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Amino Acid - Bonding

acids proteins protein molecule

Amino acids are extremely important in nature as the monomers, or individual units, that join together in chains to form copolymers (polymers made of more than one kind of monomer). The chains may contain as few as two or as many as 3,000 amino acid units. Groups of only two amino acids are called dipeptides; three amino acids bonded together are called tripeptides; if there are more than 10 in a chain, they are called polypeptides; and if there are 50 or more, they are known as proteins.

Figure 1. Illustration by Hans & Cassidy. Courtesy of Gale Group.

In 1902 the German organic chemist, Emil Fischer, first proposed that the amino acids in polypeptides are linked together between the carboxyl group of one amino acid and the amino group of the other. This bond forms when the -OH from the carboxyl end of one molecule and the hydrogen from the amino end of another molecule split off and form a small molecule byproduct, H2O or water. This type of reaction is called a condensation reaction. The new bond between the carbon atom and the nitrogen atom is called a peptide bond, also known as an amide linkage. Because every amino acid molecule has a carboxyl end and an amino end, each one can join to any other amino acid by the formation of a peptide bond.

All the millions of different proteins in living things are formed by the bonding of only 20 amino acids to form long polymer chains. Like the 26 letters of the alphabet that join together to form different words, depending on which letters are used and what the sequence is, the 20 amino acids can join together in different combinations and sequences to form proteins. But whereas words usually have only about 10 or fewer letters per word, proteins are usually made from at least 50 amino acids to more than 3,000. 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 protein is truly enormous.

The amino acids in polypeptides can be represented in three ways: by writing out the complete chemical formulas; by writing the amino acid sequence using the standard, three-letter abbreviation for each acid as in glyser-ala (which represents glycine, serine and alanine); or by naming the polypeptide as in glycylserylalanine. The name is derived by dropping the -ine or -ic ending of each amino acid along the chain and replacing it with a -yl ending. The last acid of the chain is given its full name. It is common practice to write polypeptides with the free, unbonded amino group on the left and the free carboxylic acid group on the right.

Order is important in the functioning of a protein; gly-ser-ala, gly-ala-ser, and ala-ser-gly, for example, are different peptides. In fact, there are 27 different tripeptides that are possible from these three amino acids. (Each may be used more than once.) There are about two quadrillion different proteins that can exist if each of the 20 amino acids present in humans is used only once. However, just as not all sequences of letters make sense, not all sequences of amino acids make functioning proteins and other sequences can cause undesirable effects. While small mistakes in the amino acid sequence can sometimes be tolerated in nature without serious problems, at other times malfunctioning proteins can be caused by a single incorrect amino acid in the polymer chain. Sickle cell anemia is a fatal disease caused by a single amino acid, glutamic acid being replaced by a different one, valine, at the sixth position from the end of the protein chain in the hemoglobin molecule. This small difference causes lower solubility of the sickle cell hemoglobin molecules. They precipitate out as small rods which give the cells the characteristic sickle shape and result in the often fatal disease.

The specific sequence of the amino acids along the protein chain is referred to as the primary structure of the protein. However, these chains are not rigid, but rather they are long and flexible like string. The strands of protein can twist to form helixes or fold into sheets. They can bend and fold back on themselves to form globs and several protein molecules sometimes combine into a larger molecule. All of these configurations are caused by interactions both within a single protein strand as well as between two or three separate strands of protein.

Just as proteins are formed when amino acids bond together to form long chains, they can be broken down again into their individual amino acids by a reaction called hydrolysis. This reaction is just the reverse of the formation of the peptide bond. In the process of digestion, proteins are once again broken down into their individual amino acid components. Special digestive enzymes are necessary to cause the peptide linkage to break and a molecule of water is added when the reaction occurs. The resulting amino acids are released into the small intestine where they can easily pass into the bloodstream and be carried to every cell of the organism. There, once again, each individual cell can use these amino acids to assemble the new and different proteins required for its specific functions. Life goes on by the continual breakdown of protein into the individual amino acid units followed by the buildup of new protein from these amino acids.

Of the 20 amino acids required by humans for making protein, 12 of them can be made within the body from other nutrients. But the other eight, called the essential amino acids, cannot be made by the body and must be obtained from the diet. These are isoleucine, leucine, lysine, methionine, phenlyalanine, threonine, tryptophan, and valine. In addition, arginine and histidine are believed to be essential to growing children but may not be essential to mature adults. An adequate protein is one that contains all of the essential amino acids in sufficient quantities 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 considered adequate proteins. Many plant proteins do not contain all of the essential amino acids. Corn, for example, does not contain the essential amino acids lysine and tryptophan. Rice is lacking in lysine and threonine, wheat is lacking in lysine, and soy beans are lacking in methionine. People who are vegetarians and do not consume animal proteins in their diets sometimes suffer from malnutrition because of the lack of one or more amino acids in their diets even though they may consume enough food and plenty of calories.

See also Nutrition.



Durbin, Richard, et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge: Cambridge University Press, 1999.

Lide, D. R., ed. CRC Handbook of Chemistry and Physics Boca Raton: CRC Press, 2001.

Newhouse, Elizabeth L., et al., eds. Inventors and Discoverers: Changing Our World. Washington, DC: National Geographic Society, 1994.

White, James, and Dorothy C. White, eds. Proteins, Peptides, and Amino Acids Sourcebooks. Humana Press; 2002.


Bishop, Katherine. "Baby Boomers Fight Aging by Dropping Acid (Amino)." New York Times (10 June 1992): B1(N).

Venter, J.C., et al. "The Sequence of the Human Genome." Science 291 (2001): 1304-1351.

Leona B. Bronstein


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Amino group

—An -NH2 group.

BETA-amino acid

—An amino acid in which the -NH2 (amino) group is bonded to the carbon atom.

BETA-carbon atom

—The carbon atom adjacent to the carboxyl group.

Carboxyl group

—A -COOH group; also written -CO2H.

Essential amino acid

—Amino acids that cannot be synthesized by the body and must be obtained from the diet.


—Small, individual subunits which join together to form polymers.


—Substances made up of chains of amino acids, usually fewer than 50.

Peptide bond

—The bond formed when the carboxyl group of one amino acid joins with the amino group of a second amino acid and splits off a water molecule.

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