Biomolecules: Top 4 Classes of Biomolecules

This article throws light upon the top four classes of biomolecules.

The top four classes of biomolecules are: (1) Carbohydrates (2) Lipids (3) Proteins and Amino Acids and (4) Isoprenoids and Pigments.

Biomolecules:

The living matter is composed of mainly six elements — carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. These elements together constitute about 90% of the dry weight of the human body. Several other functionally important elements are also found in the cells. These include Ca, K, Na, CI, Mg, Fe, Cu, Co, I, Zn, F, Mo and Se.

Carbon—a unique element of life:

Carbon is the most predominant and versatile element of life. It possesses a unique property to form infinite number of compounds. This is attributed to the ability of carbon to form stable covalent bonds and C—C chains of unlimited length. It is estimated that about 90% of compounds found in living system invariably contain carbon.

Chemical Molecules of Life:

Life is composed of lifeless chemical molecules. A single cell of the bacterium, Escherichia coli contains about 6,000 different organic compounds. It is believed that man may contain about 100,000 different types of molecules although only a few of them have been characterized.

Complex biomolecules:

The organic compounds such as amino acids, nucleotides and monosaccharide’s serve as the monomeric units or building blocks of complex biomolecules — proteins, nucleic acids (DNA and RNA) and polysaccharides, respectively. The important biomolecules (macromolecules) with their respective building blocks and major functions are given in Table 65.1. As regards lipids, it may be noted that they are not biopolymers in a strict sense, but majority of them contain fatty acids.

Structural hierarchy of an organism:

The macromolecules (proteins, lipids, nucleic acids and polysaccharides) form supra-molecular assemblies (e.g. membranes) which in turn organize into organelles, cells, tissues, organs and finally the whole organism.

Chemical composition of man:

The chemical composition of a normal man, weighing 65 kg, is given in Table 65.2. Water is the solvent of life and contributes to more than 60% of the weight. This is followed by protein (mostly in muscle) and lipid (mostly in adipose tissue). The carbohydrate content is rather low which is in the form of glycogen.

The basic information on the various biomolecules is essential for a better understanding of the concepts of biotechnology. The biomolecules namely nucleic acids (DNA and RNA) which are directly relevant to biotechnology are described.

Class # 1. Carbohydrates:

Carbohydrates are the most abundant organic molecules in nature. They are primarily composed of the elements carbon, hydrogen and oxygen. The name carbohydrate literally means ‘hydrates of carbon.’ Carbohydrates may be defined as polyhydroxy- aldehydes or ketones or compounds which produce them on hydrolysis. The term ‘sugar’ is applied to carbohydrates soluble in water and sweet to taste.

Functions of carbohydrates:

Carbohydrates participate in a wide range of functions:

1. They are the most abundant dietary source of energy (4 Cal/g) for all organisms.

2. Carbohydrates are precursors for many organic compounds (fats, amino acids).

3. Carbohydrates (as glycoproteins and glycolipids) participate in the structure of cell membrane and cellular functions such as cell growth, adhesion and fertilization.

4. Carbohydrates also serve as the storage form of energy (glycogen) to meet the immediate energy demands of the body.

Classification of Carbohydrates:

Carbohydrates are often referred to as saccharides (Greek: sakcharon-sugar). They are broadly classified into 3 groups—monosaccharide’s, oligosaccharides and polysaccharides. This categorization is based on the number of sugar units. Mono- and oligosaccharides are sweet to taste, crystalline in character and soluble in water, hence they are commonly known as sugars.

Monosaccharide’s:

Monosaccharide’s (Greek: mono-one) are the simplest group of carbohydrates and are often referred to as simple sugars. They have the general formula C_n(H₂O)_n, and they cannot be further hydrolysed. Based on the number of carbon atoms, the monosaccharide’s are regarded as trioses (3C), tetroses (4C), pentoses (5C), hexoses (6C) and heptoses (7C). These terms along with functional groups are used while naming monosaccharide’s. For instance, glucose is a aldohexose while fructose is a ketohexose.

Oligosaccharides:

Oligosaccharides (Greek: oligo-few) contain 2-10 monosaccharide molecules which are liberated on hydrolysis. Based on the number of monosaccharide units present, the oligosaccharides are further subdivided to disaccharides, tri- saccharides etc.

Polysaccharides:

Polysaccharides (Greek: poly-many) are poly­mers of monosaccharide units with high molecular weight (up to a million). They are usually tasteless (non-sugars) and form colloids with water. Poly­saccharides are of two types—homopoly- saccharides and heteropolysaccharides.

Monosaccharide’s:

Stereoisomerism is an important character of monosaccharide’s. Stereoisomers are the compounds that have the same structural formulae but differ in their spatial configuration. A carbon is said to be asymmetric when it is attached to four different atoms or groups. The number of asymmetric carbon atoms (n) determines the possible isomers of a given compound which is equal to 2ⁿ. Glucose contains 4 asymmetric carbons and thus has 16 isomers.

Glyceraldehyde— the reference carbohydrate:

Glyceraldehyde (triose) is the simplest mono­saccharide with one asymmetric carbon atom. It exists as two stereoisomers, and has been chosen as the reference carbohydrate to represent the structure of all other carbohydrates.

D- and L-isomers:

The D- and L-isomers are mirror images of each other. The special orientation of —H and —OH groups on the carbon atom (C₅ for glucose) that is adjacent to the terminal primary alcohol carbon determines whether the sugar is D- or L-isomer. If the —OH group is on the right side, the sugar is of D-series, and if on the left side, it belongs to L-series. The structures of D- and L-glucose based on the reference monosaccharide, D- and L-glyceraldehyde (glycerose) are depicted in Fig. 65.1

It may be noted that the naturally occurring monosaccharide’s in the mammalian tissues are mostly of D-configuration. The enzyme machinery of cells is specific to metabolize D-series of monosaccharide’s.

Optical activity of sugars:

Optical activity is a characteristic feature of compounds with asymmetric carbon atom. When a beam of polarized light is passed through a solution of an optical isomer, it will be rotated either to the right or left. The term dextrorotatory (+) and levorotatory (-) are used to compounds that respectively rotate the plane of polarized light to the right or to the left.

Glycosides:

Glycosides are formed when the hemiacetal or hemiketal hydroxyl group (of anomeric carbon) of a carbohydrate reacts with a hydroxyl group of another carbohydrate or a non-carbohydrate (e.g. methyl alcohol, phenol, and glycerol). The bond so formed is known as glycosidic bond and the non- carbohydrate moiety (when present) is referred to as aglycone.

Derivatives of Monosaccharide’s:

There are several derivatives of monosaccharide’s, some of which are physiologically important:

1. Amino sugars:

When one or more hydroxyl groups of the monosaccharide’s are replaced by amino groups, the products formed are amino sugars e.g. D-glucosamine, D-galactosamine. They are present as constituents of heteropoly- saccharides.

2. Deoxysugars:

These are the sugars that contain one oxygen less than that present in the parent molecule. The groups —CHOH and —CH₂OH become —CH₂ and —CH₃ due to the absence of oxygen. D-2-Deoxyribose is the most important deoxysugar since it is a structural constituent of DNA (in contrast to D-ribose in RNA).

3. L-Ascorbic acid (vitamin C):

This is a water- soluble vitamin, the structure of which closely resembles that of a monosaccharide.

Disaccharides:

Among the oligosaccharides, disaccharides are the most common. As is evident from the name, a disaccharide consists of two monosaccharide units (similar or dissimilar) held together by a glycosidic bond. They are crystalline, water-soluble and sweet to taste.

The disaccharides are of two types:

1. Reducing disaccharides with free aldehyde or keto group e.g. maltose, lactose.

2. Non-reducing disaccharides with no free aldehyde or keto group e.g. sucrose, trehalose.

Polysaccharides:

Polysaccharides (or simply glycans) consist of repeat units of monosaccharide’s or their derivatives, held together by glycosidic bonds. They are primarily concerned with two important functions-structural, and storage of energy.

Polysaccharides are of two types:

1. Homopolysaccharides which on hydrolysis yield only a single type of monosaccharide. They are named based on the nature of the monosaccharide unit. Thus, glucans are polymers of glucose whereas fructosans are polymers of fructose.

2. Heteropolysaccharides on hydrolysis yield a mixture of a few monosaccharide’s or their derivatives.

Homopolysaccha Rides:

Starch:

Starch is the carbohydrate reserve of plants which is the most important dietary source for higher animals, including man. High content of starch is found in cereals, roots, tubers, vegetables etc. Starch is a homopolymer composed of D-glucose units held by α-glycosidic bonds. It is known as glucosan or glucan.

Starch consists of two polysaccharide components-water soluble amylose (15-20%) and a water insoluble amylopectin (80-85%). Chemically, amylose is a long unbranched chain with 200-1,000 D-glucose units held by α (1 → 4) glycosidic linkages. Amylopectin, on the other hand, is a branched chain with α (1 → 6) glycosidic bonds at the branching points and α (1 → 4) linkages everywhere else. Amylopectin molecule containing a few thousand glucose units looks like a branched tree (20-30 glucose units per branch).

Glycogen:

Glycogen is the carbohydrate reserve in animals, hence often referred to as animal starch. It is present in high concentration in liver, followed by muscle, brain etc. Glycogen is also found in plants that do not possess chlorophyll (e.g. yeast, fungi). The structure of glycogen is similar to that of amylopectin with more number of branches. Glucose is the repeating unit in glycogen joined together by α (1 → 4) glycosidic bonds, and α (1 → 6) glycosidic bonds at branching points.

Cellulose:

Cellulose occurs exclusively in plants and it is the most abundant organic substance in plant kingdom. It is a predominant constituent of plant cell wall. Cellulose is totally absent in animal body. Cellulose is composed of β-D-glucose units linked by β (1 → 4) glycosidic bonds. Cellulose cannot be digested by mammals—including man— due to lack of the enzyme that cleaves β-glycosidic bonds (α amylase breaks α bonds only).

Certain ruminants and herbivorous animals contain microorganisms in the gut which produce enzymes that can cleave β-glycosidic bonds. Hydrolysis of cellulose yields a disaccharide cellobiose, followed by β-D-glucose.

Cellulose, though not digested, has great importance in human nutrition. It is a major constituent of fiber, the non-digestable carbohydrate. The functions of dietary fiber include decreasing the absorption of glucose and cholesterol from the intestine, besides increasing the bulk of feces.

Heteropolysaccharides:

When the polysaccharides are composed of different types of sugars or their derivatives, they are referred to as heteropolysaccharides or heteroglycans.

Mucopolysaccharides:

These are heteroglycans made up of repeating units of sugar derivatives, namely amino sugars and uronic acids. Mucopolysaccharides are more commonly known as glycosaminoglycan’s (GAG). Acetylated amino groups, besides sulfate and carboxyl groups are generally present in GAG structure.

Some of the mucopolysaccharides are found in combination with proteins to form mucoproteins or mucoids or proteoglycans. Mucoproteins may contain up to 95% carbohydrate and 5% protein. Mucopolysaccharides are essential components of tissue structure.

The extracellular spaces of tissue (particularly connective tissue-cartilage, skin, blood vessels, and tendons) consist of collagen and elastin fibers embedded in a matrix or ground substance. The ground substance is predominantly composed of GAG. The important mucopolysaccharides include hyaluronic acid, chondroitin 4-sulfate, heparin, dermatan sulfate and keratan sulfate.

Class # 2. Lipids:

Lipids (Greek: lipos-fat) are of great importance to the body as the chief concentrated storage form of energy, besides their role in- cellular structure and various other biochemical functions. As such, lipids are a heterogeneous group of compounds.

Lipids may be regarded as organic substances relatively insoluble in water, soluble in organic solvents (alcohol, ether etc.), actually or potentially related to fatty acids and utilized by the living cells. Unlike the polysaccharides, proteins and nucleic acids, lipids are not polymers. They are mostly small molecules.

Classification of Lipids:

Lipids are broadly classified (modified from Bloor) into simple, complex, derived and miscellaneous lipids, which are further subdivided.

1. Simple lipids:

Esters of fatty acids with alcohols.

These are mainly of two types:

(a) Fats and oils (triacylglycerol’s):

These are esters of fatty acids with glycerol. The difference between fat and oil is only physical. Thus, oil is a liquid while fat is a solid at room temperature.

(b) Waxes:

Esters of fatty acids (usually long chain) with alcohols other than glycerol. Cetyl alcohol is most commonly found in waxes.

2. Complex (or compound) lipids:

Esters of fatty acids with alcohols containing additional groups such as phosphate, nitrogenous base, carbohydrate, protein etc.

They are further divided:

(a) Phospholipids:

Lipids containing phosphoric acid and frequently a nitrogenous base. This is in addition to alcohol and fatty acids.

(b) Glycolipids:

These lipids contain a fatty acid, carbohydrate and nitrogenous base. The alcohol is sphingosine, hence they are also called as glycosphingolipids. Glycerol and phosphate are absent e.g., cerebrosides, gangliosides.

(c) Lipoproteins:

Macromolecular complexes of lipids with proteins.

(d) Other complex lipids:

Sulfolipids, amino- lipids and lipopolysaccharides are among the other complex lipids.

3. Derived lipids:

These are the derivatives obtained on the hydrolysis of group I and group 2 lipids which possess the characteristics of lipids. These include glycerol and other alcohols, fatty acids, mono- and diacylglycerols, lipid soluble vitamins, steroid hormones, hydrocarbons and ketone bodies.

4. Miscellaneous lipids:

These include a large number of compounds possessing the characteristics of lipids e.g., carotenoids, squalene, hydrocarbons such as pentacosane (in bees wax), terpenes etc.

5. Neutral lipids:

The lipids which are uncharged are referred to as neutral lipids. These are mono-, di-, and triacylglycerol’s, cholesterol and cholesteryl esters.

Functions of Lipids:

Lipids perform several important functions:

1. They are the concentrated fuel reserve of the body (triacylglycerol’s).

2. Lipids are the constituents of membrane structure and regulate the membrane permeability (phospholipids and cholesterol).

3. They serve as a source of fat soluble vitamins (A, D, E and K).

4. Lipids are important as cellular metabolic regulators (steroid hormones and prostaglandins).

Fatty Acids:

Fatty acids are carboxylic acids with hydrocarbon side chain. They are the simplest form of lipids.

Even and odd carbon fatty acids:

Most of the fatty acids that occur in natural lipids are of even carbons (usually 14C-20C). This is due to the fact that biosynthesis of fatty acids mainly occurs with the sequential addition of 2 carbon units. Palmitic acid (16C) and stearic acid (18C) are the most common. Among the odd chain fatty acids, propionic acid (3C) and valeric acid (5C) are well known.

Saturated and unsaturated fatty acids:

Saturated fatty acids do not contain double bonds, while unsaturated fatty acids contain one or more double bonds. Both saturated and unsaturated fatty acids almost equally occur in the natural lipids. Fatty acids with one double bond are known as monounsaturated and those with 2 or more double bonds are collectively known as polyunsaturated fatty acids (PUFA).

Shorthand representation of fatty acids:

Instead of writing the full structures, biochemists employ shorthand notations (by numbers) to represent fatty acids. The general rule is that the total number of carbon atoms is written first, followed by the number of double bonds and finally the (first carbon) position of double bonds, starting from the carboxyl end. Thus, saturated fatty acid, palmitic acid is written as 16 : 0, oleic acid as 18 : 1; 9, arachidonic acid as 20 : 4; 5, 8, 11, 14.

Essential fatty acids:

The fatty acids that cannot be synthesized by the body and, therefore, should be supplied in the diet are known as essential fatty acids (EFA). Chemically, they are polyunsaturated fatty acids, namely linoleic acid (18 : 2; 9, 12) and linolenic acid (18 : 3; 9, 12, 15). Arachidonic acid (20 : 4; 5, 8, 11, 14) becomes essential, if its precursor linoleic acid is not provided in the diet in sufficient amounts.

Triacylglycerol’s:

Triacylglycerol’s (formerly triglycerides) are the esters of glycerol with fatty acids. The fats and oils that are widely distributed in both plants and animals are chemically triacylglycerol’s. They are insoluble in water and non-polar in character and commonly known as neutral fats.

Fats as stored fuel:

Triacylglycerol’s are the most abundant group of lipids that primarily function as fuel reserves of animals. The fat reserve of normal humans (men 20%, women 25% by weight) is sufficient to meet the body caloric requirements for 2-3 months.

Structures of acylglycerols:

Monoacylglycerols, diacylglycerojs and triacylglycerol’s, respectively consisting of one, two and three molecules of fatty acids esterified to a molecule of glycerol, are known. Among these, triacylglycerol’s are the most important biochemically. Triacylglycerol’s of plants have higher content of unsaturated fatty acids compared to that of animals.

Phospholipids:

These are complex or compound lipids containing phosphoric acid, in addition to fatty acids, nitrogenous base and alcohol.

There are two classes of phospholipids:

1. Glycerophospholipids (or phosphoglycerides) that contain glycerol as the alcohol, e.g. lecithins, cephalins, phosphatidylinositol, phosphatidylserine, plasmalogens.

2. Sphingophospholipids (or sphingomyelins) that contain sphingosine as the alcohol, e.g. ceramide.

Lipoproteins:

Lipoproteins are molecular complexes of lipids with proteins. They are the transport vehicles for lipids in the circulation. There are five types of lipoproteins, namely chylomicrons, very low density lipoproteins (VLDL), low density lipoproteins (LDL), high density lipoproteins (HDL) and free fatty acid-albumin complexes.

Steroids:

Steroids are the compounds containing a cyclic steroid nucleus (or ring) namely cyclopentanoperhydrophenanthrene (CPPP). It consists of a phenanthrene nucleus (rings A, B and C) to which a cyclopentane ring (D) is attached.

There are several steroids in the biological system. These include cholesterol, bile acids, vitamin D, sex hormones and adrenocortical hormones. If the steroid contains one or more hydroxyl groups it is commonly known as sterol (means solid alcohol). The structures of steroid nucleus and cholesterol are depicted in Fig. 65.3.

Class # 3. Proteins and Amino Acids:

Proteins are the most abundant organic molecules of the living system. They occur in every part of the cell and constitute about 50% of cellular dry weight. Proteins form the fundamental basis of structure and function of life.

Functions of proteins:

Proteins perform a great variety of specialized and essential functions in the living cells. These functions may be broadly grouped as static (structural) and dynamic.

Structural functions:

Certain proteins perform ‘brick and mortar’ roles and are primarily responsible for structure and strength of body. These include collagen and elastin found in bone matrix, vascular system and other organs and a- keratin present in epidermal tissues.

Dynamic functions:

The dynamic functions of proteins are more diversified in nature. These include proteins acting as enzymes, hormones, blood clotting factors, immunoglobulin’s, membrane receptors, storage proteins, besides their function in genetic control, muscle contraction, respiration etc. Proteins performing dynamic functions are appro­priately regarded as the working horses’ of cell.

Proteins are polymers of amino acids:

Proteins on complete hydrolysis (with concen­trated HCI for several hours) yield L-α-amino acids. This is a common property of all the proteins. Therefore, proteins are the polymers of L-α-amino acids.

Amino Acids:

Amino acids are a group of organic compounds containing two functional groups—amino and carboxyl. The amino group (—NH₂) is basic while the carboxyl group (—COOH) is acidic in nature.

General structure of amino acids:

The amino acids are termed as α-amino acids, if both the carboxyl and amino groups are attached to the same carbon atom, as depicted below

The α-carbon atom binds to a side chain represented by R which is different for each of the 20 amino acids found in proteins. The amino acids mostly exist in the ionized form in the biological system (shown above).

Optical isomers of amino acids:

If a carbon atom is attached to four different groups, it is asymmetric and therefore exhibits optical isomerism. The amino acids (except glycine) possess four distinct groups (R, H, COO^–, NH₃⁺) held by α-carbon. Thus all the amino acids (except glycine where R = H) have optical isomers. The structures of L- and D-amino acids are written based on the configuration of L- and D- glyceraldehyde as shown in Fig. 65.4. The proteins are composed of L-α-amino acids

Classification 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. Amino acid classification based on the structure:

A comprehensive classification of amino acids is based on their structure and chemical nature. Each amino acid is assigned a 3 letter or 1 letter symbol. These symbols are commonly used to represent the amino acids. The 20 amino acids found in proteins are divided into seven distinct groups.

In Table 65.3, the different groups of amino acids, their symbols and structures are given.

B. Nutritional classification of amino acids:

The twenty amino acids (Table 65.3) are required for the synthesis of variety of proteins, besides other biological functions. However, all these 20 amino acids need not be taken in the diet.

Based on the nutritional requirements, amino acids are grouped into two classes—essential and non-essential:

1. Essential or indispensable amino acids:

The amino acids which cannot be synthesized by the human body and, therefore, need to be supplied through the diet are called essential amino acids. They are required for proper growth and maintenance of the individual. The ten amino acids listed below are essential for humans (and also rats):

Arginine, Valine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan.

[The code A.V. HILL, MP., T. T. (first letter of each amino acid) may be memorized to recall essential amino acids. Other useful codes are H. VITTAL, LMP and MATTVILPhLy.]

2. Non-essential or dispensable amino acids:

The body can synthesize about 10 amino acids to meet the biological needs; hence they need not be consumed in the diet. These are — glycine, alanine, serine, cysteine, aspartate, asparagine, glutamate, glutamine, tyrosine and proline.

Structure of Proteins:

Proteins are the polymers of L-a-amino acids. The structure of proteins is rather complex which can be divided into 4 levels of organization (Fig. 65.5):

1. Primary structure:

The linear sequence of amino acids forming the backbone of proteins (polypeptides).

2. Secondary structure:

The spacial arrangement of protein by twisting of the polypeptide chain.

3. Tertiary structure:

The three dimensional structure of a functional protein.

4. Quaternary structure:

Some of the proteins are composed of two or more polypeptide chains referred to as subunits. The spacial arrangement of these subunits is known as quaternary structure.

Primary Structure of Protein:

Each protein has a unique sequence of amino acids which is determined by the genes contained in DNA. The primary structure of a protein is largely responsible for its function.

Peptide bond:

The amino acids are held together in a protein by covalent peptide bonds or linkages. These bonds are rather strong and serve as the cementing material between the individual amino acids.

Formation of a peptide bond:

When the amino group of an amino acid combines with the carboxyl group of another amino acid, a peptide bond is formed (Fig. 65.6). Note that a dipeptide will have two amino acids and one peptide (not two) bond. Peptides containing more than 10 amino acids (decapeptide) are referred to as polypeptides.

Determination of primary structure:

The primary structure comprises the identifica­tion of constituent amino acids with regard to their quality, quantity and sequence in a protein structure.

A pure sample of a protein or a polypeptide is essential for the determination of primary structure which involves 3 stages:

1. Determination of amino acid composition.

2. Degradation of protein or polypeptide into smaller fragments.

3. Determination of the amino acid sequence.

Secondary Structure of Protein:

The conformation of polypeptide chain by twisting or folding is referred to as secondary structure. The amino acids are located close to each other in their sequence. Two types of secondary structures, α-helix and β-sheet, are mainly identified.

α-Helix:

α-Helix is the most common spiral structure of protein. It has a rigid arrangement of polypeptide chain. α-Helical structure was proposed by Pauling and Corey (1951) which is regarded as one of the milestones in the biochemistry research.

The salient features of a right-handed a-helix which is a stable and more commonly found structure, in the living system (Fig. 65.7) are given below:

1. The α-helix is a tightly packed coiled structure with amino acid side chains extending outward from the central axis.

2. The α-helix is stabilized by extensive hydrogen bonding. It is formed between H atom attached to peptide N, and O atom attached to peptide C.

3. All the peptide bonds except the first and last in a polypeptide chain participate in hydrogen bonding.

4. Each turn of α-helix contains 3.6 amino acids and travels a distance of 0.54 nm. The spacing of each amino acid is 0.15 nm.

5. α-Helix is a stable conformation formed spontaneously with the lowest energy.

β-Pleated sheet:

This is the second type of structure (hence β after α) proposed by Pauling and Corey. β-Pleated sheets (or simply β-sheets) are composed of two or more segments of fully extended peptide chains. In the β-sheets, the hydrogen bonds are formed between the neighbouring segments of polypeptide chain(s).

Tertiary Structure of Protein:

The three-dimensional arrangement of protein structure is referred to as tertiary structure. It is a compact structure with hydrophobic side chains held interior while the hydrophilic groups are on the surface of the protein molecule. This type of arrangement ensures stability of the molecule.

Bonds of tertiary structure:

Besides the hydrogen bonds, disulfide bonds (—S—S), ionic interactions (electrostatic bonds) and hydrophobic interactions also contribute to the tertiary structure of proteins.

Domains:

The term domain is used to represent the basic units of protein structure (tertiary) and functions. A polypeptide with 200 amino acids normally consists of two or more domains.

Quaternary Structure of Protein:

A great majority of the proteins are composed of single polypeptide chains. Some of the proteins, however, consist of two or more polypeptides which may be identical or unrelated. Such proteins are termed as oligomers and possess quaternary structure. The individual polypeptide chains are known as monomers, protomers or subunits. A dimer consist of two polypeptides while a tetramer has four.

Bonds in quaternary structure:

The monomeric subunits are held together by non-covalent bonds namely hydrogen bonds, hydrophobic interactions and ionic bonds.

Classification of Proteins:

Proteins are classified in several ways. Three major types of classifying proteins based on their function, chemical nature and solubility properties and nutritional importance are discussed here.

Functional classification of proteins:

Based on the function they perform, proteins are classified into different groups (with examples)

1. Structural proteins:

Keratin of hair and nails, collagen of bone.

2. Enzymes or catalytic proteins:

Hexokinase, pepsin.

3. Transport proteins:

Hemoglobin, serum albumin.

4. Hormonal proteins:

Insulin, growth hormone.

5. Contractile proteins:

Actin, myosin.

6. Storage proteins:

Ovalbumin, glutelin.

7. Genetic proteins:

Nucleoproteins.

8. Defense proteins:

Snake venoms, Immunoglobulin’s.

9. Receptor proteins for hormones, viruses.

Protein classification based on chemical nature and solubility:

This is a more comprehensive and popular classification of proteins. It is based on the amino acid composition, structure, shape and solubility properties. Proteins are broadly classified into 3 major groups (Table 65.4).

1. Simple proteins:

They are composed of only amino acid residues.

2. Conjugated proteins:

Besides the amino acids, these proteins contain a non-protein moiety known as prosthetic group or conjugating group.

3. Derived proteins:

These are the denatured or degraded products of simple and conjugated proteins. The above three classes are further sub-divided into different groups. The summary of protein classification is given in the Table 65.4.

Among the simple proteins, globular proteins are spherical in shape, soluble in water or other solvents and digestable e.g., albumin, globulin. Scleroproteins (fibrous proteins) are fiber like in shape, insoluble in water and resistant to digestion e.g., collagen, keratin.

The conjugated proteins may contain prosthetic groups such as nucleic acid, carbohydrate, lipid, metal etc. The primary derived proteins are produced by agents such as heat, acids, alkalies etc., while the secondary derived proteins are hydrolytic products of proteins.

Class # 4. Isoprenoids and Pigments:

Isoprenoids and pigments are organic compounds mostly distributed in plant kingdom. They perform a wide variety of functions.

Isoprenoids:

Isoprenoids are also called as terpenoids or (terpenes) as they are found in turpentine oil in high concentrations. The naturally occurring isoprenoids are composed of a five carbon isoprene unit. A majority of the isoprenoids are formed by joining of isoprene units head to tail as depicted below

Classification of terpenes:

The classification of terpenes is mainly based on the number of isoprene (C₅H₈) units present. The major classes of terpenes with selected examples are given in Table 65.5.

Pigments:

Pigments are cloured organic compounds found in the living organisms, mostly in plants, and to a minor extent in animals. Chemically, pigments are high molecular weight molecules, mostly composed of unsaturated hydrocarbons. Some of the pigments also contain cyclic structures.

The major groups of pigments are briefly described:

Tetrapyrroles:

The most abundant coloured compound in the world is chlorophyll, the photosynthetic pigment. There are different types of chlorophylls (c, d, e, a) with slight variation in colours — green, greenish blue, greenish yellow.

Structurally, chlorophylls are composed of tetrapyrroles (pyrrole   rings) with their nitrogen linked to magnesium.

Tetrapyrroles are also found in heme in certain proteins. These include hemoglobin, cytochromes, catalase and peroxidase.

Tetraterpenes (carotenoids):

The colour of carotenoids is variable, generally yellow, orange or red. A large number of carotenoids (about-600) have been identified in plant kingdom e.g. P-carotene, xanthophyll’s, lycopene.

Anthocyanins:

Anthocyanins are a group of flavonoids which represent the natural phenolic products. Anthocyanins are coloured compounds, mostly found in flowers and fruits. They contain a common ring structure called anthocyanidin.

Quinoid pigments:

Being present in trace amounts, quinoid pigments do not significantly contribute to visible colours. They however, perform some other functions e.g. involvement in electron transport chain, antioxidant functions etc. The most common quinoid pigments are benzoquinones, naphthoquinones, anthraquinones, tannins and lignins.