Class XI Unit 6 Biomolecules. Topic- Proteins By . Sarjerao Yedekar M.Sc BEd Zoology CTET

PROTEINS

• Proteins are polypeptides. These are linear chains of amino acids linked by peptide bonds.
• Essential elements in protein are C , H , O, N. Some contain sulphur(S) and phosphorus (P) also. The structural unit of protein is amino acid.
• A protein is a heteropolymer and not a homopolymer.
• Proteins are polymers of amino acids (Fisher and Hoffmeister). There are approximately 300 amino acids known to exist but only 20 types of amino acids are used in formation of proteins.
• Each amino acid is amphoteric compound because it contains one weak acidic group – COOH and a weak alkaline group – NH2.

• In protoplasm; free amino acid occurs as ions ( at iso - electric point). Iso - electric point is that point of pH at which amino acids do not move in electric field.

• Amongst proteins, 'collagen' is the most abundant protein of animal world while 'RubisCo' (Ribulose Bisphosphate Carboxylase-Oxygenase) is the most abundant protein of biosphere.

AMINO ACIDS

• The amino acids are 'structural units' as well as 'digestive end products' of proteins.
• Amino acids are organic acids with a carboxyl group
  (–COOH) and one amino group (–NH2)  on the α -carbon atom. Chemically, these are substituted  methane. Carboxyl group attributes acidic properties and amino group gives basic ones.
• There are four substituent groups occupying the four valency positions. These are hydrogen, carboxyl group, amino group and a variable group designated as R group.
• In solution, they serve as buffers and help to maintain pH. These are 20 in number, specified in genetic code and universal in viruses, prokaryotes and eukaryotes, which take part in protein synthesis,
• Except glycine, each amino acid has two isomers.

                

• Eukaryotic proteins have L- amino acid while D- amino acid occurs in bacteria and antibodies.
• Amino acids join with peptide bond and form long chains called polypeptide chains.          

• Peptidyl transferase enzyme catalyses the synthesis of peptide bond.

CLASSIFICATION OF AMINO ACIDS

Amino acids can be classified on the basis of their R (alkyl) group –

• Non-polar R-group : Non-polar side chains consist mainly of hydrocarbons. Any functional groups they contain, are unchanged at physiological pH and are incapable of participating in H–bonding.

E.g., Alanine, valine, leucine, isoleucine, proline, methionine, phenylalanine, tryptophan.

• Polar but uncharged R-group : Polar side chains contain groups that are either charged at physiological pH or groups that are able to participate in hydrogen bonding.

E.g., Glycine, serine, threonine, cysteine, tyrosine, asparagine, glutamine.

• Positively charged polar R-group : These contain 2-amino and 1-carboxyl group.

E.g., Lysine, arginine, histidine (Basic Amino acid)

• Negatively charged polar R-group : These contain 1-amino and 2-carboxyl groups.

Eg. Aspartic acid, glutamic acid (Acidic Amino acid)

 ◆PROPERTY OF PROTEIN DEPENDS

ON SEQUENCE OF AMINO ACIDS AND CONFIGURATION OF PROTEIN MOLECULES

• Simple amino acids : These have no functional group in the side chain, e.g., glycine, alanine , leucine, valine etc. Glycine is the simplest amino acid.
• Hydroxy amino acids : These have alcohol group in side chain, e.g., threonine, serine, etc.
• Sulphur containing amino acids : These have sulphur atom in side chain, e.g., methionine, cysteine and cystine.
• Basic amino acids : These have basic group (–NH2) in side chains, e.g., lysine, arginine.
• Acidic amino acids : These have carboxyl groups in side chain, e.g., aspartic acid, glutamic acid.
• Acid amide amino acids : These are the derivatives of acidic amino acids. In this group, one of the carboxyl group has been converted to amide (–CONH2), e.g., asparagine, glutamine.
• Heterocyclic amino acids : These are the amino acids in which the side chain includes a ring involving atleast one atom other than carbon, e.g., histidine, proline and hydroxyproline.
• Aromatic amino acids : These have aromatic group (benzene ring) in the side chain, e.g., phenylalanine, tyrosine and tryptophan.

ON THE BASIS OF REQUIREMENTS

On the basis of the synthesis of amino acids in the body and their requirement, these are categorized as :

• Essential amino acids : These are not synthesized in the body hence need to be provided in the diet, e.g., valine, leucine, isoleucine, threonine, lysine, tryptophan, phenylalanine, methionine etc.
• Semi-essential amino acids : Synthesized partially in the body but not at the rate to meet the requirement of individual, e.g., arginine and histidine.
• Non-essential amino acids : These amino acids are derived from carbon skeleton of lipids and carbohydrate  metabolism. In humans, there are 12 non-essential amino acids, e.g., alanine, aspartic acid, cysteine, glutamic acid etc. proline and hydroxyproline have NH (imino group) instead of NH2 hence are called imino acids.

NOTES

• All the amino acids are laevo-rotatory, except glycine which is non-rotatory.
• Amino acids which participate in protein synthesis are called protein amino acids.  Amino acids which do not participate are called non-protein amino acids, e.g. GABA, ornithine, citrulline, thyroxine etc.

CONFIGURATION OF PROTEIN MOLECULE

(1) PRIMARY STRUCTURE

A straight chain of amino acids linked by peptide bonds form primary structure of proteins. The first (or left) amino acid is called N—terminal (–NH2 group.) amino acid, and the last (or right) amino acid is called C-terminal (–COOH group) amino acid. Such proteins are non functional proteins. This structure of proteins is most unstable. Newly formed proteins on ribosomes have primary structure.

(2) SECONDARY STRUCTURE

Protein molecules of secondary structure are spirally coiled. The spiral is stabilized by straight hydrogen bonds between imide group (– NH –) of one amino acid and carbonyl group
(– CO) of fourth amino acid residue. In this way, all the imide and carbonyl groups become hydrogen bonded.

• α-helix : Right handed rotation of spirally coiled chain with approximately 3½ amino acids in each turn. This structure has intramolecular hydrogen bonding i.e. between two amino acids of the same chain e.g., keratin, myosin, tropomyosin.
• β-helix or pleated sheath structure : Protein molecule has zig - zag structure. Two or more protein molecules are held together by intermolecular hydrogen bonding. The polypeptide chain may be parallel or antiparallel, e.g. Keratin protein in birds (β– sheets parallel) and silk protein (fibroin) with antiparallel β–sheets.
• Proteins of secondary structure are insoluble in water and fibrous in appearance.
• Keratin is a fibrous, tough, resistant to digestion sclero-protein. Hardness of keratin is due to abundance of cysteine amino acid in its structure.

(3) TERTIARY CONFIGURATION OR STRUCTURE

Proteins of tertiary structure are highly folded to give a globular appearance. These are soluble in water (colloid solution) giving us a 3–dimensional view of a protein. Tertiary structure is absolutely necessary for the many biological activities of proteins. Tertiary structure is stabilised by five types of bonds:

• Peptide bonds : strongest bond in proteins.
• Hydrogen bonds : These occur between hydrogen and oxygen atoms of various groups.
• Disulphide bond : These bonds form between - SH group of amino acids (e.g., methionine, cysteine). These bonds are second strongest bond and stabilise the tertiary structure of protein.
• Hydrophobic bonds : Present  between amino acids which have hydrophobic side chains, e.g. aromatic amino acids.
• Ionic bonds : Formation of ionic bond occurs between two opposite ends of a protein molecule due to electrostatic attraction. Majority of proteins and enzymes in protoplasm exhibit tertiary structure.

(4) QUATERNARY STRUCTURE

Two or more polypeptide chains of tertiary structure united by different types of bonds to form quaternary structure of protein. Different polypeptide chains may be similar (e.g., lactic-dehydrogenase) or dissimilar types (e.g., haemoglobin, insulin). Quaternary structure is most stable structure of protein.

NOTES

Adult human haemoglobin consists of 4 subunits. Two of these are identical to each other. Hence, two subunits of α type and two subunits of β type together constitute the human
haemoglobin (Hb).

SIGNIFICANCE OF STRUCTURE OF PROTEIN

• The most important constituents of animals are proteins and their derivatives.
• In an acidic medium, the – COO– group of protein converts to – COOH and the protein itself becomes positively charged. In contrast, in an alkaline medium the – NH3+ group of protein changes to – NH2 + H2O and as a result it becomes negatively charged. Therefore, at a specific pH, a protein will possess an equal number of both negative and positive charges and it is at this specific pH, a protein becomes soluble.
• If the pH changes towards either acidic or alkaline side, then the protein begins to precipitate. This property of protein has a great biological significance. The cytoplasm of cells of organism has an approximate pH of 7 but the pH of proteins present in it is about 6 and thus, the proteins are present in a relatively alkaline medium. Therefore, the proteins are negatively charged and also are not in a fully dissolved state. It is because of this insolubility, proteins form the structural skeleton. Similarly, the pH of nucleoplasm is about 7 but the pH of proteins, namely, histones and protamines, in it is relatively more. Therefore, as a result they are positively charged and do not remain fully dissolved in the nucleoplasm forming minute organelles, the most important being the chromosomes.
• Such compounds which exhibit both acidic and alkaline properties are called amphoteric compounds or zwitterions. In the protoplasm, this dual property of proteins is utilized for neutralization of strong acids and alkalis since the protein acts as an ideal buffer in either of the situations.

Besides changes in pH, salts, heavy metals, temperature, pressure, etc. also cause precipitation of proteins.

TYPES OF PROTEINS

SIMPLE PROTEINS

Proteins which are composed of only amino acids.and it's Derivative

• Fibrous Proteins :  E.g., Collagen, elastin, keratin
• Globular Proteins : E.g., Albumin, histones, globin, protamines, prolamines (Glaidin, Gluten, Zein), Gluteline (slimy part of gluten of wheat).

CONJUGATED PROTEINS

Formed by the binding of a simple protein with a non-protein part (prosthetic group).

• Nucleoproteins - Proteins attached to nucleic acids, e.g., chromatin, ribosomes etc.
• Chromoprotein - Proteins with pigment or coloured, e.g., haemoglobin, haemocyanin, cytochromes etc.
• Lipoprotein - Proteins combined with lipids, e.g., cell membrane, lipovitelline of yolk.
• Phosphoproteins - Proteins containing phosphorus – e.g., casienogen, pepsin, ovovitelline, phosvitin.
• Glycoproteins – Proteins combined with carbohydrates, e.g., hormones like FSH, LH, TSH and HCG, blood group antigens, serum protein etc.
• Metallo-protein : Proteing with metal ions –e.g., Cu-tyrosinase, Zn-carbonic anhydrase, Mn-arginase, Mo-xanthine oxidase, Mg-kinase.

DERIVED PROTEINS

These form by denaturation or hydrolysis of protein.

• Primary derived proteins are denaturation products of normal proteins, e.g., fibrin, myosin.
• Secondary derived proteins are digestion products of proteins, e.g., proteoses, peptones.

FUNCTIONS OF PROTEINS

• Formation of cells and tissues for growth.
• Repairing of tissues.
• Formation of hormones.
• For muscle contraction (e.g., actin, myosin).
• Formation of enzymes.
• Help in blood clotting.
• For transport (e.g., haemoglobin, transferrin).
• For defence against infections (e.g., antibodies).
• Form hereditary material – nucleoproteins.
• For storage (e.g., myoglobin and ferritin).
• For support (e.g., collagen and elastin).