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4-6).Amino Acids Can Be Classified by R GroupAn understanding of the chemical properties of the standard aminoacids is central to an understanding of much of biochemistry. The topiccan be simplified by grouping the amino acids into classes based on theproperties of their R groups (Table 5-1), in particular, their polarityor tendency to interact with water at biological pH (near pH 7.0).
Thepolarity of the R groups varies widely, from totally nonpolar or hydrophobic (water-insoluble) to highly polar or hydrophilic (water-soluble).The structures of the 20 standard amino acids are shown in Figure5-6, and many of their properties are listed in Table 5-1. There arefive main classes of amino acids, those whose R groups are: nonpolarand aliphatic; aromatic (generally nonpolar); polar but uncharged;negatively charged; and positively charged. Within each class thereare gradations of polarity, size, and shape of the R groups.Chapter 5 Amino Acids and PeptidesNonpolar, aliphatic R groupscocrH 3 N-c-HHGlycineCOO"IH,N—C—HCH 3Aromatic R groupsCOO"COO"H3N-C-HCHCH3 CH3ValineAlanineCOO"IPhenylalanineIH3N-C-HH3N—C—HH—C—CH3CH 2CI13 CH3LeucineH2CCH 2H2Positively charged R groupsCH 3IsoleucineCOO"ProlineCH 2+IH3N—C-HCH 2 OHSerineCOO"CH 2CH 2H3N—C—HCH 2CHNH2NH 3C=NH 2IH3N—C—HCH3ThreonineCysteineCOO"H,N—C—HH3N—C—HCH 2AHoNOAsparaginecoo-CH 2H3N—C—HOGlutamineNonpolar, Aliphatic R Groups The hydrocarbon R groups in thisclass of amino acids are nonpolar and hydrophobic (Fig.
5-6). Thebulky side chains of alanine, valine, leucine, and isoleucine, withtheir distinctive shapes, are important in promoting hydrophobic interactions within protein structures. Glycine has the simplest aminoacid structure. Where it is present in a protein, the minimal sterichindrance of the glycine side chain allows much more structural flexibility than the other amino acids. Proline represents the oppositestructural extreme. The secondary amino (imino) group is held in arigid conformation that reduces the structural flexibility of the proteinat that point.HistidineNegatively charged R groups+ IXNH>HH •NArginineLysineCH 2CH2NC-NH2SHCOO"-, ICH 2CH 3MethionineCH 2H-C-OHCH 2S+H3N—C—HCOO"+ICH2CH 2COO"coo-H,N—C—HH3N—C—HCH 2Polar, uncharged R groupsCOO"coo+ IH3N—C—H+coo-I+H,N—C—Hcocr+115cooH3N—C—HCH 2CH 2CH 2COO"coo~AspartateGlutamateFigure 5-6 The 20 standard amino acids of proteins. They are shown with their amino and carboxyl groups ionized, as they would occur atpH 7.0.
The portions in black are those common toall the amino acids; the portions shaded in red arethe R groups.116Part II Structure and CatalysisTryptophan230 240 250 260 270 280 290 300 310Wavelength (nm)COCT+COO"IH3N-C-HH3N-C-HCH2—Cysteine—CH2Cysteine2H2HCOO"ccxrH3N-C-H H 3 N-C—HFigure 5—7 Comparison of the light absorbancespectra of the aromatic amino acids at pH 6.0. Theamino acids are present in equimolar amounts(10"3 M) under identical conditions. The light absorbance of tryptophan is as much as fourfoldhigher than that of tyrosine.
Phenylalanine absorbsless light than either tryptophan or tyrosine. Notethat the absorbance maximum for tryptophan andtyrosine occurs near a wavelength of 280 nm.Aromatic R Groups Phenylalanine, tyrosine, and tryptophan,with their aromatic side chains (Fig. 5-6), are relatively nonpolar (hydrophobic). All can participate in hydrophobic interactions, which areparticularly strong when the aromatic groups are stacked on one another. The hydroxyl group of tyrosine can form hydrogen bonds, and itacts as an important functional group in the activity of some enzymes.Tyrosine and tryptophan are significantly more polar than phenylalanine because of the tyrosine hydroxyl group and the nitrogen of thetryptophan indole ring.Tryptophan and tyrosine, and to a lesser extent phenylalanine,absorb ultraviolet light (Fig.
5-7 and Box 5-1). This accounts for thecharacteristic strong absorbance of light by proteins at a wavelength of280 nm, and is a property exploited by researchers in the characterization of proteins.Polar, Uncharged R Groups The R groups of these amino acids (Fig.5-6) are more soluble in water, or hydrophilic, than those of the nonpolar amino acids, because they contain functional groups that formhydrogen bonds with water.
This class of amino acids includes serine,threonine, cysteine, methionine, asparagine, and glutamine.The polarity of serine and threonine is contributed by their hydroxylgroups; that of cysteine and methionine by their sulfur atom; and thatof asparagine and glutamine by their amide groups.Asparagine and glutamine are the amides of two other amino acidsalso found in proteins, aspartate and glutamate, respectively, to whichasparagine and glutamine are easily hydrolyzed by acid or base.
Cysteine has an R group (a thiol group) that is approximately as acidic asthe hydroxyl group of tyrosine. Cysteine requires special mention foranother reason. It is readily oxidized to form a covalently linked dimeric amino acid called cystine, in which two cysteine molecules arejoined by a disulfide bridge. Disulfide bridges of this kind occur inmany proteins, stabilizing their structures.CystineNegatively Charged (Acidic) R Groups The two amino acids havingR groups with a net negative charge at pH 7.0 are aspartate andglutamate, each with a second carboxyl group (Fig. 5-6). These aminoacids are the parent compounds of asparagine and glutamine, respectively.Positively Charged (Basic) R Groups The amino acids in which the Rgroups have a net positive charge at pH 7.0 are lysine, which has asecond amino group at the e position on its aliphatic chain; arginine,which has a positively charged guanidino group; and histidine, containing an imidazole group (Fig.
5-6). Histidine is the only standardamino acid having a side chain with a pKa near neutrality.Chapter 5 Amino Acids and PeptidesBOX 5-1117Absorption of Light by MolecMeasurement of light absorption is an importanttool for analysis of many biological molecules. Thefraction of the incident light absorbed by a solutionat a given wavelength is related to the thickness ofthe absorbing layer (path length) and the concentration of the absorbing species. These two relationships are combined into the Lambert-Beerlaw, given in integrated form aswhere 70 is the intensity of the incident light, I isthe intensity of the transmitted light, e is themolar absorption coefficient (in units of liters permole-centimeter), c the concentration of the absorbing species (in moles per liter), and I the pathlength of the light-absorbing sample (in centimeters).
The Lambert-Beer law assumes that the incident light is parallel and monochromatic andthat the solvent and solute molecules are randomly1.0oriented. The expression log (IQ/I) is called the absorbance, designated A.It is important to note that each millimeter pathlength of absorbing solution in a 1.0 cm cell absorbsnot a constant amount but a constant fraction ofthe incident light. However, with an absorbinglayer of fixed path length, the absorbance A is directly proportional to the concentration of the absorbing solute.The molar absorption coefficient varies with thenature of the absorbing compound, the solvent, thewavelength, and also with pH if the light-absorbing species is in equilibrium with another specieshaving a different spectrum through gain or loss ofprotons.In practice, absorbance measurements are usually made on a set of standard solutions of knownconcentration at a fixed wavelength.
A sample ofunknown concentration can then be compared withthe resulting standard curve, as shown in Figure 1.r^5954080120160 200Protein concentration (fxg/mh)Cells Also Contain Nonstandard Amino AcidsIn addition to the 20 standard amino acids that are common in allproteins, other amino acids have been found as components of onlycertain types of proteins (Fig. 5-8a).
Each of these is derived from oneof the 20 standard amino acids, in a modification reaction that occursafter the standard amino acid has been inserted into a protein. Amongthe nonstandard amino acids are 4-hydroxyproline, a derivative ofproline, and 5-hydroxylysine; the former is found in plant cell-wallproteins, and both are found in the fibrous protein collagen of connective tissues. AT-Methyllysine is found in myosin, a contractileprotein of muscle. Another important nonstandard amino acid isFigure 1 Eight standard solutions containingknown amounts of protein and one sample containing an unknown amount of protein were reactedwith the Bradford reagent. This reagent contains adye that shifts its absorption maximum to 595 nmwhen it binds amino acid residues.
The A595 (absorbance at 595 nm) of the standard samples wasplotted against the protein concentration to createthe standard curve, shown here. The A595 of theunknown sample, 0.58, corresponds to a proteinconcentration of 122 /xg/mL.Part II Structure and Catalysis118HH3N—CH2—CH2—CH2—CH—COO"HO-CH2N—C—N—CH2—CH2—CH2—CH—COOCH2+6 HOrnithineH 2 C^ + / CH--COCrNH 3Citrulline(b)4-HydroxyprolineH3N-CH2-CH—CH2-CH2-CH—COO"+OHNH 35-HydroxylysineCH3-NH-CH2-CH2-CH2-CH2—CH—COO~+NH 36-iV-MethyllysineCOO"OOC—CH—CH2—CH—COO""NH 3y-Carboxyglutamatey-carboxyglutamate, found in the blood-clotting protein prothrombin as well as in certain other proteins that bind Ca 2+ in their biological function. More complicated is the nonstandard amino acid desmosine, a derivative of four separate lysine residues, found in thefibrous protein elastin.
Selenocysteine contains selenium ratherthan the oxygen of serine, and is found in glutathione peroxidase and afew other proteins.Some 300 additional amino acids have been found in cells and havea variety of functions but are not substituents of proteins. Ornithineand citrulline (Fig. 5-8b) deserve special note because they are keyintermediates in the biosynthesis of arginine and in the urea cycle.These pathways are described in Chapters 21 and 17, respectively.Amino Acids Can Act as Acids and as BasesH3NCOO"NH,(CH2)2-<CH-(CH 2 ) 2\When a crystalline amino acid, such as alanine, is dissolved in water, itexists in solution as the dipolar ion, or zwitterion, which can act eitheras an acid (proton donor):HCOO"COO"+H3NCOO"Desmosineor as a base (proton acceptor):HHSe—CH2—CH—COO~R—C-COO + HNH+NH 3Selenocysteine(a)Figure 5-8 (a) Some nonstandard amino acidsfound in proteins; all are derived from standardamino acids.
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