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by Peter Stevenson


Amino acids are the basic building blocks of proteins. Fundamentally, amino acids are joined together by peptide bonds to form the basic structure of proteins. However, owing to the many ‘side groups’ that are part of the amino acids other sorts of bonds may form between the amino acid units. These additional bonds twist and turn the protein into convoluted shapes that are unique to the protein and essential to its ability to perform certain functions within the human body. This brief paper looks at the classes of amino acids, and how they bond to form the complex structures of proteins.

The Structure of Amino Acids

Amino acids are carbon compounds that contain two functional groups: an amino group (NH2) and a carboxylic acid group (COOH). A side chain attached to the compound gives each amino acid a unique set of characteristics. Figure 1 illustrates a general model for a typical amino acid.







Figure 1 General structure of a typical alpha amino acid

Amino acids form left and right handed isomers (dextro, and levo). Only L-isomers of amino acids are found in proteins1.

Classification of Amino Acids

There are twenty amino acids that are used to form proteins in the human body, these are called the proteinogenic2 amino acids. There appear to be many different classification systems, three of which are presented here.

Timberlake3, classifies the amino acids using the system presented in Table 1. She uses a simple method of classification, identifying amino acids as polar or non-polar. A further subclassification of acidic-polar when the side chain contains a carboxylic acid, and basic-polar when the side chain contains an amino group is also introduced.

Classification Amino Acid
Nonpolar Glycine









Polar Serine






Acidic (Polar) Aspartic Acid

Glutamic Acid

Basic (Polar) Lysine



Table 1 Classification of amino acids (after Timberlake3)

Devlin4 classifies amino acids along structural lines. Devlin’s system is presented in Table 2.

Superstructure Structure Amino Acid
Monoamino, moncarboxylic   Glycine


  Unsubstituted L-Valine



  Heterocyclic L-Proline


  Aromatic L-Tyrosine


  Thioether L-Methionine
  Hydroxy L-Serine


  Mercapto L-Cysteine
  Carboxamide L-Asparagine


Monamino, dicarboxylic   L-Aspartate


Diamino, monocarboxylic   L-Lysine



Table 2 Classification of amino acids (after Devlin4)

A third method of classification, sourced from Koolman2 is presented in Table 3. This classification system is again based on structure of the side chain.

Classification Amino Acid
Alphatic (do not contain N,O,S in side chain) Glycine





Sulfur-containing Cysteine


Aromatic (benzene ring in side chain) Phenylalanine



Neutral (hydroxyl or amide groups in side chain) Serine




Acidic (carboxylate groups in side chain) Aspartic acid

Glutamic acid

Basic Lysine


Imino acid (special case) Proline

Table 3 Classification of amino acids (after Koolman2)


The Structure of Proteins

Proteins are formed from chains of amino acids, and the nature of the amino acid side chains has significant influence on the topography of the protein. The bonds between amino acid side chains generate a complex protein structure, which is considered in four stages: primary, secondary, tertiary, and quaternary.

The primary structure of a protein refers to the sequence of amino acids that make up the protein. The bonds considered in the primary structure are the peptide bonds between each amino acid.

The secondary structure refers to the shape the protein is pulled into by hydrogen bonds that form between the side chains of the amino acids. There are three common shapes formed: the a -helix, the b -pleated sheet, and the triple helix. All three shapes are very regular and exist as a result of hydrogen bonds between side chains that occur at regular intervals along the primary structure.

The tertiary structure of proteins is the result of further bonding between side chains within the protein and with any water that may be present around the protein. Polar amino acids move to the outside of the shape and non-polar amino acids move to the inside when placed in a polar solution. Bonds that are considered part of the tertiary structure include:

Bonds formed between non-polar side chains,

Disulfide bonds formed between sulfer atoms in cysteine side chains,

Ionic bonds formed between acidic and basic side chains, and

Hydrogen bonds formed between carbonyl groups and hydroxyl or amino groups.

The quaternary structure of proteins is the result of the bonding between two or more polypeptides. The bonds formed are the same as those found in the tertiary structure of proteins. Haemoglobin, the oxygen carrying component of blood, is an example of a protein in a quaternary structure.


Haemoglobin is comprised of four polypeptide subunits, two with alpha helix secondary structure and two with beta pleated sheet form. All four components carry a heme group that can bind to oxygen, and all four components must be present to form haemoglobin. The shape of the haemaglobin affects its ability to carry oxygen, and travel freely throughout the circulatory system.

A condition that is a result of a malformed haemoglobin unit is sickle-cell anemia. In this condition a particular glutamic acid is replaced by a valine, and an ionic cross-link is not formed resulting in a severe change of shape of the tertiary structure of the haemoglobin. The resultant shape is a crescent or sickle which reduces the oxygen carrying capacity of the red blood cell.

Sickle cells are removed from circulation faster than normal cells resulting in anemia. They can also clump together causing blockages, pain and organ damage3.


The shape of proteins is critical to their function, and clearly the shape is largely a result of the bonds that form between the side chains of amino acids that make the protein. It can be concluded that a primary purpose of the side chains in amino acids is to give proteins their shape, which dictates their function.


Davies, J., Shaffer Littlewood, B., Elementary Biochemistry – An Introduction to the Chemistry of Living Cells, Prentice-Hall Inc, New Jersey, 1979.

Koolman, J., Rohm, K-H, Colour Atlas of Biochemistry, Thieme, Stuttgart, 1996.

Timberlake, K.C., Chemistry – 5th Edition, Haper-Collins Publishers Inc, NY, 1992.

Devlin, T.M., The Textbook of Biochemistry – 3rd Edition, Wiley-Liss Inc, NY, 1992.


Copyright © The Australian Naturopathic Network 1998-2002. All rights reserved. 
Revised: May 18, 2002