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Amino acids

Amino acids are separated by paper chromatography, gel electrophoresis, etc. They are hjghly soluble in water and insoluble in orgaruc solvents. They have high melting points.

General formula of amino acid is

Mirror images of the amino acid.

 

Proline amino acid (cyclic) is exception to this structure:

[Racemic mixture is the mixture of D- and L-forrns of molecules.]

 

D- and L-forrns of all the optically active compounds are compared with D- and L- forms of glyceraldehydes :

 

L ( +) Amino acid                                           L(-) Glyceraldehyde

 

[The -Coo- groups of amino acid is comparable to the -CHO group of glyceraldehyde as

after reaction with an oxidizing agent, -CHO group of amino acid is oxidized to -COOH group.]

 

The a-C of all amino acids is asymmetric (attached to 4 different groups) and, thus, are

optically active, except glycine, in which a-Cis symmetric and, thus, it is optically inactive:

Optically active compounds rotate the plane of polarized light and their D and L (absolute configurations) stereoisomers, that are mirror images of each other, are possible. All naturally occuting amino acids are present in L-form, except in some cases they are found in D-form, e.g. peptidoglycan of bacterial cell wall, some antibiotics.

 

Amino acids can be:

(i)       Neutralhaving1-NH21- COOHe.g. Glycine,Alanine (ii) Basichaving2-NH21–COOHLysine,Arginine (iii) Acidichaving1-NH22 –COOHAspartic acid,Glutamic acid

 

There are 20 standard amino acids which constitute the proteins. The aromatic amino acids (R -> aromatic) absorb maximally in UV region.

Phenylalanine               Tyrosine                                  Tryptophan

 

Two amino acids are $-containing:

 

In addition to these standard amino acids, there are many non standard amino acids that are

(i)                           Found in proteins and derived from standard amino acids. Here, modification occurs after incorporation into the proteins, e.g. hydroxyl-proline, hydroxyl-lysine, etc.

 

(ii)                         Not found in proteins and are intermediates of various biosynthetic pathways (about 300 types) e.g. ornithine, citrulline.

 

Ionization of Amino Acids:

 

(i) At isoelectric poirlt (specific for each amino acid, about pH- 6) the -COOH group of amino acids becomes negatively charged and -NH2 group positively charged and the molecules at such points are called zwitter ions (dipolar ions) that is a German word, which means hybrid ions. In this situation, the molecule can act as an acid (H+ donor) or as a base (H+ acceptor) and does not migrate in an electric field.

Thus, the pH at which a molecule has equal number of positive and negative charges is known as isoelectricpoint (no net charge) and on titration with a base, the -NH3+ group acts as the H+ donor and gets neutralized to -NH2 group. Whereas, on titration with an acid, the –COOgroup acts as H+ acceptor and gets neutralized to -COOH.

ii) At lower pH (acidic), the -COO group after accepting the H+ from the acid becomes neutralized to -COOH, whereas the -NH3+ group remains as such. The amino acid thus, becomes a cation and moves towards the cathode in an electric field.

(iii) At higher pH (basic), the -NH3+group after donating a H+ becomes NH2, whereas the -COO group remains as such, and the amino acid becomes an amino and moves towards the anode in an electric field.

 

The adjacent amino acids in proteins are covalently linked by peptide bonds, that is formed by thecondensation reaction through elimination of H2O between -NH2group

of one amino acid and -COOH group of other amino acid.

 

 

After elimination of a molecule of H2Othe amino acid is known as residue and is shown by the suffix -lyl, e.g. Glycine + Alanine → Glycyl-alanine, The protein chain has -NH2group at one end (left) and -COOH group at the other end (right).

 

Derivatives of Amino Acids

Some important derivatives of amino acids are:

 

(i)                 Thyroxine: It is derivative of the amino acid tyrosine and is formed in thyroidglands. It contains four atoms of iodine (I) and helps in the regulation of growth and metabolism

(ii)               Epinephrine (adrenaline): It is also a derivative of tyrosine and is produced in adrenal medulla (above kidneys). It regulates heart beat and blood pressure.

(iii)             IAA(/ndole-3-acetic acid): It is a plant hormone and is a tryptophan derivative.

(iv)             Nicotinamide: It is a vitamin and is tryptophan derivative.

(v)               Diamino-pimelic acid: It is derivative of lysine and is found in G bacterial cell wall (peptidoglycan).

(vi)             Melanin: It is a skin pigment and is the derivative of tyrosine.

 

Classification of Proteins

1. On the basis of composition, the proteins are of two types:

(i) Simple Proteins:

They are made up of onlyamino acids (or their derivatives), e.g. albumins (in blood), globulins, histones (basic proteins), ribonuclease, etc.

 (ii) Conjugated Proteins:

In addition to amino acids, they also contain non-protein prosthetic groups, e.g. glycoproteins (immunoglobulins), phosphoproteins (casein), lipoproteins, chromoproreins (haemoglobin, where haeme is the prosthetic group, cytochromes having iron porphyrin), metalloproteins (nitrogenase has Mo, plastocyanin has Cu), etc.

2. On the basis of size, the poteins are classified as:

(i) Peptides

They contain 2-70 amino acid residues and may be present in free state (may be protein degradation products or in combination with carbohydrates (e.g. peptidoglycan or mucopeptides). Some examples are:

 Cystine, where two cysteine residues are linked by disulphide linkage (-S-S-). Glutathione, which is a tripeptide, γ-Glu-Cys~Gly.

Oxytocin consists of nine amino acids and is secreted by posterior pituitary (in brain). It helps in contraction of uterus in labour.

Vasopressin is secreted by posterior pituitary and helps in constriction of blood vessels, increases blood pressure, promotes re-absorption of water in kidney tubules.

Gramicidin, an antibiotic is produced by Bacillus brevis and is cyclic decapeptide. Tyrocidin, again an antibiotic, is a cyclic decapeptide.

(ii) Polypeptides: They contain 20-50 amino acids (molecular weight below 10,000)

(iii)Proteins: They have generally more than 50 amino acids. The proteins may contain more than one polypeptide chains. Some examples are:

Ribonuclease contains one polypeptide chain that is folded by disulphide bonds (-S-S-). It degrades RNA.

Lysozyme also contains one polypeptide chain, which is folded by disulphide bonds (–S–S-). It degrades peptidoglycan by cleaving glycosidic bonds between NAM-NAG units -.

Papain has one polypeptide chain, which is folded by disulphide bonds (-S-S-). It is a proteolytic enzyme and is obtained from the latex of papaya.

Insulin is excreted from pancreas (Islets of Langerhans) and is a hormone that converts glucose to glycogen. It was the first protein of which amino acid sequence was determined by Sanger (1951). It contains two polypeptide chains that are covalently linked by -S-S- bonds. It has 51 amino acid residues, of which 21 amino acids make

Glucagon. is a pancreatic hormone that converts glycogen into glucose and consists of 29 amino acids.

Haemoglobin. contains four polypeptides, where, two are α-chains and two are β-chains.Sickle cell anaemia is caused due to difference of only one amino acid in β-chain, so that the 6thamino acid, glutamate, is replaced by valine. In this disease, the erythrocytes becomes sickle shaped and have reduced O2exchange capacity in comparison to the normal ones.

 

Structural Levels of Proteins

Just after the protein synthesis, the protein gets folded into 3-dimensional form to attain secondary, tertiary and quaternary structures. Thus, four levels (Fig.3.9) of organizations in proteins are:

1. Primary Structure

 They consist of amino acids linked by peptide bonds and are generally non-functional, e.g.few plant proteins (Fig. 3.3). Insulin, which regulates glucose metabolism in mammals, was the first protein whose primary structure was determined by Sanger (1951).

2. Secondary Structure

Here, polypeptide chains are folded or coiled to attain second level of organization through hydrogen bonding between various functional groups,

 

Examples of such proteins are fibrous proteins (thread-like), which is mainly structural, collagen, α-keratin, fibroin, myosin in muscle. These are insoluble in water. Two main secondary structures are:

(i) α-Helix: Here, the amino acid back bone is right-handed coiled (helical) and\it is the most common coiling found in proteins (Fig. 3.4 and 3.5). It is more stable for L-amino acids than left handed coiling and has 3.6 amino acids / turn (18 a.a. /5 turns). It is hard and their examples are a-keratins, found in fur, claws, hooves, feathers, hair, nails, shell of tortoise (hardness due to extensive -S-S- bonds).

(ii) βconformation: It is 3-D (three dimensional) structure and is also known asβ-pleated sheet as the structure is folded into flat sheet with zig-zag backbone. Adjacentfibres are hydrogen-bonded (Fig. 3.6). This type of structure is flexible and some examples are β-keratin of silk fibroin, spider web fibroin, etc .

3. Tertiary Structure

These are globular proteins, where secondary level of organization is again twisted and folded. Several types of secondary structures may be present in the same polypeptide (Fig. 3.7). They are soluble in water and examples are myoglobin (first protein whose globular structure was determined by X-ray diffraction method), insulin, albumin, etc.

The tertiary structure is maintained by a number of bonds, e.g.

  1. Disulphide (-S-S-) bonds that are covalent in nature and are formed between 2 cysteine residues, e.g. ribonuclease (with four -S-S- bonds).
  2. Hydrogen bonds, though, are weak but being numerous in number provide quite stability to the protein.
  3. Ionic bonds that are formed between acidic and basic amino acids.
  4. Hydrophobic interactions occurring between hydrophobic amino acids that are organized in the interior of protein, between non-polar R-groups (in aqueous mediummaximum number of polar groups get organized towards the surrounding medium,
    whereas, the non-polar groups directed internally), etc
4. Quaternary Structure

It contains more than one polypeptide chains (subunits) that are associated together non-covalently. These subunits can be homogeneous (identical) or heterogeneous (non- identical, e.g., haemoglobin consisting oftwo α-and two β-chains) (Fig. 3.8). Most com- mon structures are dimers, trimers, tetramers, pentamers te.g. Rl’l”A polymerase) and decamers. Glutamine synthetase enzyme has 12 sub units and proteins with a maximum of 32 subunits have been reported

 

Role of Proteins

(i)                  Structural role, e.g. cell membrane, fibres, cartilage (made of collagen).

(ii)                Many proteins are enzymes, e.g. ribonuclease, glutamine synthetase.

(iii)              Many hormones are peptides or proteins, e.g. insulin, glucagon, oxytocin, vasopressingrowthhormone, etc.

(iv)               Blood proteins, e.g haemoglobin (carries 02), albumin (maintains osmotic pressure of  blood), α-, β-and γ-globulins (immunoglobulins or antibodies, which are produced by B-lymphocytes), fibrinogen (helps in blood clotting).

(v)                 Many proteins help in transport e.g., carriers in membranes, haemoglobin carries 02, myoglobin carries and stores O2 in muscles

(vi)               Movement of muscles is performed by actin and myosin (contractile proteins).

(vii)             Glutelin of wheat and rice performes storage function (cohesiveness and elasticity of dough is due to this protein, which is rich in -S-S- bonds). Egg albumin is also a storage protein.

 

 

QUESTIONS

 1.Write characteristic features of amino acids. What are zwitter ions?

2.What are the different levels of protein organization?

3.Discuss the important roles of proteins.