Protein Chemistry PDF

Protein Chemistry Protein Chemistry Introduction - Proteins are the most abundant and functional molecules in living systems. - Proteins are organic nitrogenous substances formed of amino acids linked together by peptide linkage. - Every life process depend...

Protein Chemistry Protein Chemistry Introduction - Proteins are the most abundant and functional molecules in living systems. - Proteins are organic nitrogenous substances formed of amino acids linked together by peptide linkage. - Every life process depends on this class of molecules, for example: Enzymes and polypeptide hormones direct and regulate metabolism in the body. Contractile proteins in muscle permit movement. In bone, the protein collagen forms a framework for the deposition of calcium phosphate crystals. In the bloodstream, proteins, such as hemoglobin and plasma albumin, transporter molecules essential to life. Immunoglobulins fight infectious bacteria and viruses. I. Amino Acids Amino acids are the building units of proteins. 1. Structure of the amino acids In nature, there are more than 300 different amino acids have been described, however, only 20 of them are commonly found as constituents of mammalian proteins. Amino acids are characterized by having a basic nitrogenous group, generally an amino group (- NH2), and an acidic carboxyl unit (-COOH). Most amino acids occurring naturally in proteins are α amino acid, in which NH2 is attached to the α – carbon. At physiologic pH (approximately pH = 7.4+ 0.03), the carboxyl group is dissociated, forming the negatively charged carboxylate ion (-COO-), and the amino group is protonated (-NH3+). 44  Protein Chemistry 2. Classification of amino acids: Many methods are used to classify amino acids. The most common are chemical, nutritional and metabolic classifications. 1. Chemical classification. 2. Nutritional classification. 3. Metabolic classification. I. Chemical classification According to chemical structure of the amino acids: A. Aliphatic amino acids. B. Aromatic amino acids. C. Heterocyclic amino acids. D. Imino acid A. Aliphatic amino acids: The side chain (R) is aliphatic side chain, these again can be subdivided according to their content of NH2 (basic) and COOH (acidic) groups into: I. Aliphatic neutral amino acids: which contain one NH2 and one COOH II. Aliphatic acidic amino acids: which contain one NH2 and two COOH III. Aliphatic basic amino acids: which contain one COOH and more than one NH2 I. Aliphatic neutral amino acids: They include glycine, alanine, serine, threonine, cysteine, cystine, methionine, valine, leucine and isoleucine. N.B. Serine and threonine are called hydroxyl amino acids. Cysteine and methionine are called sulfur containing amino acids. Cystine is dicysteine. Valine, leucine and isoleucine are called branched amino acids 45  Protein Chemistry II. Aliphatic acidic amino acids: They include aspartic and Glutamic. III. Aliphatic basic amino acids: They include lysine and Arginine. 46  Protein Chemistry B. Aromatic amino acids: The R contains benzene ring. They include phenylalanine, tyrosine and tryptophan. C. Heterocyclic amino acid: The R contains heterocyclic ring. It includes histidine. D. Imino and amino acids: 1. Imino acids: Proline and hydroxyproline. 2. Amino acids: Rest of amino acids. II. Nutritional classification Amino acids are classified into 3 groups: 47  Protein Chemistry A. Essential (indispensable) amino acids: - These are amino acids that cannot be formed in the body. They are essential to be taken in diet. - They are important for growth, health and protein synthesis. - They include: valine, leucine, isoleucine, lysine, phenylalanine, tryptophan, methionine and threonine. B. Semi-essential (half essential) amino acids: - These amino acids are formed in the body in amount enough for adults, but not for growing children. They include: arginine and histidine. C. Nonessential (dispensable) amino acids: - These are formed in the body in amount enough for adults and growing children. They need not be taken in diet. - They include glycine, alanine, serine, cysteine, tyrosine, glutamate, glutamine, aspartate, asparagine and proline. III. Metabolic classification Amino acids in the body are catabolized by different methods, whereby, NH2 is removed in the form of ammonia (NH3) and the carbon skeleton is converted either to glucose or ketone bodies. So amino acids are classified into: A. Glucogenic amino acids: which give glucose in the body. B. Ketogenic amino acids: which give ketone bodies. Leucine is the only purely ketogenic amino acid. C. Glucogenic and ketogenic: They give both glucose and ketone bodies. They are phenylalanine, tyrosine, tryptophan, lysine and isoleucine. Optical properties of amino acids - The Presence of asymmetric carbon atom, accepts the amino acid an optical activity and an optical isomerism. - All amino acid, except glycine, have asymmetric α-carbon atom. 48  Protein Chemistry - [Note: Glycine is the exception because its α-carbon has two hydrogen substituents and, therefore, it is optically inactive.] - Amino acids that have an asymmetric α -carbon can exist in two forms, designated D and L, that are mirror images of each other. Acidic and basic properties of amino acids - Amino acids in aqueous solution can act as a weak acid, as it contains α-carboxyl group (-COO-) and weak base, as it contains α-amino group (-NH3+). - Note: Acid is a proton donor, while base is a proton acceptor. - Thus, free amino acids can act as buffers. Peptide Bond Formation: - As both the amine and carboxylic acid groups of amino acids can react to form peptide bond and a molecule of water. - It Is a covalent bond formed between the carboxyl group of one amino acid and the amino group of another. - It Is formed by removal of water. 49  Protein Chemistry - Peptide formation needs energy, getting from hydrolysis of a high energy phosphate compound e.g. ATP. - II. Peptides Peptides are compounds formed of less than 50 amino acids linked together by peptide bonds. Dipeptide (2 amino acids, one peptide bond) Tripeptide (3 amino acids, two peptide bonds) Oligopeptide (4-10 amino acids) Polypeptide (11-50 amino acids) At one end of the peptide chain, there is a free NH2 group (to the left side) and at the other end, there is free COOH (to the right side), called N-terminal and C-terminal respectively. Biologically Active Peptides Peptides include many active compounds as: 1- Hormones: Insulin and glucagon from pancreas. 50  Protein Chemistry Vasopressin and oxytocin from posterior pituitary gland. Adrenocorticosteroid hormone (ACTH) from anterior pituitary gland. 2- Bradykinin: Potent smooth muscle relaxant. It causes vasodilation and hypotension. 3- Antibiotics: e.g. valinomycin. 4- Glutathione: It is a tripeptide formed of glutamic, cysteine and glycine (γ glutamyl- cysteinyl – glycine). It is abbreviated as: G-SH. Functions of glutathione: The main function performed by glutathione is ability to lose and accept hydrogen 2GSH GS-SG Reduced Oxidized It protects the cells and RBCs against damage due to H2O2 generated during aerobic metabolism. H2O2 + GSH H2O + GS - SG It plays a role in the transport of amino acids across the intestinal membrane (absorption of amino acids). Defense mechanism against toxic drugs and carcinogens. Inactivation of insulin hormone. 51  Protein Chemistry Clinical uses of glutathione supplements: - Preventing aging. - Treating or preventing cancer and heart disease, hepatitis, liver diseases. - In diseases which impair the body defense system e.g., AIDS. - Alzheimer's, memory loss and osteoarthritis A. Aspartame: It Is a dipeptide (aspartic acid and phenylalanine) that serves as sweetening agent. It Is used In replacement of cane sugar. III. Proteins Proteins are macromolecules formed of repeated units of L-α-amino acids amino acids. Proteins may be classified according to their functional roles into: ▪ Regulatory proteins: enzymes, hormones and DNA binding protein. ▪ Transporter proteins: hemoglobin and albumin. ▪ Storage proteins: ferritin and myoglobin. ▪ Structural proteins: collagen and proteoglycans. ▪ Protective proteins: blood clotting factors and immunoglobulins. ▪ Contractile proteins: actin and myosin of the muscle. Proteins may be also classified according to their shapes into: A. Globular proteins: They have a spherical form, the ratio of the length to the width is less than 10, for example hemoglobin. B. Fibrous proteins: They have rod like structure, the ratio of the length to the width is more than 10, e.g. collagen and elastin. 52  Protein Chemistry Structure of Proteins Proteins are formed of 20 amino acids; these amino acids are linked together by peptide bonds. Each protein in its native state, has three-dimensional structure (primary, secondary, tertiary), which is known ''conformation''. Proteins which are formed from more than one polypeptide chain have additional quaternary structure. A. Primary structure of protein: - The sequence of amino acids in a protein is called the primary structure of the protein. - The sequence of amino acids, in a primary structure, is destined by the sequence of nucleotides in DNA. The force stabilizes the primary structure is peptide bond. Naming the peptide: - For a peptide chain, the free amino end (N-terminal) is written to the left and the free carboxyl end (C- terminal) is written to the right. - In the peptide chain, the amino acid sequence is read from N-terminal to C-terminal. B. Secondary structure of proteins: Further folding of polypeptide backbone into α- helix or β- sheets is known as secondary structure. - The bond stabilizes the secondary structure is the hydrogen bond. 1. α- helix. - The α- helix is the most common type of secondary structure. - It is a spiral structure, consisting of a coiled polypeptide backbone core. 53  Protein Chemistry - An α- helix is stabilized by extensive hydrogen bonds extend up the spiral from the carbonyl oxygen of one peptide bond to the -NH- group of a peptide linkage four residues ahead in the polypeptide. - Hydrogen bonds are individually weak, but extensive number of hydrogen bonds stabilize the helix. - Example: Myosin, Keratin, Myoglobin and Hemoglobin. - The α- helical structure may be further arranged in a fibrous form, as in keratin, or a globular form as in myoglobin. 2- β- sheets - It is another form of secondary structure in which the surfaces of β -sheets appear "pleated”. The β -sheet can be formed from two or more separate polypeptide chains or segments of polypeptide chains that are arranged parallel or antiparallel to each other. Example: Skin Fibers or Fibroin. C. Tertiary structure of proteins Final folding of the polypeptide chain to take its final shape of protein, either globular or fibrous form, is known as tertiary structure. - Polypeptide chains that are greater than 200 amino acids in length generally consist of two or more domains. - The primary structure of a polypeptide chain determines its tertiary structure. There are 2 types: 1. Fibrous: form long rodlike filaments, are relatively inert or water-insoluble, and provide structural support in the extracellular environment. 54  Protein Chemistry e.g., collagen, elastin and ß keratin. 2. Globular: are spherical in overall shape. They are usually water-soluble, possessing many hydrophilic amino acids on their outer surface, facing the aqueous environment. More nonpolar amino acids face the interior of the protein, providing hydrophobic interactions to further stabilize the globular structure. e.g., troponin, albumin, globulin and myoglobin. Interactions stabilizing tertiary structure The unique three-dimensional structure of each polypeptide is determined by its amino acid sequence. Interactions between the amino acid side chains guide the folding of the polypeptide to form a compact structure. - Four types of interactions cooperate in stabilizing the tertiary structures of globular proteins. 1. Disulfide bonds: -A disulfide bond is a covalent linkage formed from the sulfhydryl group (-SH) of each of two cysteine residues, to produce a cystine residue. These strong, covalent bonds help stabilize the structure of proteins, and prevent them from becoming denatured in the extracellular environment. 2. Hydrophobic interactions: - Amino acids with nonpolar side chains tend to be located in the interior of the polypeptide molecule, where they associate with other hydrophobic amino acids. In contrast, amino acids with polar or charged side chains tend to be located on the surface of the molecule in contact with the polar solvent. 3. Hydrogen bonds: 55  Protein Chemistry 4. Ionic interactions: Negatively charged groups, such as the carboxyl group (-COO-) in the side chain of aspartate or glutamate, can interact with positively charged groups, such as the amino group (- NH3+) in the side chain of lysine. D. Quaternary structure of proteins Many proteins consist of a single polypeptide chain, and are defined as monomeric proteins. However, others may consist of two or more polypeptide chains that may be structurally identical or totally unrelated. The arrangement of these polypeptide subunits is called the quaternary structure of the protein. Note: If there are two subunits, the protein is called "dimeric", if three subunits "trimeric", and, if several subunits, "multimeric."] Protein subunits are held together by noncovalent interactions (for example, hydrogen bonds, ionic bonds, and hydrophobic interactions). Examples of proteins having the quaternary structure: Hemoglobin: the oxygen carrying protein of the blood contains 4 subunits ''tetramer'' (two α and two β subunits) arranged in the form, α2β2. 56  Protein Chemistry Insulin''dimer'':2 subunits lactate dehydrogenase ''tetramer:4 subunits Creatine kinase ''dimer'': 2 subunits Denaturation of proteins It is a change of protein from its native form. Protein denaturation means unfolding and disorganization of the protein due to disruption of its secondary, tertiary and quaternary structures with loss of biological activity of protein. Native protein: is the protein whose chemical structure, amino acid sequences secondary, and quaternary structure are not changed from the natural state. Causes: A- Physical factors: Heat. U.V rays and X-rays and ultrasound. High pressure. Repeated freezing and thawing. B. Chemical factors: Strong acid, alkali Alcohol Acetone Salts of heavy metals. They form ionic bond with negative charged ions on proteins molecules, so the electrostatic bonds are disrupted e.g. Hg, Pb, Ag. 57  Protein Chemistry Irradiation. Digestive enzymes. Effects of protein denaturation: - Increase viscosity. - Decrease solubility. - loss of biological activity - loss of antigenicity. Desaturated proteins cannot induce antibody formation when injected. - Increased digestibility by proteolytic enzymes. IV. Classification of Proteins Proteins can be classified on the basis of: 1. Nutritional value. 2. Chemical composition and properties. 1. Classification according to nutritional value A. High biological value proteins: Contain high amounts of essential amino acids and easily digested e.g., meat, milk, fish, poultry, and liver. B. Low biological value proteins: Deficient in essential amino acids and not easily digested e.g., collagen and plant proteins. 2. Classification according to chemical composition and properties: A. Simple proteins. B. Conjugated proteins. C. Derived proteins. A. Simple proteins Simple proteins are defined as those proteins, which on hydrolysis yield only amino acids or their derivatives and they include: 58  Protein Chemistry 1- Albumins The albumins are soluble in water and coagulated by heat. Examples include egg albumin, myosin of muscle, serum albumin of blood, lactalbumin of milk. Albumin functions: - carrier of some mineral as calcium and free fatty acids. - responsible for osmotic pressure of blood, low albumin level leads to escape of water to extracellular space, a condition named edema 2- Globulins The globulins are insoluble in pure water and are heat coagulable. Examples include ovoglobulin of egg yolk, serum globulin of blood, phaseolin of beans and peas. Globulins functions: - Serum globulin of blood is responsible for transport of bilirubin and steroid hormones in blood. 3- Globins (histones) and protamines: Both are basic proteins i.e., rich in basic amino acids. Globin protamine Type of basic amino acid Histidine Lysine and arginine Solubility salt solution salt solution & ethanol (70%) Sources: - Combined with DNA to form - In fish, combined with DNA nucleoproteins. to form nucleoprotein. - Combined with heme form hemoglobin. 4- Gliadins and glutelins: - Both are acidic proteins i.e., rich in acidic amino acids: glutamic acid. - Both are present in cereals. - Both are soluble in diluted acids and alkalis. - Gliadins also soluble in 70% ethanol. 59  Protein Chemistry 5- Scleroproteins (Albuminoids): They include: keratin, collagen, elastin and reticulin. 1. α- Keratins: a) Location: They are found in hair, nail, enamel of teeth and outer layer of skin. b) Structure: - They are α- helical polypeptide chains. - They are rich in cysteine (which provides disulfide bonds between adjacent polypeptide chains). c) Functions: Keratin is a tough fibrous protein that strengthens skin, hair and nails with its tight strands. d) Solubility: It is insoluble due to their high content of hydrophobic amino acids. 2. Collagens: a) Types of collagens: - There are more than 12 types of collagens. In human body type I constitute 90% of cell collagens. - Collagens form about 30% of total body proteins. b) Location: - It Is the protein of connective tissue present in skin, bones, tendons and blood vessels. - Collagen may be present as a gel e.g. in extracellular matrix or in vitreous humor of the eye. c) Functions: - Collagen provides the framework for various organs such as the kidneys and lymph nodes. 60  Protein Chemistry - Collagen also gives great support and strength to structures such as the bones, tendons and blood vessels. d) Structure of collagen: - Collagen molecules are simple protein, consist of 3 a polypeptide chains. - They are held together by hydrogen bonds. - Each chain is about 300 nm in length and 1.5 nm in diameter. - Each chain is formed of 1050 amino acids. Amino acids composition: Collagen contains 33% glycine (the smallest amino acid), 10% proline, 10% hydroxy proline and 1% hydroxylysine. Every third amino acid in the α- chain is glycine. Collagen molecule has very firm structure due to: - Each helical turn contains only 3 amino acids. For other proteins, each turn contains 3.6 amino acids. - Glycine (the smallest amino acid) forms 33% of total molecule. This makes the polypeptide chains compact. - The high content of hydroxyproline and hydroxylysine increase the number of hydrogen bonds. Collagen synthesis: - Collagens are formed by connective tissue cells called fibroblasts. - Intracellular location: The polypeptide chains of preprocollagen are synthesized on the rough endoplasmic reticulum, where preprocollagen is cleaved to Procollagen + Signal (pre) sequence. - Proline and lysine residues are hydroxylated by a reaction that requires O2 and vitamin C. - Glycosylation: by glucose and galactose that added to hydroxylysine residues. - The procollagen (In the form of triple helix) Is secreted from the cell and cleaved to Collagen. - Cross links are produced. Solubility and denaturation: - Solubility: Collagen is insoluble in all solvents. It is protein of low biological value and not digestible. - Denaturation: 61  Protein Chemistry 1- When collagen is heated, it loses all of its structure. The triple helix unwinds and the chains are separated. Then when this desaturated mass cools down, it soaks up all the surrounding water like sponge, forming gelatin. ii- Gelatin is soluble in water and digestible. Gelatin is given for patients during convalescence (in the form of jelly). h) Collagen diseases: (Scurvy): It is due to a deficiency in ascorbic acid (vitamin C). 62  Protein Chemistry 3. Elastin: a) Characters: It is connective tissue protein. It is rubber like i.e., it can be stretched to several times as their normal length, but recoil to their original shape when the stretching force is relaxed. b) Location: It is present in lungs, the walls of large blood vessels and elastic ligaments. c) Structure: - Elastin is formed of 4 polypeptide chains. - Elastin is similar to collagen, being rich in glycine (1/3 of its amino acids) and proline. It is poor in hydroxyproline and hydroxylysine. - The 4 polypeptide chains interconnected through their lysine residues. The 4 lysine residues are linked together to form a cyclic structure termed: desmosine. Elastin is capable of undergoing 2-way stretch, due to its content of desmosine. 63  Protein Chemistry Functions: Elastin is a protein that coil and recoils like a spring within the elastic fibers of connective tissue and accounts for the elasticity of structures such the lungs, blood vessels and ligaments. Role of α-1-antitrypsin (α-1-AT) in elastin degradation: - α-1-antitrypsin an enzyme produced mainly by liver. It Is also produced by blood cells monocytes and macrophage. - It Is present in blood and other body fluids. - It Inhibits a number of enzymes and destroys proteins. · - Role of α-1-AT in the lungs: in the normal lung, the alveoli are exposed to low levels of elastase enzyme released from neutrophils. Their proteolytic activity can destroy the elastin in alveolar walls. This elastase enzyme activity is inhibited by α-1-antitrypsin. Deficiency of α-1-antitrypsin: Leads to destruction of connective tissue of alveolar walls by neutrophils elastase. This leads to lung disease called emphysema. Elastin and William’s syndrome. Williams syndrome (WS), also known as Williams–Beuren syndrome (WBS), is a rare neurodevelopmental disorder characterized by: a distinctive, "elfin" facial appearance, along; and cardiovascular problems, such as supravalvular aortic stenosis and transient high blood calcium. There deletion of elastin gene. 64  Protein Chemistry Patients with Williams syndrome has wide mouth with full lower lip. He had small, irregular, widely spaced, peg shaped primary teeth with extensive caries. These are the typical anomalies of primary teeth in Williams syndrome. In adulthood teeth tend to be crowded. B- Conjugated Proteins Conjugated or complex proteins are composed of simple proteins (Apoprotein) combined with some non-protein substance. The non-protein group is referred to as the prosthetic group. 1- Nucleoproteins The nucleoproteins are composed of simple basic proteins (protamins or histones) in combinations with nucleic acids. Examples: a) Chromosomes: These are proteins conjugated with DNA. b) Ribosomes: These are proteins conjugated with RNA. 2- Glycoproteins and proteoglycans. See carbohydrate chemistry chapter. 3- Chromoprotein The chromoproteins are composed of simple proteins united with a colored prosthetic group e.g., hemoglobin. 4- Phosphoproteins Phosphoric acid is linked to protein e.g. casein of milk and vitellin of egg yolk. 5- Lipoproteins: See lipid chemistry chapter. 6- Metalloproteins: According to the type of metal, they are classified into: a) Metalloproteins containing Iron: b) The iron may be in the form of heme or nonheme iron: 65  Protein Chemistry I. Heme Iron: Hemoglobin, myoglobin, and some enzymes as cytochromes, catalase, peroxidase, tryptophan pyrrolase). II. Nonheme Iron: - Ferritin: Is the storage form of iron, present in liver, spleen, bone marrow and intestinal cells. - Transferrin: Is the iron carrier protein in the plasma. - Hemosiderin: Formed as a result of Iron toxicity (over dosage)as in case of repeated blood transfusion. III. Metalloproteins containing copper: - Ceruloplasmin: Is plasma protein, responsible for the oxidation of ferrous ions (Fe'') into ferric ions (Fe"'). - Erythrocuprein: Present in red cells. - Hepatocuprein: Present in liver. - Cerebrocupreln: Present in brain. - Oxidase enzymes: Contain cupper e.g. cytochrome oxidase. IV. Metalloproteins containing zinc: - Insulin hormone. - Some enzymes e.g., carbonic anhydrase. V. Metalloproteins containing magnesium: - Some enzymes as kinase and phosphatase. VI. Metalloproteins containing selenium: - Glutathione peroxidase. C- Derived Proteins This class of proteins, as the name implies, includes those substances derived from simple and conjugated proteins. Derived proteins are subdivided into: Primary derived proteins: Denaturating proteins: 1- Coagulated albumin and globulins. 66  Protein Chemistry 2- Gelatin derived by. boiling of collagen. Secondary derived proteins: hydrolytic products of proteins The complete hydrolytic decomposition of a natural protein molecule into amino acids generally progresses through successive stages as follows: protein → metaproteins →proteose → peptone → peptides → amino acids. 67