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voet 04 - 4 Amino Acids This chapter introduces you to the...

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4 Amino Acids This chapter introduces you to the structure and chemistry of amino acids. The chapter begins by discussing the zwitterionic character of amino acids at physiological pH, followed by a brief introduction to the amide linkage known as the peptide bond. Amino acids are categorized by the chemistry of their unique R groups and by their mode of biosynthesis. The standard amino acids are specified by the genetic code; nonstandard amino acids include the D stereoisomers and modified forms of the standard amino acids. This chapter also introduces you to the conventions used to describe stereoisomers, namely the Fischer convention and the RS system. Amino acids contain ionizable groups, so this chapter discusses the acid–base properties of amino acids and introduces you to the concept of the isoelectric point. A clear understanding of the acid–base properties of amino acids is critical for appreciating the structural and catalytic behavior of proteins. The chapter closes with a brief discussion of the biological significance of some amino acid derivatives. Essential Concepts Amino Acid Structure 1. All proteins are composed of 20 standard amino acids, which are specified by the genetic code. 2. The standard amino acids are called α -amino acids because they have a primary amino group and a carboxyl group bound to the same carbon atom (the α carbon). Only proline has a secondary amino group attached to the α carbon, but it is still commonly referred to as an α -amino acid. 3. The generic structure of an amino acid at pH 7 is shown below. At pH 7, the amino acid is a zwitterion, or dipolar ion. A unique side chain, or R group, characterizes each amino acid.
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Chapter 4 Amino Acids 38 4. Amino acids are polymerized by condensation reactions to form a chain called a polypeptide. Each polypeptide is polarized: One end has a free amino group and the other end has a free carboxyl group, referred to as the N-terminus and the C-terminus, respectively. 5. The R groups of the standard 20 amino acids are classified into three categories based on their polarities and charge at pH 7: the nonpolar amino acids, the polar uncharged amino acids, and the charged amino acids (see Table 4-1). 6. Among the nonpolar amino acids, glycine (shorthand Gly or G) has a hydrogen atom as its R group. Alanine (Ala; A), valine (Val; V), leucine (Leu; L), isoleucine (Ile; I), and methionine (Met; M) have aliphatic chains as R groups (Met has a sulfur rather than a methylene group). Tryptophan (Trp; W) and phenylalanine (Phe; F) contain bulky indole and phenyl groups, respectively. 7. The polar uncharged amino acids include asparagine (Asn; N), glutamine (Gln; Q), serine (Ser; S), threonine (Thr; T), tyrosine (Tyr; Y), and cysteine (Cys; C). Amide functional groups occur in Gln and Asn. Alcoholic functional groups occur in Ser and Thr. Tyrosine and cysteine are characterized by a phenolic group and a thiol group, respectively.
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