9.2: Amino Acids
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- To recognize amino acids and classify them based on the characteristics of their side chains.
The proteins in all living species, from bacteria to humans, are polymers constructed from the same set of 20 amino acids, so called because each contains an amino group attached to a carboxylic acid. The amino acids in proteins are α-amino acids, which means the amino group is attached to the α-carbon of the carboxylic acid. Humans can synthesize only about half of the needed amino acids; the remainder must be obtained from the diet and are known as essential amino acids.
Amino Acid Structure
Every amino acid contains an amino group, (–NH2), a carboxyl group, (–COOH), and a side chain or R group, which are all attached to the alpha-carbon (the one directly bonded to the carboxyl functional group). Therefore, amino acids are commonly called alpha-amino acids. The figure 9.2.1 shows the structure of a generic α-amino acid.
Figure \(\PageIndex{1}\): An α-amino acid. The three parts to an amino acid include the amino group, the carboxyl group, and the side-chain or R group all attached to the α-carbon. The R group is the part that distinguishes one amino acid from the next.
Recall from earlier that a carboxylic acid is a weak acid (H+ ion donor) and an amine is a weak base (H+ ion acceptor). Both functional groups are present in the same molecule and so the structure of the amino acid allows it to act as both an acid and a base in the same molecule. The properties of amino acids reflect this acid-base property. The amino acids are soluble in water, colorless, nonvolatile, crystalline solids, melting and decomposing at temperatures above 200°C. These melting temperatures are more like those of inorganic salts than those of amines or organic acids and indicate that the structures of the amino acids in the solid state and in neutral solution are best represented as having both a negatively charged group and a positively charged group. Such a species is known as a zwitterion.
Figure \(\PageIndex{2}\): Zwitterion vs Uncharged Molecule.
Classification
In addition to the amino and carboxyl groups, amino acids have a side chain or R group attached to the α-carbon. Each amino acid has unique characteristics arising from the size, shape, solubility, and ionization properties of its R group. As a result, the side chains of amino acids exert a profound effect on the structure and biological activity of proteins. Although amino acids can be classified in various ways, one common approach is to classify them according to whether the functional group on the side chain at neutral pH is nonpolar, polar neutral, negatively charged, or positively charged. The nonpolar and the polar neutral amino acids exist as zwitterions at physiological pH. Amino acids are overall negatively charged when they have a carboxylic acid in their sidechains and are also call polar acidic amino acids. Amino acids are overall positively charged when they have an amine functional group in their side chain and are addressed as polar basic.
The structures and names of the 20 amino acids, their one- and three-letter abbreviations, and some of their distinctive features are given in Table \(\PageIndex{1}\).
| Common Name | Abbreviation | Structural Formula at physiological pH | Molecular Weight (amu) | Distinctive Feature |
|---|---|---|---|---|
| Amino acids with a nonpolar side chain (nonpolar amino acids) | ||||
| glycine | gly (G) |  |
75 | _ |
| alanine | ala (A) |  |
89 | — |
| valine | val (V) |  |
117 | a branched-chain amino acid |
| leucine | leu (L) |  |
131 | a branched-chain amino acid |
| isoleucine | ile (I) |  |
131 | an essential amino acid because most animals cannot synthesize branched-chain amino acids |
| phenylalanine | phe (F) |  |
165 | also classified as an aromatic amino acid |
| tryptophan | trp (W) |  |
204 | also classified as an aromatic amino acid |
| methionine | met (M) |  |
149 | side chain has a sulfide functional group and functions as a methyl group donor |
| proline | pro (P) |  |
115 | contains a secondary amine group |
| Amino acids with a polar but neutral side chain (polar neutral amino acids) | ||||
| serine | ser (S) |  |
105 | found at the active site of many enzymes |
| threonine | thr (T) |  |
119 | named for its similarity to the sugar threose |
| cysteine | cys (C) |  |
121 | oxidation of two cysteine molecules yields disulfide bridge in proteins |
| tyrosine | tyr (Y) |  |
181 | also classified as an aromatic amino acid |
| asparagine | asn (N) |  |
132 | contains the amide of aspartic acid |
| glutamine | gln (Q) |  |
146 | contains the amide of glutamic acid |
| Amino acids with a negatively charged side chain (polar acidic/polar negative amino acids | ||||
| aspartic acid | asp (D) |  |
132 | carboxylic acid functional groups are ionized at physiological pH; also known as aspartate |
| glutamic acid | glu (E) |  |
146 | carboxylic acid functional groups are ionized at physiological pH; also known as glutamate |
| Amino acids with a positively charged side chain (polar basic/polar basic amino acids) | ||||
| histidine | his (H) |  |
155 | at physiological pH the side chain exists as a cation |
| lysine | lys (K) |  |
147 | at physiological pH the side chain exists as a cation |
| arginine | arg (R) |  |
175 | at physiological pH the side chain exists as a cation |
The first amino acid to be isolated was asparagine in 1806. It was obtained from protein found in asparagus juice (hence the name). Glycine, the major amino acid found in gelatin, was named for its sweet taste (Greek glykys, meaning “sweet”). Glutamic acid is named as such because it was first isolated from gluten. The crystalline salt of glutamic acid is called monosodium glutamate (MSG), which naturally occurs in some foods but is also added to as a savory or "umami" flavor enhancer. In some cases an amino acid found in a protein is actually a derivative of one of the common 20 amino acids (one such derivative is hydroxyproline). The modification occurs after the amino acid has been assembled into a protein.
Summary
Amino acids can be classified based on the characteristics of their distinctive side chains as nonpolar, polar neutral, negatively charged, or positively charged.