Amino Acids - Introduction
Introduction: Proteins are probably the most important class of biochemical molecules, although of course lipids and carbohydrates are also essential for life. Proteins are the basis for the major structural components of animal and human tissue. Proteins are natural polymer molecules consisting of amino acid units. The number of amino acids in proteins may range from two to several thousand. Amino Acids: Although we are studying only about 20 amino acids, there are about six more found in the body. Many others are also known from a variety of sources. Amino acids are the building blocks used to make proteins and peptides. The different amino acids have interesting properties because they have a variety of structural parts which result in different polarities and solubilities. Each amino acid has at least one amine and one acid functional group as the name implies. See graphic on the left. The different properties result from variations in the structures of different R groups. The R group is often referred to as the amino acid "side chain". Amino acids have special common names, however, a three letter abreviation for the name is used most of the time. Consult the amino acid table on the next page for structure, names, and abbreviations. Zwitterion: Amino acid physical properties indicate a "salt-like" behavior. Amino acids are crystalline solids with relatively high melting points, and most are quite soluble in water and insoluble in non-polar solvents. In solution, the amino acid molecule appears to have a charge which changes with pH. An intramolecular neutralization reaction leads to a salt-like ion called a zwitterion. The accepted practice is to show the amino acids in the zwitterion form. (1) The carboxyl group can lose a hydrogen ion to become negatively charged. |
Introduction: Proteins are probably the most important class of biochemical molecules, although of course lipids and carbohydrates are also essential for life. Proteins are the basis for the major structural components of animal and human tissue. Proteins are natural polymer molecules consisting of amino acid units. The number of amino acids in proteins may range from two to several thousand. See Amino Acids. Primary Protein Structure: The primary protein structure is defined as the specific sequence of amino acids in the protein. In order to function properly, peptides and proteins must have the correct sequence of amino acids. In the section on peptide bonds, it was shown that a dipeptide consisting of two different amino acids could have two different sequences as in the example gly - ala or ala - gly. Remember that as written left to right in gly-ala, the glycine has the "free" amine terminal end and alanine has the "free" carboxyl acid terminal end. If three different amino acids (gly, ala, leu) are used to make a tripeptide, how many different sequences are possible? There are six possible sequences: gly - ala - leu; gly - leu - ala; ala - gly - leu; Review example: gly-ala-leu - Chime in new window In the protein hormone insulin, 51 amino acids are found. Using 51 amino acids there are 1.55 x 1066different possible sequences. Many other proteins contain many more amino acids then insulin, but only the correct precise sequence is produced by the body. The procedure used to synthesize the correct sequence of amino acids in proteins is guided by the genetics of DNA and RNA.
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Introduction: The secondary protein structure is the specific geometric shape caused by intramolecular and intermolecular hydrogen bonding of amide groups. The geometry assumed by the protein chain is directly related to molecular geometry concepts of hybridization theory. Experimental evidence shows that the amide unit is a rigid planar structure. This is derived from the planar triangle geometry of the carbonyl unit ( C = O ). See the graphic on the left. The geometry around the nitrogen is derived from an unusual situation with a planar triangle geometry. Apparently, the double bond on oxygen can alternate to make a double bond between carbon and nitrogen. Rotation around bonds C-C and N-C does take place. The C=O and NH are always in a rigid plane. Notice that the carbonyl group and the hydrogen on nitrogen are almost always trans to each other. The result is that chains of amino acids as peptides with amide bonds reflect this geometry. As a result of studying X-ray photographs and constructing molecular models, Linus Pauling and Robert Cory, in 1951, proposed that the protein structures were either in the form of an alpha helix or the beta pleated sheet.
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