Protein and Its Structures 1st year Biology Notes

 PROTEIN 

Of all the macromolecules found in the cell, the proteins are chemically and physically more diverse. They are important constituents of the cell forming more than 50 per cent of the cell’s dry weight. The term protein was coined by Dutch chemist G.J. Mulder (1802—1880) and is derived from Greek word proteios, which means “of the first rank”. Proteins serve as the chief structural material of protoplasm and play numerous other essential roles in living systems. They form enzymes—globular proteins specialized to serve as catalysts in virtually all biochemical activities of the cells. Other proteins are antibodies (immunoglobulins), transport proteins, storage proteins, contractile proteins, and some hormones. In every living organism, there are thousands of different proteins, each fitted to perform a specific functional or structural role. Indeed, a single human cell may contain more than 10,000 different protein molecules. Chemically, proteins are polymers of amino acids. 1. Amino acids. Nobel Laureate Emil Fischer (1902) discovered that all proteins consist of chains (linear sequence) of smaller units that he named amino acids. There are about 20 different amino acids which occur regularly as constituents of naturally occurring proteins. An organic compound containing one or more amino groups (–NH2) and one or more carboxyl groups (—COOH) is known as amino acid. The amino acids occur freely in the cytoplasmic matrix and constitute the so called amino acid pool.

The sole exception is proline, where the amino group forms part of a ring structure. The central or alpha carbon atom of each amino acid is covalently bonded to four groups :  (1) A hydrogen atom, (2) an amino group (—NH2), (3) an acid (or carboxyl) group, and (4) a side chain called an R-group. It is the particular chemical structure of the R-group that distinguishes one amino acid from another.

 Types of proteins.

Many different methods have been used to classify proteins, no method of their classification being entirely satisfactory :

 (1) Classification based on biological functions. 

According to their biological functions, proteins are of two main types :

 1. Structural proteins which include keratin, the major protein component of hair (cortex), wool, fur, nail, beak, feathers, hooves and cornified layer of skin; and collagen, abundant in skin, bone, tendon, cartilage and other connective tissues.

2. Dynamic or functional proteins which include the enzymes that serve as catalysts in metabolism, hormonal proteins, respiratory pigments, etc.

(2) Cl assification based on shape of proteins. 

According to the shape or conformation, two major types of proteins have been recognized : 

(a) Fibrous proteins. Fibrous proteins are water-insoluble, thread-like proteins having greater length than their diameter. They contain secondary protein structure and occur in those cellular or extracellular structures, where strength, elasticity and rigidity are required, e.g., collagen, elastin, keratin, fibrin (blood-clot proteins) and myosin (muscle contractile proteins).

 (b) Globular proteins. Globular proteins are water-soluble, roughly spheroidal or ovoidal in shape. They readily go into colloidal suspension. They have tertiary protein structure and are usually functional proteins, e.g., enzymes, hormones and immunoglobulins (antibodies). Actin of micro- filaments and tubulins of microtubules are also globular proteins (see Alberts et al., 1989). 

(3) Classification based on solubility characteristics. According to this criterion proteins can be classified into two main types :

 (A) Simple proteins. These proteins contain only amino acids in their molecules and they are of following types : 

(i) Albumins. These are water soluble proteins found in all body cells and also in blood stream, e.g., lactalbumin, found in milk and serum albumin found in blood.

 (ii) Globulins. These are insoluble in water but are soluble in dilute salt solutions of strong acids and bases, e.g., lactoglobulin found in milk and ovoglobulin.

 (iii) Glutelins. These plant proteins are soluble in dilute acids and alkalis, e.g., glutenin of wheat.

 (iv) Prolamines. These plant proteins are soluble in 70 to 80 per cent alcohol, e.g., gliadin of wheat and zein of corn.

 (v) Scleroproteins. They are insoluble in all neutral solvents and in dilute alkalis and acids, e.g., keratin and collagen.

 (vi) Histones. These are water soluble proteins which are rich in basic amino acids such as arginine and lysine. In eukaryotes histones are associated with DNA of chromosomes to form nucleoproteins.

(vii) Protamines. These are water soluble, basic, light weight, arginine rich polypeptides. They are bound to DNA in spermatozoa of some fishes, e.g., salmine, of salmon and sturine in sturgeons.

 (B) Conjugated proteins. These proteins consist of simple proteins in combination with some non-protein components, called prosthetic groups. The prosthetic groups are permanently associated with the molecule, usually through covalent and/or non-covalent linkages with the side chains of certain amino acids. Conjugated proteins are of following types : 

(i) Chromoproteins. Chromoproteins are a heterogeneous group of conjugated proteins which are in combination with a prosthetic group that is a pigment, e.g., respiratory pigments such as haemoglobin, myoglobin and haemocyanin; catalase, cytochromes, haemerythrins; visual purple or rhodopsin of rods of retina of eye and yellow enzymes or flavoproteins.

 (ii) Glycoproteins. Glycoproteins are proteins that contain various amounts (1 to 85 per cent) of carbohydrates. Of the known 100 monosaccharides, only nine are found to occur as regular constituents of glycoproteins (e.g., glucose, galactose, mannose, fucose, acetylglucosamine, acetylgalactosamine, acetylneuraminic acid, arabinose and xylose). Glycoproteins are of two main types : 

1. Intracellular glycoproteins which are present in cell membranes and have an important role in membrane interaction and recognition. They also serve as antigenic determinants and receptor sites.

 2. Secretory glycoproteins are plasma glycoproteins secreted by the liver ; thyroglobulin, secreted by the thyroid gland ; immunoglobulins secreted by the plasma cells ; ovoalbumins secreted by the cells of oviduct of hen ; ribonucleases and deoxyribonucleases. Mucus and synovial fluid are also glycoproteins with lubricative properties.

 (iii) Lipoproteins. Lipid containing proteins are called lipoproteins. Their lipid contents are 40 to 90 per cent of their molecular weight and this tends to affect the density of the molecule. There are four types of lipoproteins :

 1. High density lipoproteins (HDL) or αlipoproteins; 

2. Low density lipoproteins (LDL) or β- lipoprotiens ; 

3. Very low density lipoproteins (VLDL) or pre- β-lipoproteins; and

 4. Chylomicrons. Lipoproteins include some of the blood plasma proteins, various types of membrane proteins, lipovitellin of egg yolk and proteins of brain and nerve tissue.

(iv) Nucleoproteins. Nucleoproteins are proteins in combination with nucleic acids (DNA and RNA). However, these proteins are not true conjugated proteins since the nucleic acid involved cannot be regarded as prosthetic groups. Nucleoproteins are of two types :

 1. Histones which are quite similar in all plants and animals. Their highly basic nature accounts for the close associations histones form with the nucleic acids. Histones are involved in the tight packing of DNA molecules during the condensation of chromatin into chromosomes for the mitosis.

 2. Nonhistones have great heterogeneous amino acid composition and are acidic in nature. They have selective combination with certain stretches of nuclear DNA and, thus, are involved in the regulation of gene expression. 

(v) Metalloproteins. Metalloproteins are proteins conjugated to metal ions which are not part of the prosthetic group, e.g., carbonic anhydrase enzyme contains zinc ions and amino acids in its molecule; caeruloplasmin, an oxidase enzyme containing copper; and siderophilin contains iron. 

(vi) Phosphoproteins. Phosphoproteins are proteins in combination with a phosphate group, e.g., casein of the milk and ovovitellin of eggs. 

3. Structural levels of proteins. 

The protein as synthesized on the ribosome is a linear sequence of amino acids, polymerized by the elimination of water between successive amino acids to form the peptide bond, and existing as a randomly coiled chain without specific shape and possessing no biological (i.e., catalytic) activity. Within seconds of synthesis being completed, the protein folds into a specific three-dimensional form, which is the same for all molecules of the same type of protein and which now is capable of doing catalysis. According to their mode of folding the following four levels of protein organization have been recognized :

 (a) Primary protein structure. The primary protein structure is defined as the particular sequence of amino acids found in the protein. It is determined by the covalent peptide bondings between amino acids. Primary structure also includes other covalent linkages in proteins, for example the linkages that may exist between sulphur atoms of cysteine amino acids located in the chain of the protein insulin. The first protein to have its primary structure determined was of insulin, the pancreatic hormone that regulates glucose metabolism in mammals. Insulin has a molecular weight of 5,800 daltons and contains 51 amino acids. Insulin consists of two polypeptide chains of 21 and 30 amino acid residues, called the A and B chains, respectively . (An amino acid residue is that which is left when the elements of water are split out during polymerization). 

Since the elucidation of the primary structure of insulin in 1953 by F. Sanger (for which Sanger

received a Nobel Prize), several hundred proteins have been fully sequenced. Among the fully sequenced proteins are ribonuclease and nearly 100 types of haemoglobin. For example, Stein and his coworkers established the amino acid sequence (i.e., primary structure) of the enzyme ribonuclease. This enzyme is produced by the pancreas and secreted into the small intestine where it catalyzes the hydrolytic digestion of polyribonucleotide chains (RNA). The ribonuclease consists of a single 124 amino acid polypeptide having a molecular weight of about 12,000. 

(b) Secondary protein structure. Secondary structure of the protein is any regular repeating organization of the polypeptide chain. There are three types of secondary protein structure :

 (1) Helical structure (e.g., α-keratin and collagen);

(2) Pleated sheet structure or β- structure (e.g., fibroin of silk); and

(3) Extended configuration (e.g., stretched keratin). Most fibrous proteins have secondary structure. In globular protein, too, it is not uncommon for half of all the residues of each polypeptide to be organized into one or more specific secondary structures. Collagen. The collagens (the source of leather, gelatin, glue, etc.) are a family of highly characteristic fibrous proteins found in all multicellular animals (e.g., in connective tissues). They are secreted by the fibroblasts constituting most abundant (up to 25 per cent of total body’s proteins) proteins of mammals. The characteristic feature of collagen (or tropocollagen) molecules is their stiff, triple-stranded helical structure (which was discovered by Rich, Crick and Rama-chandran). Three collagen polypeptide chains are lefthanded α-helices or alpha chains, each is about 1000 amino acid residues long. These chains are wound around one another in a regular superhelix to generate a rope-like collagen or tropocollagen molecule which is about 300 nm long and 1.5 nm is diameter . Collagens are exceptionally rich in proline (and hydroxyproline; both accounting for more than 20 per cent of collagen’s amino acids) and glycine. Other dominant amino acids of collagens are lysine and alanine. 

(C) Tertiary protein structure. Tertiary protein structure refers to a more compact structure in which the helical and non-helical regions of a polypeptide chain are folded back on themselves. This structure is typical of globular protein structure, in which it is the non-helical region that permits the folding. The folding of a polypeptide chain is not random but occurs in a specific fashion, thereby imparting certain steric (i.e., three-dimensional) properties to the protein. For example, in enzymes folding brings together active amino acids, which are otherwise scattered along the chain, and may form a distinctive cavity or cleft in which the substrate is bound. 

(d) Quaternary protein structure. In proteins that are composed of two or more polypeptide chains, the quaternary structure refers to the specific orientation of these chains with respect to one another and the nature of the interactions that stabilize this orientation. The individual polypeptide chains of the protein are called sub-units and the active protein itself is called multimer. While multimeric proteins containing up to 32 subunits have been described, the most common multimers are dimers, trimers, tetramers, pentamers (e.g., RNA polymerase) and decamers (e.g., DNA polymerase III) . If the protein consists of identical sub-units, it is called homopolymers and is said to have homogeneous quaternary structure, e.g., the isozymes H4 and M4 of lactic dehydrogenase (LDH), enzyme phosphorylase and L-arabinose isomerase. The enzyme β-galactosidase consists of four identical polypeptide chains. Lastly, when the sub-units of the protein are different, the protein is called heteropolymer and is said to have a heterogeneous quaternary structure, e.g., haemoglobin and immunoglobulins.Quaternary proteins are usually joined by hydrophobic forces. Hydrogen bonds, ionic bonds and possibly disulphide bonds may also participate in forming quaternary structures.