1. Biochemistry I BIOCA2301

2. Topics Carbohydrates Lipids Proteins Nucleic acids Enzymes Metabolism Carbohydrates Lipids Proteins Nucleic acids Enzymes Metabolism

3. The Remaining Part.. Proteins - Classification - Properties of proteins - Denaturing Factors of proteins Proteins - Classification - Properties of proteins - Denaturing Factors of proteins

4. The isoelectric Point (pI) If placed in an electric field, the amino acid will therefore migrate toward the cathode (negative electrode) at low pH and toward the anode (positive electrode) at high pH. At some intermediate pH, called the isoelectric point (pI), the amino acid will have a net charge of zero. It will be unable to move toward either electrode. Each of the amino acids has a characteristic isoelectric points 4

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6. Secondary Structure Review Polypeptide chains can fold into regular structures. Two types of secondary structure elements: 1. α-helix 2. β-sheet 6

7. 1. α-helix Is a coiled structure stabilized by intrachain hydrogen bonds. Each turn of the helix contains a bout 3.6 amino acids. Hair & wool are examples of protein with helical structure, both contain keratin. Is a coiled structure stabilized by intrachain hydrogen bonds. Each turn of the helix contains a bout 3.6 amino acids. Hair & wool are examples of protein with helical structure, both contain keratin. 7

8. β-sheet Beta sheets are stabilized by hydrogen bonding between polypeptide strands. The β- sheet is composed of 2 or more polypeptide chains called β- strands. A β- strand is almost fully extended rather than being tightly coiled as in the α- helix. The distance between adjacent amino acids along a β- strand is approximately 3.5 Å, in contrast with a distance of 1.5 Å along an α- helix. point in opposite directions. The side chains of adjacent amino acids point in opposite directions. Beta sheets are stabilized by hydrogen bonding between polypeptide strands. The β- sheet is composed of 2 or more polypeptide chains called β- strands. A β- strand is almost fully extended rather than being tightly coiled as in the α- helix. The distance between adjacent amino acids along a β- strand is approximately 3.5 Å, in contrast with a distance of 1.5 Å along an α- helix. point in opposite directions. The side chains of adjacent amino acids point in opposite directions. 8

9. 9 The structure of a β- strand. The side chains (green) are alternatively above and below the plane of the strand. The bar shows the distance between two residues Examples of proteins with β-sheet are protein in silk (fibroin), and proteins that bind fatty acids

10. Classification of Proteins Proteins can be classified into three classes: 1. Simple protein 2. Conjugated proteins 3. Derived proteins Proteins can be classified into three classes: 1. Simple protein 2. Conjugated proteins 3. Derived proteins 10

11.  Simple proteins they give amino acids or their derivative (polypeptides) upon hydrolysis  Conjugated proteins they give amino acids and other compounds (non protein compound) upon hydrolysis  Derived proteins Are produced from simple or conjugated proteins upon chemical or enzymatic action on proteins. As derived proteins one can consider proteoses, peptones, polypeptides, tripeptides, and dipeptides.  Simple proteins they give amino acids or their derivative (polypeptides) upon hydrolysis  Conjugated proteins they give amino acids and other compounds (non protein compound) upon hydrolysis  Derived proteins Are produced from simple or conjugated proteins upon chemical or enzymatic action on proteins. As derived proteins one can consider proteoses, peptones, polypeptides, tripeptides, and dipeptides. 11

12. Classification Of Proteins According To Solubility Simple proteins are classified according to their solubility in various solvents and also as to whether they are coagulated by heat. 12

13. Classification Of Proteins According To Composition Conjugated proteins can be classified into different types: 1.Nucleoproteins: (nucleic acid/ chromosomes) 2.Glycoproteins: (carbohydrates/ mucin in saliva) 3.Phosphoproteins: (Phosphate/ casein in milk) 4.Chromoproteins: (Chromophore/ hemoglubin, cytochrome) 5.Lipoproteins: (lipids/ fibrin in blood) 6.Metalloproteins: Metals/ ceruloplasmin Conjugated proteins can be classified into different types: 1.Nucleoproteins: (nucleic acid/ chromosomes) 2.Glycoproteins: (carbohydrates/ mucin in saliva) 3.Phosphoproteins: (Phosphate/ casein in milk) 4.Chromoproteins: (Chromophore/ hemoglubin, cytochrome) 5.Lipoproteins: (lipids/ fibrin in blood) 6.Metalloproteins: Metals/ ceruloplasmin 13

14. Classification Of Proteins According To Function 1.Structural proteins: Collagen (in connective tissues), keratin (in hair). 2.Contractile proteins: Myosin, actin (muscle contraction) 3.Storage proteins: Ferritin (storage of iron) 4.Transport proteins: Hemoglobin (transfers oxygen) 1.Structural proteins: Collagen (in connective tissues), keratin (in hair). 2.Contractile proteins: Myosin, actin (muscle contraction) 3.Storage proteins: Ferritin (storage of iron) 4.Transport proteins: Hemoglobin (transfers oxygen) 14 5.Hormones: Insulin ( metabolism of carbohydrates) 6.Enzymes: Pepsin (digestion of proteins) 7.Protective proteins: γ-globulin (antibody formation) 8.Toxin: Venoms (poisons) 5.Hormones: Insulin ( metabolism of carbohydrates) 6.Enzymes: Pepsin (digestion of proteins) 7.Protective proteins: γ-globulin (antibody formation) 8.Toxin: Venoms (poisons) According to their biological function, proteins can be classified into various classes:

15. Classification Of Proteins According To Shape 1. Globular proteins: Folded into a shape of ball. Are soluble in water or form colloidal dispersions. Examples: Hemoglobin, Albumin, globulins Enzymes are globular 2. Fibrous proteins Consist of parallel polypeptide chains that are coiled and stretch out. Are insoluble in water. Examples: collagen, elastin, myosin. 1. Globular proteins: Folded into a shape of ball. Are soluble in water or form colloidal dispersions. Examples: Hemoglobin, Albumin, globulins Enzymes are globular 2. Fibrous proteins Consist of parallel polypeptide chains that are coiled and stretch out. Are insoluble in water. Examples: collagen, elastin, myosin. 15

17. Properties of Proteins Proteins have two characteristic properties: 1.Colloidal Nature 2.Denaturation Proteins have two characteristic properties: 1.Colloidal Nature 2.Denaturation 17

18. 1. Colloidal Nature When proteins are in water, they form a colloidal dispersion. Due to this property, proteins will not pass through a membrane. This is very important because proteins present in bloodstream can not pass through the capillaries & should remain in blood-stream. Therefore there should be no protein in the urine. So if there is a protein in urine, it indicates that there is a damage in the kidney membranes- possibly nephritis. When proteins are in water, they form a colloidal dispersion. Due to this property, proteins will not pass through a membrane. This is very important because proteins present in bloodstream can not pass through the capillaries & should remain in blood-stream. Therefore there should be no protein in the urine. So if there is a protein in urine, it indicates that there is a damage in the kidney membranes- possibly nephritis. 18

19. 2. Denaturation Unfolding & rearrangement of secondary and tertiary structure of a protein without breaking the peptide bonds. A denatured protein loses its activity If denaturing conditions are mild, protein will restore their active structure if these conditions of denaturing are reversed. If denaturation is drastic, the process is irreversible; the protein will coagulate or precipitate from solution. Unfolding & rearrangement of secondary and tertiary structure of a protein without breaking the peptide bonds. A denatured protein loses its activity If denaturing conditions are mild, protein will restore their active structure if these conditions of denaturing are reversed. If denaturation is drastic, the process is irreversible; the protein will coagulate or precipitate from solution. 19

20. Factors or Reagents Causing Denaturation 1. Alcohol (ethanol) - It causes irreversible denaturation. - Alcohols form hydrogen bonds, that compete with original hydrogen bonds 1. Alcohol (ethanol) - It causes irreversible denaturation. - Alcohols form hydrogen bonds, that compete with original hydrogen bonds 20

21. 2. Salts of heavy metals HgCl 2 (mercuric chloride) and AgNO 3 (silver nitrate) cause irreversible denaturation by disrupting salt bridges & disulfide bridges. 3. Heat -If heat is gentle, protein will denature reversibly. -If heat is vigorous, protein will denature irreversibly by disrupting several types of bonds. 2. Salts of heavy metals HgCl 2 (mercuric chloride) and AgNO 3 (silver nitrate) cause irreversible denaturation by disrupting salt bridges & disulfide bridges. 3. Heat -If heat is gentle, protein will denature reversibly. -If heat is vigorous, protein will denature irreversibly by disrupting several types of bonds. 21

22. Examples: 1.Egg-white coagulates on heating. 2. In bacteria heat destroys & coagulates proteins, hence in hospitals, the sterilization of instruments and clothing for use, need high temperature. 3. Determination of proteins present in urine can be done by heating a sample of urine which will cause the coagulation of any protein present. Examples: 1.Egg-white coagulates on heating. 2. In bacteria heat destroys & coagulates proteins, hence in hospitals, the sterilization of instruments and clothing for use, need high temperature. 3. Determination of proteins present in urine can be done by heating a sample of urine which will cause the coagulation of any protein present. 22

23. 4. Alkaloidal Reagents (tannic acid & picric acid) -Both form insoluble compounds with proteins. They denature proteins irreversibly by dis- rupting salt bridges and hydrogen bonds. 5. Radiation UV & X-ray cause coagulation of proteins. They denature proteins irreversibly by disrupting the hydrogen bonds and hydropho- bic bonds. 4. Alkaloidal Reagents (tannic acid & picric acid) -Both form insoluble compounds with proteins. They denature proteins irreversibly by dis- rupting salt bridges and hydrogen bonds. 5. Radiation UV & X-ray cause coagulation of proteins. They denature proteins irreversibly by disrupting the hydrogen bonds and hydropho- bic bonds. 23

24. 6.pH Changing the pH will disrupt hydrogen bonds and salt bridges causing irreversible denaturing. (H 2 SO 4, HCl, HNO 3 ). 7. Oxidizing & reducing agents - Bleach (chlorine), nitric acid, both oxidizing agents. - SO 3 2- (sulfites) & oxalates are reducing agents. Both denature proteins by disrupting disulfide bridges. 6.pH Changing the pH will disrupt hydrogen bonds and salt bridges causing irreversible denaturing. (H 2 SO 4, HCl, HNO 3 ). 7. Oxidizing & reducing agents - Bleach (chlorine), nitric acid, both oxidizing agents. - SO 3 2- (sulfites) & oxalates are reducing agents. Both denature proteins by disrupting disulfide bridges. 24

25. 8. Salting out: -The vast majority of proteins are insoluble in saturated salt solutions and precipitate out unchanged. -It is possible to separate proteins from other proteins in a mixture by placing the mixture in a saturated solution of (NH 4 ) 2 SO 4, Na 2 SO 4 or NaCl. -The protein is precipitated out and removed by filtration. 8. Salting out: -The vast majority of proteins are insoluble in saturated salt solutions and precipitate out unchanged. -It is possible to separate proteins from other proteins in a mixture by placing the mixture in a saturated solution of (NH 4 ) 2 SO 4, Na 2 SO 4 or NaCl. -The protein is precipitated out and removed by filtration. 25