proteins and its classification

institute of agriculture sciences
BANARAS HINDU UNIVERSITY

1. INSTITUTE OF AGRICULTURAL SCIENCES ASSIGNMENT SUBMITTED TO: DR.YADUVEER SINGH SUBMITTED BY: 1.ABHISHEK SUMAN(14005) 2.AJIT KUMAR(14008) 3.AKANkSHA SINGH(14009) 4.AKASH TRIVEDI(14010) 5.AMIT KUMAR(14013 )-LEADER DEPARTMENT OF SOIL SCIENCES AND AGRICULTURAL CHEMISTRY GROUP “A”

2. CLASSIFICATION OF PROTEINS

3. Protein Can Be Classified By: Structure Biological function Shape and solubility Composition Nutritional basis

4. CLASSIFICATION BY STRUCTURE

5. Primary Structure The primary structure of proteins is defined as a linear sequence of amino acids joined together by peptide bonds. Peptide bonds and disulfide bonds are responsible for maintaining the primary structure.

6. Secondary Structure The secondary structure of a protein is defined as a local spatial structure of a certain peptide segment, that is, the relative positions of backbone atoms of this peptide segment. H-bonds are responsible for stabilizing the secondary structure. Repeating units of Ca-C(=O)-N(-H)-Ca constitute the backbone of peptide chain. Six atoms, Ca-C(=O)-N(-H)-Ca , constitute a planer peptide unit.

7. Tertiary Structure The tertiary structure is defined as the three-dimensional arrangement of all atoms of a protein.

8. Quaternary structure The quaternary structure is defined as the spatial arrangement of multiple subunits of a protein. These subunits are associated through H-bonds, ionic interactions , and hydrophobic interactions

9. CLASSIFICATION BY BIOLOGICAL FUNCTION

10. Enzymes Those proteins which are highly specialized in their function with catalytic activity. These proteins regulate almost all biological reactions going on inside all living cells. There are about 2000 different enzymes has been recognized; each capable of catalyzing a different kind of biochemical reaction.

11. Transport Proteins are those proteins which help in transportation of life sustaining chemicals vital gases and nutrients. Carry essential substances throughout the body. Example: - Haemoglobin is a globular protein present in RBC of blood can binds with oxygen when blood passes though longs and distributes oxygen through out the body cells to affect cellular respiration. - Blood plasma contains lipoprotein which carries lipids from the liver to other organs.

12. Storage Proteins are those stored inside the cells or tissue as reserved food and can be mobilized at the time of nutrient requirement to provide energy. Store nutrients. Example: - Casein stores protein in milk. - Ferritin stores iron in the spleen and liver.

13. Contractile/Motile Proteins Move muscles. the ability to contract to change the shape or to move about. These proteins includes. Actin and myosin; which are present in form of filamentous protein in muscle cells for functioning in the contractile systems.

14. Structural Proteins This type of protein form major component of tendons, cartilages and bones. These are fibrous proteins named collagen. Ligaments are contains special structural protein capable of stretching in two dimensions called as elastin . Hairs finger nails, feathers of birds consists of tough insoluble protein named keratin. Major component of silk fibers , threads of spider web contain structural protein named fibroin.

15. Defense proteins Many proteins in body of organisms posses defending action against the invasion and attack of foreign entities or protect the body from injury. Among these proteins special globular protein named immunoglobulin's or antibodies in vertebrate’s body is the most indispensible protein. It synthesized by lymphocytes and they can neutralize the foreign protein produced by bacteria, virus and other harmful microbes called antigens through precipitation or glutination .

16. Regulatory Protein Some proteins help to regulate cellular or physiological activity. Among them are many hormones, such as insulin; which is a regulatory protein formed in pancreatic tissue help to regulate the blood sugar level. Growth hormones of pituitary and parathyroid hormones regulate Ca++ and phosphate transport in body. Other proteins called repressors regulate biosynthesis of enzymes.

17. Other Functional Proteins There are number of proteins whose functions are not yet specified and are rather exotic. These includes – Monelin : -  A protein of an African plant has an intensely sweet taste and used as non toxic food sweetener for human use. Antifreeeze :  A protein present in blood plasma of Antarctic fisher which protect their blood freezing in ice cold water. Resillin :  A type of protein present in wing hinges of some insects with elastic properties.

18. Classification by Shape & Solubility

19. Fibrous Proteins these proteins have a rod like structure. They are not soluble in water. (a)    These are made up of polypeptide chain that are parallel to the axis & are held together by strong hydrogen and disulphide bonds.  (b)    They can be stretched & contracted like thread.  Examples: -Collagen -Keratin -Fibrinogen -Muscle protein

20. Globular proteins these proteins more or less spherical in nature. Due to their distribution of amino acids (hydrophobic inside, hydrophillic outside) they are very soluble in aqueous solution. Examples Myoglobin , albumin, globulin, casein, haemoglobin, all of the enzymes, and protein hormones.

21. Membrane proteins These are protein which are in association with lipid membranes. Those membrane proteins that are embedded in the lipid bilayer have extensive hydrophobic amino acids that interact with the non-polar environment of the bilayer interior. Membrane proteins are not soluble in aqueous solution.

22. Classification By Composition

23. Simple proteins are those which on hydrolysis yield only amino acids and no other major organic or inorganic hydrolysis products. They usually contain about 50% carbon,7% hydrogen, 23% oxygen, 16% nitrogen and 0–3% sulphur. Example: -Egg (albumin) -Serum (globulins) -Wheat ( Glutelin ) -Rice ( Coryzenin )

24. Conjugated Proteins are those which on hydrolysis yield not only amino acids but also organic or inorganic components. The non-amino acid part of a conjugated protein is called prosthetic group. Conjugated proteins are classified on the basis of the chemical nature of their prosthetic groups.

25. Nutritional Basis

26. Complete Proteins A complete protein contains an adequate amount of all of the essential amino acids that should be incorporated into a diet. Some protein contains all the amino acids needed to build new proteins, which generally come from animal and fish products. A complete protein must not lack even one essential amino acid in order to be considered complete. Sources: The following foods are examples of complete proteins, which need not be combined with any other food to provide adequate protein: Meat, Fish, Poultry, Cheese, Eggs, Yogurt, Milk

27. Incomplete Proteins An incomplete protein is any protein that lacks one or more essential amino acids in correct proportions. These can also be referred to as partial proteins. Even if the protein contains all the essential amino acids, they must be in equal proportions in order to be considered complete. If not, the protein is considered incomplete. Sources of Incomplete Proteins: Grains, Nuts, Beans, Seeds, Peas, Corn

28. Combining Incomplete Proteins to Create Complete Proteins By combining foods from two or more incomplete proteins, a complete protein can be created. The amino acids that may be missing from one type of food can be compensated by adding a protein that contains that missing amino acid. When eaten in combination at the same meal, you are providing your body with all the essential amino acids it requires. These are considered complementary proteins when they are combined to compensate for each other's lack of amino acids.

29. Samples of Complementary Proteins create a complete protein in one meal include: Grains with Legumes - sample meal: lentils and rice with yellow peppers. Nuts with Legumes -  sample meal: black bean and peanut salad. Grains with Dairy - sample meal: white cheddar and whole wheat pasta. Dairy with Seeds - sample meal: yogurt mixed with sesame and flax seeds. Legumes with Seeds - sample meal: spinach salad with sesame seed and almond salad dressing.

30. Properties of proteins Physical Properties Chemical Properties

31. Physical properties contains carbon, hydrogen, oxygen, nitrogen and small amount of sulphur. composed of amino acids that are linked together by peptide bonds  act as catalysts, enzymes that speed up the rate of chemical reactions  provides structural support for cells transports substances across cell membrane  provides a defense mechanism against pathogens (antibodies)  responds to chemical stimuli  secretes hormones.

32. To determine molecular nature In order to determine the nature of the molecular and ionic species that are present in aqueous solutions at different pH's, we make use of the  Henderson - Hasselbalch Equation.

33. isoelectric point the negatively and positively charged molecular species are present in equal concentration. This behavior is general for simple (difunctional) amino acids.

34. Electrophoresis The distribution of charged species in a sample can be shown experimentally by observing the movement of solute molecules in an electric field, using the technique of  electrophoresis .

35. Chemical properties Denaturation of Proteins Denaturation is a process in which  proteins  or  nucleic acids  lose the  quaternary structure ,  tertiary structure  and  secondary structure  which is present in their  native state , by application of some external stress or compound such as a strong  acid  or  base , a concentrated  inorganic  salt, an  organic solvent (e.g.,  alcohol  or  chloroform ), radiation or  heat .

36. Denaturation occurs because the bonding interactions responsible for the secondary structure (hydrogen bonds to amides) and tertiary structure are disrupted. In tertiary structure there are four types of bonding interactions between "side chains" including: hydrogen bonding, salt bridges, disulfide bonds, and non-polar hydrophobic interactions. which may be disrupted. Therefore, a variety of reagents and conditions can cause denaturation . The most common observation in the denaturation process is the precipitation or coagulation of the protein.

37. Heat can be used to disrupt hydrogen bonds and non-polar hydrophobic interactions. This occurs because heat increases the kinetic energy and causes the molecules to vibrate so rapidly and violently that the bonds are disrupted. The proteins in eggs denature and coagulate during cooking. Other foods are cooked to denature the proteins to make it easier for enzymes to digest them. Medical supplies and instruments are sterilized by heating to denature proteins in bacteria and thus destroy the bacteria. HEAT

38. Alcohol Disrupts Hydrogen Bonding: Hydrogen bonding occurs between amide groups in the  secondary protein structure . Hydrogen bonding between "side chains" occurs in t ertiary protein structure  in a variety of amino acid combinations. All of these are disrupted by the addition of another alcohol. A 70% alcohol solution is used as a disinfectant on the skin. This concentration of alcohol is able to penetrate the bacterial cell wall and denature the proteins and enzymes inside of the cell. A 95% alcohol solution merely coagulates the protein on the outside of the cell wall and prevents any alcohol from entering the cell. Alcohol denatures proteins by disrupting the side chain intramolecular hydrogen bonding. New hydrogen bonds are formed instead between the new alcohol molecule and the protein side chains.

39. Acids and Bases Disrupt Salt Bridges: Salt bridges  result from the neutralization of an acid and amine on side chains. The final interaction is ionic between the positive ammonium group and the negative acid group. Any combination of the various acidic or amine amino acid side chains will have this effect. The  denaturation  reaction on the salt bridge by the addition of an acid results in a further straightening effect on the protein chain as shown in the graphic on the left.

40. Heavy Metal Salts Heavy metal salts act to denature proteins in much the same manner as acids and bases.  Heavy metal salts usually contain Hg +2 , Pb +2 , Ag +1  Tl +1 , Cd +2  and other metals with high atomic weights. Since salts are ionic they disrupt salt bridges in proteins. The reaction of a heavy metal salt with a protein usually leads to an insoluble metal protein salt. This reaction is used for its disinfectant properties in external applications. For example AgNO 3  is used to prevent gonorrhea infections in the eyes of new born infants. Silver nitrate is also used in the treatment of nose and throat infections, as well as to cauterize wounds. Mercury salts administered as Mercurochrome or Merthiolate have similar properties in preventing infections in wounds.

41. Acids Acidic  protein denaturants include: Acetic acid [8] Trichloroacetic acid  12% in water Sulfosalicylic acid Solvents Most organic  solvents  are denaturing, including: Ethanol Methanol Cross-linking reagents Cross-linking  agents for proteins include: [ citation needed ] Formaldehyde Glutaraldehyde Chaotropic agents Chaotropic agents  include: Urea  6 – 8  mol/l Guanidinium chloride  6 mol/l Lithium perchlorate  4.5 mol/l Disulfide bond reducers [ edit ] Agents that break  disulfide bonds  by reduction include: [ citation needed ] 2-Mercaptoethanol Dithiothreitol TCEP  ( tris (2-carboxyethyl) phosphine ) Other Picric acid Radiation Temperature

42. Example of denaturation that occurs in our living: 1. Denaturation of human hair The extent to which fatty acid oxygenases are activated in the normal epidermis is not known 2. In cooking eggs cooking eggs turns them from runny to solid cooking food makes it more digestible. 3. Milk forms a solid curd on standing ·        bacteria in milk grows ·        forms lactic acid ·         protonates carboxylate groups ·        becomes isoelectric ·        coagulates into a solid curd

43. Separation of Amino Acids and Proteins Chromatography – the method of separating amino acids on the basis of differences in absorption, ionic charges, size and solubility of molecules Electrophoresis – effects separation in an electric field on the basis of differences in charges carried by amino acids and proteins under specific condition 3. Ultracentrifugation – effects separation on the basis of molecular weight when large gravitational forces are applied in the ultracentrifuge. 4. Precipitation Methods – salts as sodium sulfate, ammonium sulfate, cadmium nitrate, silver nitrate and mercuric chloride at specific conc. precipitate some proteins while others remain in solution 5. Dialysis – is for the removal of small, crystalloidal molecules from protein solution.

44. Chromatography Much of modern biochemistry depends on the use of column chromatographic methods to separate molecules. Chromatographic methods involve passing a solution (the mobile phase) through a medium (the immobile phase) that shows selective solute components. The important methods of chromatography are: 1. Ion-Exchange Chromatography 2. Antibody Affinity Chromatography 3. Gel Filtration Chromatography 4. HPLC (High Performance Liquid Chromatography)

45. HPLC

46. Gel Filtration Chromatography

47. Precipitation of proteins

48. Biuret Test

49. Chemical Reaction in the Biuret test

50. Proteomics Proteomics is the science of protein expression of all the proteins made by a cell Proteome pertain to all proteins being made according to the transcriptome (RNA profile). It is often visualized by a system interaction map as seen in the proteogram.

51. Procedures of the Proteomics Commonly used procedures by Proteomics are: Mass Spectrophotometry – detects exact mass of small peptides (molecular weight). X-ray Crystallography – determines 3D shape of molecules mathematically NMR Spectroscopy – magnetic signal indicates distances between atoms

52. Biochemical Importance of Amino Acids Amino Acids Systematic name Importance Glycine Aminoetha- noic acid Helps trigger the release of oxygen to the energy requiring cell-making process Important in the manufacture of hormones for strong immune system Alanine α -amino propanoic acid Important AA as it is an energy source for the liver, muscles, and CNS Strengthens the immune system by producing antibodies Helps in the metabolism of sugars and organic acids

53. Valine α -amino 3-methylbutanoic acid Essential AA Promotes mental vigor, muscle coordination and calm emotions Leucine α -amino 4-methyl pentanoic acid Essential AA Provides necessary substances for energy production Stimulants to the upper brain and helps to be more alert Isoleucine α -amino 3-methylpentanoic acid Essential AA Same functions as leucine

54. Phenylalanine α -amino 3-phenylpropanoic acid Essential AA Used by the brain to produce norepinephrine, Reduces hunger pains Functions as antidepressant Helps improve memory Tyrosine α -amino 3-(4-hydroxyphenyl)propanoic acid Transmits nerve impulses to the brain; helps overcome depression; improves memory; increases mental alertness; promotes the healthy functioning of the endocrine glands Tryptophan α - amino 3-indole propanoic acid Essential AA A natural relaxant, helps alleviate insomia by inducing normal sleep Reduces anxiety and depression Helps in the treatment of migraines and headaches Helps stabilize the immune system Helps reduce risk of artery and heart spasms Works with lysine in reducing cholesterol levels

55. Methionine α -amino 4-methyl thiol butanoic acid Essential AA Principal supplier of sulfur which prevents disorder of the hair, skin and nails Helps lower cholesterol levels by increasing the liver’s production of lecithin A natural chelating agent for heavy metals Regulates the formation of ammonia and creates ammonia-free urine which reduces bladder irritation Influences hair follicles and promotes hair growth

56. Cysteine 2-amino 3-mercaptopropanoic acid Functions as an antioxidant and is a powerful aid to the body in protecting against radiation and pollution Helps slow down the aging process, deactivate free radicals, neutralizes toxins Aids in protein synthesis and promotes cellular repair Necessary for skin formation, in the recovery from burns and surgical operations Serine 2-amino 3 hydroxy propanoic acid A storage source of glucose by the liver and muscles Helps strengthen immune system by providing antibodies Synthesizes fatty acid sheath around nerve fibers Threonine 2-amino 3 hydroxy butanoic acid Essential AA Important constituent of collagen , Assists metabolism and assimilation Helps the digestive and intestinal tracts functions normally Helps prevents fat build-up in the liver

57. Histidine α -amino 3 (1H-imidazol-4-yl) propanoic acid Essential AA Found abundantly in hemoglobin Used in the treatment of rheumatoid arthritis, allergic diseases, ulcers, anemia Lysine 2,6 diamino hexanoic acid Essential AA Insures adequate absorption of calcium Helps form collagen (which makes up bone and cartilages) Aids in the production of antibodies, hormones and enzymes Arginine α -amino 5-guanidino pentanoic acid Helps improve immune responses to bacteria, viruses and tumor cells Promotes wound healing and regeneration of the liver Causes the release of growth hormones Crucial for optimal muscle growth and tissue repair

58. Aspartic Acid α -amino butanedioic acid Most easily used as energy source Aids in the expulsion of toxic ammonia from the body Located most closely to the TCA cycle, the site of energy production Found in increased levels in people with epilepsy and in decreased amounts in some cases of depression Glutamic acid α -amino pentanedioic acid Considered to be nature’s “brain food” by improving mental capacities Helps speed the healing of ulcers; gives a “lift” from fatigue Helps control alcoholism, schizophrenia and the craving of sugar, Parkinson’s disease, mental retardation, and muscular dystrophy Asparagine α -amino 3 carbamoyl propanoic acid Found in the surfaces of proteins where they can interact with water molecules

59. Glutamine α -amino 4 carbamoyl butanoic acid Found in the surfaces of proteins where they can interact with water molecules The polar amide groups can also form hydrogen bonds with atoms in the side chains of other polar amino acids Proline Pyrrolidine-2-carboxylic acid Non-essential AA Important for the proper functioning of joints and tendons Helps maintain and strengthen heart muscles Helps repair processes after cell injury or for any type of wound healing Hydroxy lysine Hydroxy hexanoic acid It is a hydroxy derivative of lysine. It is most widely known as a component of collagen

60. Biologically Important Proteins Protein No. of AA Function Insulin 51 Enzyme for sugar metabolism Cytochrome C 104 Enzyme for cell respiration Growth hormone 191 Used as anti-aging treatment Hemoglobin 574 Oxygen transport in blood Hexokinase 730 Enzyme for glycolysis Gamma globulin 1320 Part of immune system in blood Myosin 6100 Muscle action

61. Blood Proteins Albumins Create osmotic pressure and transport other molecules Immunoglobulins Participate in immune system Fibrinogens Blood coagulation Alpha-1-Antitrypsin Neutralize trypsin that has leaked from the digestive system Regulatory proteins Regulation of gene expression

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