Chapter Outline (3-1) Amino acids are three-dimensional (3-2) Structures and properties of amino acids (3-3) Amino acids can act as both acids and bases (3-4) The peptide bond (3-5) Small peptides with physiological activity
Amino Acids Are Three-Dimensional • Amino acids - Include an amino group and a carboxyl group, both of which are bonded to the - carbon • Amino group: —NH2 functional group • Carboxyl group: —COOH functional group that disassociates to give the carboxylate anion, — COO–, and a hydrogen ion
• -carbon - Bonded to a hydrogen and to the side chain
group, R • Side chain group: Portion of an amino acid that determines its identity • Two stereoisomers of amino acids are designated as L- and D-amino acids based on similarity to glyceraldehyde • Stereoisomers: Molecules that differ from each other only in their configuration
Structure and Properties of Amino Acids • With the exception of glycine, all amino acids have at least one chiral center (the -carbon) and are chiral (stereoisomers) • Vast majority of -amino acids have the L configuration at the -carbon • Proline is usually in the L form • Side chain carbons in amino acids other than glycine are designated with Greek symbols, starting at - carbon (β-, γ-, δ-, ε-, and ω-) • Amino acids can be referred to by three-letter or one- letter codes
Nonpolar Amino Acids • Group of amino acids that has nonpolar side chains • Glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, and methionine • Alanine, valine, leucine, and isoleucine contain aliphatic hydrocarbon group • Proline has an aliphatic cyclic structure • In phenylalanine, the hydrocarbon group is aromatic • In tryptophan, the side chain contains an indole ring, which is aromatic • In methionine, the side chain contains a sulfur atom in addition to aliphatic hydrocarbon groupings
Acidic Amino Acids: Glutamic Acid and Aspartic Acid • Glutamic acid and aspartic acid have carboxyl groups in their side chains in addition to the one present in all amino acids • Carboxyl group can lose a proton, forming carboxylate anions • Side chains are negatively charged at neutral pH
Basic Amino Acids • Histidine, lysine, and arginine have basic side chains • Side chains are positively charged at or near neutral pH 7 • In lysine, side-chain amino group is attached to an aliphatic hydrocarbon chain • In arginine, side chain is a guanidino group bonded to an aliphatic hydrocarbon chain • In histidine, side chain is an imidazole group
• Average pKa of an –carboxyl group is 2.19, which
makes it a considerably stronger acid than acetic acid (pKa 4.76) • Greater acidity is due to the electron-withdrawing inductive effect of the –NH3+ group • Compared with a value of 10.76 for a 2° alkylammonium ion, average value of pKa for an – NH3+ group is 9.47
Basicity: –NH3+ groups • Guanidine group - Side chain of arginine is a considerably stronger base than an aliphatic amine • Basicity of the guanidino group is attributed to the large resonance stabilization of the protonated form relative to the neutral form • Imidazole group - Side-chain imidazole group of histidine is a heterocyclic aromatic amine
Example 3.1 - Structures and Properties of Amino Acids • In the following group, identify the amino acids with nonpolar side chains and those with basic side chains: • Alanine, serine, arginine, lysine, leucine, and phenylalanine • pKa of the side-chain imidazole group of histidine is 6.0 • What is the ratio of uncharged to charged side chains at pH 7.0?
Example 3.1 - Solution • Amino acids with nonpolar and basic side chains • Nonpolar - Alanine, leucine, and phenylalanine • Basic - Arginine and lysine • Serine is not in either category because it has a polar side chain • Ratio of uncharged to charged side chains at pH 7.0 • Ratio is 10:1 because the pH is one unit higher than the pKa
Titration of Amino Acids • When an amino acid is titrated, its titration curve represents the reaction of each functional group with a hydrogen ion • Titration curve of: • Alanine is that of a diprotic acid • Histidine is that of a triprotic acid
Isoelectric pH (pI) • pH at which a molecule has no net charge • Known as isoelectric point pK a1 + pK a2 pI = 2 • pI for glycine falls midway between the pKa values for the carboxyl and amino groups
Example 3.2 - Amino Acid Titrations • Aspartic acid, alanine, arginine, glutamic acid, leucine, and lysine • Which of the these amino acids has a net charge of +2 at low pH? • Which has a net charge of –2 at high pH?
Example 3.2 - Solution • Arginine and lysine have net charges of +2 at low pH because of their basic side chains • Aspartic acid and glutamic acid have net charges of − 2 at high pH because of their carboxylic acid side chains • Alanine and leucine do not fall into either category because they do not have titratable side chains
Peptide Bond • Amide bond between amino acids in a protein • Individual amino acids can be linked by forming covalent bonds • Bond is formed between α-carboxyl group of one amino acid and the α-amino group of the next one • Peptides: Molecules formed by linking two to several dozen amino acids by amide bonds
Peptide Bond (continued 2) • Carbon–nitrogen bond in a peptide bond is usually written as a single bond, with one pair of electrons shared between the two atoms • Single bond can be written as a double bond with a shift in the position of pair of electrons • Resonance structures: Structural formulas that differ from each other only in the position of electrons • Peptide bond can be represented as a resonance hybrid of two structures • Peptide bond has partial double bond character making it stronger than single bonds • Rotation around it is restricted
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