isoelectric point have both positive and negative charges and are known as a zwitterion, which comes from the German word Zwitter meaning "hermaphrodite".^[18] Amino acids can exist as zwitterions in solids and in polar solutions such as water, but not in the gas phase.^[19] Zwitterions have minimal solubility at their isolectric point and an amino acid can be isolated by precipitating it from water by adjusting the pH to its particular isolectric point.

Occurrence and functions in biochemistry

A polypeptide is an unbranched chain of amino acids.

Standard amino acids

See also: Primary structure and Posttranslational modification

Amino acids are the structural units that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched, with each amino acid within the chain attached to two neighbouring amino acids. The process of making proteins is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome.^[20] The order in which the amino acids are added is read through the genetic code from an mRNA template, which is a RNA copy of one of the organism's genes. Twenty-two amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids.^[8]

The amino acid selenocysteine

Non-standard amino acids

Aside from the twenty-two standard amino acids, there are a vast number of "non-standard" amino acids. Two of these can be specified by the genetic code, but are rather rare in proteins. Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.^[21] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG.^[22] Other non-standard amino acids found in proteins are formed by post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations,^[23] and the hydroxylation of proline is critical for maintaining connective tissues.^[24] Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue.^[25] Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane.^[26]

β-alanine and its α-alanine isomer

Examples of nonstandard amino acids that are not found in proteins include lanthionine, 2-aminoisobutyric acid, dehydroalanine and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids — for example ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below).^[27] A rare exception to the dominance of α-amino acids in biology is the β-amino acid beta alanine (3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B5), a component of coenzyme A.^[28]

In human nutrition

Further information: Protein in nutrition and Amino acid synthesis

When taken up into the body in the diet, the twenty-two standard amino acids are either used to synthesize proteins and other biomolecules or oxidized to urea and carbon dioxide as a source of energy.^[29] The oxidation pathway starts with the removal of the amino group by a transaminase, the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle.^[30] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.^[31]

Of the twenty-two standard amino acids, eight are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.^[32] However, the situation is quite complicated since cysteine, taurine, tyrosine, histidine and arginine are semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed.^[33][34] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.

Essential	Nonessential
Isoleucine	Alanine
Leucine	Asparagine
Lysine	Aspartic Acid
Methionine	Cysteine*
Phenylalanine	Glutamic Acid
Threonine	Glutamine*
Tryptophan	Glycine*
Valine	Proline*
	Serine*
	Tyrosine*
	Arginine*
	Histidine*

(*) Essential only in certain cases.^[35][36]

Non-protein functions

Further information: Amino acid neurotransmitter

In humans, non-protein amino acids also have important roles as metabolic intermediates, such as in the biosynthesis of the neurotransmitter gamma-aminobutyric acid. Many amino acids are used to synthesize other molecules, for example:

• Tryptophan is a precursor of the neurotransmitter serotonin.^[37]
• Glycine is a precursor of porphyrins such as heme.^[38]
• Arginine is a precursor of nitric oxide.^[39]
• Ornithine and S-adenosylmethionine are precursors of polyamines.^[40]
• Aspartate, glycine and glutamine are precursors of nucleotides.^[41]

However, not all of the functions of other abundant non-standard amino acids are known, for example taurine is a major amino acid in muscle and brain tissues, but although many functions have been proposed, its precise role in the body has not been determined.^[42]

Some non-standard amino acids are used as defenses against herbivores in plants.^[43] For example canavanine is an analogue of arginine that is found in many legumes,^[44] and in particularly large amounts in Canavalia gladiata (sword bean).^[45] This amino acid protects the plants from predators such as insects and can cause illness in people if some types of legumes are eaten without processing.^[46] The non-protein amino acid mimosine is found in other species of legume, particularly Leucaena leucocephala.^[47] This compound is an analogue of tyrosine and can poison animals that graze on these plants.

Uses in technology

Amino acids are used for a variety of applications in industry but their main use is as additives to animal feed. This is necessary since many of the bulk components of these feeds, such as soybeans, either have low levels or lack some of the essential amino acids: lysine, methionine, threonine, and tryptophan are most important in the production of these feeds.^[48] The food industry is also a major consumer of amino acids, particularly glutamic acid, which is used as a flavor enhancer,^[49] and Aspartame (aspartyl-phenylalanine-1-methyl ester) as a low-calorie artificial sweetener.^[50] The remaining production of amino acids is used in the synthesis of drugs and cosmetics.^[48]

Amino acid derivative	Pharmaceutical application
5-HTP (5-hydroxytryptophan)	Experimental treatment for depression.[51]
L-DOPA (L-dihydroxyphenylalanine)	Treatment for Parkinsonism.[52]
Eflornithine	Drug that inhibits ornithine decarboxylase and is used in the treatment of sleeping sickness.[53]

Chemical building blocks

Further information: Asymmetric synthesis

Amino acids are important as low-cost feedstocks. These compounds are used in chiral pool synthesis as enantiomerically-pure building blocks.^[54]

Amino acids have been investigated as precursors chiral catalysts, e.g. for asymmetric hydrogenation reactions, although no commercial applications exist.^[55]

Biodegradable plastics

Further information: Biodegradable plastics and Biopolymers

Amino acids are under development as components of a range of biodegradable polymers. These materials have applications as environmentally-friendly packaging and in medicine in drug delivery and the construction of prosthetic implants. These polymers include polypeptides, polyamides, polyesters, polysulfides and polyurethanes with amino acids either forming part of their main chains or bonded as side chains. These modifications alter the physical properties and reactivities of the polymers.^[56] An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture.^[57] Due to its solubility and ability to chelate metal ions, polyaspartate is also being used as a biodegradeable anti-scaling agent and a corrosion inhibitor.^[58][59] In addition, the aromatic amino acid tyrosine is being developed as a possible replacement for toxic phenols such as bisphenol A in the manufacture of polycarbonates.^[60]

Reactions

As amino acids have both a primary amine group and a primary carboxyl group, these chemicals can undergo most of the reactions associated with these functional groups. These include nucleophilic addition, amide bond formation and imine formation for the amine group and esterification, amide bond formation and decarboxylation for the carboxylic acid group.^[61] The multiple side chains of amino acids can also undergo chemical reactions.^[62] The types of these reactions are determined by the groups on these side chains and are therefore different between the various types of amino acid.

The Strecker amino acid synthesis

Chemical synthesis

Main article: Peptide synthesis

Several methods exist to synthesize amino acids. One of the oldest methods, begins with the bromination at the α-carbon of a carboxyic acid. Nucleophilic substitution with ammonia then converts the alkyl bromide to the amino acid.^[63] Alternatively, the Strecker amino acid synthesis involves the treatment of an aldehyde with potassium cyanide and ammonia, this produces an α-amino nitrile as an intermediate. Hydrolysis of the nitrile in acid then yields a α-amino acid.^[64] Using ammonia or ammonium salts in this reaction gives unsubstituted amino acids, while substituting primary and secondary amines will yield substituted amino acids.^[65] Likewise, using ketones, instead of aldehydes, gives α,α-disubstituted amino acids.^[66] The classical synthesis gives racemic mixtures of α-amino acids as products, but several alternative procedures using asymmetric auxiliaries ^[67] or asymmetric catalysts ^[68][69] have been developed.^[70]

Currently the most adopted method is an automated synthesis on a solid support (e.g. polystyrene beads), using protecting groups (e.g. Fmoc and t-Boc) and activating groups (e.g. DCC and DIC).

Peptide bond formation

For more details on this topic, see Peptide bond.

The condensation of two amino acids to form a peptide bond

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.^[71] This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond.^[72] As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their N-terminus and moving towards their C-terminus.

However, not all peptide bonds are formed in this way. In a few cases, peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids.^[73] In the first step gamma-glutamylcysteine synthetase condenses cysteine and glutamic acid through a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione.^[74]

In chemistry, peptides are synthesized by a variety of reactions. One of the most used in solid-phase peptide synthesis, which uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.^[75] The ability to easily synthesize vast numbers of different peptides by varying the types and order of amino acids (using combinatorial chemistry) has made peptide synthesis particularly important in creating libraries of peptides for use in drug discovery through high-throughput screening.^[76]

Biosynthesis and catabolism

In plants, nitrogen is first assimilated into organic compounds in the form of glutamate, formed from alpha-ketoglutarate and ammonia in the mitochondrion. In order to form other amino acids, the plant uses transaminases to move the amino group to another alpha-keto carboxylic acid. For example, aspartate aminotransferase converts glutamate and oxaloacetate to alpha-ketoglutarate and aspartate.^[77] Other organisms use transaminases for amino acid synthesis too. Transaminases are also involved in breaking down amino acids. Degrading an amino acid often involves moving its amino group to alpha-ketoglutarate, forming glutamate. In many vertebrates, the amino group is then removed through the urea cycle and is excreted in the form of urea. However, amino acid degradation can produce uric acid or ammonia instead. For example, serine dehydratase converts serine to pyruvate and ammonia.^[78]

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosyl methionine,^[42] while hydroxyproline is made by a posttranslational modification of proline.^[79]

Microorganisms and plants can synthesize many uncommon amino acids. For example, some microbes make 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged derivative of alanine. Both of these amino acids are found in peptidic lantibiotics such as alamethicin.^[80] While in plants, 1-aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is a key intermediate in the production of the plant hormone ethylene.^[81]

Hydrophilic and hydrophobic amino acids

Depending on the polarity of the side chain, amino acids vary in their hydrophilic or hydrophobic character.^[8] These properties are important in protein structure and protein-protein interactions. The importance of the physical properties of the side chains comes from the influence this has on the amino acid residues' interactions with other structures, both within a single protein and between proteins. The distribution of hydrophilic and hydrophobic amino acids determines the tertiary structure of the protein, and their physical location on the outside structure of the proteins influences their quaternary structure.^[8]

For example, soluble proteins have surfaces rich with polar amino acids like serine and threonine, while integral membrane proteins tend to have outer rings of hydrophobic amino acids that anchor them into the lipid bilayer. In the case part-way between these two extremes, peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. Similarly, proteins that have to bind to positively-charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine. Recently a new scale of hydrophobicity based on the free energy of hydrophobic association has been proposed.^[82]

The hydrophilic and hydrophobic interactions of proteins are not always the result of the properties of their amino acid sidechains. This is because a range of posttranslational modifications can attach other chemical groups to the amino acids in proteins. For example, these modifications can produce hydrophobic lipoproteins,^[83] or hydrophilic glycoproteins.^[84] These type of modification allow the reversible targeting of a protein to a membrane. For example, the addition and removal of the fatty acid palmitic acid to cysteine residues in some signaling proteins causes the proteins to attach and then detach from cell membranes.^[85]

Table of standard amino acid abbreviations and side chain properties

Main article: Proteinogenic amino acid

Amino Acid	3-Letter[86]	1-Letter[86]	Side chain polarity[86]	Side chain charge (pH 7)[86]	Hydropathy index[87]	Absorbance λmax(nm)[88]	ε at λmax (x10-3 M-1 cm-1)[88]
Alanine	Ala	A	nonpolar	neutral	1.8
Arginine	Arg	R	polar	positive	-4.5
Asparagine	Asn	N	polar	neutral	-3.5
Aspartic acid	Asp	D	polar	negative	-3.5
Cysteine	Cys	C	nonpolar	neutral	2.5	250	0.3
Glutamic acid	Glu	E	polar	negative	-3.5
Glutamine	Gln	Q	polar	neutral	-3.5
Glycine	Gly	G	nonpolar	neutral	-0.4
Histidine	His	H	polar	neutral	-3.2	211	5.9
Isoleucine	Ile	I	nonpolar	neutral	4.5
Leucine	Leu	L	nonpolar	neutral	3.8
Lysine	Lys	K	polar	positive	-3.9
Methionine	Met	M	nonpolar	neutral	1.9
Phenylalanine	Phe	F	nonpolar	neutral	2.8	257, 206, 188	0.2, 9.3, 60.0
Proline	Pro	P	nonpolar	neutral	-1.6
Serine	Ser	S	polar	neutral	-0.8
Threonine	Thr	T	polar	neutral	-0.7
Tryptophan	Trp	W	nonpolar	neutral	-0.9	280 219	5.6, 47.0
Tyrosine	Tyr	Y	polar	neutral	-1.3	274, 222, 193	1.4, 8.0, 48.0
Valine	Val	V	nonpolar	neutral	4.2

In addition to the specific amino acid codes, placeholders are used in cases where chemical or crystallographic analysis of a peptide or protein can not conclusively determine the identity of a residue.

Ambiguous Amino Acids	3-Letter	1-Letter
Asparagine or aspartic acid	Asx	B
Glutamine or glutamic acid	Glx	Z
Leucine or Isoleucine	Xle	J
Unspecified or unknown amino acid	Xaa	X

Unk is sometimes used instead of Xaa, but is less standard.

Additionally, many non-standard amino acids have a specific code. For example, several peptide drugs, such as Bortezomib or MG132 are artificially synthesized and retain their protecting groups, which have specific codes. Bortezomib is Pyz-Phe-boroLeu and MG132 is Z-Leu-Leu-Leu-al. Additionally, To aid in the analysis of protein structure, photocrosslinking amino acids are available. These include photoleucine (pLeu) and photomethionine (pMet).^[89]

See also

• Amino acid dating
• Beta amino acid
• Degron
• Glucogenic amino acid
• Homochirality
• Leucines
• Proteinogenic amino acid (including chemical structures)
• Table of codons, 3-nucleotide sequences that encode each amino acid

References and notes

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Further reading

• Doolittle, R.F. (1989) Redundancies in protein sequences. In Predictions of Protein Structure and the Principles of Protein Conformation (Fasman, G.D. ed) Plenum Press, New York, pp. 599–623
• David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd edition, 2000, Worth Publishers, ISBN 1-57259-153-6
• Meierhenrich, U.J.: Amino acids and the asymmetry of life, Springer-Verlag, Berlin, New York, 2008. ISBN 978-3-540-76885-2
• Morelli, Robert J. "Studies of amino acid absorption from the small intestine." San Francisco: Morelli, 1952.

External links

• Amino acids overview physical-chemistry properties, 3D structures, etc
• List of Standard Amino Acids The Detailed PDF List of Standard Amino Acids (including 3D depictions)
• Nomenclature and Symbolism for Amino Acids and Peptides IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)
• Molecular Expressions: The Amino Acid Collection - Has detailed information and microscopy photographs of each amino acid.
• Amino acid properties - Properties of the amino acids (a tool aimed mostly at molecular geneticists trying to understand the meaning of mutations)
• Synthesis of Amino Acids and Derivatives
• Learn the 20 proteinogenic amino acids online
• The origin of the single-letter code for the amino acids

v • d • e The 20 Common Amino Acids ("dp" = data page) Branched-chain amino acids Isoleucine (dp) · Leucine (dp) · Valine (dp) Non Branch-chain Alanine (dp) · Arginine (dp) · Asparagine (dp) · Aspartic acid (dp) · Cysteine (dp) · Glutamic acid (dp) · Glutamine (dp) · Glycine (dp) · Histidine (dp) · Lysine (dp) · Methionine (dp) · Phenylalanine (dp) · Proline (dp) · Serine (dp) · Threonine (dp) · Tryptophan (dp) · Tyrosine (dp) Other classifications Essential amino acids · Ketogenic amino acid · Glucogenic amino acid Major families of biochemicals Saccharides/Carbohydrates/Glycosides · Amino acids/Peptides/Proteins/Glycoproteins · Lipids/Terpenes/Steroids/Carotenoids · Alkaloids/Nucleobases/Nucleic acids · Cofactors/Phenylpropanoids/Polyketides/Tetrapyrroles

v • d • e Protein primary structure and posttranslational modifications General Peptide bond · Protein biosynthesis · Proteolysis · Racemization · N-O acyl shift N terminus Acetylation · Carbamylation · Formylation · Glycation · Methylation · Myristoylation (Gly) C terminus Amidation · Glycosyl phosphatidylinositol (GPI) · O-methylation · Sumoylation · Ubiquitination Specific AAs Serine/ Threonine Phosphorylation · Glycosylation · Methylidene-imidazolone (MIO) formation Tyrosine Phosphorylation · Sulfation · Porphyrin ring linkage · Flavin linkage · p-Hydroxybenzylidene-imidazolone formation · Lysine tyrosyl quinone (LTQ) formation · Topaquinone (TPQ) formation Cysteine Disulfide bond · Palmitoylation · Prenylation Aspartate Succinimide formation Glutamate Carboxylation · Methylation · Polyglutamylation · Polyglycylation Asparagine Deamidation · Glycosylation Glutamine Transglutamination Lysine Methylation · Acetylation · Acylation · Hydroxylation · Ubiquitination · Sumoylation · Desmosine · ADP-ribosylation · Deamination and Oxidation to aldehyde Arginine Citrullination · Methylation Proline Hydroxylation ←Amino acids Secondary structure→

v • d • e Metabolism: amino acid metabolism · synthesis and catabolism enzymes (essential in CAPS) K→acetyl-CoA LYSINE→ Saccharopine dehydrogenase · Glutaryl-CoA dehydrogenase LEUCINE→ Branched chain aminotransferase · Branched-chain alpha-keto acid dehydrogenase complex · Isovaleryl coenzyme A dehydrogenase · Methylcrotonyl-CoA carboxylase · Methylglutaconyl-CoA hydratase · 3-hydroxy-3-methylglutaryl-CoA lyase TRYPTOPHAN→ Indoleamine 2,3-dioxygenase/Tryptophan 2,3-dioxygenase · Arylformamidase · Kynureninase · 3-hydroxyanthranilate oxidase · Aminocarboxymuconate-semialdehyde decarboxylase · Aminomuconate-semialdehyde dehydrogenase PHENYLALANINE→tyrosine→ (see below) G G→pyruvate →citrate glycine→serine→ Serine hydroxymethyltransferase · Serine dehydratase glycine→creatine: Guanidinoacetate N-methyltransferase · Creatine kinase alanine→ Alanine transaminase cysteine→ D-cysteine desulfhydrase threonine→ L-threonine dehydrogenase G→glutamate→ α-ketoglutarate HISTIDINE→ Histidine ammonia-lyase · Urocanate hydratase · Formiminotransferase cyclodeaminase proline→ Proline oxidase · Pyrroline-5-carboxylate reductase · 1-Pyrroline-5-carboxylate dehydrogenase/ALDH4A1 · PYCR1 arginine→ Ornithine aminotransferase · Ornithine decarboxylase · Agmatinase →alpha-ketoglutarate→TCA Glutamate dehydrogenase Other cysteine+glutamate→glutathione: Gamma-glutamylcysteine synthetase · Glutathione synthetase · Gamma-glutamyl transpeptidase glutamate→glutamine: Glutamine synthetase · Glutaminase G→propionyl-CoA→ succinyl-CoA VALINE→ Branched chain aminotransferase · Branched-chain alpha-keto acid dehydrogenase complex · Enoyl-CoA hydratase · 3-hydroxyisobutyryl-CoA hydrolase · 3-hydroxyisobutyrate dehydrogenase · Methylmalonate semialdehyde dehydrogenase ISOLEUCINE→ Branched chain aminotransferase · Branched-chain alpha-keto acid dehydrogenase complex · 3-hydroxy-2-methylbutyryl-CoA dehydrogenase METHIONINE→ generation of homocysteine: Methionine adenosyltransferase · Adenosylhomocysteinase regeneration of methionine: MTR/Homocysteine methyltransferase · Betaine-homocysteine methyltransferase conversion to cysteine: Cystathionine beta synthase · Cystathionine gamma-lyase THREONINE→ Threonine aldolase →succinyl-CoA→TCA Propionyl-CoA carboxylase · Methylmalonyl CoA epimerase · Methylmalonyl-CoA mutase G→fumarate PHENYLALANINE→tyrosine→ Phenylalanine hydroxylase · Tyrosine aminotransferase · 4-Hydroxyphenylpyruvate dioxygenase · Homogentisate 1,2-dioxygenase · Fumarylacetoacetate hydrolase tyrosine→melanin: Tyrosinase G→oxaloacetate asparagine→aspartate→ Asparaginase/Asparagine synthetase · Aspartate transaminase see also disorders, intermediates

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