Protein Chemistry Lecture Notes PDF

SHORT NOTES ON PROTEIN CHEMISTRY FOR FIRST YEAR STUDENTS OF COLLEGE OF DENTISTRY BY: Prof.DR. Azza Mohamed kamel abdu allah  Structure and Functions of Proteins Nature of proteins: ❑Proteins are large molecules ❑They are linear unbranched polymers formed of 20 differen...

SHORT NOTES ON PROTEIN CHEMISTRY FOR FIRST YEAR STUDENTS OF COLLEGE OF DENTISTRY BY: Prof.DR. Azza Mohamed kamel abdu allah  Structure and Functions of Proteins Nature of proteins: ❑Proteins are large molecules ❑They are linear unbranched polymers formed of 20 different -amino acids Functions & Biomedical Importance of Proteins 1. Proteins are the most abundant and multifunctional molecules in living systems 2. Most of enzymes are proteins 3. Polypeptide hormones e.g. Insulin and Growth hormone direct and regulate metabolism in the body 4. Cellular receptors that recognize hormones and neurotransmitters are proteins 5. Contractile proteins in muscle permit movement 6. In bone, the protein collagen forms a framework for the deposition of calcium phosphate crystals 7. Control of genetic expression: ❑Repressor molecules that suppress certain DNA sequences are proteins ❑ Initiation and termination factors which serve in transcription and translation phases of gene function are proteins 8. In the bloodstream, proteins, such as hemoglobin carries O2 and plasma albumin, carries molecules essential to life, whereas immunoglobulins proteins fight infectious bacteria and viruses  Functions & Biomedical Importance of Amino Acids 1. There is over 300 naturally occurring amino acids but only 20 amino acids constitute the monomer units of proteins. 2. Only L- α -amino acids are the monomer units occur in proteins 3. L-α-amino acids and their derivatives participate in some cellular functions e.g.: a) Nerve transmission e.g. glutamate, serotonine & dopamine b) Biosynthesis of porphyrins, purines, pyrimidine and urea c) Thyroid hormones and adrenaline are synthesized from tyrosine d) Some hormones, hormone-releasing factors, neuromodulators, or neurotransmitters are peptides  Amino Acids Structure and Properties ❑An amino acid is composed of an amino group + α carboxyl group attached to a carbon atom called -carbon with a distinctive side chain Classification of Amino Acids A. Classification of Amino Acids Based on Chemical Structure: B. Classification of Amino Acids Based on Nutritional Requirements: Essential amino Partially essential amino Non-essential amino acids acids acids 1. Isoleucine 1. Arginine 1. Alanine 2. Leucine 2. Histidine 2. Aspartic acid 3. Lysine 3. Asparagin 4. Methionine 4. Cysteine 5. Phenylalanine 5. Glutamic acid 6. Threonine 6. Glutamin 7. Tryptophan 7. Glycine 8. Valine 8. Proline 9. Serine 10.Tyrosine C. Classification of Amino Acids Based on Metabolism (Metabolic Fate): ❑ The carbon skeleton of amino acids can serve as a precursor for the synthesis of glucose (glycogenic) or fat (ketogenic) or both. 1. Glucogenic amino acids: ❑ These amino acids serve as precursors of gluconeogenesis (for glucose or glycogen synthesis) ❑ Glycine, Alanine, Methionine, Aspartic acid 2. Ketogenic amino acids: ❑ These amino acids breakdown to form ketone bodies for fat synthesis. ❑ Leucine and Lysine 3. Glucogenic and ketogenic amino acids: ❑ These amino acids breakdown to form precursors for both ketone bodies (fats) and glucose. ❑ Isoleucine, Phenylalanine, Tryptophan and Tyrosine  General Reactions of Amino Acids I. Reactions Due to Carboxyl Group A. Decarboxylation: The amino acids will undergo alpha decarboxylation to form the corresponding amine producing some important amines. For example: 1) Histidine → Histamine + CO2 2) Tyrosine → Tyramine + CO2 3) Tryptophan → Tryptamine + CO2 4) Lysine → Cadaverine + CO2 5) Glutamic acid → Gamma amino butyric acid (GABA) + CO2 B. Amide Formation: ❑The -COOH group of dicarboxylic amino acids (other than alpha carboxyl) can combine with ammonia to form the corresponding amide. For example: Aspartic acid + NH3 → Asparagine Glutamic acid + NH3 → Glutamine ❑ These amides are also components of protein structure. The amide group of glutamine serves as the source of nitrogen for nucleic acid synthesis. II. Reactions Due to Amino Group A. Transamination: ❑ The alpha amino group of amino acid can be transferred to alpha keto acid to form the corresponding new amino acid and another alpha keto acid. ❑This is an important reaction in the body for the inter-conversion of amino acids and for synthesis of non-essential amino acids. B. Oxidative Deamination: ❑ The alpha amino group is removed from the amino acid to form the corresponding keto acid and ammonia ❑ In the body, Glutamic acid is the most common amino acid to undergo oxidative deamination.  Importance of Amino Acid Derivatives 1. Gamma amino butyric acid (GABA) ❑ It is a neurotransmitter derived from glutamic acid. 2. Hydroxyproline and hydroxylysine: ❑ They are present in collagen and gelatin helping cross linkage which make these proteins strong. 3. Histamine ❑ It synthesized from histidine, and it is the mediator of allergic reactions. 4. Thyroxine (synthesized from tyrosine) is an important thyroid hormone.  The peptide bond ❑It is the bond formed between the -carboxyl group of one amino acid and the -amino group of another, with removal of one molecule of H2O ❑This process needs energy (Endergonic)  Peptides and Polypeptides ❑ Joining amino acid residues together with peptide bonds produces polypeptide chains and proteins. ❑ Peptides are distinguished from proteins on the basis of size, as peptides contain approximately 50 or fewer amino acids. ❑ Smaller peptides are present and are biologically important e.g. 1. Glutathione (3 amino acids) consists of -glutamyl:::cysteinyl:::glycine (glu-cys-gly) 1. Vasopressin also called antidiuretic hormone (ADH) (9 amino acids) 2. Glucagon (29 amino acids)  Biological Value of Proteins I. Nutritionally Rich Proteins: ❑ They contain all the essential amino acids ❑They are called High Biological Value Proteins e.g., casein of milk and animal meat II. Nutritionally Poor Proteins: ❑ They lack one or more essential amino acids ❑They are called Low Biological Value Proteins e.g., gelatin and vegetable proteins e.g., zein present in corn lack tryptophan and lysine  Classification of Proteins A.Classification based on functions: 1) Catalytic proteins e.g., enzymes 2) Structural proteins e.g., collagen, elastin 3) Contractile proteins e.g., myosin, actin 4) Transport proteins e.g., hemoglobin, albumin, transferrin 5) Regulatory proteins or hormones e.g., ACTH, Insulin, growth hormone 6) Genetic proteins e.g., histones 7) Protective proteins e.g., immunoglobulins, interferon, clotting factors B. Classification based on composition and solubility: I. Simple proteins contain only amino acids e.g.: 1. Albumin: 2. Globulins: a. Coagulable by heating a. Coagulable by heating b. Soluble in water b. Insoluble in water c. Examples: serum albumin, lactalbumin c. Examples: serum globulin and egg albumin 4. Globin: a. It is rich in histidine and lysine 3. Histones: b. It combines with heme to form a. Non coagulable by heating hemoglobin in RBCs b.Soluble in water c. Rich in lysine and arginine (basic 5. Sclero-proteins (fibrous proteins): amino acids) a. They have supportive and protective d.Present with nucleic acid in the cell function b. Examples: collagen, keratin, and elastin II. Conjugated proteins: ❑ They contain amino acids + non-protein part e.g. 1) Glycoproteins contain carbohydrates e.g., blood group antigens and mucin 2) Lipoproteins contain lipids e.g., VLDL, LDL and HDL 3) Nucleoproteins are proteins attached to nucleic acids e.g., histones 4) Chromoproteins are proteins with colored non protein part e.g., hemoglobin 5) Phosphoproteins contain phosphate groups e.g., casein of milk 6) Metalloproteins contain metal ions e.g., hemoglobin contains iron, tyrosinase contains copper, carbonic anhydrase contains zinc 7) Derived proteins: proteins derived by hydrolysis or denaturation of other proteins e.g., coagulable egg albumin  Protein Structure Levels of Protein Structure: ❑There are four levels of protein structures: primary, secondary, tertiary and quaternary structure (may not present in every protein) 1. Primary Structure of Proteins ❑The primary structure of a protein is its linear sequence of its amino acids formed by peptide bonds and also the location of any disulfide (-S-S-) bonds ❑Denaturation of the protein does not alter the primary structure  2. Secondary Structure of Proteins It results from folding of polypeptides into structures such as: A. α-Helix B. β-Pleated sheet A. α-Helix Structure: ❑ It is the most common and stable structure for a polypeptide chain ❑ The alpha helix is a rod-like structure in which the polypeptides form spiral structure where the peptide bonds form the backbone, and the side chains of amino acids extend outside ❑ The alpha helix structure is maintained by hydrogen bonds between peptide bonds near to each other B. The β-pleated sheet secondary structure of protein ❑β-pleated sheet are adjacent polypeptide chains either run in opposite directions (antiparallel) or run in the same direction (parallel) ❑The β-pleated sheet structure is maintained by hydrogen bonds between peptide bonds in 2 adjacent polypeptide chains  3. Tertiary Structure of Proteins ❑ It describes the three-dimensional structure and final confirmation of a single polypeptide chain ❑ -helices and -sheets of the secondary structure are folded (arranged) in domains ❑ The protein molecule may contain one or more domains ❑ These domains are the shape suitable for a protein function e.g., catalytic site of an enzyme, binding a receptor etc. ❑ Correct domain formation is necessary for proteins to perform their functions  4. Quaternary Structure of Proteins ❑ Quaternary structure is the assembly of several protein units together. ❑Complexes of two polypeptides called a dimer while complexes of more polypeptides (multiple subunits) are called multimers. ❑Multimers made up of identical subunits are referred to with a prefix of "homo-" e.g., CK-MM and LD (HHHH) while those made up of different subunits are referred to with a prefix of "hetero-" e.g., hemoglobin molecule consists of 2 α-subunits and 2 β- subunits ❑ The protein will lose its function when the subunits are separated  Denaturation of proteins ❑Protein denaturation means loss of secondary, tertiary and quaternary structures ❑The primary structure is preserved due to stable peptide bonds Causes of denaturation Results of protein denaturation 1. High temperature 1.Loss of catalytic activity of enzymes 2. High pressure 2.Loss of biological functions of hormones 3. Vigorous shaking 4. Strong acids and 3.Decreased solubility alkalis 4.Increased viscosity 5. UV light and 5.Increased digestibility e.g., cooking meat & irradiation eggs by boiling 6. X- ray  Fibrous Proteins ❑Fibrous protein has a rod-like shape ❑They are water insoluble ❑They have structural and supportive functions ❑Examples are collagen, elastin, and keratins