The amino acids that we are familiar with and all of those incorporated into mammalian protein are "alpha"-amino acids. By definition, they have a carboxyl-carbon group and an amino nitrogen group attached to a central a-carbon ( Fig...2.1). Amino acids differ in structure by substitution of one of the two hydrogens on the a-carbon with another functional group. Amino acids can be characterized by their functional groups, which are often classified at neutral pH as (a) nonpolar, (b) uncharged but polar, (c) acidic (negatively charged), and (d) basic (positively charged) groups.
Figure 2.1. Structural formulas of the 21 common a-amino acids. The a-amino acids all have (a) a carboxyl group, (b) an amino group, and (c) a differentiating functional group attached to the a-carbon. The generic structure of amino acids is shown in the upper left corner with the differentiating functional marked R. The functional group for each amino acid is shown below. Amino acids have been grouped by functional class. Proline is the only amino acid whose entire structure is shown because of its "cyclic" nature.
Within any class there are considerable differences in shape and physical properties. Thus, amino acids are often arranged in other functional subgroups. For example, amino acids with an aromatic group—phenylalanine, tyrosine, tryptophan, and histidine—are often grouped, although tyrosine is clearly polar and histidine is also basic. Other common groupings are the aliphatic or neutral amino acids (glycine, alanine, isoleucine, leucine, valine, serine, threonine and proline). Proline differs in that its functional group is also attached to the amino group, forming a five-member ring. Serine and threonine contain hydroxy groups. The branched-chain amino acids (BCAAs: isoleucine, leucine, and valine) share common enzymes for the first two steps of their degradation. The acidic amino acids, aspartic acid and glutamic acid, are often referred to as their ionized, salt forms: aspartate and glutamate. These amino acids become asparagine and glutamine when an amino group is added in the form of an amide group to their carboxyl tails.
The sulfur-containing amino acids are methionine and cysteine. Cysteine is often found in the body as an amino acid dimer, cystine, in which the thiol groups (the two sulfur atoms) are connected to form a disulfide bond. Note the distinction between cysteine and cystine; the former is a single amino acid, and the latter is a dimer with different properties. Other amino acids that contain sulfur, such as homocysteine, are not incorporated into protein.
All amino acids are charged in solution: in water, the carboxyl group rapidly loses a hydrogen to form a carboxyl anion (negatively charged), while the amino group gains a hydrogen to become positively charged. An amino acid, therefore, becomes "bipolar" (often called a zwitterion) in solution, but without a net charge (the positive and negative charges cancel). However, the functional group may distort that balance. Acidic amino acids lose the hydrogen on the second carboxyl group in solution. In contrast, basic amino acids accept a hydrogen on the second N and form a molecule with a net positive charge. Although the other amino acids do not specifically accept or donate additional hydrogens in neutral solution, their functional groups do influence the relative polarity and acid-base nature of their bipolar portion, giving each amino acid different properties in solution.
The functional groups of amino acids also vary in size. The molecular weights of the amino acids are given in T.a.ble 2 2.. Amino acids range from the smallest, glycine, to large and bulky molecules (e.g., tryptophan). Most amino acids crystallize as uncharged molecules when purified and dried. The molecular weights given in Table 2.2 reflect their molecular weights as crystalline amino acids. However, basic and acidic amino acids tend to form much more stable crystals as salts, rather than as free amino acids. Glutamic acid can be obtained as the free amino acid with a molecular weight of 147 and as its sodium salt, monosodium glutamate (MSG), which has a crystalline weight of 169. Lysine is typically found as a hydrogen chloride-containing salt. Therefore, when amino acids are represented by weight, it is important to know whether the weight is based on the free amino acid or on its salt.
Table 2.2 Common Amino Acids in the Body
Another important property of amino acids is optical activity. Except for glycine, which has a single hydrogen as its functional group, all amino acids have at least one chiral center: the a-carbon. The term chiral comes from Greek for hand in that these molecules have a left (levo or L) and right (dextro or D) handedness around the a-carbon atom. The tetrahedral structure of the carbon bonds allows two possible arrangements of a carbon center with the same four different groups bonded to it, which are not superimposable; the two configurations, called stereoisomers, are mirror images of each other. The body recognizes only the L form of amino acids for most reactions in the body, although some enzymatic reactions will operate with lower efficiency when given the D form. Because we do encounter some D amino acids in the foods we eat, the body has mechanisms for clearing these amino acids (e.g., renal filtration).
Any number of molecules could be designed that meet the basic definition of an amino acid: a molecule with a central carbon to which are attached an amino group, a carboxyl group, and a functional group. However, a relatively limited variety appear in nature, of which only 20 are incorporated directly into mammalian protein. Amino acids are selected for protein synthesis by binding with transfer RNA (tRNA). To synthesize protein, strands of DNA are transcribed into messenger RNA (mRNA). Different tRNA molecules bind to specific triplets of bases in mRNA. Different combinations of the 3 bases found in mRNA code for different tRNA molecules. However, the 3-base combinations of mRNA are recognized by only 20 different tRNA molecules, and 20 different amino acids are incorporated into protein during protein synthesis.
Of the 20 amino acids in proteins, some are synthesized de novo in the body from either other amino acids or simpler precursors. These amino acids may be deleted from our diet without impairing health or blocking growth; they are nonessential and dispensable from the diet. However, several amino acids have no synthetic pathways in humans; hence these amino acids are essential or indispensable to the diet. T§ble 2.2. lists the amino acids as essential or nonessential for humans. Both the standard 3-letter abbreviation and the 1-letter abbreviation used in representing amino acid sequences in proteins are also presented in Table.2.2. for each amino acid. Some nonessential amino acids may become conditionally essential under conditions when synthesis becomes limited or when adequate amounts of precursors are unavailable to meet the needs of the body (6, 7 and 8). The history and rationale of the classification of amino acids in T.a.bJ.e 2 2. is discussed in greater detail below.
Beside the 20 amino acids that are recognized by, and bind to, tRNA for incorporation into protein, other amino acids appear commonly in the body. These amino acids have important metabolic functions. For example, ornithine and citrulline are linked to arginine through the urea cycle. Other amino acids appear as modifications after incorporation into proteins; for example, hydroxy-proline, produced when proline residues in collagen protein are hydroxylated, and 3-methylhistidine, produced by posttranslational methylation of select histidine residues of actin and myosin. Because no tRNA codes for these amino acids, they cannot be reused when a protein containing them is broken down (hydrolyzed) to its individual amino acids.
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