Chapter 1 Amino Acids: Structure, Physical & Chemical Properties PDF

Chapter 1 Amino Acids I: Structure, Physical & Chemical Basic Biochemistry 03040346 Prepared by Dr. Yousef Abu-Zaitoon  1.1 Structure of the amino acids Proteins: are the most abundant and functionally diverse molecules in living systems. All proteins share the com...

Chapter 1 Amino Acids I: Structure, Physical & Chemical Basic Biochemistry 03040346 Prepared by Dr. Yousef Abu-Zaitoon  1.1 Structure of the amino acids Proteins: are the most abundant and functionally diverse molecules in living systems. All proteins share the common structural feature of being linear polymers of amino acids. Each amino acids (except for proline, which has a secondary amino group) has a carboxyl group, a primary amino group, and a distinctive side chain(R- group). Bonded to the α-carbon atom Figure 1.1: Comparison of the secondary amino group found in proline with the primary amino group found in other amino acids, such as alanine Figure 1.2: Structural features of amino acids (shown in their fully protonated form). Figure 1.3: Peptide bonds between amino acids  At physiologic pH (7.4) the carboxyl group is dissociated, forming the negatively charged carboxylate ion(COO-) and the amino group is protonated (NH3+). In proteins, almost all of these carboxyl and amino groups are combined through peptide linkage and, in general, are not available for chemical reaction except for hydrogen bond formation. Figure 1.4: Hydrogen bond between the phenolic hydroxyl group of tyrosine and another molecule containing carbonyl group  Amino acids are classified according to the properties of their side chains to polar (have uneven distribution of electrons such as acids and bases) and non polar (have even distribution of electrons).  1.2 Amino acids with nonpolar side chains They do not gain or lose protons or participate in hydrogen or ionic bonds. Their side chains promote hydrophobic interactions. In aqueous solutions (polar environments); the side chains of the nonpolar amino acids tend to cluster together in the interior of the protein. This phenomenon, known as the hydrophobic effect. Figure 1.5: Location of nonpolar amino acids in soluble and membrane proteins  1.3 Amino acids with uncharged polar side chains These amino acids have zero net charge at neutral pH, although the side chains of cysteine and tyrosine can lose a proton at an alkaline pH. Serine, threonine, and tyrosine each contain a polar hydroxyl group (OH-) that can participate in hydrogen bond formation. The side chains of asparagine and glutamine each contain a carbonyl group and an amide group, both of which can participate in hydrogen bonds. Figure 1.6: Classification of the 20 amino acids commonly found in proteins, according to the charge and polarity of their side chains at acidic pH (continued from Figure 1.4). Each amino acid is shown in its fully protonated form, with dissociable hydrogen ions represented in red print. The pK values for the α-carboxyl and α-amino groups of the nonpolar amino acids are similar to those shown for glycine. Figure 1.7: Nonpolar amino acids Figure 1.8: Uncharged polar amino acids and acidic amino acids.  1.4 Amino acids with acidic side chains Aspartic and glutamic acids are proton donors. At physiologic pH, their side chains are fully ionized (contain a negatively charged carboxlate group). They are called aspartate or glutamate).  1.5 Amino acids with basic side chains The side chains of basic amino acids accept protons. At physiologic pH, the side chains of lysine and arginine are fully ionized and positively charged. Histidine is weakly basic, and the free amino acid is largely uncharged at physiologic pH. When histidine is incorporated into a protein, its side chain can be either positively charged or neutral, depending on the ionic environment provided by the polypeptide chains of the protein  1.6 Abbreviation and symbols of amino acids Each amino acid name has an associated three- letter abbreviation and a one-letter symbol. Figure 1.9: Abbreviations and symbols for the commonly occurring amino acids.  1.7 Optical properties of amino acids The α-carbon of an amino acid is attached to 4 different chemical groups and is, therefore, a chiral or optically active carbon atom. Glycine is the exception because its α-carbon has 2 hydrogen substituents and, therefore is optically inactive. Amino acids that have an asymmetric center at the α-carbon can exist in 2 forms, designated D, and L, that are mirror images of each other.  The 2 forms in each pair are termed stereoisomers, optical isomers, or enantiomers. All amino acids found in proteins are of the L- configuration. D-amino acids are found in some antibiotics and in plant and bacterial cell walls. Figure 1.10: D and L forms of alanine are mirror images. The carbons are lined up vertically, with the chiral atom in the center. The carbons in these molecules are numbered beginning with the terminal carboxyl carbon, from top to bottom the R group of the amino acid (in this case the methyl group of alanine) is always below the α-carbon. L-amino acids are those with the α-amino group on the left, and D-amino acids have the α-amino group on the right 1. Lippincott’s Illustrated Reviews; Biochemistry. Richard Harvey and Denise Ferrier. Fifth Edition 2011.