The role of amino acids in life as the building blocks of proteins is readily apparent. 3 Amino Acids CHAPTER

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1 APTER 3 Amino Acids 3.1 Proteins Are Built from a Repertoire of 20 Amino Acids 3.2 Amino Acids ontain a Wide Array of Functional Groups 3.3 Essential Amino Acids Must Be btained from the Diet In Lewis arroll s wonderful tale Through the Looking Glass, Alice enters a world of delightful curiosities. ad Alice been a biochemist, she might have wondered if the stereochemistry of the amino acids in Looking Glass proteins were mirror images of the amino acids in her normal world. [The Granger ollection.] The role of amino acids in life as the building blocks of proteins is readily apparent in health food stores. Indeed, their shelves are stocked with powdered amino acids for use as dietary supplements so that body builders can enhance muscle growth. owever, amino acids are key biochemicals in their own right. Some amino acids function as signal molecules such as neurotransmitters, and all amino acids are precursors to other biomolecules, such as hormones, nucleic acids, lipids and, as just mentioned, proteins. In this chapter, we examine the fundamental chemical properties of amino acids. 32

2 3.1 Proteins Are Built from a Repertoire of 20 Amino Acids Amino acids are the building blocks of proteins. An a-amino acid consists of a central carbon atom, called the a carbon, linked to an amino group, a carboxylic acid group, a hydrogen atom, and a side chain, called the R group. Each kind of amino acid has a different R group Amino Acid Structure Most Amino Acids Exist in Two Mirror-Image Forms With four different groups connected to the tetrahedral -carbon atom, -amino acids are chiral: they may exist in one or the other of two mirror-image forms, called the L isomer and the D isomer (Figure 3.1). R R α α 3 L isomer D isomer 3 Figure 3.1 The L and D isomers of amino acids. The letter R refers to the side chain. The L and D isomers are mirror images of each other. nly L amino acids are constituents of proteins. Although considerable effort has gone into understanding why amino acids in proteins have the L absolute configuration, no satisfactory explanation has been reached. It seems plausible that the selection of L over D was arbitrary but, once made, the selection was fixed early in evolutionary history. All Amino Acids ave at Least Two harged Groups Free amino acids in solution at neutral p exist predominantly as dipolar ions (also called zwitterions). In the dipolar form, the amino group is protonated ( 3 ) and the carboxyl group is deprotonated ( ). The ionization state of an amino acid varies with p (Figure 3.2). In acid solution (e.g., p 1), the R R R Zwitterionic form Both groups deprotonated oncentration Both groups protonated p Figure 3.2 Ionization state as a function of p. The ionization state of amino acids is altered by a change in p. The zwitterionic form predominates near physiological p.

3 34 3 Amino Acids amino group is protonated ( 3 ) and the carboxyl group is not dissociated ( ). As the p is raised, the carboxylic acid is the first group to give up a proton, because its pk a is near 2. The dipolar form persists until the p approaches 9, when the protonated amino group loses a proton. Under physiological conditions, amino acids exist in the dipolar form. 3.2 Amino Acids ontain a Wide Array of Functional Groups Twenty kinds of side chains varying in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity are commonly found in proteins. Many of these properties are conferred by functional groups. The amino acid functional groups include alcohols, thiols, thioethers, carboxylic acids, carboxamides, and a variety of basic groups. Most of these groups are chemically reactive. All proteins in all species bacterial, archaeal, and eukaryotic are constructed from the same set of 20 amino acids with only a few exceptions. This fundamental alphabet for the construction of proteins is several billion years old. The remarkable range of functions mediated by proteins results from the diversity and versatility of these 20 building blocks. Although there are many ways to classify amino acids, we will assort these molecules into four groups, on the basis of the general chemical characteristics of their R groups: 1. ydrophobic amino acids with nonpolar R groups 2. Polar amino acids with neutral R groups but the charge is not evenly distributed 3. Positively charged amino acids with R groups that have a positive charge at physiological p 4. egatively charged amino acids with R groups that have a negative charge at physiological p ydrophobic Amino Acids ave Mainly ydrocarbon Side hains The amino acids having side chains consisting only of hydrogen and carbon are hydrophobic. The simplest amino acid is glycine, which has a single hydrogen atom as its side chain. With two hydrogen atoms bonded to the -carbon atom, glycine is unique in being achiral. Alanine, the next simplest amino acid, has a methyl group ( 3 ) as its side chain (Figure 3.3). The three-letter abbreviations and one-letter symbols under the names of the amino acids depicted in Figure 3.3 and in subsequent illustrations are an integral part of the vocabulary of biochemists. Larger hydrocarbon side chains are found in the branched-chain (aliphatic) amino acids valine, leucine, and isoleucine. Methionine contains a largely aliphatic side chain that includes a thioether ( S ) group. The different sizes and shapes of these hydrocarbon side chains enable them to pack together to form compact structures with little empty space. Proline also has an aliphatic side chain, but it differs from other members of the set of 20 in that its side chain is bonded to both the -carbon and the nitrogen atom. Proline markedly influences protein architecture because its ring structure makes it more conformationally restricted than the other amino acids. Two amino acids with relatively simple aromatic side chains are also classified as hydrophobic (see Figure 3.3). Phenylalanine, as its name indicates, contains a phenyl ring attached in place of one of the methyl hydrogens of alanine. Tryptophan has an indole ring joined to a methylene ( 2 ) group; the indole group comprises two fused rings and an group.

4 The hydrophobic amino acids, particularly the larger aliphatic and aromatic ones, tend to cluster together inside the protein away from the aqueous environment of the cell. This tendency of hydrophobic groups to come together is called the hydrophobic effect (pp ) and is the driving force for the formation of the The 20 Amino Acids Glycine (Gly, G) Alanine (Ala, A) S S Valine (Val, V) 3 Leucine (Leu, L) 3 Isoleucine (Ile, I) 3 Methionine (Met, M) 2 Proline (Pro, P) Figure 3.3 ydrophobic amino acids. Phenylalanine (Phe, F) Tryptophan (Trp, W)

5 36 3 Amino Acids unique three-dimensional architecture of water-soluble proteins. The different sizes and shapes of these hydrocarbon side chains enable them to pack together to form compact structures with little empty space. Polar Amino Acids ave Side hains That ontain an Electronegative Atom The next group of amino acids that we will consider are those that are neutral overall, yet they are polar because the R group contains an electronegative atom that hoards electrons. Three amino acids, serine, threonine and tyrosine contain hydroxyl ( ) groups (Figure 3.4). The electrons in the bond are attracted to the oxygen atom, making it partially negative, which in turn makes the hydrogen partially positive. Serine can be thought of as a version of alanine with a hydroxyl group attached to the methyl group, whereas threonine resembles valine with a hydroxyl group in place of one of the valine methyl groups. Tyrosine is similar to phenylalanine, but contains a hydrophilic hydroxyl group attached to the large aromatic ring. The hydroxyl groups on serine, threonine, and tyrosine make them more hydrophilic (water loving) and reactive than their respective nonpolar counterparts alanine, valine, and phenylalanine. ysteine is structurally similar to serine but contains a sulfhydryl, or thiol ( S), group in place of the Serine (Ser, S) Threonine (Thr, T) Tyrosine (Tyr, Y) S S Figure 3.4 Polar amino acids. ysteine (ys, ) Asparagine (Asn, ) Glutamine (Gln, Q)

6 The 20 Amino Acids Lysine (Lys, K) Arginine (Arg, R) istidine (is, ) Figure 3.5 Positively charged amino acids. hydroxyl group. The sulfhydryl group is much more reactive than a hydroxyl group and can completely lose a proton at slightly basic p to form the reactive thiolate group. Pairs of sulfhydryl groups in close proximity may form disulfide bonds, covalent bonds that are particularly important in stabilizing some proteins, as will be discussed in hapter 4. In addition, the set of polar amino acids includes asparagine and glutamine, which contain a terminal carboxamide. Positively harged Amino Acids Are ydrophilic We now turn to amino acids having positively charged side chains that render these amino acids highly hydrophilic (Figure 3.5). Lysine and arginine have relatively long side chains that terminate with groups that are positively charged at neutral p. Lysine is topped by an amino group and arginine by a guanidinium group. ote that the R groups of lysine and arginine have dual properties the four-carbon chains constitute a hydrocarbon backbone, similar to the amino acid leucine, but the chain is terminated with a positive charge. Such combinations of characteristics contribute to the wide array of chemical properties of amino acids. istidine contains an imidazole group, an aromatic ring that also can be positively charged. With a pk a value near 6, the imidazole group of histidine is unique in that it can be uncharged or positively charged near neutral p, depending on its local environment (Figure 3.6). Indeed, histidine is often found in the active sites of enzymes, where the imidazole ring can bind and release protons in the course of enzymatic reactions. Lysine is an essential amino acid (p. 39), which means that human beings cannot synthesize lysine and must obtain it in the diet. In experimental animals, kept on a cereal-based diet, inadequate dietary lysine increased stress-induced anxiety. Recent studies suggest that this response to lysine deprivation may be true for human beings, too Guanidinium Imidazole 2 2 Figure 3.6 istidine ionization. istidine can bind or release protons near physiological p.

7 38 3 Amino Acids Monosodium glutamate (MSG), which is glutamate with sodium bound to an acid group, is commonly used as a taste enhancer. In fact, the taste of glutamate and aspartate (called umami, from the Japanese word for deliciousness ) is, along with sweet, sour, bitter, and salty, one of the five primary tastes. QUIK QUIZ ame three amino acids that are positively charged at neutral p. ame three amino acids that contain hydroxyl groups Aspartate (Asp, D) Glutamate (Glu, E) Figure 3.7 egatively charged amino acids. egatively harged Amino Acids ave Acidic Side hains The two amino acids in this group, aspartic acid and glutamic acid, have acidic side chains that are usually negatively charged under intracellular conditions (Figure 3.7). These amino acids are often called aspartate and glutamate to emphasize the presence of the negative charge on their side chains. In some proteins, these side chains accept protons, which neutralize the negative charge. This ability is often functionally important. Aspartate and glutamate are related to asparagine and glutamine in which a carboxylic acid group in the former pair replaces a carboxamide in the latter pair. The Ionizable Side hains Enhance Reactivity and Bonding Seven of the 20 amino acids tyrosine, cysteine, arginine, lysine, histidine, and aspartic and glutamic acids have readily ionizable side chains. These seven amino acids are able to form ionic bonds as well as to donate or accept protons to facilitate reactions. The ability to donate or accept protons is called acid base catalysis and is an important chemical reaction for many enzymes. We will see the importance of histidine as an acid base catalyst when we examine the protein-digesting enzyme chymotrypsin in hapter 8. Table 3.1 gives equilibria and typical pk a values for the ionization of the side chains of these seven amino acids. Table 3.1 Typical pk a values of ionizable groups in proteins Group Acid Δ Base Typical pk a Terminal -carboxyl group 3.1 Aspartic acid Glutamic acid 4.1 istidine 6.0 Terminal -amino group 8.0 ysteine 8.3 S S Tyrosine 10.9 Lysine 10.8 Arginine 12.5 ote: Values of pk a depend on temperature, ionic strength, and the microenvironment of the ionizable group.

8 Table 3.2 Basic set of 20 amino acids onessential Alanine Arginine Asparagine Aspartate ysteine Glutamate Glutamine Glycine Proline Serine Tyrosine Essential istidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine Essential Amino Acids 3.3 Essential Amino Acids Must Be btained from the Diet Most microorganisms can synthesize the entire basic set of 20 amino acids, whereas human beings cannot make nine of them. Amino acids that cannot be generated in the body must be supplied by the diet and are termed essential amino acids. The others are called nonessential amino acids (Table 3.2). These designations refer to an organism under a particular set of conditions. For example, a human adult can synthesize enough arginine to meet his or her needs, but a growing child requires more arginine than the body can provide. linical Insight Pathological onditions Result If Protein Intake Is Inadequate The importance of amino acids in the diet (usually ingested as proteins) is illustrated by kwashiorkor, a particular form of malnutrition. Kwashiorkor means the disease of the displaced child in the language of Ga, a Ghanaian dialect; that is, the condition arises when a child is weaned because of the birth of a sibling. This condition was first defined in the 1930s in Ghana. It is a form of malnutrition that results when protein intake is not sufficient. Initial symptoms of the disease are generalized lethargy, irritability, and stunted growth. If treated early enough, the effects of the disease are reversible. owever, if not corrected early enough, many physiological systems fail to develop properly, including the brain. For instance, children will suffer from various infectious diseases because their immune systems, composed of many different proteins, cannot be constructed to function adequately. Likewise, the lack of protein prevents the complete development of the central nervous system, with resulting neurological problems. The most common characteristic of a child suffering from kwashiorkor is a large protruding belly (Figure 3.8). The large belly is a sign not of excess calories but of edema, another result of the lack of protein. Edema is swelling that results from too much water in tissue. Insufficient protein in a child s blood distorts the normal distribution of water between plasma and surrounding capillaries. Although the swollen belly is most obvious, the limbs of a child suffering from kwashiorkor also are often swollen. Such suffering children are a devastating display of the centrality of protein to life. Figure 3.8 A child suffering from kwashiorkor. ote the swollen belly and limbs. This swelling (edema) is due to fluid collecting in the tissues because there is not enough protein in the blood. [Stephen Morrison/epa/orbis.]

9 40 3 Amino Acids SUMMARY 3.1 Proteins Are Built from a Repertoire of 20 Amino Acids Proteins are linear polymers of amino acids. Each amino acid consists of a central tetrahedral carbon atom linked to an amino group, a carboxylic acid group, a distinctive side chain, and a hydrogen atom. These tetrahedral centers, with the exception of that of glycine, are chiral; only the L isomer exists in natural proteins. All natural proteins are constructed from the same set of 20 amino acids. 3.2 Amino Acids ontain a Wide Array of Functional Groups The side chains of these 20 building blocks vary tremendously in size, shape, and the presence of functional groups. They can be grouped as follows on the basis of the chemical properties of the side chains: (1) hydrophobic side chains glycine, alanine, valine, leucine, isoleucine, methionine, proline as well as the aromatic amino acids phenylalanine and tryptophan; (2) polar amino acids serine, threonine, tyrosine, asparagine and glutamine; (3) positively charged amino acids lysine, arginine, and histidine; and (4) negatively charged amino acids aspartic acid and glutamic acid. 3.3 Essential Amino Acids Must Be btained from the Diet Most microorganisms are capable of making all 20 of the amino acids from simpler molecules. Although human beings can make 11 amino acids, 9 must be acquired from the diet. These 9 amino acids are called essential amino acids because they are required for healthy growth and development. Key Terms side chain (R group) (p. 33) L amino acid (p. 33) dipolar ion (zwitterion) (p. 33) essential amino acids (p. 39) Answer to QUIK QUIZ Lysine, arginine, and histidine are positively charged at neutral p. Three amino acids containing hydroxyl groups are serine, threonine, and tyrosine. Problems 1. idden message. Translate the following amino acid sequence into one-letter code: Glu-Leu-Val-Ile-Ser-Ile-Ser- Leu-Ile-Val-Ile-Asn-Gly-Ile-Asn-Leu-Ala-Ser-Val-Glu-Gly- Ala-Ser. 2. Identify. Examine the following four amino acids: What are their names, three letter abbreviations, and oneletter symbols? A B D

10 Problems Properties. In reference to the amino acids shown in problem 2, which are associated with the following characteristics: (a) ydrophobic side chain (b) Basic side chain (c) Three ionizable groups (d) pk a of approximately 10 in proteins (e) Modified form of phenylalanine 4. Match em. Match each amino acid in the left-hand column with the appropriate side-chain type in the right-hand column. (a) Leu (1) hydroxyl-containing (b) Glu (2) acidic (c) Lys (3) basic (d) Ser (4) sulfur-containing (e) ys (5) nonpolar aromatic (f) Trp (6) nonpolar aliphatic 5. Solubility. In each of the following pairs of amino acids, identify which amino acid would be most soluble in water: (a) Ala, Leu; (b) Tyr, Phe; (c) Ser, Ala; (d) Trp, is. 6. Bonding is good. Which of the following amino acids have R groups that have hydrogen-bonding potential? Ala, Gly, Ser, Phe, Glu, Tyr, Ile, and Thr. 7. Minor species. For an amino acid such as alanine, the major species in solution at p 7 is the zwitterionic form. Assume a pk a value of 8 for the amino group and a pk a value of 3 for the carboxylic acid. Estimate the ratio of the concentration of the neutral amino acid species (with the carboxylic acid protonated and the amino group neutral) to that of the zwitterionic species at p 7.