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The 20 amino acids of proteins are often referredto as the standard, primary, or normal amino acids, to distinguishthem from amino acids within proteins that are modified after theproteins are synthesized, and from many other kinds of amino acidspresent in living organisms but not in proteins.

The standard aminoacids have been assigned three-letter abbreviations and one-lettersymbols (Table 5-1), which are used as shorthand to indicate the composition and sequence of amino acids in proteins.We note in Figure 5-2 that for all the standard amino acids exceptone (glycine) the a carbon is asymmetric, bonded to four different substituent groups: a carboxyl group, an amino group, an R group, and ahydrogen atom. The a-carbon atom is thus a chiral center (see Fig.3-9). Because of the tetrahedral arrangement of the bonding orbitalsaround the a-carbon atom of amino acids, the four different substituent groups can occupy two different arrangements in space, which arenonsuperimposable mirror images of each other (Fig.

5-3). These twoforms are called enantiomers or stereoisomers (see Fig. 3-9). Allmolecules with a chiral center are also optically active—i.e., theycan rotate plane-polarized light, with the direction of the rotation differing for different stereoisomers.COO"L-AlanineD-Alanine(b)COO"COCT+Proteins can be reduced to their constituent amino acids by a variety ofmethods, and the earliest studies of proteins naturally focused on thefree amino acids derived from them.

The first amino acid to be discovered in proteins was asparagine, in 1806. The last of the 20 to be found,threonine, was not identified until 1938. All the amino acids have trivial or common names, in some cases derived from the source fromwhich they were first isolated. Asparagine was first found in asparagus, as one might guess; glutamate was found in wheat gluten; tyrosine was first isolated from cheese (thus its name is derived from theGreek tyros, "cheese"); and glycine (Greek glykos, "sweet") was sonamed because of its sweet taste.II.H3N—C—HH—C—NH 3L-AlanineD-Alanine(c)Figure 5—3 (a) The two stereoisomers of alanine.L- and D-alanine are nonsuperimposable mirrorimages of each other, (b, c) Two different conventions for showing the configurations in space ofstereoisomers.

In perspective formulas (b) thewedge-shaped bonds project out of the plane of thepaper, the dashed bonds behind it. In projectionformulas (c) the horizontal bonds are assumed toproject out of the plane of the paper, the verticalbonds behind. However, projection formulas areoften used casually without reference to stereochemical configuration.Chapter 5 Amino Acids and Peptides113Table 5-1 Properties and conventions associated with the standard amino acidsAbbreviatedAmino acidNonpolar, aliphaticR groupsGlycineAlanineValineLeucineIsoleucineProlineAromatic R groupsPhenylalanineTyrosineTryptophanPolar, unchargedR groupsSerineThreonineCysteineMethionineAsparagineGlutamineNegatively chargedR groupsAspartateGlutamatePositively chargedR groupsLysineArginineHistidinepi^ipiHydropathyindex*Occurrencein Proteins (%)f5.976.015.975.986.026.48-0.41.84.23.84.5-1.67.59.06.97.54.64.65.485.665.892.8-1.3-0.93.53.51.113.6013.6010.285.685.875.075.745.415.65-0.8-0.72.51.9-3.5-3.57.16.02.81.74.43.99.609.673.654.252.773.22-3.5-3.55.56.28.959.049.1710.5312.486.009.7410.767.59-3.9-4.5-3.27.04.72.1pK2Mr(—COOH)(—NH3+)GAVLIP75891171311311152.342.342.322.362.361.999.609.699.629.609.6810.96PbeFTrp1651812041.832.202.389.13YW9.391051191211491321462.212.111.962.282.022.179.159.628.189.218.809.131331471.882.191461741552.182.171.82namesGlyAlaValLeuHeProSerCyssTCMetAsnMNGinQThtAspGluLysArgHisD•' EKEH:(R group)91110.07* A scale combining hydrophobicity and hydrophilicity; can be used to predict which aminoacids will be found in an aqueous environment (- values) and which will be found in ahydrophobic environment ( + values).

See Box 10-2. From Kyte, J. & Doolittle, R.F. (1982)J. Mol. Biol. 157, 105-132.t Average occurrence in over 200 proteins. From Klapper, M.H. (1977) Biochem. Biophys. Res.Commun. 78, 1018-1024.THOHO^(UHCHOH—C—OH3CH2OHD-GlyceraldehydeCH2OHL-GlyceraldehydeCOO'The classification and naming of stereoisomers is based on the absolute configuration of the four substituents of the asymmetric carbon atom.

For this purpose a reference compound has been chosen, towhich all other optically active compounds are compared. This reference compound is the 3-carbon sugar glyceraldehyde (Fig. 5-4), thesmallest sugar to have an asymmetric carbon atom. The naming ofconfigurations of both simple sugars and amino acids is based on theabsolute configuration of glyceraldehyde, as established by x-ray diffraction analysis. The stereoisomers of all chiral compounds having aconfiguration related to that of L-glyceraldehyde are designated L (forlevorotatory, derived from levo, meaning "left"), and the stereoisomersrelated to D-glyceraldehyde are designated D (for dextrorotatory, derived from dextro, meaning "right").

The symbols L and D thus refer tothe absolute configuration of the four substituents around the chiralcarbon.COOCH3L-AlanineD-AlanineFigure 5-4 Steric relationship of the stereoisomersof alanine to the absolute configuration of L- andD-glyceraldehyde. In these perspective formulas, thecarbons are lined up vertically, with the chiral atomin the center.

The carbons in these molecules arenumbered beginning with the aldehyde or carboxylcarbons on the end, or 1 to 3 from top to bottomas shown. When presented in this way, the R groupof the amino acid (in this case the methyl groupof alanine) is always below the a carbon. L-Aminoacids are those with the a-amino group on the left,and D-amino acids have the a-amino group on theright.Part II Structure and Catalysis114Proteins Contain L-Amino AcidsNearly all biological compounds with a chiral center occur naturally inonly one stereoisomeric form, either D or L. The amino acids in proteinmolecules are the L stereoisomers.

D-Amino acids have been found onlyin small peptides of bacterial cell walls and in some peptide antibiotics(see Fig. 5-19).It is remarkable that the amino acids of proteins are all L stereoisomers. As we noted in Chapter 3, when chiral compounds are formed byordinary chemical reactions, a racemic mixture of D and L isomers results. Whereas the L and D forms of chiral molecules are difficult for achemist to distinguish and isolate, they are as different as night andday to a living system. The ability of cells to specifically synthesize theL isomer of amino acids reflects one of many extraordinary propertiesof enzymes (Chapter 8). The stereospecificity of the reactions catalyzedby some enzymes is made possible by the asymmetry of their activesites. The characteristic three-dimensional structures of proteins(Chapter 7), which dictate their diverse biological activities, requirethat all their constituent amino acids be of one stereochemical series.Amino Acids Are Ionized in Aqueous SolutionsCOOHH2N—C—HRNonionicformCOO"H3N-C-HRZwitterionicformFigure 5—5 Nonionic and zwitterionic forms ofamino acids.

Note the separation of the + and charges in the zwitterion, which makes it an electric dipole. The nonionic form does not occur in significant amounts in aqueous solutions. The zwitterion predominates at neutral pH.Amino acids in aqueous solution are ionized and can act as acids orbases. Knowledge of the acid-base properties of amino acids is extremely important in understanding the physical and biological properties of proteins. Moreover, the technology of separating, identifying,and quantifying the different amino acids, which are necessary stepsin determining the amino acid composition and sequence of proteinmolecules, is based largely on their characteristic acid-base behavior.Those a-amino acids having a single amino group and a singlecarboxyl group crystallize from neutral aqueous solutions as fully ionized species known as zwitterions (German for "hybrid ions"), eachhaving both a positive and a negative charge (Fig.

5-5). These ions areelectrically neutral and remain stationary in an electric field. The dipolar nature of amino acids was first suggested by the observation thatcrystalline amino acids have melting points much higher than those ofother organic molecules of similar size. The crystal lattice of aminoacids is held together by strong electrostatic forces between positivelyand negatively charged functional groups of neighboring molecules,resembling the stable ionic crystal lattice of NaCl (see Fig.

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