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This is the third edition of Through the Microscope. A new edition has just been published. Please go to the Table of contents for the fourth edition
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As with nucleic acids, primary structure refers to the ordered sequence of the different amino acids in a protein. The carboxyl group and the amino group of amino acids are reactive. As shown in Figure 2-9, cells synthesize proteins by attaching the carboxyl group of one amino acid to the amine group the next, with polymerization taking place at the ribosome. This is termed a peptide bond. Since each amino acid has a carboxyl group and an amino group, hundreds of amino acids can be linked together.
Figure 2.9 A peptide bond. The peptide bond between an alanine residue and a valine residue is identified by the arrow. Peptide bonds can form between any two of the 20 amino acids and link the carboxyl group of one amino acid and the amine group of the next.
There are 20 common amino acids found in proteins and these amino acids can be roughly classified into 3 groups: polar, non-polar and charged. Polar and charged amino acids are hydrophilic and are often found on the surface of a protein, interacting with the surrounding water. In contrast, non-polar (or hydrophobic) amino acids avoid water. While this categorization is adequate for most purposes, you should recognize that it is a bit simplistic. For example, arginine does have a charged hydrophilic group at one end, but the -CH2- backbone that makes up most of the amino acid is actually quite hydrophobic. Figure 2-10 shows the chemical structure of all 20 common amino acids.
Figure 2.10 The common amino acids. In the figure, the amino acids are organized into their chemical type and characteristics. Acidic and basic amino acids carry a charge, amino acids with a sulfur or hydroxyl comonent are polar, and aliphatic and aromatic amino acids are non-polar.