Proteins Chapter 4 PDF

What are PROTEINS? An extraordinary number of different proteins, each with a different function, exist in the human body. A typical human cell contains about 9,000 different kinds of proteins, and the human body contains about 100,000 different proteins. Proteins are important for the synthe...

What are PROTEINS? An extraordinary number of different proteins, each with a different function, exist in the human body. A typical human cell contains about 9,000 different kinds of proteins, and the human body contains about 100,000 different proteins. Proteins are important for the synthesis of enzymes, certain hormones, and some blood components, for the maintenance and near of esisting issues, for the synthesis of new tissue, and sometimes for energy. GENERAL CHARACTERISTICS OF PROTEINS Proteins are the most abundant substances in nearly all cells next to water. They account for about 15% of a cell's overall mass. All proteins contain the elements carbon, hydrogen, oxygen, and nitrogen. The presence of nitrogen in proteins set them apart from carbohydrates and pids, which most often do not contain nitrogen. Other elements such as sulfur, phosphorus, and iron are essential constituents of certain spectailzed proteins. Casein, the main protein of milk, contains shophorus, an element which is very important in the e diet of infants and children. Hemoglobin, the oxygen transporting protein of blood, contains iron AMINO ACIDS: THE BUILDING BLOCKS OF PROTEINS An amino acid is an organic compound that contains both an amino (NH2) group and a carboxyl (- COOH) groups. The amine acids found in proteirs are always alpha amino acids. An alpha-amino acid Is an amino acid in which the amino group and the cartioxyl group are attached to the alpha a carbon atom. As with carbohydrates, it is traditional to use the D and I nomenclature with amino acids based on the configuration of glyceraldehyde. Naturally occurring amino acids generally have the same configuration as L-glyceraldehyde (S configuration at the alpha-carbon. GENERAL STRUCTURE OF AMINO ACIDS The general formula for alpha-amino acid is shown below: It is called an alpha-amino acid because both amino and carboxyl groups are attached to the alpha carbon atom. All of the 20 amino acids found in proteins have a common denominator: a carboxy group and an amino group bonded to the same carbon atom. The amino acids differ from each other in their side chains, or R groups, which vary in structure, size, electric charge, and solubility in water. Examination of the above formula discloses the fact that the alpha carbon atoms have 4 different groups attached to it (except for the case where R is H like glycine), so this carbon is asymmetric, and because of the presence of this asymmetric carbon atom, amino acids are capable of optical rotation, except glycine, because the phenomena of optical rotation is due to asymmetry. Amino acids are optically active molecules and asymmetry of their mirror images is not superimposable (except in the case of glycine where the R-group is hydrogen). GENERAL CHARACTERISTICS OF AMINO ACIDS Amino acids are colorless crystalline substances soluble in water and insoluble in organic solvent with a high melting point. Arginine Valine Alanine Lysine CLASSIFICATION OF AMINO ACIDS Various ways of classifying the amino acids on the basis of their R groups have been proposed. The most meaningful is based on their polarity, ie, their tendency to interact with water at biological pH (near pH 7.0). There are 5 main families of amino acids based on the polarity of their R-groups or side chains. Amino acids are classified on the basis of the structure of R. 1. Aliphatic side chains - hydrophobic 2. Polar side chains - text classifies as HO-, 5-, and amide containing – hydrophilic 3. Acidic - hydrophilic  4. Basic - hydrophilic 5. Heterocyclic/Aromatic - hydrophilic or hydrophobic ANOTHER WAY OF CLASSIFYING AMINO ACIDS A. Neutral amino acids - they are monoamine-monocarboxylic (with one as well as other substituents distinguish these amino acids from each other). 1. Straight-chain a) Glycine b) Alanine c) Serine d) Threonine 2. Branched-chain amino acids a) Valine. b) Leucine c) Isoleucine B. Aromatic amino acids - these consists of amino acids with phenyl hydroxyphenyl, or indole rings substituted on alanine. 1. Phenylalanine - contains the phenyl ring 2. Tyrosin - contains the hydroxyphenyl ring 3. Tryptophan - contains the indole ring C. Essentials and Non-essentials amino acids 1. Cysteine 2. Homocysteine 3. Methionine D. Basic amino acid 1. Lysine 2. Arginine 3. Histidine E. Acidic amino acids 1. Aspartic acid 2. Glutamic acid F. Imino acids - a molecule that contains both imine (CNH) and carboxyl (-C-C)-OH) functional groups 1. Proline 2. Hydroxyproline PHYSICAL PROPERTIES OF AMINO ACIDS 1. Solubility - amino acids exhibit a wide range of solubilities, in general, amino acids are minimally soluble at their isoelectric points. Those amino acids with longer aliphatic side chains are less solubile (eg, leu, lie, Val) than those with shorter chains (eg, Gly, Ala) polar groups such as carbonyl and hydroxyl, tend increase solubility. 2. Melting point - amino acids possess' high melting points, usually above 200°C 3. Tastes of amino acids - amino acids are usually sweet, tasteless, or bitter. Glycine, alanine, valine, and serine are sweet. Leucine in tasteless; isoleucine is bitter. 4. Appearance - the amino acids are white crystalline substance; the crystal from being characteristic for each one. 5. Ultraviolet absorption spectrum of aromatic amino acids - the aromatic amino acids tryptophan, tyrosine, and phenylalanine absorb ultraviolet light. Most of the UV absorption of proteins is due to their tryptophan content. 6. Optical properties of amino acids - the alpha carbon atoms of all the amino acids except glycine are asymmetric, so they show optical activity, The rotations of the amino acids vary according to the pli of the solution, which determines the lonic state of the amino acid. 7. Acid-base properties of amino acids - amino acids in aqueous solution are ionized and can act as acids or bases. Those amino acids having a single amino group and a single carboxyl group crystallize from neutral aqueous solutions in a fully ionized species called dipolar ion of zwitterion. These dipolar and negative charges. Below is the formula of zwitterion: Since the amino acids have both amino and carboxyl groups; they are amphoteric which means that they can react act either as an acid (proton donor) or a base (proton acceptor). Substances with amphoteric properties are called ampholytes. Amino acids may be either positively or negatively charged depending on the pH or hydrogen ion concentration of the environment. Isoelectric pH (pl or lpH) It is that characteristic pH which the amino acids have no net charge and is not attached to either electrode of the electrophoretic system. If the dipolar or zwitterions from an amino acid is titrated with an acid such as HCI, the following reaction takes place. The addition of an acid depresses the ionization of the carboxyl group, and the dipolar ion accepts a proton, thus placing a net positive charge on the amino acid molecule. CHEMICAL REACTIONS OF AMINO ACIDS The chemical reactions of the amino acids are relatively numerous because the different reactive groups that are present in the same molecule. The 3 important components which give the different amino acids their characteristic reactivities are the following: 1. The amino or NH2 group 2. The carboxyl or COOH group 3. The various R groups which identify them from one another Although we shall not examine all such organic reactions of amino acids, here are two important reactions that are widely used for the detection, measurement, and identification of amino acids: A. Ninhydrin reaction If a solution of an alpha amino acid is boiled with ninhydrin (triketohydrindene hydrate) a powerful oxidizing agent, carbon dioxide dioxide+ ammonia aldehyde is formed together with reduced ninhydrin. The reduced ninhydrin then reacts with the liberated ammonia, forming a purple product (ruhemann's purple). Proline and hydroxyproline will give a yellow color. The purple to blue color forms the basis of a quantitative test for &-amino acids. The intensity of color produced can be used to measure amino acid concentration calorimetrically. The visualization of amino acids on paper chromatography and the quantitative determination of amino acids after ion-exchange chromatography usually involve the ninhydrin reaction. B. Reaction with Sanger's reagent Sanger's reagent is 1-fluoro-2, 4-dinitrobenzene (FDNB). In mildly alkaline solution FDNB reacts with & amino acids to yields 2, 4-dinitrophenyl derivatives, useful in the identification of individual amino acids. Most of the DNP-amino acids are colored bright yellow. This reaction is important in determining the amino acids sequence of peptides. SPECIAL AMINO ACIDS PRESENT IN SOME PROTEINS 1. Hydroxyproline and hydroxylysine - found in the collagen of connective tissue 2. N-Methyllysine - found in myosin, a muscle protein functioning in contraction 3. Gamma-carboxyglutamic acid - found in the blood clotting protein prothrombin. 4. Desmosine - a derivative of lysine, found only in the fibrous protein elastin PEPTIDES Peptides are chains of amino acids. Two amino acid molecules can be covalently joined through a peptide bond, to yield a dipeptide. Such linkage is formed by removal of the elements of water from the carboxyl group of one amino acid and the alpha-amino group of the other by the action of strong condensing agents. Three amino acids can be joined by two peptide bonds in a similar manner to form a tripeptide; similarity, we have tetrapeptides and pentapeptides. When there are more than 10 amino acids joined in this fashion, the structure is called polypeptide. The amino acid units in a peptide are usually called residues. The amino acids residue at the end of the peptide having a free alpha amino group is the amino-terminal (also called N-terminal) residue; at the opposite end, the residue which has a free carboxyl group is the carboxyl-terminal (also C-terminal) residue. Peptides are named from the sequence of their constituent amino acids beginning from the N- terminal residue as amino acid number 1. Ser-gly-tyr-ala-leu (seryglycity rosin alanyl leucine) The above structure is a pentapeptide. The N-terminal amino acid residue is serine; the C-terminal residue is leucine; the 3d amino acid residue is tyrosine. Some Peptides with Biological Activity 1. Insulin - a hormone secreted by the B cells of the pancreas stimulates the capacity of cells to use glucose as a metabolic fuel. 2. Oxytocin - a hormone with 9 amino acid residues secreted by the posterior pituitary gland which stimulates uterine contractions. 3. Brakdykin - a substance that inhibits inflammation of tissues. 4. Enkephalins - a short peptide formed in the central nervous system; it binds to specific receptors in certain cells of the brain and induces analgesia, deadening of pain sensations. 5. Corticotrophin - a hormone of the pituitary gland that stimulates the adrenal cortex. Biological Functions of Proteins 1. Enzymatic catalysis - all known enzymes are proteins 2. Transport proteins - hemoglobin of red blood cells bind oxygen as the blood passes through the lungs and carries it to the peripheral tissues. 3. Nutrient proteins - examples are ovalbumin, the major protein of egg white and casein, the major protein of milk. 4. Storage proteins - ferritin of animal tissues stories iron. 5. Contractile proteins - actin and myosin are filamentous proteins function in the contractile system of skeletal muscle.. 6. Structural proteins - examples are: a) Collagen- the major component of tendons and cartilage; this fibrous protein has very tensile strength. b) Elastin - found in ligaments is a structural protein capable of stretching in two dimensions.  c) Keratin - a tough, insoluble protein found in hair, fingernails, and features. d) Fibrin - the major component of silk fibers and spider webs. 7. Defense proteins - examples are: a) Immunoglobulins or antibodies are specialized proteins by lymphocytes which can recognize and precipitate or neutralize invading bacteria, viruses, and other pathogenic microorganisms. b) Prothrombin and fibrinogen are blood-clotting proteins that prevent loss of blood when the vascular is injured. 8. Regulatory proteins - examples are polypeptides or peptide hormones that help regulate cellular or physiological activity. From the foregoing items, it is clear that proteins are among the most important substances which make up the human body, carrying out the regulation of almost every aspect of biological activity. Classification of Proteins This classification is based on the composition, physical and chemical properties of the proteins: I. Simple proteins - defined as those proteins which upon hydrolysis yield only amino acids or their derivatives. A. Albumin - soluble in water, coagulated by heat; deficient in glycine Examples: lactalbumin from milk, ovalbumin from the egg white. B. Globulins - insoluble in water, coagulated by heat; contain glycine Examples: ovoglobulin of egg yolk, serum globulin of blood. C. Glutelins - soluble in dilute acids and alkali, insoluble in neutral solvents; coagulated by heat Examples: glutamine of wheat, oryzenin of rice. D. Prolamines of gladins - they are soluble proteins; plant proteins found principally in seeds. Examples: zein of corn, gliadin of wheat E. Scleroproteins of Albumniods - the least soluble of all the proteins; insoluble in water, salt solutions, dilute acids and alkalies and alcohol. They are entirely animal proteins and are the chief constituents of exoskeletal structures such as hair, horn, hoofs and nails, and of the organic materials of cartilage and bones. They are the protein of supportive tissues. The two principal classes are collagens and keratins, Gelatin is a degenerated albuminoid. F. Histones - characterized by a high content of basic amino acids, they appear to occur in combination with the nucleic acid in the nuclei of the somatic cells of many organisms. Examples: histones of nucleoproteins, globin of hemoglobin. G. Protamines they are the simplest of the proteins and may be regarded as large polypeptides. They are strongly basic and yield chiefly basic amino acids upon hydrolysis, particularly arginine. Example: salmine of salmon sperm. II. Conjugated proteins - they are composed of simple proteins combined with some non-protein substance. The non-protein group is referred to as the prosthetic group. A. Nucleoproteins - the prosthetic group is a nucleic acid, they are the proteins of cell nuclei and apparently are the chief constituent of chromatin Example: nucleohistone B. Glycoproteins and mucoproteins - these are compounds with carbohydrate prosthetic group (mucopolysaccharides). The distinction between glycoproteins and mucoproteins is based on the amount of carbohydrates glycoproteins contain less 4% of carbohydrates in the molecule and mucoproteins contain more than 4%. C. Phosphoteins - the prosthetic group is phosphoric acid. Example: casein of milk D. Chromoproteins - composed of simple united with a colored prosthetic group, which is believed to be a pigment. Example: heme of hemoglobin E. Lipoproteins - simple conjugated to lipids such as phospholipids and cholesterol.  F. Metalloproteins - protein plus metallic elements such as Fe, Cu, Mn Example: copper of ceruloplasmin. IIL Derived proteins - these proteins include those substances formed from simple and conjugated proteins. This category includes the artificially synthesized protein-like compounds and those resulting from the decomposition of proteins. a. Primary derived proteins - those protein derivatives are formed by a process which causes only slight changes in the protein molecule and its properties. There is no hydrolytic cleavage of peptide bonds. They are synonymous with denatured proteins. 1. Proteins they are insoluble products formed by the incipient action of water, very dilute acids and enzymes. 2. Metaproteins - formed by further action of acids and alkalies upon proteins. 3. Coagulate proteins - they are insoluble products formed by the action of heat or alcohol upon natural proteins. b. Secondarily derived proteins - they are formed in the progressive hydrolytic cleavage of the peptide union of proteins molecules. 1. Proteases - they are hydrolytic products of protein which are soluble in water, not coagulated by heat. 2. Peptones - a product of further hydrolytic decompositions. They are of simpler structure than the proteases. 3. Peptides - a compound of 2 or more amino acids, either synthesized or resulting from the hydrolysis of proteins. Proteins can also be classified on the basis of their shape: 1. Globular proteins - is the kind of proteins wherein the peptide chain is tightly folded into compact spherical or globular shape. They are usually soluble in aqueous systems and diffuse readily; most have a mobile or dynamic function. Nearly all enzymes are globular proteins, as are blood transport proteins, antibodies and nutrient storage proteins. 2. Fibrous proteins - consist of polypeptide chains arranged in a parallel fashion along a single axis, to yield long fibers or sheets. They are physically tough and are soluble in water or dilute salt solutions, They are the basic structural elements in the connective tissue of higher animals Examples are collagen of tendons of bone matrix, & -keratin of hair skin, nails, and features and elastin of elastin connective tissues. Bonds Responsible for Protein Structure Protein structures are stabilized by 2 dasses of strong bonds (peptide and disulfide) and 2 classes of weak bonds (hydrogen and hydrophobic). 1. Peptide bonds - the primary structure of proteins derives ultimately from the linkage or alpha amino acids by peptide bonds. 2. Disulfide bonds - the disulfide bond may interconnect 2 parallel peptide chains through cysteine residues within each polypeptide. This is relatively stable and is not really broken under the usual conditions of denaturation. 3. Hydrogen bonds - the hydrogen bond results from the sharing of hydrogen atoms between the nitrogen and the carbonyl oxygen or different peptide bonds. These may be contributed by amino acid residues in the name or different polypeptide chains. 4. Hydrophobic bonds - the non-polar side chains of neutral amino acids tend to nonstoichiometric; hence no true bond may be said to exist so that it is better called hydrophobic interaction. 5. Electrostatic or ionic bonds - these are salt bonds formed between oppositely charged groups in the side chains of amino acids. Levels of Structural Organizations of Proteins Levels of Structural Organizations of Proteins A. Primary structure of proteins This is concerned with the quantitative amino acid composition (i.e., the number of amino acid residue) of the protein and the sequence of these constituents in the peptide chain. Secondary structure chain and this gives rise to the following or twisting of the primary structure. Alpha Helix Beta sheet The Alpha-helix, the Beta pleated sheets, and collagen helices are examples of secondary structure. B. The tertiary structure of proteins It so called the 3-dimensional or conformational structure of proteins. This structure results when attractive forces between amino acid residues cause a linking or winding attractive of the secondary structure. This structure refers to the manner in which the polypeptide chain is bent or folded to form the compact, tightly folded structure of globular proteins. It is maintained by an interaction between the different R groups of the amino acids composing the peptide chain. C. Quaternary structure of proteins It denotes the manner in which the polypeptide chains of a protein having more than one peptide chain are arranged or clustered in space. This level of structural organization is exhibited only by proteins that contain more than one polypeptide chain and this structure refers to the way in which the chains are packed together or how the chains are arranged in relation to each other. Oligomeric proteins - these are proteins with 2 or more polypeptide chain; their component chains subunits or protomer. An example of an oligomeric protein is hemoglobin which consists of 4 polypeptide chain. Properties of Proteins 1. Pure proteins are odorless - they turn brown and char upon heating and give an odor of burning hair. 2. Proteins are viscous and their viscosity is dependent upon the kind of protein and concentration, long molecules are higher viscosity then these that are major or less globular. 3. Proteins are very large molecules; hence, they are colloidal in nature. They polypeptides of different proteins may have been anywhere from about 100 to as many as 1800 or more amino acid residues. 4. Amphoteric behavior since proteins contain both acidic and basic amino acids, they are amphoteric and are capable of donating and accepting. In an acid environment, containing excess protons the protein molecules have a net positive charge, whereas in alkaline medium proteins molecules have a net negative charge. As with amino acids, there exists a pH at which the net charge is zero, the isoelectric point. A protein is least soluble at its isoelectric pH and consequently, it is most easily precipitated. 5. lon bonding of proteins - since proteins are either positive or negative in charge on either side of their isoelectric point, they may form salts its various anions and cations. 6. Solubility each homogenous protein has a definite and characteristic solubility in a solution on fixed salt concentration and pH. The solubility of proteins is at a minimum at the isoelectric point and increase with increasing acidity and alkalinity. Denaturation of Proteins It is defined as a disruption of the secondary, tertiary and quaternary organization of protein, due to the cleavage of non-covalent bonds. This disorganization results in alterations of the chemical, physical and biological characteristics of the protein. Denaturing Agents a. Physical agents b. chemical agents 1. Heat 1. Organic solvent 2. Surface action a) acids and alkaline 3. Ultraviolet light b) urea and guanidine 4. High pressure 2. Detergents Chemical alterations brought about by denaturation 1. Decreased solubility at the protein's isoelectric point. 2. As a result of the unfolding process in denaturation, many chemical groups which were rather inactive awing be shielding of the native state become exposed and more readily detectable. The change in a protein that is produced by several agents is known as denaturation. Proteins in their natural state are called native proteins; after the change, they are denatured proteins. Physical alterations brought about by denaturation 1. Increases in the viscosity of the solution, so the rate of diffusion of the protein molecules decrease. 2. Increased levorotation 3. Denatured proteins cannot be crystallized since the formation of a crystal depends upon a high degree of organization of the molecules. Biological alterations brought about by denaturation 1. Increased digestibility by proteolytic enzymes 2. Enzymatic or hormonal activity is usually destroyed by denaturation. 3. The antigenic or antibody functions of proteins are frequently altered as well. 1. Simple Proteins Definition: Made up of only amino acids and no other chemical groups. They yield only amino acids when broken down. Types: o Globular Proteins: ▪ Rounded and mostly water-soluble, making them adaptable for functions in body fluids. ▪ Examples: ▪ Albumins: Soluble in water and found in blood plasma and egg whites, they help with maintaining fluid balance. ▪ Globulins: Soluble in salt solutions and found in blood serum, they function in immune responses. ▪ Glutelins: Soluble in dilute acids and bases, commonly found in cereals (e.g., wheat gluten). ▪ Prolamines: Soluble in alcohol, these are found in seeds (e.g., gliadin in wheat, which is part of gluten). ▪ Histones: Basic proteins, highly soluble in water, associated with DNA in the cell nucleus, helping with DNA packaging. ▪ Globins: Found in hemoglobin and myoglobin, these proteins bind oxygen in the blood and muscles. ▪ Protamines: Highly basic proteins, soluble in water, typically found in fish sperm cells and bind tightly to DNA. o Scleroproteins (also known as Fibrous Proteins): ▪ Long, fibrous, and mostly water-insoluble, they provide structural support to various tissues. ▪ Examples: ▪ Collagens: Found in connective tissues like skin, tendons, and bones, providing structural strength. ▪ Elastins: Found in elastic tissues such as blood vessels and lungs, allowing tissues to stretch and recoil. ▪ Keratin: Found in hair, nails, and outer layers of skin, providing durability and protection. 2. Conjugated Proteins Definition: Made up of a protein part (apoprotein) combined with a non-protein component (prosthetic group), which often defines the protein's function. Types: o Nucleoproteins: Have nucleic acids (DNA or RNA) as their prosthetic group. Found in cell nuclei, they help with genetic information storage and expression (e.g., chromosomes). o Glycoproteins: Contain carbohydrates as their prosthetic group. Found on cell surfaces and in body fluids, they play roles in cell recognition and immune responses (e.g., mucins in mucus). o Mucoproteins: A type of glycoprotein with a high carbohydrate content. Found in mucus, they protect and lubricate surfaces. o Lipoproteins: Contain lipids (fats) as the prosthetic group. They transport fats through the blood and form part of cell membranes. o Phosphoproteins: Contain phosphate groups. They are important in cellular regulation and found in milk and other sources (e.g., casein in milk). o Chromoproteins: Contain a colored prosthetic group, often involved in oxygen transport or enzyme function (e.g., hemoglobin in blood, which has a heme group for oxygen transport). o Metalloproteins: Contain metal ions as the prosthetic group. They play roles in electron transport and storage (e.g., ferritin stores iron, cytochromes involved in cellular respiration). 3. Derived Proteins Definition: Proteins that result from the modification or breakdown of simple or conjugated proteins, usually by chemical or physical processes such as hydrolysis or denaturation. Types: o Primary Derived Proteins: ▪ Proteins that have undergone mild changes, retaining some of their original structure. ▪ Examples: ▪ Coagulated Proteins: Proteins that have been denatured by heat or acids, causing them to lose their native structure (e.g., egg white protein when cooked). ▪ Proteans: Intermediate products from the initial breakdown of proteins, they are insoluble and precipitate out. ▪ Metaproteins: Formed by the partial hydrolysis of proteins and are generally less soluble than the original protein. o Secondary Derived Proteins: ▪ More extensively broken-down protein products, closer to their simplest forms. ▪ Examples: ▪ Proteoses: Intermediate products in protein digestion; still somewhat soluble and functional. ▪ Peptones: Further breakdown products that are even smaller than proteoses; used in nutrient media for bacterial growth. ▪ Polypeptides and Peptides: Short chains of amino acids resulting from advanced hydrolysis, these are small enough to be absorbed by cells and used in metabolism. In summary: Simple Proteins are just amino acids, either as globular (rounded, soluble) or scleroproteins (fibrous, structural). Conjugated Proteins have additional components, like carbs in glycoproteins or metals in metalloproteins. Derived Proteins are modified or broken-down proteins, either partially (primary) or almost fully (secondary).