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Chapter 3

After studying this chapter, you should be able to:

• Name, and draw the structures of, the 20 amino acids present in proteins.
• Write the three- and one-letter designations for each of the common amino acids.
• List the ionizable groups of the common amino acids and their pKa values.
• Calculate the pH of an unbuffered aqueous solution of a polyfunctional amino acid and the change in pH that occurs following the addition of a given quantity of strong acid or alkali.
• Define pI and indicate its relationship to the net charge on a polyfunctional electrolyte.
• Explain how pH, pKa and pI can be used to predict the mobility of a polyelectrolyte, such as an amino acid, in a direct-current electrical field.
• Describe the contribution of each type of R group of the common amino acids to their chemical properties.
• Describe the directionality, nomenclature, and primary structure of peptides.
• Identify the bond in a peptide that exhibits partial double-bond character and its conformational consequences in a peptide.
• Identify those bonds in the peptide backbone that are capable of free rotation and the Greek letters used to designate them.

In addition to providing the monomer units from which the long polypeptide chains of proteins are synthesized, the L-α-amino acids and their derivatives participate in cellular functions as diverse as nerve transmission and the biosynthesis of porphyrins, purines, pyrimidines, and urea. Short polymers of amino acids called peptides perform prominent roles in the neuroendocrine system as hormones, hormone-releasing factors, neuromodulators, or neurotransmitters. Humans and other higher animals lack the capability to synthesize 10 of the 20 common L-α-amino acids in amounts adequate to support infant growth or to maintain health in adults. Consequently, the human diet must contain adequate quantities of these nutritionally essential amino acids. While human proteins contain only L-α-amino acids, microorganisms make extensive use of D-α-amino acids. Bacillus subtilis, for example, secretes a mixture of D-methionine, D-tyrosine, D-leucine, and D-tryptophan to trigger biofilm disassembly, and Vibrio cholerae incorporates D-leucine and D-methionine into the peptide component of their peptidoglycan layer. Many bacteria elaborate peptides that contain both D- and L-α-amino acids, several of which possess therapeutic value, including the antibiotics bacitracin and gramicidin A and the antitumor agent bleomycin. Certain other microbial peptides are toxic. The cyanobacterial peptides microcystin and nodularin are lethal in large doses, while small quantities promote the formation of hepatic tumors.

The Genetic Code Specifies 20 L-α-Amino Acids

Of the over 300 naturally occurring amino acids, 20 constitute the predominant monomer units of proteins. While a three-letter genetic code could potentially accommodate more than 20 amino acids, several amino acids are specified by multiple codons (see Table 37–1). Redundant usage limits the available codons to the 20 L-α-amino acids listed in Table 3–1. Both one- and three-letter abbreviations ...

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