General Features

All peptides and proteins, regardless of their origin, are constructed from a set of about 20 common amino acids that are covalently linked together, usually in a linear sequence (Davies, 1985). The structures and selected chemical features of the most common amino acids are given in Table 2-1. Amino acids have distinctive side chains that give each amino acid a characteristic size and shape, and properties that dictate solubility and electrochemical characteristics. With such diverse building blocks, it should be easy to visualize that peptides and proteins can be designed for complex activities (Darby 1993).

The first chemical description of an amino acid appeared in 1806. The last of the common amino acids to be described was threonine in 1938. The names for amino acids largely are derived from Greek terms. For example, the designation glycine is derived from the Greek glykos (sweet), because glycine has a sweet taste.

Although each amino acid is unique, the chemical properties of amino acids do have a number of common features. As the term amino acid implies, each contains an amino group and an acid moiety a carboxylic acid group. Both of these functional moieties are bonded directly to a central carbon atom designated as the a-carbon (Fig. 2-1). Except for glycine, the a-carbon for each of the amino acids has four different functional groups bonded to it: an amino group, a carboxylic acid group, hydrogen, and a "side chain" or "R" group.

The presence of these four different functional groups creates what is called a chiral center. A chiral center exists when an arrangement around a given molecule cannot be superimposed. For all the amino acids (with the exception of glycine), there are two non-superimposable, mirror-image forms. These two forms are referred to as stereoisomers, designated as l- and d-isomers. This terminology comes from the Latin, laevus and dexter, and the Greek, levo and dextro, meaning left and right, respectively That is, the use of the designation l or d in combination with the given name of an amino acid infers a specific spatial configuration around the amino acid's a-carbon. Although there are other systems of assigning stereochemistry (e.g., the RS system used in organic chemistry), the l and d designations remain in common usage for most amino acids.

Molecules with a chiral center are optically active. The presence of a chiral center causes the rotation of plane-polarized light.

L-lsomer D-lsomer

Figure 2-1. General structure for the a-amino acids. Stereoisomers are shown in their l and d forms. Note the position of the a-carbon. The four valences of carbon result in chemical bonds that may be viewed as an equilateral tetrahedron. When a carbon atom has four different substituents, two distinct spatial arrangements are possible. Fisher projections are used to depict the l and d isomers. In a Fisher projection, bonds pointing horizontally are viewed as coming out of the plane on which they are depicted, whereas those pointing vertically go below the plane. A zwitterion is also depicted, wherein the arrows designate the potential balance and interaction between the positive (+) charge of the amino group and the negative (-) charge of the carboxylate group.

TABLE 2-1 Common Amino Acids

Neutral R Groups cooh cooh cooh cooh cooh

TABLE 2-1 Common Amino Acids

Neutral R Groups cooh cooh cooh cooh cooh

h2n-

1 1 -c-h h2n-c-h

h2n-

-c-h

h2n-c-h

ch3 A"

hn cho 1 1

h-

-c-ch3

ch,

h3c ch3

hgc ch2

h-

-c-h ch3

c-h / \ h3c ch3

Amino Acid

Alanine

Valine

Proline

Leucine

Isoleucine

Abbreviation

Ala, A

Val, V

Pro, P

Leu, L

Ile, I

Molecular Weight

89

117

115

131

131

Occurrence (%)"

9-10

6-7

4-5

7-8

4-5

Pka

-cooh

2.34

2.32

1.99

2.36

2.36

-nh2

9.69

9.62

10.6

9.68

9.68

-RH

P/

6.01

.5.97

6.48

5.98

6.02

Hydropathy Index

0.5 [16.7]

1.5 [8.3]

-3.3 [162]

1.8 [2.4]

2.5 [4.1]

(kcal/moQb and

[Solubility in H20

(g/100 mL) at 25°c]

Nutritional Essentiality*"

*

*

Acidic R Groups cooh

h2n-c-h

cooh h2n-c-h cooh cooh cooh

cooh cooh

h2n-c-h

cooh

Amino Acid

Phenylalanine

Tyrosine

Tryptophan

Aspartate

Glutamate

Abbreviation

Phe, F

Tyr, Y

Trp, W

Asp, D

Giù, E

Molecular Weight

165

181

204

133

147

Occurrence (%)•

3-4

3-4

1-1.5

5-6

6-7

pka

-COOH

1.83

2.20

2.38

2.09

2.19

-nh2

9.13

10.07

9.39

9.82

9.67

-RH

9.11 (-OH)

3.86 (-COOH)

4.25 (-COOH)

p'

5.48

5.66

5.89

2.77

3.22

Hydropathy Index

2.5 [2.96]

2.3 [0.045]

3.4 [1.14]

-7.4 [0.5]

-9.4 [0.84]

(kcal/moQb and

[Solubility in H20

(g/100 mL) at 25°C]

Nutritional Essentiality0

*

t

*

Table continued

on following page

The direction and magnitude differ among the various amino acids. Furthermore, optical rotation of amino acids is dependent on other factors, such as pH (the hydrogen ion concentration) and the degree of ionization of the carboxylic acid or amine group(s). Optical rotation may also be influenced by the nature of the solvent in which the amino acid is dissolved.

In proteins and peptides, amino acids are found almost exclusively in the L form, although occasionally D-amino acids are found in bacterial proteins and peptides (Da-vies, 1985). This has a number of important connotations and underscores the importance of appreciating properties of compounds that contain chiral centers. For example, that proteins are constructed largely of L-amino acids

TABLE 2-1

Common Amino Acids Continued

Positively Charged R Groups cooh

hon-c-h

ch2 h2c ch2 h2c nh2

cooh

h2n-c-h

ch2 ch2 ch2

h2n-c-h ch2

Amino Acid

Lysine

Arginine

Histidine

Abbreviation

Lys, K

Arg, R

His, H

Molecular Weight

146

174

154

Occurrence (%)"

7

4-5

2

pK„

-cooh

2.18

2.17

1.82

-nh2

8.95

9.04

9.17

-rh

10.53 (-NH2)

12.48 (-NH=CH-NH2)

6.0 (imidazole ring)

P'

9.74

10.76

7.59

Hydropathy Index

-4.2 [freely soluble]

-11.2 [freely soluble]

0.5 [15]

(kcal/moI)b and

[Solubility in HzO

(jg/100 mL) at 25°C]

Nutritional Essentiality1

*

t

*

Polar, Uncharged R groups

cooh cooh

cooh

cooh |

cooh

cooh 1

cooh 1

h2n-c-h

h2n-c-h

h2n-c-h

h2n-c-h

h2n-c-h ^ ]

h2n-c~h 1

¿ 1

h

h2c

choh |

ch2

ch3

ch2 1 *

ch2

ho

h3c

sh

h2c s ch3

conh2

h2c conh2

Amino Acid

Glycine

Serine

Threonine

Cysteine

Methionine

Asparagine

Glutamine

Abbreviation

Gly G

Ser, S

Thr, T

Cys, C

Met, M

Asn, D

Gin, Q

Molecular Weight

75

105

119

121

149

132

146

Occurrence (%)"

7-8

7-8

6

1-2

3-4

4-5

3-4

PKa

-COOH

2.34

2.21

2.63

1.71

2.28

2.04

2.17

-nh2

9.60

9.15

10.43

10.78

9.31

9.82

9.13

-RH

8.33 (-SH)

Pi

5.97

5.68

5.87

5.07

6

5.41

5.65

Hydropathy Index

0 [25]

-0.3

0.4

-2.8

1.3 [18]

-0.2 [3.4]

-0.3 [4.7]

(kcal/moI)b and

[freely

[freely

[freely

[Solubility in H20

soluble]

soluble]

soluble]

(jg/100 mL) at 25°C]

Nutritional Essentiality

Í

*

f

*

"Distribution, expressed as a percentage of the total amino acids found in common proteins.

The hydropathy index combines measures of hydrophobicity and hydrophilicity and is used to predict which amino acids will most likely be found in an aqueous environment (- values) or a nonpolar environment (+ values). Hydrophobicities are usually measured by estimating the distribution of the amino acid between a nonpolar solvent and water. Note that hydrophobicity does not relate directly to solubility in water, because a number of factors related to the orientation of the R group and its configuration (see value for proline) can directly influence how the amino acid interacts with water.

The designation (*) indicates that higher order animals have a nutritional requirement for the amino acid. The designation (—) indicates that in most instances the amino acid is sufficiently synthesized at critical periods in growth or development. The designation (t) implies that for some animals there may be a conditional need; i.e., sufficient quantities may not be synthesized. For example, in the rapidly growing and feathering chick, there is a conditional need for glycine, an amino acid abundant in connective tissue proteins and feathers (i.e., glycine is not synthesized in sufficient amounts).

indicates that reactions involving amino acids are highly stereospecific. The metabolic pathways for amino acid synthesis create predominantly amino acids in their l form. Moreover, the biological machinery required for protein assembly recognizes l-amino acids almost exclusively (Davies, 1985).

Regarding other important properties, purified amino acids are colorless and nonvolatile crystalline solids in the physiological pH range. Decomposition usually requires temperatures above 200°C. In aqueous solutions, amino acids are easily ionized. An amino group and carboxyl group bonded to a common carbon atom result in a zwitterion, a term used to designate a dipolar, chemical structure with both a positive and negative charge (see Fig. 2-1). Although the zwitterion portion of an amino acid is water soluble in the physiological pH range, it is ionically neutral because the positive charge of the amino group cancels out the negative charge associated with the carboxylate group. The zwitter-ionic character causes amino acids to be held together by electrostatic forces in a crystalline lattice (i.e., analogous to the crystalline lattice of sodium chloride and other salt crystals). In this regard, the high decomposition temperature is related to the zwitterionic characteristics of amino acids and their ability to form crystalline lattices.

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