Amino acids are a group of organic compounds containing two functional groups--amino (-NH2) and carboxyl (-COOH).The Amino group is basic and the carboxyl group is acidic in nature.These are structural unit of protein.Proteins are polymers of amino acids, with each amino acid residue joined to its neighbour by a specific type of covalent bond namely peptide bond that reflects the loss of the elements of water during joining of two amino acid.Proteins can be broken down( hydrolyzed) to their constituent amino acids by a variety of methods.
Atoms in amino acids structure : C,O,N,H and S.
General structure of Amino Acids :
Standard amino acids :
As many as 300 amino acids occure in nature, of these only 20 amino acids known as standard amino acids are repeatedly found in protein structure,isolated from different forms of life such animal,plant and microbial.The first to be discovered was asparagine, in 1806.The last of the 20 to be found,threonine, was not identified until 1938.
Structures of 20 standard amino acids :
Selenocystein - the 21 st amino acid : In recent years a 21 st amino acid namely selenocystein has been added.It is found in at the active sites of certain enzymes / proteins (selenoproteins), e.g. glutathione peroxidase,glycine reductase, thioredoxine reductase, 5'-deiodinase.
Pyrrolysine - in 2002 some researchers have described another amino acid namely pyrrolysine as the 22 nd amino acid. The stop codon UAG can code for pyrrolysine.
Non standard amino acids :
amino acids that have been chemically modified after they have been incorporated into a protein (termed a “posttranslational modification”) and those amino acids that occur in living organisms but are not found in proteins .Among these modified amino acids is γ-carboxyglutamic acid, a calcium-binding amino acid residue found in the blood-clotting protein prothrombin
(as well as in other proteins that bind calcium as part of their
biological function). The most abundant protein by mass in vertebrates
is collagen.
Some nonstandard amino acids are not found in proteins. Examples include lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids — for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below). A rare exception to the dominance of α-amino acids in biology is the β-amino acid beta alanine (3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B5), a component of coenzyme A.
Common structural features of amino acids :
1. All 20 of the common amino acids are a α-amino acids.They have a carboxyl group and an amino group bonded to the same carbon atom (α carbon)
2. They differ from each other in their side chains , or R groups , which vary in structure, size, and electric charge , and which infuence the solubility of the amino acids in water.
3. The common amino acids of proteins have been assigned three-letter abbreviations and one-letter symbols,which are used as shorthand to indicate the composition and se quence of amino asids polymerized in proteins.
4. The additional carbons in an R group are commonly designated β, γ, δ, ε and so forth proceeding out from the α carbon .
5. For most other organic molecules , carbon atoms are simply numbered from one end, giving highest priority(C-1) to the carbon with the substituent containing the atom of highest atomic number.Within this lattter convention , the carboxylic carbon of an amino acid would be C-1 and the α carbonwould be C-2 . Amino acids with heterocyclick R groups, the greek lettering system is ambigous and the numbering convention is therfore used.
Lysin
6. The α carbon is known as chiral carbon (except glycine) because four different groups : a carboxylic group, an amine group, an R group, and a hydrogen bind to this carbon.
7. Amino acids have two possible sterioisomers because of the tetrahydral arrangement of bonding orbitals around the α-carbon atom. All molecules with chiral center are also optically active i.e., they rotate plane -polarized light.
Classificattion of amino acids :
There are different ways of classifying the amino acids based on the structure and chemical nature, nutritional requirement, metabolic fate etc.
A.
Classification based on the structure :
1. Amino acids with aliphatic side chains : These are monoamino monocarboxylic acids.The amino acids of this class are glycine, alanine, valine, leucine, and isoleucine.The last three amino acids contain branched aliphatic side chains ,hence they are reffered to as branched chain amino acids.
2. Hydroxyl group containing amino acids: Serine, threonine,and tyrosine are hydroxyl group containing amino acids.
3. Sulfur containing amino acids : cysteine with sulfhydryl group and methionine with thioether group and cystine with two molecule of cystein joining by disulfied bond.
4. Acidic amino acids and their amides : Aspartic acid and glutamic acids are dicarboxylic monoamino acids while asparagine and glutamine are their respective amide derivatives.
5. Basic amino acids : The three amino acids lysine , arginine(with guanido group) and histidine (with imidazole group) are monocarboxylic acids but basic in character.
6. Aromatic amino acids : Phenylalanine ,tyrosine,and tryptophan( with indole group) are aromatic amino acids.
7. Imino acids : proline containing pyrrolidine ring is a unique amino acid with an iminogroup(= NH).
B. Classification based on polarity : Amino acids are classified into four groups based on their polarity.
1.
Non-polar amino acids : These are hydrophobic ( water hating ).They have no charge in R group.The amino acids include in this class alanine, leucine,isoleucine ,valine , methionine, phenyl alanine tryptophan,and proline.
2. Polar amino acids with no charge on R group : The amino acids of this class do not carry charge on the R groups.They possege groups such as hydroxyl, sulfhydral , and amide .e.g. Glycine,serine, threonine, cystein,glutamine, asparagine and tyrosine.
3. Polar amino acids with positive R group : The three amino acids lysine ,arginine ,and histidine are included in this group.
4. Polar amino acids with negative R group : The dicarboxylic monoamino acids- aspartic acid and glutamic acid are considered in this group.
C. Classification Based on Nutrition : The twenty common amino acids are classified into two classes based on their nutritional requirement those are required for the synthesis of variety of proteins and biological functions.
1. 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 maintanence of the individual.The ten amino acids are essential for human :
Arginine, Valine, Histidin, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine,Threonine, Tryptophan.
Semi-essential amino acids : There are two amino acids namely Arginine and Histidine are partly synthesized by the adult body hence htey are known as semi essential amino acids.Thus 8 are absolutely essential while 2 are semi essential amino acids.
2. Non-essential or dispensable amino acids : The amino acids which can be synthesized by the body to meet the biological needs known as non-essential amino acids. These are - Glycine, Alanine, Serine, Cystein, Asparagine, Aspartate, Glutamate, Glutamine,Tyrosine and proline.
D.
Classification based on their metabolic fate : The carbon skeleton of amino acids cn serve as a precursor for the synthesis of glucose or fat or both. From metabolic view amino acids are divided into three classes :
1. Glycogenic amino acids : the amino acids which act as precursor of the glucose or glycogen biosynthesis e.g. Alanine, aspartate, glycine, methionine etc.
2. Ketogenic amino acids : the amino acids act as precursors for fat biosynthesis. Two amino acids are ketogenic leucine and lysine are exclusively ketogenic.
3. Glycogenic and Ketogenic amino acids : The four amino acids isoleucine, phenylalanine, tryptophan, tyrosine are precursors for the synthesis of glucose as well as fat.
Physiochemical propeties of Amino acids :
A.
Physical properties :
1. Solubility : Most of the amino acids are usually soluble in water and insoluble in organic solvents .
2. Melting point : Amino acids are generally melt at higher temparatures, often avobe 200 degree centigrade.
3. Taste : Amino acids may be sweet (gly,ala,val), tasteless(leu), or bitter(Arg,Ile).
4. Optical properties : All the amino acids except glycine posseses optical isomers i.e.D-and L-Amino Acids due to the presence of asymmetric carbon atom. Some amino acids also have a second asymmetric carbon e.g. isoleucine, threonine.
5. Amino acids as ampolytes : Amino acids contain both acidic (-COOH) and basic (-NH2) groups. They can donate a proton or accept a proton ,hence amino acids regarded as ampolytes.
6. Each Amino acids has characteristic pH (e.g. leucine pH 6.0) at which it carries both positive and negative chargesand exsts as Zwitterion.
7. Amino acids have characteristic Titration curves.
B.
Chemical properties :
1. The common chemical properties of all amino acids result from the presence of both α-carboxylic and α-amino groups in their molecules. The reactions connected with specific features of the side chains allow to distinguish individual amino acids or some groups of amino acids.It refers to both free amino acids and those bound in peptide or protein molecules. Reaction with ninhydrin – a common reaction for all amino acids All amino acids and peptides, which contain a free α-amino group, react with ninhydrin forming a blue-violet product, whereas proline and hydroxyproline, which contain free imino groups, form a yellow product. During the ninhydrin reaction the amino acid undergoes decarboxylation and deamination. The released ammonia (NH3) binds to ninhydrin forming a blue-violet product. The reaction is presented on
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Characteristic reactions for individual amino acids
2.The aromatic rings of phenylalanine, tyrosine and tryptophan submitted to the action of nitric acid (HNO3) form yellow nitroderivative products. This process is known as a xantoprotein reaction.
Tyrosine, like other phenols, reacts with Millon reagent, which is a mixture of mercury nitrates (V) and mercury nitrates (III) in nitric acid solution. The nitrophenols, resulting from the interaction of tyrosine with nitric acid (V) form red colour complexes with mercury. The heating of mixture containing free or peptide bound tyrosine with Millon reagent results in formation of red flocky sediment.
3.Sulphur-containing amino acids: cysteine and methionine – in strongly alkaline medium – are degraded releasing the sulphide ions (S2-), which react with lead (II) acetate forming brown-black lead (II) sulphide.
4. The guanidine group of arginine reacts with α-naphtol oxidised with bromate (I), releasing ammonia (NH3), and red colour complex.
5. The indol ring of tryptophan reacts with glyoxalic acid - in the presence of sulphuric (VI) acid - forming red-violet product. The glyoxalic acid exists as a contaminating component in commercial preparation of concentrated (glacial) acetic acid.
6. The imidazole ring of histidine, in the presence of sodium nitrite, reacts with sulphanilic acid forming yellow product.
Occurance and function in Biochemistry :
1.Amino acids are primary building blocks of various biologically active proteins.
2.Amino acids can be metabolized to produce energy. This is especially
important during fasting, when the breakdown of muscle protein is a major
energy source.
3.Some amino acids act as neurotransmitters, and some act as starting
materials for the biosynthesis of neurotransmitters, hormones, and other
important biochemical compounds.
Amino acids useful as drugs :
There are certain non-standard amino acids that are used as drugs .
- D-peniciline (D- dimethylglycine), a metabolite of peniciline is employed in the chelation therapy of Willson's disease.
- N-Acetylcysteine is used in cystic fibrosis and chrionic renal insufficiency ,as it can function as an antioxidant.
- Gabapentin (γ- aminobutyrate linked to cytohexane) is used as an anticonvulsant.
Sources and biological function of amino acids.
