Protein Biochemistry Lecture II PDF

Chemistry of protein Lecture II By Dr. Nashwa Abdel-Ghaffar Abdel-Rahman Lecturer at Medical Biochemistry Department  Objectives ❑ Bonds Responsible For Protein Structure ❑ Structure of Proteins ❑ Denaturation of proteins ❑ Classification of P...

Chemistry of protein Lecture II By Dr. Nashwa Abdel-Ghaffar Abdel-Rahman Lecturer at Medical Biochemistry Department  Objectives ❑ Bonds Responsible For Protein Structure ❑ Structure of Proteins ❑ Denaturation of proteins ❑ Classification of Proteins ❑ Biological importance of Proteins  Bonds Responsible For Protein Structure Bonds Responsible For Protein Structure I- Strong bonds: ✓ Peptide bonds (primary bond). ✓ Disulfide bonds (secondary bond). II- Weak bonds: ✓ Hydrogen bond. ✓ Hydrophobic bond. ✓ Electrostatic bond.  Strong bonds Peptide bonds (primary bond): ▪ It is a covalent bond formed by a reaction between amino group of one amino acid and a carboxylic group of the next amino acid with the loss of H2O that required ATP. ▪ It is the strongest bond in the protein molecule that resists denaturation ▪ It is called primary because it is the only bond in the primary structure of the polypeptide. Disulfide bonds (secondary bond): ▪ The disulfide bond is formed between the SH groups of two cysteine residues within same (intra-chain) or two different polypeptide chains (inter-chain). ▪ It maintain secondary structure of a peptide chain or connects two polypeptide chains together in the tertiary structure. ▪ It follows the peptide bond in strength but liable to denaturation.  Weak bonds Hydrogen bond ▪ Hydrogen bond is a weak bond formed between the hydrogen atom of –NH of a peptide bond on one peptide chain and the oxygen of C=O of another peptide bond on an adjacent peptide chain or a loop belongs to same peptide chain. Hydrophobic bonds ▪ The non polar side chains of neutral amino acids tend to associate in hidden core of protein molecule away from solvent. Electrostatic bonds( Ionic bond) ▪ These are salt bonds formed between oppositely charged groups in the side chains of amino acids e.g. ε-amino group of lysine and the carboxyl group of asparatic acid  Structure of Proteins ▪ There are 4 levels or orders of organization of the structure protein molecule; ✓ primary, ✓ secondary, ✓ tertiary and ✓ quaternary structures. ▪ This complication gives the molecule its functional domain to explain its structure- function requirements that if changes due to mutation will give non-functional protein and, therefore, a disease  Primary Structure ▪ It is the arrangement and number of amino acids that enter in the structure of protein. ▪ Peptide bonds are covalent bonds responsible for primary structure.  Secondary Structure ▪ It is spatial relationship of adjacent amino acid residues (first and fourth). ▪ They are 2 forms : a-helix or P-pleated sheets ▪ Hydrogen bonds are responsible for secondary structure  Tertiary Structure ▪ It is the spatial relationship of more distant amino acid residues. ▪ Hydrogen, hydrophobic, electrostatic and disulfide bonds are responsible for tertiary structure There are 2 forms of tertiary structure : fibrous (extended) and globular (com pact) form  Quaternary structure ▪ It is the arrangement of proteins having more than one subunit. ▪ Hydrogen , electrostatic and hydrophobic bonds are responsible for quaternary structure. Definition of Denaturation ▪ Unfolding and loss of secondary, tertiary and quaternary structure. ▪ Does not affect primary structure i.e. not accompanied by hydrolysis of peptide bond. ▪ Denaturation may be reversible (in rare cases) Denaturating factors include: 1. Heat: causes coagulation and precipitation of certain proteins like albumin. 2. Strong acids or bases: : cause disruption of hydrogen and electrostatic bonds 3. Heavy metals: as lead and mercury salts: 4. Enzymes: e.g. Digestive enzymes. 5. Urea, ammonium sulphate and sodium chloride: cause precipitation of proteins. 6. Repeated freezing and thawing: cause disruption of hydrogen and other bonds. Effects (or fate) of Denaturation 1. Physical changes: Increase in viscosity, decreased solubility (insoluble). 2. Chemical changes: as loss of hydrogen, hydrophobic and electrostatic bonds but not of the peptide or disulfide bonds. This leads to loss of secondary tertiary and quaternary structures but not of the primary structure. 3. Biological changes: which include loss of enzymatic, hormonal and other biological properties of proteins.. Significance and Application of denaturation 1. Denatured proteins, e.g., cooked meat are easily digested 2. Blood samples to be analyzed for small molecules, e.g., uric acid and glucose are first treated with acid such as trichloroacetic acid or phosphotungestic acid to precipitate the plasma proteins (by denaturation). 3. Detection of albumin in urine by heat coagulation test is based on denaturation by heat. 4. Several approaches for stoppage of bleeding and treatment of burns is based on precipitation and denaturation of a superficial protein layer. 5. Avoidance of denaturation is important for biological samples used for determination of enzymatic, hormonal or protein contents. I. According to the biological importance of the protein: ✓ Proteins of high biological value ✓ Proteins of low biological value II. According to the axial ratio of the protein molecule: Axial ratio = Length/Width of the protein molecule ✓ Fibrous proteins ✓ Globular proteins III. According to the chemical composition of the Protein: ✓ Simple Proteins ✓ Conjugated proteins ✓ Derived Proteins  According to the biological importance of the protein Proteins of high biological value ▪ These are all proteins of animal origin (with a few exceptions) and some proteins of plant origin, that contain all the 10 essential amino acids in well balanced amounts and are easily digestible. ▪ Examples of animal proteins include; milks and its products, egg, liver, fishes, red and white meats. ▪ Examples of the few plant proteins of high biological value are lentils and broad beans  Proteins of low biological value ▪ These are proteins that ✓ are deficient in one or more of the essential amino acids or ✓ containing very little amount of one of them or ✓ are indigestible. ▪ Most of plant protein are of low biological value and a very few animal proteins are also of low biological value such are ✓ collagen because is deficient in tryptophan and cysteine and ✓ keratins because they are indigestible.  According to the axial ratio of the protein molecule I. Fibrous proteins ▪ They have an axial ratio of more than 10. Axial ratio = Length/Width of the protein molecule. ▪ They are ✓ fairly stable proteins in which the straight polypeptide chains lie parallel (or antiparallel) to one another along a single axis forming fibers or sheets. ✓ usually insoluble and non motile. ▪ Examples:- a. Keratin proteins in hairs, wool and skin. b. Myosin is the major protein of muscles  II. Globular proteins ▪ Their axial ratio is less than 10. ▪ Their one or more peptide chains are folded or coiled on themselves in a very compact manner. ▪ They are ✓ less stable than fibrous proteins ✓ usually soluble and motile. ▪ Examples are albumin, globulins, and insulin. According to the chemical composition of the Protein  I. Simple Proteins ▪ These are proteins which on hydrolysis produce amino acids only Albumins & Globulins Albumin Globulin - Soluble in water and salt solution - Soluble in salt solution. - M.W.: 68 KDa. - M.W.: 150 KDa. -Precipitated by full saturation with -Precipitated by half saturation with ammonium sulfate. ammonium sulfate. -They are present in: serum, egg, milk They are present in: serum,milk, eggs - It functions as transporting protein for - It functions in transport also but its elements, vitamins, and hormones other major function is being antibodies. than keeping blood osmosis.  Scleroproteins (Albuminoids) ▪ Scleroproteins are characterized by their extreme insolubility in water, dilute acids and the most common reagents. ▪ They are extracellular fibrous proteins and never present inside the cells. ▪ Their main function is the protection of the body. ▪ Hairs, nails, natural silk and connective tissues, contain scleroproteins. ▪ They are never present in plants. ▪ The main important groups of scleroproteins are: ✓ Keratins ✓ Collagens ✓ Elastins ✓ Reticulins  Keratins ▪ Keratin is a typical fibrous protein. ▪ It consists of long polypeptide chains. ▪ Keratins are present in ✓ hairs, nails and superficial layer of the skin. ✓ They form the intermediate filaments of the cytoskeleton in the epithelial cells. ▪ Keratins are highly insoluble compounds. ✓ They are insoluble in all protein solvents, and are not digestible by proteolytic enzymes. ▪ The sulfur content of keratin is high. It is present in the form of cystine, which is responsible for the stability and insolubility of keratins.  Collagens ▪ They are present in white fibrous connective tissues, tendons and bones. ▪ They form about 30% of total body protein. ▪ Collagen molecules consist of 3 polypeptide chains, ✓They are twisted around each other forming triple helix molecule. ✓They are held together by hydrogen bonds. ✓Each helical turn contains only 3 amino acids. ▪ There are 19 types of collagen formed of different combinations of 30 type of subunits (polypeptides). ▪ Collagen is rich in glycine, proline and hydroxy proline but low in sulfur containing amino acids. ▪ Glycine, proline and hydroxy proline form about 2/3 of the total amount of amino acids present in the collagen molecule. ▪ Collagen is low biological value protein, because of ✓its high content of glycine and ✓it is deficient in tryptophan. ▪ When Collagen is boiled for a long time with water, it changes to gelatin. Thus, gelatin is a derived protein obtained from the partial hydrolysis of collagen  II. Conjugated proteins ▪ They are simple proteins combined with a non-protein group called prosthetic group. So on hydrolysis, they give amino acids and prosthetic group. ▪ They include: ✓ Phosphoproteins: as in casein (milk), vitellin (egg yolk). ✓ Lipoproteins. As in VLDL, HDL. ✓ Glycoproteins. ✓ Metalloproteins. As in Trasnferrin & ferritin (Iron binding proteins) ✓ Chromoproteins. As in hemoglobin  III. Derived Proteins ▪ They include: ✓ Primary derived proteins: Denatured protein: e.g., coagulated albumin or globulin or gelatin ✓ Secondary derived proteins : Hydrolytic product of protein: e.g. Protein  Proteoses  Peptone  Polypeptide. 1. Nutritional role: Provide the body with essential amino acids, nitrogen and sulfur. 2. Catalytic role: All enzymes are proteins in nature. 3. Hormonal role: Most of hormones and all cellular receptors are protein in nature. 4. Defensive role: The antibodies (immunoglobulins) that play an important role in the body’s defensive mechanisms are proteins in nature. 5. Osmotic pressure Plasma proteins are responsible for most effective osmotic pressure of the blood. 6. Transport role: Proteins carry lipids in the blood, hormones, e.g., thyroid hormones and minerals, e.g., calcium, iron and copper. Hemoglobin (a chromo- protein) carries O2 from the lung to tissues is a protein. 7. Structural role: Proteins are the main structural component in bone, muscles cyto-skeleton and cell membrane. 8. Blood clotting: coagulation factors are proteins. 9. Control of gene expression: Most factors required for DNA replication transcription and mRNA translation are protein in nature Which amino acid can form disulfide bonds? a- Glycine b- Proline c- Glutamate d- Cysteine Which of the following pairs of amino acids might contribute to protein conformation by forming electrostatic interactions? a- Glycine and leucine b- Glutamate and lysine c- Phenylalanine and tyrosine d- Lysine and arginine The highest concentration of cystine can be found in: a- Melanin b- Keratin c- Collagen d- Myosin Glycine and proline are the most abundant amino acids in the structure of: a- Hemoglobin b- Myoglobin c- Insulin d- Collagen Keratin is a derived protein a- True b- False