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Amino Acids |
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/>.
McGraw-Hill Science & Technology Encyclopedia:
Amino acids |
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).
Amino acids | R |
|---|---|
Glycine | Hydrogen |
Alanine, valine, leucine, isoleucine | Unsubstituted aliphatic chain |
Serine, threonine | Aliphatic chain bearing a hydroxyl group |
Aspartic acid, glutamic acid | Aliphatic chain terminating in an acidic carboxyl group |
Asparagine, glutamine | Aliphatic chain terminating in an amide group |
Arginine, lysine | Aliphatic chain terminating in a basic amino group |
Cysteine, cystine, methionine | Sulfur-containing aliphatic chain |
Phenylalanine, tyrosine | Terminates in an aromatic ring |
Tryptophan, proline, histidine | Terminates in a heterocyclic ring |
*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.
Oxford Food & Nutrition Dictionary:
amino acids |
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.
Oxford Food & Fitness Dictionary:
amino acids |
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)
Oxford Companion to the Body:
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
Oxford Dictionary of Sports Science & Medicine:
amino acids |
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.
Gale Nutrition Encyclopedia:
Amino Acids |
| Essential amino acids | Nonessential amino acids |
| Histidine | Alanine |
| Isoleucine | Arginine |
| Leucine | Asparagine |
| Lysine | Aspartic acid |
| Methionine | Cysteine |
| Phenylalanine | Glutamic acid |
| Threonine | Glutamine |
| Tr yptophan | Glycine |
| Valine | Proline |
| Serine | |
| Tyrosine |
Columbia Encyclopedia:
amino acid |
Dictionary of Cultural Literacy: Science:
amino acids |
Wiley Dictionary of Flavors:
Amino Acid |
Oxford Dictionary of Biochemistry:
amino acid |
| amino, aminergic, amine oxidase | |
| amino acid exchange matrix, amino acid index, amino acid transporter |
Saunders Veterinary Dictionary:
amino acid |
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.
Mosby's Dental Dictionary:
amino acid |
An organic acid in which one of the CH hydrogen atoms has been replaced by NH2. Amino acids are the building blocks of proteins.
Random House Word Menu:
categories related to 'amino acid' |
Bradford's Crossword Solver's Dictionary:
amino acid |
See crossword solutions for the clue Amino-acid.
Wikipedia on Answers.com:
Amino acid |
Amino acids (
/əˈmiːnoʊ/, /əˈmaɪnoʊ/, or /ˈæmɪnoʊ/) are molecules containing an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen. They are particularly important in biochemistry, where the term usually refers to alpha-amino acids.
An alpha-amino acid has the generic formula H2NCHRCOOH, where R is an organic substituent;[1] the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (the α–carbon). Other types of amino acid exist when the amino group is attached to a different carbon atom; for example, in gamma-amino acids (such as gamma-amino-butyric acid) the carbon atom to which the amino group attaches is separated from the carboxylate group by two other carbon atoms. The various alpha-amino acids differ in which side-chain (R-group) is attached to their alpha carbon, and can vary in size from just one hydrogen atom in glycine to a large heterocyclic group in tryptophan.
Amino acids serve as the building blocks of proteins, which are linear chains of amino acids. Amino acids can be linked together in varying sequences to form a vast variety of proteins.[2] Twenty amino acids are naturally incorporated into polypeptides and are called proteinogenic or standard amino acids. These 20 are encoded by the universal genetic code. Nine standard amino acids are called "essential" for humans because they cannot be created from other compounds by the human body, and so must be taken in as food.
Amino acids are important in nutrition and are commonly used in nutrition supplements, fertilizers, food technology and industry. In industry, applications include the production of biodegradable plastics, drugs, and chiral catalysts.
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The first few amino acids were discovered in the early 19th century. In 1806, the French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named 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.[4][6] Glycine and leucine were also discovered around this time, in 1820.[7] Usage of the term amino acid in the English language is from 1898.[8]
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 carboxyl 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.[9] 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.[10] 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.[9] The chemical structures of the 22 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.[9] In chemical terms, proline is, therefore, an imino acid, since it lacks a primary amino group,[11] although it is still classed as an amino acid in the current biochemical nomenclature,[12] and may also be called an "N-alkylated alpha-amino acid".[13]
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 all of the amino acids found in proteins during translation in the ribosome, D-amino acids are found in some proteins produced by enzyme posttranslational modifications after translation and translocation to the endoplasmic reticulum, as in exotic sea-dwelling organisms such as cone snails.[14] They are also abundant components of the peptidoglycan cell walls of bacteria,[15] and D-serine may act as a neurotransmitter in the brain.[16] 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, in theory, be synthesized (D-glyceraldehyde is dextrorotary; L-glyceraldehyde is levorotary). In alternative fashion, 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.[17] Cysteine is unusual since it has a sulfur atom at the second position in its side-chain, which has a larger atomic mass than the groups attached to the first carbon, which is attached to the α-carbon in the other standard amino acids, thus the (R) instead of (S).
The amine and carboxylic acid functional groups found in amino acids allow them to have amphiprotic properties.[9] Carboxylic acid groups (-CO2H) can be deprotonated to become negative carboxylates (-CO2- ), and α-amino groups (NH2-) can be protonated to become positive α-ammonium groups (+NH3-). At pH values greater than the pKa of the carboxylic acid group (mean for the 20 common amino acids is about 2.2, see the table of amino acid structures above), the negative carboxylate ion predominates. At pH values lower than the pKa of the α-ammonium group (mean for the 20 common α-amino acids is about 9.4), the nitrogen is predominantly protonated as a positively charged α-ammonium group. Thus, at pH between 2.2 and 9.4, the predominant form adopted by α-amino acids contains a negative carboxylate and a positive α-ammonium group, as shown in structure (2) on the right, so has net zero charge. This molecular state is known as a zwitterion, from the German Zwitter meaning hermaphrodite or hybrid.[18] Below pH 2.2, the predominant form will have a neutral carboxylic acid group and a positive α-ammonium ion (net charge +1), and above pH 9.4, a negative carboxylate and neutral α-amino group (net charge -1). The fully neutral form (structure (1) on the right) is a very minor species in aqueous solution throughout the pH range (less than 1 part in 107). Amino acids also exist as zwitterions in the solid phase, and crystallize with salt-like properties unlike typical organic acids or amines.
At pH values between the two pKa values, the zwitterion predominates, but coexists in dynamic equilibrium with small amounts of net negative and net positive ions. At the exact midpoint between the two pKa values, the trace amount of net negative and trace of net positive ions exactly balance, so that average net charge of all forms present is zero.[19] This pH is known as the isoelectric point pI, so pI = ½(pKa1 + pKa2). The individual amino acids all have slightly different pKa values, so have different isoelectric points. For amino acids with charged side-chains, the pKa of the side-chain is involved. Thus for Asp, Glu with negative side-chains, pI = ½(pKa1 + pKaR), where pKaR is the side-chain pKa. Cysteine also has potentially negative side-chain with pKaR = 8.14, so pI should be calculated as for Asp and Glu, even though the side-chain is not significantly charged at neutral pH. For His, Lys, and Arg with positive side-chains, pI = ½(pKaR + pKa2). Amino acids have zero mobility in electrophoresis at their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids. Zwitterions have minimum solubility at their isolectric point and some amino acids (in particular, with non-polar side-chains) can be isolated by precipitation from water by adjusting the pH to the required isoelectric point.
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 neighboring 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 naturally incorporated into polypeptides and are called proteinogenic or natural amino acids.[9] Of these, 20 are encoded by the universal genetic code. The remaining 2, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of 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, which is normally a stop codon in other organisms.[22] This UAG codon is followed by a PYLIS downstream sequence.[23]
Aside from the 22 standard amino acids, there are many other amino acids that are called non-proteinogenic or non-standard. Those either are not found in proteins (for example carnitine, GABA), or are not produced directly and in isolation by standard cellular machinery (for example, hydroxyproline and selenomethionine).
Non-standard amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during 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,[24] and the hydroxylation of proline is critical for maintaining connective tissues.[25] Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue.[26] 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.[27]
Some nonstandard amino acids are not found in proteins. Examples 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).[28] 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.[29]
When taken up into the human body from the diet, the 22 standard amino acids either are used to synthesize proteins and other biomolecules or are oxidized to urea and carbon dioxide as a source of energy.[30] 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.[31] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.[32]
Pyrrolysine trait is restricted to several microbes, and only one organism has both Pyl and Sec. Of the 22 standard amino acids, 9 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.[33] In addition, cysteine, taurine, tyrosine, and arginine are semiessential amino-acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed.[34][35] 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 |
|---|---|
| Histidine | Alanine |
| Isoleucine | Arginine* |
| Leucine | Asparagine |
| Lysine | Aspartic acid |
| Methionine | Cysteine* |
| Phenylalanine | Glutamic acid |
| Threonine | Glutamine* |
| Tryptophan | Glycine |
| Valine | Ornithine* |
| Proline* | |
| Selenocysteine* | |
| Serine* | |
| Taurine* | |
| Tyrosine* |
(*) Essential only in certain cases.[36][37]
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:
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.[43]
Some non-standard amino acids are used as defenses against herbivores in plants.[44] For example canavanine is an analogue of arginine that is found in many legumes,[45] and in particularly large amounts in Canavalia gladiata (sword bean).[46] 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.[47] The non-protein amino acid mimosine is found in other species of legume, particularly Leucaena leucocephala.[48] This compound is an analogue of tyrosine and can poison animals that graze on these plants.
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.[49] In this industry, amino acids are also used to chelate metal cations in order to improve the absorption of minerals from supplements, which may be required to improve the health or production of these animals.[50]
The food industry is also a major consumer of amino acids, in particular, glutamic acid, which is used as a flavor enhancer,[51] and Aspartame (aspartyl-phenylalanine-1-methyl ester) as a low-calorie artificial sweetener.[52] Similar technology to that used for animal nutrition is employed in the human nutrition industry to alleviate symptoms of mineral deficiencies, such as anemia, by improving mineral absorption and reducing negative side effects from inorganic mineral supplementation.[53]
The chelating ability of amino acids has been used in fertilizers for agriculture to facilitate the delivery of minerals to plants in order to correct mineral deficiencies, such as iron chlorosis. These fertilizers are also used to prevent deficiencies from occurring and improving the overall health of the plants.[54] The remaining production of amino acids is used in the synthesis of drugs and cosmetics.[49]
| Amino acid derivative | Pharmaceutical application |
|---|---|
| 5-HTP (5-hydroxytryptophan) | Experimental treatment for depression.[55] |
| L-DOPA (L-dihydroxyphenylalanine) | Treatment for Parkinsonism.[56] |
| Eflornithine | Drug that inhibits ornithine decarboxylase and is used in the treatment of sleeping sickness.[57] |
Since 2001, 40 non-natural amino acids have been added into protein by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins.[58][59]
Amino acids are important as low-cost feedstocks. These compounds are used in chiral pool synthesis as enantiomerically-pure building blocks.[60]
Amino acids have been investigated as precursors chiral catalysts, e.g., for asymmetric hydrogenation reactions, although no commercial applications exist.[61]
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.[62] An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture.[63] 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.[64][65] 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.[66]
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.[67] The combination of these functional groups allow amino acids to be effective polydentate ligands for metal-amino acid chelates.[68] The multiple side-chains of amino acids can also undergo chemical reactions.[69] 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.
Several methods exist to synthesize amino acids. One of the oldest methods begins with the bromination at the α-carbon of a carboxylic acid. Nucleophilic substitution with ammonia then converts the alkyl bromide to the amino acid.[70] In alternative fashion, 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.[71] Using ammonia or ammonium salts in this reaction gives unsubstituted amino acids, while substituting primary and secondary amines will yield substituted amino acids.[72] Likewise, using ketones, instead of aldehydes, gives α,α-disubstituted amino acids.[73] The classical synthesis gives racemic mixtures of α-amino acids as products, but several alternative procedures using asymmetric auxiliaries [74] or asymmetric catalysts [75][76] have been developed.[77]
At the current time, 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).
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.[78] 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.[79] 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.[80] 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.[81]
In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in solid-phase peptide synthesis 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.[82] 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.[83]
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.[84] Other organisms use transaminases for amino acid synthesis, too.
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,[43] while hydroxyproline is made by a posttranslational modification of proline.[85]
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.[86] 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.[87]
Degradation of an amino acid often involves deamination by moving its amino group to alpha-ketoglutarate, forming glutamate. This process involves transaminases, often the same as those used in amination during synthesis. 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.[89] After removal of one or more amino groups, the remainder of the molecule can sometimes be used to synthesize new amino acids, or it can be used for energy by entering glycolysis or the citric acid cycle, as detailed in image at right.
The 20 amino acids encoded directly by the genetic code can be divided into several groups based on their properties. Important factors are charge, hydrophilicity or hydrophobicity, size, and functional groups.[9] These properties are important for protein structure and protein–protein interactions. The water-soluble proteins tend to have their hydrophobic residues (Leu, Ile, Val, Phe, and Trp) buried in the middle of the protein, whereas hydrophilic side-chains are exposed to the aqueous solvent. The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them into the lipid bilayer. In the case part-way between these two extremes, some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. In similar fashion, 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. There are different hydrophobicity scales of amino acid residues.[90]
Some amino acids have special properties such as cysteine, that can form covalent disulfide bonds to other cysteine residues, proline that forms a cycle to the polypeptide backbone, and glycine that is more flexible than other amino acids.
Many proteins undergo a range of posttranslational modifications, when additional chemical groups are attached to the amino acids in proteins. Some modifications can produce hydrophobic lipoproteins,[91] or hydrophilic glycoproteins.[92] 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.[93]
| Amino Acid | 3-Letter[94] | 1-Letter[94] | Side-chain polarity[94] | Side-chain charge (pH 7.4)[94] | Hydropathy index[95] | Absorbance λmax(nm)[96] | ε at λmax (x10−3 M−1 cm−1)[96] |
|---|---|---|---|---|---|---|---|
| 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 | polar | 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 | positive(10%)
neutral(90%) |
−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, there are two additional amino acids that are incorporated by overriding stop codons:
| 21st and 22nd amino acids | 3-Letter | 1-Letter |
|---|---|---|
| Selenocysteine | Sec | U |
| Pyrrolysine | Pyl | O |
In addition to the specific amino acid codes, placeholders are used in cases where chemical or crystallographic analysis of a peptide or protein cannot 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.
In addition, many non-standard amino acids have a specific code. For example, several peptide drugs, such as Bortezomib and 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. To aid in the analysis of protein structure, photocrosslinking amino acid analogues are available. These include photoleucine (pLeu) and photomethionine (pMet).[97]
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