Amino Acids

By: Dhiraj Kr. ChaudharyIAAS, Lamjung

• Amino acids are biologically important organic compounds composed of 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.

• Amino acids are the building blocks of proteins.• Amino acids are joined together with peptides bonds to form proteins.

General Structure of Amino Acids:• Each amino acid is a nitrogenous compound having both an acidic

carboxyl (-COOH) and a basic (- NH2) group. R stands for the side chains that are different for each amino acid.

• R can be as simple as a hydrogen atom (H) or a methly group (-CH3) or a more complex structure.

• The first carbon is a the part of the carboxyl group. The second carbon, to which amino group is attached is called the α- carbon.

• The α- carbon in all the amino acids is asymmetric except in Glycine where the α- carbon is symmetric.

• Due to this asymmetry, the amino acids exist in two optically active forms: -those having -NH2 group to the right are designated as D- forms and those having - NH2 group to the left as L- forms.

Electrochemical Properties of Amino acids:• All molecules possessing both acidic and basic groups might exist as

uncharged molecules or in ionic form or as a mixture of both.• Calculation have revealed that an aqueous solution of most amino acids,

glycine for e.g., can have only one part of uncharged molecules in one lakh parts of the ionic form.

• In the ionic form, the proton migrates from the carboxyl to amino group, thus producing carboxylate (COO- ) and ammonim (NH+

3) ions.• Amino acids react with both acids and bases. Hence, they are amphoteric

in nature. In acid solution , the COO- ion acquires a proton and the amino acid

becomes an ammonium salt of the acid. Conversely, in alkaline solution, the NH+

3 ion loses a proton and the amino acid becomes the anion salt.

These reactions are of reversible nature and depend on the pH of the medium.

Henceforth, amino acids serves as buffers and tend to prevent pH change when an acid or a base is added.

Zwitterion Form of Amino acids:• The amine and carboxylic acid functional groups found in amino acids

allow them to have amphiprotic properties.• Carboxylic acid groups (−CO2H) can be deprotonated to become negative

carboxylates (−CO2− ), and α-amino groups (NH2−) can be protonated to

become positive α-ammonium groups (+NH3−). • At pH between 2.2 and 9.4, the predominant form adopted by α-amino

acids contains a negative carboxylate and a positive α-ammonium group, as shown in structure.

• This form of amino acid has net zero charge. • This molecular state is known as a zwitterion, from the

German Zwitter meaning hermaphrodite or hybrid.• Below pH 2.2, the predominant form will have a neutral carboxylic acid

group and a positive α-ammonium ion (net charge +1), and above pH 9.4, a negative carboxylate and neutral α-amino group (net charge −1).

Fig: Zwitterion form of Amino anids

Standard, Primary or Normal Amino Acids

• Although over 100 amino acids have been shown to present in various plants and animals, only 20 of them are found as constituent of most proteins.

• These 20 amino acids of proteins are referred to as standard, primary or normal amino acids to distinguish them from others.

• The 20 amino acids that are found within proteins convey a vast array of chemical versatility. 

• The precise amino acid content, and the sequence of those amino acids, of a specific protein, is determined by the sequence of the bases in the gene that encodes that protein.

Structures of 20 Standard Amino acids

Amino Acids Symbol Amino Acids Symbol

Alanine Ala Leucine Leu

Arginine Arg Lysine Lys

Asparagine Asn Methionine Met

Aspartic acid Asp Phenylalanine Phe

Cysteine Cys Proline Pro

Glutamic acid Glu Serine Ser

Glutamine Gln Threonine Thr

Glycine Gly Tryptophan Trp

Histidine His Tyrosine Tyr

Isoleucine Ile Valine Val

Table: Amino acids & their Symbols

Classification of Amino acids:• There are several basis of classification of Amino acids:A. On the Basis of Requirements:1. Essential amino acids• Essential amino acids cannot be made by the body. As a result, they must

come from food.• The nine essential amino acids are: histidine, isoleucine, leucine, lysine,

methionine, phenylalanine, threonine, tryptophan, and valine.2. Nonessential amino acids• "Nonessential" means that our bodies produce an amino acid, even if we

don't get it from the food we eat.• They include: alanine, asparagine, aspartic acid, and glutamic acid.3. Conditional amino acids• Conditional amino acids are usually not essential, except in times of illness

and stress.• They include: arginine, cysteine, glutamine, tyrosine, glycine, proline,

and serine.

Essential Nonessential

Histidine Alanine

Isoleucine Arginine*

Leucine Asparagine

Lysine Aspartic acid

Methionine Cysteine*

Phenylalanine Glutamic acid

Threonine Glutamine*

Tryptophan Glycine

Valine Ornithine*

Proline*

Selenocysteine*

Serine*

Tyrosine*

(*) Essential only in certain cases.

B. On the basis of the composition of the side chain or R group:• Based on the composition of the side chain, the twenty amino acids, may be

grouped into following 8 categories:i. Simple amino acids:• These have no functional group in their side chain, e.g.: Glycine, Alanine,

valine, leucine, and isoleucine.ii. Hydoxy amino acids:• These amino acids contain a hydoxyl group in their side chain. E.g. serine

and threonine.iii. Sulfur- containing amino acids:• These possess a sulfur atom in the side chain, e.g. Cysteine and methionine.iv. Acidic amino acids:• These have a carboxyl group in the side chain, e.g., Aspartic acid and

Glutamic acid.v. Amino acid amides:• These are derivatives of acidic amino acids in which one of the carboxyl

group has been transformed into an amide group (-CONH2 ), e.g., Asparagine and Glutamine.

vi. Basic amino acids: • These possess an amino group in the side chain, e.g. lysine, and arginine.vii. Heterocyclic amino acids:• These amino acids, have in their side chain a ring which possesses at

least one atom other than the carbon.e.g., Tryptophan, histidine, and Proline.

viii. Aromatic amino acids:• These have a benzene ring in the side chain, e.g., Phenylalanine and

Tyrosine

C. On the basis of the number of amino and carboxylic groups.:• McGilvery and Goldstein (1979) have classified various amino acids as

follows :I. Monoamino-monocarboxylic amino acids :

1. Unsubstituted = Glycine Alanine, Valine, Leucine, Isoleucine2. Heterocyclic = Proline3. Aromatic = Phenylalanine, Tyrosine,Tryptophan4. Thioether = Methionine5. Hydroxy = Serine, Threonine6. Mercapto = Cysteine7. Carboxamide = Asparagine, Glutamine

II. Monoamino-dicarboxylic amnino acids : Aspartic acid, Glutamic acid

III. Diamino-monocaryboxylic amino acids : Lysine, Arginine, Histidine

D. On the basis of polarity of the side chain or R group: A more meaningful classification of amino acids is, however, based on the

polarity of the R groups present in their molecules, i.e., their tendency to interact with water at biological pH (near pH 7.0):

This system recognizes following 4 categories :I. Amino acids with nonpolar R groups.II. Amino acids with polar but uncharged R groups.III. Amino acids with negatively charged (= acidic) R groups.IV. Amino acids with positively charged (=basic) R groups.

I. Amino acids with nonpolar R groups:• The R groups in this category of amino acids are hydrocarbon in nature and

thus hydrophobic. • This group includes:

-five amino acids with aliphatic R groups (alanine, valine, leucine isoleucine, proline),- two with aromatic rings (phenylalanine, tryptophan) and -one containing sulfur (methionine).

II. Amino acids with polar but uncharged R groups: The R groups of these amino acids are more soluble in water i.e., more

hydrophilic than those of the nonpolar amino acids because they contain functional groups that form hydrogen bonds with water.

This category includes 7 amino acids, viz., glycine, serine, threonine, tyrosine, cysteine, asparagine and glutamine.

The polarity of these amino acids may be due to either a hydroxyl group (serine, threonine, tyrosine) or a sulfhydryl group (cysteine) or an amide group (asparagine, glutamine).

The R group of glycine, a single hydrogen atom, is too small to influence the high degree of polarity.

III. Amino acids with negatively charged (= acidic) R groups:• These are monoaminodicarboxylic acids. • In other words, their side chain contains an extra carboxyl group with a

dissociable proton. • The resulting additional negative charge accounts for the electrochemical

behaviour of proteins.• The two amino acids which belong to this category are aspartic and

glutamic.

IV. Amino acids with positively charged (=basic) R groups:• These are diaminomonocarboxylic acids. • In other words, their side chain contains an extra amino group which

imparts basic properties to them.• Lysine, arginine and histidine belong to this category.

NONSTANDARD PROTEIN AMINO ACIDS :• In addition to the above-mentioned twenty standard amino acids which are

building blocks of proteins having a wide range of distribution, several other amino acids exists which have a limited distribution.

• As an example, hydroxyproline has a limited distribution in nature but constitutes as much as 12% of the composition of collagen.

• Similarly, hydroxylysine is also a component of collagen.• N-methyllysine is found in myosin, a contractile protein of muscle. • γ-carboxyglutamate is found in the blood-clotting protein, prothrombin.

F. NONPROTEIN AMINO ACIDS:• There are some 300 additional amino acids which are never found as

constituents of proteins but which either play metabolic roles or occur as natural products.

• Among the important nonprotein amino acids, which play metabolic roles, are L-ornithine, L-citrulline, β-alanine, creatine and γ-aminobutyrate.

Function of Amino Acids: It is the building blocks of Proteins. Major Component of Peptidoglycan Functions as a Buffers. Serves as a precursor of several enzymes and component Act as a nitrogen source