3.2. CLASSIFICATION OF PROTEINS Proteins show a wide range of structural and functional diversity. It is quite difficult to classify this diverse group of biological macromolecules on the basis of one single property or characteristic. Thus, there is no general or universal system of classification of proteins. Some of the common basis of classification of proteins are given below and are discussed subsequently. Shape and structure © Products of hydrolysis * Biological function 3.2.1 Classification on the Basis of Shape and Structure Proteins adopt a wide range of shapes depending on their composition and the nature of folding of polypeptide chains. On the basis of their overall shape the proteins are further categorised into two broad classes. These are Globular proteins e Fibrous proteins Globular Proteins These are also called spheroproteins or corpuscular proteins and contain compactly folded coils of polypeptide chains which give them a shape of spheroids (a sphere) or ellipsoids (an ellipse). These have low axial ratio (<10, usually 3-4) i., the ratio of length to the width, These proteins contain a number of structural units, called domains which are of single strand polypeptide chains containing alternating c-helices and B-strands (structures adopted by proteins; discussed later). These are usually soluble in water or aqueous solutions of acids, bases or alcohols. Due to the compact shape these proteins diffuse quite easily. Albumins, globulins, lysozyme. histones and protamines - the proteins of animal origin and prolamines and glutelins found in the food grains belong to this classProteins 1p @ (b) BAL (a) Lysozyme-a globular protein and (b) Collagen-a fibrous protein. The globular proteins have low axial ratios as compared to the fidreus proteins Fibrous Proteins The proteins belonging to this class have an elongated shape and look somewhat like fibres or threads and have axial ratio of more than 10. These are insoluble in water and aqueous solutions of acids and bases. Fibrous proteins have high mechanical strength and form skeletal and connective tissues in anin nals. The peptide chains in these proteins can be arranged in many ways, and depending on these, fibrous proteins can be further divided into following special types. () ce Keratins: c:-Keratins are found in protein fibres of hair. skin and wool and are constituted of a number of a-helices that are twisted together like the strands of a rope. These are rich in cystine and poor in proline and hydroxyproline. Fibrin, the protein involved in the coagulation of blood also has a o-keratin structure. B-Keratins: B-Keratin type of fibrous proteins are found in hard tissues such as nails. horns, spider's web. fish scales, porcupine quills, and bird feathers etc. These are rich in small uncharged amino acids like glycine and alanine and poor in cysteine, proline and hydroxyproline and acquire a B-pleated sheet structure. Silk fibroin obtained from the cocoons of silk moth has B-keratin structure (iii) Collagens: Collagens are the main components of bone. teeth, connective tissues of tendons and ligaments etc. These are rich inamino acids like glycine, alanine, proline and hydroxyproline and poor in cysteine, cystine, methionine, tyrosine and tryptophan. In collagen the polypeptide chain acquires an elongated left handed o-helical structure and three such helices spiral around each other like the strands of a rope. On heating with water these proteins swell up to give colloidal gelatin. (iv) Elastins: These are closely related to collagens and constitute ligaments, the walls of blood vessels ete. Elastins are rich in amino acids like, alanine, leucine, proline and valine and are deficient in cysteine, cystine, methionine and histidine. Structurally, elastin is similar to collagen, the difference being in the nature of cross linking of different polypeptide chains. Further, it does not swell up in water like collagen. 3.2.2 Classification on the Basis of Products of Hydrolysis ‘On the basis of the products obtained on hydrolysis (or the composition) proteins can be classified into three categories as: * Simple proteins © Conjugated proteins * Derived proteins Simple Proteins These are composed of amino acids only and do not contain any non- protein part attached to them, These are further classified on the basis of their solubility, precipitability and thermocoagulability which in turn depend on the size and shape of the proteins. Most of the simple proteins are of globular type, scleroproteins being exception as these are fibrous in nature Major classes in this type include the following, G@_ Albumins: These are soluble in water and aqueous solutions of acids, bases and salts. Albumins generally have low isoelectric point: pl and act as acidic proteins under physiological conditions. These can be reprecipitated by full saturation with ammonium sulphate and are easily thermocoagulable. These are generally deficient in glycine. Serum albumin in blood plasma, ovalbumin in egg white and lactoalbumin in milk are common animal albumins while leucosin in cereals, legumelin in legumes and ricin in castor beans are common plant albumins. Gi) Globulins: These are ellipsoidal in shape, having lower solubilities as compared to albumins and are insoluble in water but dissolve in aqueous solutions of acids, bases and dilute salt solutions (5% sodium chloride).‘These can be precipitated by half-saturation with ammonium sulphate and are also easily thermocoagulable. These usually contain the amino acid, glycine. Serum globulin in blood plasma, myosin in muscles and lactoglobulin in milk and thyroglobulin from the thyroid gland are common animal globulins while edestin in hemp seed is an example of plant globulin (iii) Histones: These are a small group of closely related basic (iv) ~ wip nucleoproteins (proteins found in the nucleus of the cell) containing a good fraction of lysine, histidine or arginine and lack tryptophan and are deficient in cysteine and methionine residues. These can be isolated from the sperm cells, red blood corpuscles (RBCs) and white blood corpuscles (WBCs). Histones dissolve in water and dilute aqueous solutions of acids and bases but are insoluble in dilute ammonia. These are not easily thermocoagulable. Protamins: Protamins, like histones, are also basic proteins that are soluble in-water and dilute aqueous solutions of acids, bases and ammonia and are not easily thermocoagulable. These occur almost entirely in animals and are the main components of sperm cells of certain fishes. Salmine and clupeine are the protamins found in the sperm cells of salmon and herring fish respectively. The protamins are quite small in size and have relatively low molecular mass of the order of ~5000 Daltons. These proteins are quite rich in basic amino acid, arginine and behave more like a polypeptide. Prolamins: This is a very small class of plant proteins found in grain stuff. These proteins are insoluble in either water or alcohol and are not thermocoagulable but can be extracted with 60-80% alcohol or dilute aqueous solutions of acids and bases. These are rich in glutamic acid and proline but poor in histidine. lysine and arginine etc. Gliadin from wheat, hordenine from barley and zein from maize etc. are common examples of prolamins Glutelins: These. like prolamins are plant proteins found in grains. ‘These are insoluble in either water or alcohol but can be extracted with dilute aqueous solutions of acids and bases. Due to their reasonable size these can be thermocoagulated. It is in contrast to prolamins. which are not thermocoagulable. Glutelins in a way supplement prolamins as these contain lysine and tryptophan. Glutenin in wheat flour, glutelin in corn and oryzenin in rice are common examples of glutelins. Scleroproteins: Scleroproteins are fibrous proteins of animal origin. These are insoluble in water and dilute aqueous solutions of acids.bases and salts and also in 60-80% alcohol. However, these dissolve in concentrated acids and bases and include &- and B- keratins, collagens and elastins discussed above. Conjugated or Complex Proteins When the proteins form complexes with some nonprotein components these are called conjugated proteins. The protein part of conjugated proteins is called apoprotein and the nonprotein part is referred to as the prosthetic Broup. The entire molecule is called a haloprotein. The conjugated proteins are generally globular in nature and can be further subdivided on the basis of the nature of prosthetic group present. Major classes in this type include the following. (@ Phosphoproteins: These proteins contain phosphoric acid as prosthetic group and do not include phosphate containing substances like nucleic acids etc. The phosphoric acid group is connected through ester linkage to a hydroxy group on the pélypeptide chain. Casein, the milk protein and ovovitellin obtained from egg yolk are common phosphoproteins. The phosphoric acid group of these proteins can be removed enzymatically or with the help of aqueous sodium hydroxide. Gi) Metattoprot In metalloproteins. the protein molecule is linked with metal ions which may be strongly bound or weakly associated Siderophilin, an important plasma protein, constituting about a third of plasma proteins, has a very strong affinity for iron and in fact is involved in iron transport. Cerulopiasmin, another plasma protein has affinity for copper ions. In addition, a number of enzymes also need metal ions for their activity. For example. carbonic anhydrase requires Zn™ while cytochrome oxidase needs Cu** and Fe** ions to perform their functions. (iii) Chromoproteins: Chromoproteins are proteins containing coloured Pigments like flavins, carotenoids, porphyrins etc. as their prosthetic groups. This class includes proteins involved in respiratory functions ¢-g., haemoglobin, myoglobin and cytochrome ete. A number of enzymes like, catalase, peroxidase. cytochrome oxidase belong to this group. Chloroplastin, the plant protein containing chlorophyll is also a chromoprotein. (iv) Glycoproteins and mucopolysaccharides: This group refers to the Proteins containing a carbohydrate component as the prosthetic group. The prosthetic group is an integral part of the structure and may constitute from less than 4% to more than 80% of the glycoproteins. ‘The oligosaccharide chains are joined with the polypeptide through aO-glycosidic linkage with the hydroxy] group of serine or threonine residues or by N-glycosidic linkage with the amide side chain of asparagine. Glycoproteins include immunoglobulins, many enzymes and some hormones like, thyrotropin or thyroid stimulating hormone (TSH), follicle stimulating hormone (FSH) and lutenising hormone(LH) etc. These hormones are secreted by anterior pituitary glands Mucopolysachharides, on the other hand. contain a small protein component in a carbohydrate structure. These are found in the supportive and connective tissues in animals. Hyaluronic acid present in the vitreous humour of the eye is one of the simplest mucopolysachharides and is made up of N-acetylglucosamine and p-glucoronic acid. Heparin, the natural anticoagulant and chondroitin sulphate isolated from cartilages and tendons are some of the other examples of mucopolysaccharides (y) Nucleoproteins: Nucleoproteins are complexes containing nucleic acids and basic proteins like protamines and histones. The protein and the nucleic acids are bound primarily through electrostatic interactions. These complexes adopt very compact structures and are important constituents of chromosomes, ribosomes. and some viruses. (vi) Lipoproteins: This group includes proteins complexed with lip and have a variable composition. The nonpolar side chains of the apoprotein and the lipids are bound through hydrophobic interactions. These are important constituents of blood plasma, cellular membranes, milk and egg yolk etc. Lipoproteins are further classified on the basis of their densities which in turn depend on the protein content. The lipoproteins of lowest density are called as chylomicrons and contain up to 2% protein. The fraction containing about 9% of the proteins is referred to as very low density lipoproteins (VLDL); the one having about 21% protein are called low density lipoproteins (LDL) while the lipoproteins containing about 33% proteins are known as high density lipoproteins (HDL). These lipoprotein complexes are closely related to heart diseases. Increased concentration of LDL in the blood increases the risk of arteriosclerosis —the thickening of arterial walls Derived Proteins These are the degradation products derived on subjecting the native proteins to different physical or chemical agents like, heat, acid, alkali or enzyme. Artificially produced polypeptides are also included in this ci The derived proteins are further classified into following types(i) Primary or denatured derived proteins: These are obtained by the action of water, acids, alkalies, heat, radiations etc. on the native protein which denature the protein without hydrolysing it. It implies that the perturbing conditions do not hydrolyse the peptide backbone, only the weaker forces like hydrogen bonding. hydrophobic interactions, salt linkages etc: responsible for maintaining the native structure of protein are disrupted. In these, proteins molecular mass does not change. only the properties like solubility, precipitation etc, are altered e.g., ovalbumin, a soluble globular protein changes to insoluble fibrous protein on heating or treating with urea (i) Secondary derived proteins: These are obtained by the processes that cause progressive hydrolysis of the native protein. The products obtained in the initial'stages of the hydrolysis, with dilute acids, alkalies and enzymes, are called proteoses; these are soluble in water and are heat coagulable. The primary proteoses also called metaproteins are insoluble in water but dissolve in acids and alkalis, These can be salted out by half saturation with ammonium sulphate. However, the secondary proteoses—the second stage hydrolysis products need full saturation. The next stage of hydrolysis generates peptones which are soluble in water and are not coagulated by heat and also cannot be salted out by ammonium sulphate. Further hydrolysis gives polypeptides and simple peptides. which also behave like peptones. The ultimate product of the hydrolysis is a mixture of amino acids These are soluble in water and sparingly soluble in organic solver The products obtained at different stages of protein hydrolysis and their properties can be summarised as follows: Proteins Stage-1 Metaproteins or primary proteoses : can be salted out by halt saturation Stage-I Y Secondary proteoses can be saltec out by full saturation Stage-li! Y Peptones nonthermocoagulable and do not salt out Stage-IVy Simple peptides / polypeptides = Nonthermocoagulable and do not salt out Stage-V y Mixture of amino acids soluble in water3.2.3 Classi ication on The Basis of Biological Functions Since proteins perform a variety of functions in the body, the biological functions performed provide another basis for their classification. The different classes of proteins on the basis of their biological function are as follows. w Gi Gi) Gv) w wid (ii) Enzymes: These are also called as biochemical catalysts and are proteins involved in catalysing biological reactions e.g dehydrogenases, catalysing dehydrogenation reactions and, kinases, involved in transfer of phosphate group etc. Chapter 4 gives a detailed account of enzymes in terms of their structure and function ete. Storage proteins: These proteins are entrusted with the job of stori important species in the living cell. Myoglobin (responsible for oxygen storage in skeletal muscles) and ferritin (involved in the storage of iron in the liver) belong to this category Regulatory proteins: As the name suggests, these proteins control many aspects of cell functions including metabolism and reproduction. Several hormones such as insulin and glucagons that regulate body functions are also proteins. Structural proteins: These provide mechanical support to large animals and provide them with their outer covering, e.g. proteoglycan ‘These proteins are also major structural components of ceilular membranes and cell organelles. Our hair and finger nails are lar; composed of keratin. a type of fibrous protein. Collagen - another fibrous protein provides mechanical strength to our teeth. bones and tendons and is responsible for the stability of our body. Protective (or defense) proteins: These proteins defend the body against infection and are related to the immune system. These are collectively called as immunoglobulins or antibodies which bind specifically to an antigen (foreign substances / organisms causing infection) and cause its destruction. Venoms and toxins also belong to this class Transport proteins: These proteins are engaged in carrying materials from one place t another in the body. These are generally involved in transport of food molecules. energy sources etc. across the cell membrane or in the body fluids. For example, haemoglobin is associate: with the transport of oxygen while the protein called transferrin is used for transporting ferric ions in the plasma Contractile and mobile proteins: These are engaged in ail forms of movement for example, actin and myosin are responsible for heart and muscle movement, tubulin for sperm movement etc.