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Protein-An overview

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Protein-An overview

  1. 1. PROTEIN: UNIQUE MOLECULE
  2. 2. Presented by Dr. N. Sannigrahi, Associate Professor, Department of Botany, Nistarini College, Purulia ( W.B) India
  3. 3. Life is a millions of biochemical reactions and the four elements build up the most of the molecules essentially required for the execution of life since the origin of life started in this blue planet. Besides carbohydrates and lipids along with nucleic acids, another macromolecule essentially required to build up the life is protein. As garland made up of flower like protein are made up of amino acids joined to one another by means of chemical thread called peptide bonds. Irrespective of the structural complexity and functional attributes, it is difficult to find out the beat of life without protein. From acellular virus to multicellular most complex human beings via unicellular prokaryotes like bacteria, protein is everywhere. Staring from physical and chemical activities, biological membrane, enzymes, hormones, muscular contraction, cell to cell transport, motion to flexibility, defence along with to overcome unavoidable stress, the saga of protein must be sung. In a word, from birth to death, protein is the main actor in the magic of the reality of life.
  4. 4. AMINO ACIDS: Proteins, a kind of macromolecules are mostly treated as the polymer of amino acids. Thus, amino acids are building block materials or structural units of all proteins and these monomer are joined to each other by peptide bonds as stated earlier. The name protein was first suggested by Berzelius (1838). The amino acids are basically of 20 types and they almost constitute at 1011 different kind of proteins . Human beings 40000 different kind of proteins while E. coli has 3000 kinds of proteins. The polymer contains the elements in the following percentage: C= 50-55%, H= 6-8%, O= 20-23%, N=15-18%, S= 0-4% The distribution of amino acids ins not uniform in all proteins. Nearly 40% by weight of fibroin and 25% by weight of collagen are accounted for by glycine. Serine and threonine predominate in casein and phosvitin.
  5. 5. STRUCTURE OF AMINO ACIDS Amino acids consist of -NH2 and – COOH group bonded to the same carbon, Amino acid both basic and acidic in nature, The carbon adjacent to carboxyl group is called α-carbon to which the amino group is attached, The α-carbon of most amino acid is joined by covalent bonds to 4 different groups- carboxyl group, amino group, residue ® and hydrogen atom, The R stands for side chains that are different for each amino acids. R can be simply as only one H as in glycine amino acid or may be a methyl group as in alanine or more complex structure, α-carbon in all amino acids is asymmetric except in glycine .
  6. 6. For this reason, all amino acids except glycine exhibit optical isomerism- Dextro and Levo form just like monosaccharide & D- glyceraldehydes, Isolecucine and threonine have two asymmetric carbon atoms, hence each have4 2*2=4 optical isomers. Most of the naturally occurring amino acids are L-isomers. At neutral pH, the amino and carboxyl groups of an amino acids are ionized, the amino group with + charge and carboxyl group with –ve charge. Thus in aqueous solution, at pH 7.0, an amino acid behaves like a dipole. This dipolar ion is known as Zwitterions. The molecular structure of the 20 amino acids are arranged on the basis of the polarities of R groups as follows:
  7. 7. On the basis of the composition of side chain or R group, amino acids are as followed: i. Simple amino acids-no functional group in the side chain like glycine, alanine, valine, leucine, isoleucine, ii. Hydroxy-amino acids- one hydroxy group in the side chain like serine, threonine, iii. Sulphar containing amino acids- A single sulfur atom in the side chain like cysteine, methionine, iv. Acidic amino acids- A carboxyl group in the side chain like aspartic acid & glutamic acid, v. Amino acids amides- derivatives of acidic amino acids in which one of the carboxyl group has been transformed into an –amide group (- CO.NH2), vii. Basic amino acids- amino group in the side chain like lysine & arginine, viii. Heterocyclic amino acids- side chain consists a ring having one atom other than carbon like tryptophan, histidine, proline
  8. 8. viiii. Aromatic amino acids- Have a benzene ring in the side chain like Phenylalanine, tyrosine . B. On the basis of the number of amino & carboxyl group- 1. Mono-amino mono-carboxylic amino acids- a. Unsubstitted- Glycine, alanine, Valine, Leucine, Isoleucine b. Heterocyclic- Proline, c. Aromatic- Phenylalanine, Tyrosine, Tryptophan, d. Thio-ether- Methionine e. Hydroxy- Serine, Threonine f. Mercapto- Cysteine g. Carboxyamide- Asparagines, Glutamine. Thus amino acids are classified on the basis of the number of the functional groups required for the same.
  9. 9. C. On the basis of the polarity of the side chains---- i. With non-polar (hydrophobic) R group (insoluble ) in water- Here the R group simply Hydrocarbon in nature and thus hydrophobic. This group includes both aliphatic (alanine, valine, leucine, isoleucine And methionine) and aromatic (Phenylalanine and tryptophan) amino acids along with glycine. ii. With uncharged polar R group- This group contain amino acids having R group as a. Hydroxyl (-OH) as in serine, threonine and tyrosine, b. Sulf-hydryl group( -SH) as in cysteine, c. amide (-NH2) as in asparagine and glutamine. iii. Amino acids with + vely charged R groups( Basic amino acids)- This group includes with + vely charged R groups such as Lysine, arginine and histidine. These are basic in nature as they contain 2 or more + vely charged and one – vely charge making ultimately positive.
  10. 10. iv. With –vely charged R group (acidic amino acids)- this group includes two carboxylic acids like aspartic acid and glutamic acid. These contain two acidic (-ve) and one basic (+vely ) group thus making the net charge –ve and acidic in nature. NONSTANDARD AMINO ACIDS There is a wide distribution in proteins , several other amino acids exist. These have4 a limited distribution but may be present in high amounts in a few proteins and hence deserve mention. Hydroxyproline has limited distribution in nature but constitutes 12% of the composition of collagen, important animal protein . Similarly hydroxylysine in collagen, N- methyllysine as found in myosin also belong to this category. NON-PROTEIN AMINO ACIDS –About 250 different amino acids have been detected are not proteniceous in nature like L- ornithine, L-citruline, Creatine, GABA, Histamine, Dopamine, Thyroxine . Their function is important and have allelopathic effect.
  11. 11. PEPTIDE BOND A peptide bond is a chemical bond produced in between two amino acids. Formation of peptide bonds leads to the synthesis of oligopepetide and polypeptides that are converted into protein. If 2 –amino acids are linked by peptide bond, it is called dipeptide, If 3 amino acids are joined by peptide bond , it is called tripeptide, If 10 or less than 10 amino acids are joined by peptide bonds are called oligopeptides, If more than 10 amino acids are joined together by peptide bonds are called polypeptides. A peptide bond is generated when the alpha carboxylic acid group of one amino acids is joined to the α-amino group of another amino acids by secondary linkage with the liberation of one molecule of water.
  12. 12. 1. A peptide bond is a specialized amide linkage and is actually a bond between C and N. 2. Peptide bond is the backbone of the protein polypeptide3 chain, 3. A peptide chain has the amino group at the one end (left) and the carboxyl group (right) at the other end, 4. The amino acid end is known as the amino terminus or N- terminus and the carboxyl end is called carboxyl terminus or C-terminus, 5. The N-terminus amino acid residue is the first amino acid and the C-terminus amino acid is the last amino acid of the polypeptide chain, 6. The C-N bond is a strong bond and only to be hydrolyzed by the action of the enzyme-peptidase and can be artificially synthesized at normal temperature and pH by the action of enzyme peptidyl transferase.
  13. 13. PROTEIN CLASSIFICATION Proteins on the basis of source traditionally divided into two well- defined groups-animal proteins and Plant proteins. Animal proteins are treated as higher –quality proteins having the adequate amount of all the essential amino acids while the plant proteins are called lower quality as they have a low content of one or more of the essential amino acids like methionine, lysine, threonine and tryptophan. On the basis of the shape of the protein molecule, proteins have grouped under two categories- Globular & fibrous. GLOBULAR or CORPUSCULAR : Due to less axial ratio (length: width) of less than 10, appear spherical or ovoid in shape, soluble in water or aqueous medium containing acids, bases, salt, alcohol, complex in conformation, mostly tertiary & quaternary belong to this group; enzymes , plant hormones, blood transport proteins, antibodies and storage proteins belong to this group.
  14. 14. FIBROUS OR FIBRILLAR PROTEIN: Here, the axial ratio more than 10, long ribbons or fibers shape, mainly animal in origin, insoluble in almost all common solvents like water, acids, salt, alcohol; strong and possess two important properties of elastomers- They can stretch and later recoil to their original length, They have the tendency to creep i.e if stretched for a long time, their basic length increases and equals the stretched length but if the tension of the two ends of the fiber is relaxed, they creep to their shorter and shorter length. It is heterogeneous groups and includes the proteins of connective tissues, bones, blood vessels, hairs, nails, wool, silk etc. The most important are- Collagens that build up the total protein in the mammalian body, Elastine being the major constituents of yellow elastic tissues like ligaments, Keratin with large amount of sulfur in the form of human hair and Fibroin being the principal constituent of fibers of silk
  15. 15. CLASSIFICATION ON THE BASIS OF SOLUBILITY 3 major groups- Simple or Holoproteins, Conjugated or complex or Heteroproteins and Derived. SIMPLE PROTEIN Mostly globular includes proteins containing only amino acids as structural components and their decomposition with acids liberate constituent amino acids, It may be different as per solubility like Protamines & histones ( Salamine and nucleohistones), albumins( Ovalbumin), Globulins(serum globulin), Glutelins (Glutelin from corn), Prolamines (gliadin from wheat), scleroproteins or albuminoids Collagen from bones)etc. CONJUGATED PROTEIN: Proteins linked with a separable non- protein portion called prosthetic group either metal or compound and on decomposition with acids produce amino acids & prosthetic group. They may be metalloprotein, chromoproteins, glycoprotein, phosphoproteins, lipoproteins, nucleoproteins etc.
  16. 16. 1. Metalloproteins -Proteins linked with various metals like hg, Au, Cu, Zn strongly bind with collagen, albumins. Ca binds weakly with proteins but Na & K do not couple with proteins. Siderophilin, ceruloplasmin are the two examples in this regard 2. Chromoproteins - Proteins coupled with colored pigment, mostly found in enzymes like cartalase, perxidase and flavoproteins. Myglobin, hemoglobin, cytochromes. Haemocyanin are some examples. 3. Glycoprotein- Proteins containing carbohydrate as prosthetic group. Glycoprotein like albumin, elastin and mucoproteins like mucin, ovomucoid are belonged to this group. 4. Phosphoproteins- proteins linked with phosphoric acid like casein from milk and ovovitelin from egg yolk belong to this group. 5. Lipoproteins- Proteins associated with lipid like cephalin,
  17. 17. lecithin, cholesterol , highly insoluble in water. Lipoproteins may be VHDL, HDLs, LDLS, VLDLs belong to this group. 6. Nucleoproteins-Compounds containing nucleic acid like protamines and histones, usually salt like compounds either present in nuclear substances or cytoplasm. DERIVED PROTEINS Derivatives of protein resulting from the action of heat, enzymes or chemical agents and it also includes artificially induced polypeptides. i. Primary derived proteins like proteans, metaproteins and coagulated proteins belong to this. ii. Secondary derived proteins-These are derivatives of protein in which the hydrolysis has certainly considered. Proteases, Pep[tones, polypeptides belong to this group. Thus, on the basis of source and the degree of the occurrence of the different other components, proteins can be studied in the different forms.
  18. 18. LEVELS OF PROTEIN STRUCTURE The proteins have specific molecular configurations leading to four types of structural levels of organization - primary, Secondary, Tertiary and Quaternary, the first three types of structures composed of one polypeptide chain only while the quaternary structures exist in protein molecule composed of more than two polypeptides chain in a complex manner. In the secondary, tertiary and quaternary structure of the protein, apart from the normal polypeptide bond, a variety of chemical bonds bonds exist either in the same polypeptide chain or in between different polypeptide chain. These chemical bonds are Hydrogen bond, Ionic or electrostatic bond, Non-polar or hydrophobic bond Disulphide bond. Protein conformation basically speaks about combined secondary, tertiary and quaternary structure.
  19. 19. PRIMARY STRUCTURE I. It is the linear sequence and the number of amino acid residues that make the polypeptide chain II. Ii. The amino acids residues are linked by polypeptide bonds formed between α-carboxyl group of one amino acid residue to the α amino group of the other. III. The peptide bond is a special amide linkage and it construct the backbone of the protein chain, IV. The primary structure of a protein is to start from the amino- terminus (N) end to the carboxyl-terminal (C) end. V. All peptide bonds in proteins occur in trans configuration Glycine, Proline etc.
  20. 20. SECONDARY STRUCTURE The primary structure of the protein chain is folded by hydrogen bonds to produce secondary structure which may be helical structure as in α-helices and β-helices. As observed in an atomic-resolution structure. In this structure, the hydrogen bond is formed in between the amine hydrogen of one amino acid residue with the carboxyl oxygen atom of a different amino acid residue of the same chain. The α-helix and β pleated sheet structure were first proposed by Nobel prize winner, Linus Pauling et al in 1951. The α-helix is a rod like structure whose inner part is formed by the tightly coiled polypeptide chain. All the main chain carboxyl and amino groups are hydrogen bonded. All the naturally occurring α-helices are right handed. Each complete coil in each helix consists of 3.6 amino acid residues and the rise of the helix per turn is 5.4Å (ii) β-plated sheet is different from the α-helix in that it is a sheet rather than being tightly coiled. The several polypeptides are being parallel to one another in a plane , with
  21. 21. Hydrogen bonds between the adjacent chains. The β-pleated sheets may have two structures-parallel and anti-parallel. If the chains run in the same direction, then it is treated as parallel and if it run in alternate opposite direction, then it is known as anti-parallel β- sheet. Examples : α-helix: Keratin wool, β-pleated sheet: silk, certain synthetic fibres like nylon, orlon etc. Many long helices form a multi-stranded rope like structure. i. Protofibril of hair having 3-right handed helices round around each other to form a left-handed super-coil of 20Å in diameter. ii. Coiled coil having identical α-helices and non-polar repeating side chains twist around in each other to produce a stable structure as in α-keratin fiber.
  22. 22. TARTIARY STRUCTURE In this structure of [protein, a polypeptide chain is extensively coiled and folded to produce a complex and rigid structure . The folding are due to interact between the amino acid residues relatively present far apart in the primary sequence , produce different type of bonding such as hydrogen bond, hydrophobic(non-polar), ionic and disulphide bond. The tertiary structure of a protein involves folding of its secondary structural elements and specifies the position of atoms, bonds other than normal bonds of residue. And those of the side chains. The helices in globular protein undergo folding sequences due to the above four additional bonds and in turn, they achieve a globular or spherical structure. A protein having tertiary structure with a large polypeptide chain containing more than 200 amino acids residues fold into globular spherical clusters to form domains that give the protein bi- or multi –lobed appearance.
  23. 23. A domain may consists of around one-two hundred residues having diameter approximately 25Å. The adjacent domains are also well connected by chemical bond. However, small spherical proteins have many independent domains. EXAMPLES: I. Myoglobin- a hem protein found in muscle tissue contains 153 residues and a single Fe porphyrin group in horse heart with molecular weight 16, 700. ii. Ribonuclease - of bovine pancreas contains 124 residues having 4 disulphide bridges, iii. Lysozyme has 129 residues with 40 α-helices and 12 β- structures, iv. Cytochrome C with 104 residues, v. Chymotrypsin with 247 residues, vi. Carboxypeptidase with 307 residues having 38 α-helices & 17 β-structures
  24. 24. QUATERNARY SATRUCTURE Here, the very complex structure are formed due to the protein- protein interactions and develop two or more than two interacting polypeptide chains. Each of then known as subunit . Thus, a large size globular protein is formed giving a quaternary structure. The same bonds involved in the formation of tertiary structure like H bond, ionic, disulphide bonds and also involved to link the various polypeptide chains in the quaternary structure. EXAMPLES: I. Tobacco Mosaic Virus (TMV) protein containing 158 residues are rod like, tubular structure measuring 3000 Å in length and 180 Å in diameter, II. Blood hemoglobin containing 4 polypeptide chains of two types- α and β chains roughly spherical in shape with mol. wt. 64,450; α-chain with 141 residues & β chains with -146 residues, the two chains are joined together with ionic & hydrogen bond. The 2 pairs are then joined to each other by H, ionic and hydrophobic bond.
  25. 25. iii. Glutamate dehydrogenase of bovine liver: consists of 40 chains with 83000 residues having molecular weight 1000000. iv. Glutamate synthetase of E. coli having 12 subunits, v. Ribulose bis-phosphate carboxylase oxygenase (RUBISCO) –a kind of dual enzymes performs oxidation and reduction during photosynthesis and photorespiration contains 16 sub units ; 8 in upper view and 8 in lower view. DNA polymerase, I, II, III associated with DNA replication
  26. 26. ISOELECTRIC POINT As in amino acids, we have observe that in aqueous solution, proteins are either positively or negatively charged and migrate towards positive or negative pole. But at certain condition, they neither behave positively or negatively charged , rather behaves like a dipole just like Zwitterions form of dipolar amino acids. The Isoelectric pH of the proteins depend upon the number of basic (+ ve ) and acidic (- ve) group which are provided by the amino acids residues. Proteins like Pepsin, ovalbumin like substances contain more acidic amino acids and this make the isoelectric pH of 2.7 and 4.6 respectively. Lysozyme of egg white has high number of basic amino acids and the isoelectric pH is 11.0.some proteins like milk casein readily precipitated at or near the isoelectric point and this phenomenon is called isoelectric precipitation. The isoelectric point is a valuable information to the biochemists and some of the proteins and their isoelectric point are attached herewith.
  27. 27. Sl. No. Proteins along with no. of chains Molecular weight Isoelectric point 1. Cytochrome C (1) 12,500 9.8 2. Myglobin of horse (1) 16,700 7.0 3. Fibrinogen 4,50, 000 5.5 4. Catalase 2,50,000 5.6 5. Insulin of bovine 5,733 5.4 6. Urease 4,80,000 5.0 7. Pepsin 35,500 2.7
  28. 28. DENATURATION OF PROTEIN Spatial arrangement of polypeptides chain within protein molecules can be altered for diverse purposes. Protein denaturation is the process of the alteration of the spatial arrangement of the polypeptide chain within a protein molecule with an aim to keep the primary structure retained. It was first coined by Kauzamann (1959). The physical and chemical properties of the native protein is altered. In many cases , it is followed by coagulation when the denatured protein molecules form large aggregate and precipitate in the solution. The different types of agents are employed for the denaturation process as followed: 1. PHYSICAL AGENTS- This process include mechanical action like shaking, rubbing, heat treatment , high hydrostatic pressure varying from 5000-10000 atm., ultraviolet rays, ionizing radiations etc are used for the same. Heating and the pH alteration changes the conformation of protein leading to the denaturation.
  29. 29. 2. CHEMICAL AGENTS- Different types of chemical agents like acetone, alcohol, aromatic anions like salicylates, anionic detergents like sodium dodecyl sulphate, mineral acid and alkynes, picric acid, trichloroacetic acid, tangustic acid are some of the compounds used for the chemical denaturation of protein. These agents generally cleave the hydrogen and salt linkages or other chemical bonds present in the protein to unfold the polypeptide chain. The unfolding of the polypeptide chain by denaturation causing disorganization of the protein structure . The denaturized proteins are more easily hydrolyzed as the denaturation causes freed the hydrogen bond in between the two polypeptide chains and the free sulphohahydryl group (-SH) are set free by the denaturation process. Denaturation causes the cessation of biochemical activity of enzymes and hormones; decrease solubility; change the size and shape along with the increase of activity of some radicals present in protein molecule like –SH, -S-S-, -COOH group etc.
  30. 30. TYPES OF DENATURATION Depending on the nature of the denaturation, it may be of the following types- i. Irreversible type- Denatured proteins by external agents can not be brought back to its previous original position and conformation. ii. Reversible type- In some cases, denatured proteins can be brought back to its original position called reversible type. The process of regaining the normal state of the protein from the denatured one is called renaturation. In some cases, antibodies may cause refolding of the protein chains restoring the original bonds to bring back the original state. Examples:i.Trypsin- If trypsin is exposed to the high temperature ( 80-90℃), it denatures but when cooled at room temperature (37℃), the solubility and the activity of the enzyme is restored. ii. RNAase- The enzyme RNAase can be denatured by keeping it in 8M urea solution containing 2-mercaptoethnol. If after dialyzing the urea and mercaptoethanol, RNAase activity is regained at pH 8 in O2 exposure.
  31. 31. FUNCTION OF PROTEINS Proteins extend a number of biological role as a part of the structural and functional mode as stated below: i. Components of tissues- As a part of the structural attributes, protein serve as components of tissues like skeletal systems and collagen as connective tissues. ii. It acts as central key components in the architecture of organisms, iii. Catalysts-acts as catalysts to perform diverse biological functions, iv. Biological membranes- key components of cell membrane, v. Transport functions-The mechanism of active transport into cell and out of cell requires protein expedited by energy, vi. Hormones-mostly proteins act as chemical messenger to control multiple physiological functions,
  32. 32. vii. Signal transduction-Communication in between cells during signal transduction takes place by proteins, Viii .Chromosomes - Histone and non- histone proteins build up the structure of chromosomes, ix. Cellular toxicity- Under different stress condition, the cell accumulates the different toxic substances and these are the accumulation of the different denatured protein components, x. Interferon-these are low molecular weight, regulatory, glycoprotein's produced by many eukaryotic cells in response to numerous inducers like virus infection, dsRNA , endotoxins, antigenic stimuli, mutagenic agents, and many more.
  33. 33. References: 1. Google for images, 2. Different open sources of information of WebPages 3. Biochemistry- Lehninger 2. Biomolecules & Cell Biology- Arun chandra Sahu, 3. A textbook of Botany (Vol. II) Ghosh, Bhattacharya, Hait 4. Fundamentals of Biochemistry- Jain, Jain, & Jain, 5.A Textbook of Genetics- Ajoy Paul DISCLAIMER: This presentation has been made to enrich open source of learing without any financial interest. The presenter acknowledges Google for images and other open sources of information to develop this PPT.

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