Amino Acids

 

Amino acid

Amino acids are biologically important organic compounds made from amine (-NH₂) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid.

The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. The amino function may have any position α, β, γ, δ etc. with respect to the acidic function and accordingly amino acids may further be classified as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids respectively. Other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur etc.) Aminoethanoic acid (Glycin; NH₂CH₂CO₂H), 3-Aminopropanoic acid (NH₂CH₂CH₂CO₂H) and 4-aminobutanoic acid (NH₂(CH₂)₃CO₂H) are examples of α-, β- and γ-amino acids respectively. The α-amino acids, which are obtained from naturally occurring proteins by the process of hydrolysis, are twenty two in number and they are the units of proteins. Ten out of twenty two are considered to be essential for life. These α-amino acids contain –CO2H group as acidic function and may further be classified, depending on the relative number of amino and acidic functions they contain, as follows:

(a) Neutral amino acids: A compound of this class contains the same number of amino and carboxyl groups. Example: glycine (aminoacetic acid, NH₂CH₂CO₂H) is a neutral amino acid.

(b) Basic amino acids: When numbers of amino groups exceed the number of carboxyl groups in an amino acid compound then these class of amino acids are called basic amino acids. Example: Lysine, NH₂CH(CH₂)₄(NH₂)CO₂H, is an example of basic amino acids.

(c) Acidic amino acids: Each compound of the class contains more carboxyl functions than amino functions; aspartic acid, CO₂H.CH₂CH(NH₂)CO₂H, is a member of the class.

In the form of proteins, amino acids comprise the second largest component (after water) of human muscles, cells and other tissues.

Selenocysteine (abbreviated as Sec or U, in older publications also as Se-Cys) is the 21st proteinogenic amino acid.

It exists naturally in all kingdoms of life as a building block of selenoproteins.

Selenocysteine is a cysteine analogue with a selenium-containing selenol group in place of the sulfur-containing thiol group. It is present in several enzymes (for example glutathione peroxidases, tetraiodothyronine 5' deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases, selenophosphate synthetase 1, methionine-R-sulfoxide reductase B1 (SEPX1), and some hydrogenases).

Selenocysteine was discovered by Theresa Stadtman, wife of biochemist Earl R. Stadtman, at the National Institutes of Health.

Pyrrolysine (abbreviated as Pyl or O) is a naturally occurring, genetically coded amino acid used by some methanogenic archaea and one known bacterium in enzymes that are part of their methane-producing metabolism. It is similar to lysine, but with an added pyrroline ring linked to the end of the lysine side chain. It forms part of an unusual genetic code in these organisms, and is considered the 22nd proteinogenic amino acid.

Ornithine and citrulline are among those 300 amino acids but are very important as they act as an intermediate in the arginine biosynthesis and urea cycle.

Essential amino acids:

Essential amino acids are "essential" not because they are more important to life than the others, but because the body does not synthesize them. They must be present in the diet or they will not be present in the body.

In addition, the amino acids arginine, cysteine, glycine, glutamine, histidine, proline, serine and tyrosine are considered conditionally essential, meaning they are not normally required in the diet, but must be supplied exogenously to specific populations that do not synthesize them. 

Essential	Nonessential
Histidine	Alanine
Isoleucine	Arginine
Leucine	Aspartic acid
Lysine	Cysteine
Methionine	Glutamic acid
Phenylalanine	Glutamine
Threonine	Glycine
Tryptophan	Proline
Valine	Serine
	Tyrosine
	Asparagine
	Selenocysteine

 

Hydropathy index

The hydropathy index of an amino acid is a number representing hydrophobic or hydrophilic properties of its side chain. It was proposed in 1982 by Jack Kyte and Russell F. Doolittle. The larger the number is, the more hydrophobic the amino acid. The most hydrophobic amino acids are isoleucine (4.5) and valine (4.2). The most hydrophilic ones are arginine (-4.5) and lysine (-3.9). This is very important in protein structure; hydrophobic amino acids tend to be internal (with regard to the protein's 3 dimensional shape) while hydrophilic amino acids are more commonly found towards the protein surface.

UV absorption of amino acids

Tryptophan and tyrosine, and to a much lesser extent phenylalanine, absorb ultraviolet light. This accounts for the characteristic strong absorbance of light by most proteins at a wavelength of 280 nm, a property exploited by researchers in the characterization of proteins.

Dipolar ions

Since amino acids contain one or more amino group (-NH₂) and more carboxyl group (-CO₂H), they are amphoteric. In the dry solid state, amino acids form inner salts which are called dipolar ions or zwitter ions or ampholytes. In the dipolar ion form the carboxyl group remains as a carboxylate (CO₂^-) and the amino group exists as an ammonium (-NH₃⁺) group. However, in the aqueous medium, an equilibrium exists involving the dipolar ion, the anionic forms of the amino acids. 

⁺NH₃CH(R)CO₂H ⇋  ⁺H₃NCH(R)CO₂^- ⇋ H₂NCH(R)CO₂^-

 

 

 

 The pH of the solution and the nature of the amino acid determine the predominant form of an amino acid in a solution. In a strongly acidic medium (pH<2) all amino acids remain primarily as cations; while in a strongly basic solution, they remain as anions (at a pH>11). at the optimum pH (2<pH<11), the concentration of the dipolar ion is the highest and the concentration of cations and anions are equal. A dipolar ion is electrically neutral since its electric charge is zero; and consequently if an amino acid is placed in an electric field at the pH at which the concentration of its dipolar ion is maximum, the amino acid does not migrate to any electrode and the pH is called the isoelectronic point. Isoelectronic point is also considered as the pH at which the dipolar ion of an amino acid has the maximal concentration in the presence of salts; while the pH at which the concentration of dipolar ion is maximum in presence of hydrogen ion is called isoionic point. Every amino acid has its own isoelectronic point. However, the isoelectronic point of a monoamino monocarboxylic acid, for example, the isoelectric point of glycine can be calculated as,

⁺NH₃CH₂COOH ⇋ ⁺NH₃CH₂COO- + H⁺

 

⁺NH₃CH₂CO₂^- ⇋ NH₂CH₂COO^- + H⁺

 

K1 = [Dipolar ion][H⁺] where K1 = equilibrium constant

[cA] = [Dipolar ion] [H⁺]/K1

Similarly,

K2 = [cB][H⁺]/[Dipolar ion] where K2= equilibrium constant

[cB] = K2[Dipolar ion]/[H⁺]

At the isoelectric point the concentration of the dipolar ion being maximum and the net charge of the ion being zero, [cA] = [cB]

Or, [dipolar ion] [H⁺]/K1 = K2[Dipolar ion]/[H⁺]

Or, [H⁺]² = K1K2

2X –log₁₀[H⁺] = -log₁₀K1-log10K2

2pH = pK1 + pK2

PH = [pK1+pK2]/2 = Pi, the isoelectric point

For glycine the pK1 and pK2 have value 2.4 and 9.6 respectively.

Pi =[2.4+9.6]/2 = 6.0

Here it is needless to mention that a neutral amino acid like glycine has two pK values, one as an acid and another as a base since it has two functional groups of acidic and basic characters.

The pK values of amino acids were derived from the titrations of amino acids. Example: for glycine it gives a quantitative measure of the pKa of each of the two ionizing groups:

2.34 for the -COOH group

9.60 for the -NH3  group. This amino acid has two regions of buffering power pH region:   2.34 ± 1 and 9.60 ± 1

 The optical rotatory power differs from group to group because of their different polarisability. Therefore, the optical rotatory powers of a carboxyl (-CO₂H) group and the corresponding carboxylate (-CO₂^-) group are different. The same is the case with amino (-NH₂) group and ammonium (-NH₃⁺) group. As a consequence, the specific rotations of dipolar ion and those of the cation (cA) and the anion are different. So at different pHs an amino acid has different specific rotations. In an acidic medium, the amino acids primarily becomes RCH(NH₃⁺)CO₂H and in the basic medium it becomes RCH(NH₂)CO₂^-, while at the iosoelectric point the same remains primarily as a dipolar ion, RCH(NH₃⁺)CO₂^- . Therefore, the specific rotation of an amino acid is pH dependent and specific rotation of an amino acid is measured at its isoelectric point. However, the presence of dipolar ion in the solid state has been proved by the fact that the solid amino acids conduct electricity and they have high boiling, melting point and solubility in polar solvents. It is interesting to note that the amino acids have high normally the lowest solubility in water at the isoelectric points. Perhaps zwitter ions are less hydrated than the corresponding cations and anions. At pi the concentrations of cA an cB are equal but least, and that of the dipolar ion is highest; the latter, however, does not get hydrated appreciably and thus an amino acid has the least solubility in water at pi. At a pH at which the concentration of either cation (pH<2) or anion (pH>11) is maximum and thereby the amino acid in the cationic or in the anionic form gets maximum hydrated and becomes most soluble in water. This property of solubility of amino acid could be utilised to separate amino acids which have appreciably different pi. For example, a mixture of glycine (pi = 6.0) and glutamic acid (pi = 3.20) may be separated at a pH = 6, the pi of glycine, by fractional crystallisation at which glycine is least soluble but glutamic acid is not. Therefore, the former could be filtered out. Similarly, a mixture of glutamic acid and lysine (pi = 9.5) could be separated by fractional crystallization at a pH = 9.5 when lysine will remain mostly as insoluble solid and glutamic acid will remain soluble and, therefore, can be separated by the process of filtration. Electrophoresis may also be used for the purpose of separation.