THE AMINO ACIDS

AMINO ACIDS

DEFINITION

Amino acids are basic building block unit of protein. They are group of organic compound containing two functional groups. The amino acids are named because both amino (-NH₂) and carboxyl (-COOH) groups are present in a single molecule. The amino (-NH₂) group is basic and carboxyl (-COOH) group is acidic in nature. They are precursor molecules of many important biological molecules e.g. Neurotransmitter, enzymes, proteins, N-bases etc.

STRUCTURE OF THE AMINO ACIDS

Although more than 300 different amino acids have been described in nature, only 20 are commonly found as constituents of mammalian pro­teins. Each amino acid (except for proline, which has a secondary amino group) has a carboxyl group, a primary amino group, and a distinctive side chain (“R-group”) bonded to the α-carbon atom. At physiologic pH (approximately pH 7.4), the carboxyl group is dissociated, forming the negatively charged carboxylate ion (– COO^–), and the amino group is protonated (– NH₃⁺). In proteins, almost all of these carboxyl and amino groups are combined through peptide linkage and, in general, are not available for chemical reaction except for hydrogen bond formation. Thus, it is the nature of the side chains that ultimately dictates the role an amino acid plays in a protein. It is, therefore, useful to classify the amino acids according to the properties of their side chains, that is, whether they are nonpolar (have an even distribution of electrons) or polar (Figures 1).

ABBREVIATIONS AND SYMBOLS FOR COMMONLY OCCURRING AMINO ACIDS

Each amino acid name has an associated three-letter abbreviation and a one-letter symbol. The one-letter codes are deter­mined by the following rules:

1. Unique first letter: If only one amino acid begins with a particular letter, then that letter is used as its symbol. For example, I = isoleucine.

2. Most commonly occurring amino acids have priority: If more than one amino acid begins with a particular letter, the most com­mon of these amino acids receives this letter as its symbol. For example, glycine is more common than glutamate, so G = glycine.

3. Similar sounding names: Some one-letter symbols sound like the amino acid they represent. For example, F = phenylalanine, or W = tryptophan (“twyptophan” as Elmer Fudd would say).

4. Letter close to initial letter: For the remaining amino acids, a one-letter symbol is assigned that is as close in the alphabet as possi­ble to the initial letter of the amino acid, for example, K = lysine. Furthermore, B is assigned to Asx, signifying either aspartic acid or asparagine, Z is assigned to Glx, signifying either glutamic acid or glutamine, and X is assigned to an unidentified amino acid (Figure 2).

                                    

 Figure 1: Structural features of amino acids

(Shown in their fully protonated form)

   Figure 2: Abbreviations and symbols used for amino acids

CLASSIFICATION OF AMINO ACIDS:

1. Classification of amino acids on the basis of nature of side chains:

A. Amino acids with nonpolar side chains

Each of these amino acids has a nonpolar side chain that does not gain or lose protons or participate in hydrogen or ionic bonds. The side chains of these amino acids can be thought of as “oily” or lipid-like, a property that promotes hydrophobic interactions (Figure 3).

Figure 3: Structures of amino acids with non-polar side chains

B. Polar amino acids with no charge on 'R‘ group:

These amino acids, as such, carry no charge on the 'R‘ group. They however possess groups such as hydroxyl, sulfhydryl and amide and participate in hydrogen bonding of protein structure. The simple amino acid glycine (where R = H) is also considered in this category. The amino acids in this group are glycine, serine, threonine, cysteine, glutamine, asparagine and tyrosine (Figure 4).

Figure 4: Structures of polar amino acids with no charge R groups

C. Amino acids with acidic side chains

The amino acids aspartic and glutamic acid are proton donors. At physiologic pH, the side chains of these amino acids are fully ionized, containing a negatively charged carboxylate group (–COO^–). They are, therefore, called aspartate or glutamate to emphasize that these amino acids are negatively charged at physiologic pH (Figure 5).

Figure 5: Structures of amino acids with acidic side chains

D. Amino acids with basic side chains

The side chains of the basic amino acids accept protons. At physiologic pH the side chains of lysine and arginine are fully ionized and positively charged. In contrast, histidine is weakly basic, and the free amino acid is largely uncharged at physiologic pH. However, when histidine is incorporated into a protein, its side chain can be either positively charged or neutral, depending on the ionic environment provided by the polypeptide chains of the protein. This is an important property of histidine that contributes to the role it plays in the functioning of proteins such as hemoglobin (Figure 6).

Figure 6: Structures of amino acids with basic side chains

2. Nutritional classification of amino acids:

The twenty amino acids are required for the synthesis of variety of proteins, besides other biological functions. However, all these 20 amino acids need not be taken in the diet. Based on the nutritional requirements, amino acids are grouped into two classes essential and nonessential.

A. Essential or indispensable amino acids:

The amino acids which cannot be synthesized by the body and, therefore, need to be supplied through the diet are called essential amino acids. They are required for proper growth and maintenance of the individual. The ten amino acids listed below are essential for humans (and also rats): Arginine, Valine, Histidine, lsoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, and Tryptophan (For remembrance use the code 'PVT TIM HALL'). The two amino acids namely arginine and histidine can be synthesized by adults and not by growing children, hence these are considered as semi-essential amino acids. HA

Thus, 8 amino acids are absolutely essential while 2 are semi-essential.

B. Non-essential or dispensable amino acids:

The body can synthesize about '10 amino acids to meet the biological needs, hence they need not be consumed in the diet. These are glycine, alanine, serine, cysteine, aspartate, asparagi ne, glutamate, glutamine, tyrosine and proline.

3. Amino acid classification based on their metabolic fate

The carbon skeleton of amino acids can serve as a precursor for the synthesis of glucose (glycogenic) or fat (ketogenic) or both. From metabolic view point, amino acids are divided into three groups.

A. Glycogenic amino acids:

These amino acids can serve as precursors for the formation of glucose or glycogen. E.g. alanine, aspartate, glycine, methionine etc.

B. Ketogenic amino acids:

Fat can be synthesized from these amino acids. Two amino acids leucine and lysine are exclusively ketogenic.

C. Glycogenic and ketogenic amino acids:

The four amino acids isoleucine, phenylalanine, tryptophan, tyrosine are precursors for synthesis of glucose as well as fat.

PROPERTIES OF AMINO ACIDS

A. Physical Properties of Amino acids:

The amino acids differ in their physicochemical properties which ultimately determine the characteristics of proteins.

1. Solubility:

            Most of the amino acids are usually soluble in water and insoluble in organic solvents.

2. Melting points:

            Amino acids generally melt at higher temperatures, often above 200°C.

3. Taste:

            Amino acids may be sweet (Gly, Ala, Val), tasteless (Leu) or bitter (Arg, lle). Monosodium glutamate (MSC; ajinomoto) is used as a flavoring agent in food industry, and Chinese foods to increase taste and flavor. Some individuals are intolerant to MSC.

4. Optical property:

The α-carbon of an amino acid is attached to four different chemical groups and is, therefore, a chiral or optically active carbon atom. Glycine is the exception because its α-carbon has two hydrogen substituents and, therefore, is optically inactive. Amino acids that have an asymmetric center at the α-carbon can exist in two forms, designated D (Dextro-dextrorotatory) and L (Levo-levorotatory) that are mirror images of each other. The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers. All amino acids found in proteins are of the L-configuration. However, D-amino acids are found in some antibiotics and in plant and bacterial cell walls (Figure 7).

Figure 7: Mirror imaging of optical isomers of amino acids

5. Amino acids as Ampholytes:

Amino acids contain both acidic (-COOH) and basic (-NH₂) groups. They can donate a proton or accept a proton; hence amino acids are regarded as ampholytes. Zwitterion or dipolar ion: The name zwitter is derived from the German word which means hybrid. Zwitter ion (or dipolar ion) is a hybrid molecule containing positive and negative ionic groups. The amino acids rarely exist in a neutral form with free carboxylic (-COOH) and free amino (-NH₂) groups. In strongly acidic pH (low pH), the amino acid is positively charged (cation) while in strongly alkaline pH (high pH), it is negatively charged (anion). Each amino acid has a characteristic pH (e.g. leucine, pH 6.0) at which it carries both positive and negative charges and exists as zwitterion. Isoelectric pH (symbol pl) is defined as the pH at which a molecule exists as a zwitterion or dipolar ion and carries no net charge. Thus, the molecule is electrically neutral.

Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and weakly basic α-amino groups. In addition, each of the acidic and basic amino acids contains an ionizable group in its side chain. Thus, both free amino acids and some amino acids combined in peptide linkages can act as buffers. Recall that acids may be defined as proton donors and bases as proton acceptors. Acids (or bases) described as “weak” ionize to only a limited extent. The concentration of protons in aqueous solution is expressed as pH, where pH = log 1/[H⁺] or –log [H⁺]. The quantitative relationship between the pH of the solu­tion and concentration of a weak acid (HA) and its conjugate base (A^–) is described by the Henderson-Hasselbalch equation.

B. Chemical Properties of Amino acids:

The general reactions of mostly due to the presence groups namely carboxyl (-COOH) group and amino (-NH₂) group.

Reactions due to -COOH group:

1. Salt formation: Amino acids form salts (-COONa) with bases and esters (-COOR') with alcohols.

2. Decarboxylation: Amino acids undergo decarboxylation to produce corresponding amines.

           

R-CH(NH₃+ )-COO   ®        R-CH₂(NH₃+) + CO₂

This reaction assumes significance in the living cells due to the formation of many biologically important amines. These include histamine, tyramine and g-amino butyric acid (GABA) from the amino acids histidine, tyrosine and glutamate, respectively.

3. Reaction with ammonia: The carboxyl group of dicarboxylic amino acids reacts with NH3 to form amide

                        Aspartic acid + NH₃              ®        Asparagine

                        Glutamic acid + NH₃             ®        Glutamine

Reactions due to -NH₂ group:

4. Acts as bases: The amino groups behave as bases and combine with acids (e.g. HCI) to form salts (-NH₃⁺Cl^-).

5. Reaction with ninhydrin: In the pH range of 4-8, all α- amino acids react with ninhydrin (triketohydrindene hydrate), a powerful oxidizing agent to give a purple colored product (diketohydrin) termed Rhuemann’s purple. All primary amines and ammonia react similarly but without the liberation of carbon dioxide. The imino acids proline and hydroxyproline also react with ninhydrin, but they give a yellow colored complex instead of a purple one. Besides amino acids, other complex structures such as peptides, peptones and proteins also react positively when subjected to the ninhydrin reaction (Note: Proline and hydroxyproline give yellow color with ninhydrin).

6. Color reactions of amino acids: Amino acids can be identified by specific color reactions:

a. Xanthoproteic acid test

Aromatic amino acids, such as Phenyl alanine, tyrosine and tryptophan, respond to this test. In the presence of concentrated nitric acid, the aromatic phenyl ring is nitrated to give yellow colored nitro-derivatives. At alkaline pH, the color changes to orange due to the ionization of the phenolic group.

                    

b. Pauly's diazo Test

This test is specific for the detection of Tryptophan or Histidine. The reagent used for this test contains sulphanilic acid dissolved in hydrochloric acid. Sulphanilic acid upon diazotization in the presence of sodium nitrite and hydrochloric acid results in the formation a diazonium salt. The diazonium salt formed couples with either tyrosine or histidine in alkaline medium to give a red coloured chromogen (azo dye). 

c. Millon's test

Phenolic amino acids such as Tyrosine and its derivatives respond to this test. Compounds with a hydroxybenzene radical react with Millon’s reagent to form a red colored complex. Millon’s reagent is a solution of mercuric sulphate in sulphuric acid.

d. Histidine test

This test was discovered by Knoop. This reaction involves bromination of histidine in acid solution, followed by neutralization of the acid with excess of ammonia.  Heating of alkaline solution develops a blue or violet coloration.

e. Hopkins cole test

This test is specific test for detecting tryptophan. The indole moiety of tryptophan reacts with glyoxilic acid in the presence of concentrated sulphuric acid to give a purple colored product. Glyoxilic acid is prepared from glacial acetic acid by being exposed to sunlight.

f. Sakaguchi test

Under alkaline condition, α- naphthol (1-hydroxy naphthalene) reacts with a mono-substituted guanidine compound like arginine which upon treatment with hypobromite or hypochlorite produces a characteristic red color.

g. Lead sulphide test

Sulphur containing amino acids, such as cysteine and cystine upon boiling with sodium hydroxide (hot alkali), yield sodium sulphide. This reaction is due to partial conversion of the organic sulphur to inorganic sulphide, which can be detected by precipitating it to lead sulphide, using lead acetate solution.

                                    

h. Folin's McCarthy Sullivan Test

Imino acids such as Proline and hydroxyproline condense with isatin reagent under alkaline condition to yield blue colored adduct. Addition to sodium nitroprusside [Na₂Fe(CN)₅NO]  to an alkaline solution of methionine followed by the acidification of the reaction yields a red color. This reaction also forms the basis for the quantitative determination of methionine.  

i. Isatin test

Imino acids such as Proline and hydroxyproline condense with isatin reagent under alkaline condition to yield blue colored adduct.

7. Transamination: Transfer of an amino group from an amino acid to a keto acid to form a new amino acid is a very important reaction in amino acid metabolism.

8. Oxidative deamination: The amino acids undergo oxidative deamination to liberate free ammonia.

References:

Lippincott's Bichemistry

&

Satyanarayan's Text Book of Biochemistry