NO AC DS, PEPT PROTE NS, ENZYMES, AND NUCLE T he chemistry of life is largely the chemistry of polyfunctional organic com- pounds. The functional groups usually are of types that interact rather strongly as, for example, the hydroxyl and carbonyl functions of carbohydrates (Chap- ter 20). The interaction between amino and carboxyl functions of amino acids figures greatly in the present chapter. We will approach the very important chemistry of amino acids and their derivatives in three stages. First, simple a-amino acids will be considered with emphasis on how the properties of amine functions and of acid functions are modified in molecules that possess both groups. Then we shall discuss some important properties of peptides and proteins, which are substances made up of amino acids linked together by amide bonds. Attention also will be given to the chemical problems presented by enzymes, which are protein molecules able to act as efficient catalysts for specific chemical reactions, and to the role of nucleic acids in protein synthesis. 25-1 TYPES OF BIOLOGICALLY IMPORTANT AMINO ACIDS 25-1A Protein Amino Acids The amino acids that occur naturally as constituents of proteins have an amino group (NH,) and a carboxylic acid group (C0,H) attached to the same 25-1A Protein Amino Acids carbon. They are called a-amino acids and have the general formula They differ only in the nature of the R group on the a carbon and, with few exceptions, they are chiral molecules with the L configuration at the chiral a carbon:l L-amino acid (S-amino acid) The structures and names of some particularly important a-amino acids are shown in Table 25-1. You will notice that the names in common use for amino acids are not descriptive of their structural formulas; but at least they have the advantage of being shorter than the systematic names. The abbrevia- tions Gly, Glu, and so on, that are listed in Table 25-1 are particularly useful in designating the sequences of amino acids in proteins and peptides, as will become evident later in the chapter. The nature of the substituent R varies considerably. In some amino acids, R is a hydrocarbon group, whereas in others it possesses functional groups such as OH, SH, SCH,, CQ,H, or NH,. Amino acids that have amine or other basic functions in the R group are called basic amino acids (lysine and arginine), whereas those with acidic groups are called acidic amino acids (aspartic and glutamic acids). Three of the amino acids listed in Table 25-1 (cysteine, cystine, and methionine) contain sulfur in -SH, -S-S-, and -SCH, groups. Cysteine and cystine can be interconverted readily with a wide variety of oxidizing and reducing agents according to the general reaction [OI 2RSH d RSSR. This is an important process in the biochemistry of [HI sulfur-containing peptides and proteins (Section 25-8A). The a-amino function of the common amino acids is primary -NH, in all except proline and hydroxyproline. Several of the amino acids have aromatic R groups (phenylalanine, tyrosine, tryptophan), while histidine and tryptophan have azarene R groups. lA number of D-amino acids have been found to be constituents of peptides in the cell walls of bacteria. 25 Amino Acids, Peptides, Proteins, Enzymes, and Nucleic Acids 25-1A Protein Amino Acids Table 25-1 (continued) Amino Acids Important as Constituents of Proteins Abbreviations Name 3-letter 1- letter Structurea histidine His H phenylalaninec Phe tyrosine TYr tryptophan proline Pro hydroxyprolined Hyp ?! Q "For convenience only, the structures are represented as neutral nonpolar molecules. In reality, ionic and dipolar forms are present in aqueous f solution in amounts dependent on the pH (Section 25-2A). 0 bWater solubility at isoelectric point of the L isomer in g/100 g at 20°C. The D,L mixtures are usually less soluble. "Must be included in diet for maintenance of proper nitrogen equilibrium in normal adult humans. dFound only in collagen. 25-1 B Nonprotein Amino Acids 1216 Exercise 25-1 Select the amino acids in Table 25-1 that have more than one chiral center and draw projection formulas for all the possible stereoisomers of each which possess the L configuration at the a carbon. Exercise 25-2 Which of the amino acids in Table 25-1 are acidic amino acids and which basic amino acids? Which of the structures shown would have the most basic nitrogen? The least basic amino nitrogen? Give the reasons for your choices. (Review Section 23-7.) 25-1 B Nonprotein Amino Acids The most abundant amino acids are those that are protein constituents and these are always a-amino acids. However, there are many other amino acids that occur naturally in living systems that are not constituents of proteins, and are not a-amino acids. Many of these are rare, but others are common and play important roles in cellular metabolism. For example, 3-aminopropanoic acid is a precursor in the biosynthesis of the vitamin, pantothenic acid,2 I/ H2NCH2CM2C-OH 3-aminopropanoic acid (p-alanine) ew3 ow o I I /I ~OCH2-C-c-~ pantothen~ca cid I I CH3 H and 4-aminobutanoic acid is involved in the transmission of nerve impulses. 0 I I H2NCH2CII[2Cw2C-ON[ 4-aminobutanoic acid (y-aminobutyric) Homocysteine3 and homoserine are among the important a-amino acids that are not constituents of proteins. These substances are precursors in the bio- synthesis of methionine. NH2 NH2 homocysteine homoserine 2Pantothenic acid is in turn a precursor for the synthesis of coenzyme A, which is essential for the biosynthesis of fats and lipids (Sections 18-8F and 30-5A). The prefix homo implies an additional carbon in the longest chain. 1212 25 Amino Acids, Peptides, Proteins, Enzymes, and Nucleic Acids 25-2 THE ACID-BASE PROPERTIES OF a-AMINO ACIDS The behavior of glycine is reasonably typical of that of the simple amino acids. Because glycine is neither a strong acid nor a strong base, we shall expect a solution of glycine in water to contain four species in rapid equilibrium. The proportions of these species are expected to change with pH, the cationic conjugate acid being the predominant form at low pH and the anionic conjugate base being favored at high pH: conjugate acid dipolar ion conjugate base of glycine o r of glycine (dominant at pH 1) zwitterion (dominant at pH 12) neutral glycine Spectroscopic measurements show that the equilibrium between neutral gly- cine and the dipolar ion favors the dipolar ion by at least 100 to 1. This is to 0 be expected because the H3N- group of the dipolar ion will stabilize the 0 -co,@ end while the -CO,~ group will stabilize the H,N- end. 0 The acid-ionization constant of H3NCH2C02Wi s 4.5 x 10-YpK, = 2.34, Equation 25-I), which is about 25 times greater than K, for ethanoic acid. (Section 18-2). This is expected because of the electron-attracting 0 0 electrostatic effect of the H3N- group. Ionization of the H,N- group of the dipolar ion (K, = 2.0 x 10-lo; pK = 9.60; Equation 25-2) is oppositely affected by the electrostatic effect of the -CO,@ group and is 10 times less than of ethanammonium ion (Section 23-7B). The manner in which the concentrations of the charged glycine species change with pH is shown in Figure 25- 1. Notice that, between pH 3 and pH 8, almost all of the glycine is in the form of the dipolar ion. The pH at the center of this range, where the concentration of 0 0 H,NCH,CO,H is equal to the concentration of H,NCH,CO,, is called the isoelectric point, pl, and usually corresponds to the pH at which the amino acid has minimum water solubility. Isoelectric points for the amino acids are shown in Table 25- 1. The isoelectric points are the average of the pK, values for dissociation of the monocation and the dipolar ion forms of the amino acid. + For glycine, pl = (2.34 9.60)/2. 25-2 The Acid-Base Properties of a-Amino Acids concentration, moles liter-' 0 0 Figure 25-4 Concentrations of H,NCH,CO,H, H,NCH,CO,~, and H,NCH,- CO,@ as a function of pH for a 0.1M solution of glycine in water @ pKa' = pf-H $. loglo [ H ~ N C H ~ C=O 9~ -6~0I [H,NCH~CO,@] Exercise 25-3 How would the general features of the plot of concentration of dipolar ion and charged species versus pH for glycine (Figure 25-1) change for 6-amino- hexanoVica cid, which has pK, values of 4.43 and 10.75? Give special attention to the position of the isoelectric point and the width of the pH range over which the dipolar ion is expected to be the most stable species present. Exercise 25-4 Use Equations 25-1 and 25-2 to show that the isoelectric point of glycine is the average of the two pK, values for the acid dissociation of glycine. The pH behavior of amino acids with either acidic or basic functional groups attached to the side chains is more complicated than of simple amino 4214 25 Amino Acids, Peptides, Proteins, Enzymes, and Nucleic Acids acids. For example, there are three acid dissociations starting with the di- conjugate acid of lysine: diconjugate conjugate base acid of lysine of lysine The pKa values for the side-chain functions of acidic and basic amino acids are given in Table 25- 1. 0 We already have mentioned how the H3N- group of the conjugate acid of glycine enhances the acid strength of the carboxyl group compared to 0 0 ethanoic acid and how the -C02 group reduces the acidity of the H3N- group of the dipolar ion relative to ethanammonium ion. These effects will be smaller the farther away the charged group is from the ionizable group. As a result, one would predict that the carboxyl groups of aspartic acid would have different pKa values, and indeed this is so: C H ~ aspartic acid I 25-3 Physical and Spectroscopic Properties 11 29 5 Similarly; the side-chain ammonium group of lysine is less acidic than that of the ammonium group close to the carboxyl group: (CH2)4 conjugate acid of lysine I Exercise 25-5 a. The equations for the acid-base equilibria of lysine on p. 1214 'show possible involvement of three forms of the monocation and three forms of the neutral acid. Arrange the three forms of each set in expected order of stability. Give your reasoning. b. The conjugate acid of glutamic acid (Table 25-1) has three acid dissociation steps with pK, values of 2.19, 4.25 and 9.67. Write equations for the equilibria involved and assign pKa values to each. Do the same for arginine (Table 25-1) with pKa values of 2.17, 9.04 and 12.48. Calculate the isoelectric point for glutamic acid and for arginine. 25-3 PHYSICAL AND SPECTROSCOPIC PROPERTIES 0 0 The a-amino acids crystallize as the dipolar forms, H,N-CHR-CO,, and the strong intermolecular electrical forces in the crystals lead to higher melting points than those of simple amines or monocarboxylic acids (see Table 25-1). The melting points are so high that decomposition often occurs on melting. The solubility characteristics of amino acids in water are complex because of the acid-dissociation equilibria involved, but they are least soluble at their isoelectric points. The dipolar structures of amino acids greatly reduce their solubility in nonpolar organic solvents compared to simple amines and car- boxylic acids. The infrared spectra of a-amino acids in the solid state or in solution do not show a carbonyl absorption band at 1720 cm-l characteristic of a carboxyl group. Rather, they show a strong absorption near 1600 cm-I typical of the carboxylate anion. The N-El stretch appears as a strong, broad band between 3 100-2600 cm-l: