Introduction To Protein And Protein Structures, Lecture notes of Biochemistry

Download Introduction To Protein And Protein Structures and more Lecture notes Biochemistry in PDF only on Docsity! Biochemistry of Macromolecules: Proteins Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. All amino acids have the same basic structure. Each molecule has a central carbon atom (a- carbon) linked together with a basic amino group, a carboxylic acid group, a hydrogen atom and an R-group or side-chain group. The general structure of Amino acids is H2NCH RCOOH, which can be written as: COOH HaN - f -H R Therefore, the major key elements of amino acids are carbon, hydrogen, nitrogen, oxygen. Each amino acid hence has 4 different groups attached to a- carbon atom. These 4 groups are: e Amino group, * COOH, e Hydrogen atom, eR group - Side chain Although numerous numbers of amino acids exist in nature (about 500 amino acids are known), only 20 amino acids are most important. These twenty amino acids make up proteins and appear in the genetic code. All amino acids have the same basic structure, differing only in the R-group (or side chain). Amino acids are the building blocks that form polypeptides and hence the building blocks that form proteins. Consequently, amino acids are fundamental components of the human body and are vital for physiological functions such as protein synthesis, tissue repair and nutrient absorption in the body Classification of amino acids Classification of amino acids is necessary because it gives the grouping between the 20 amino acids and also gives a basic outline for grouping. Classification gives a clear idea of picking the particular amino acid type needed and also creates an easy understanding between each amino acid. Amino acids can be classified in various ways such as classification based on the R group, polarity and R group, distribution in protein, nutritional requirements, number of amino and carboxylic groups present etc. 1. Based on R-Group: Amino acids can be further classified into the following sub-groups based on the R-group. e Simple amino acids: these have no functional group in their side chain. Example: glycine, valine, alanine, leucine, isoleucine ¢ Hydroxy amino acids: these have a hydroxyl group in their side chain e.g threonine, serine tyrosine. ¢ Sulfur containing amino acids: have sulfur in their side chain e.g: cysteine, methionine Aromatic amino acids: have benzene ring in their side chain e.g: phenylalanine, tyrosine * Heterocyclic amino acids: having a side chain ring which possess at least one atom other than carbon e.g: Tryptophan, histidine, proline * Amine group containing amino acids: derivatives of amino acids in which one of carboxyl group has been transformed into an amide group e.g: Asparagine, glutamine ¢ Branched chain amino acids: A branched-chain amino acid is an amino acid having aliphatic side-chains with a branch e.g: leucine, isoleucine, and valine ¢ Acidic amino acids: have carboxyl group in their side chain e.g: Aspartic and Glutamic acid Basic amino acids: contain amino group in their side chain e.g: Lysine, Arginine Imino acid: Amino acids containing a secondary amine group e.g: Proline 2. Polarity and R Group: the following sub-groups are in this group Amino acids with non-polar R group: these are hydrocarbons in nature and are hydrophobic. They have aliphatic and aromatic groups a) * Aliphatic R groups: e.g: Alanine, Valine, Leucine, Isoleucine, Proline. * Aromatic groups: e.g: Phenylalanine, Tryptophan, Methionine (sulfur) b) Amino acids with polar but uncharged R Group: these amino acids are polar and possess neutral pH value. e.g: Glycine, Serine, Threonine, Cysteine, Tyrosine, Glutamine, Asparagine. c) Negatively charged amino acids: their side chain [R Group] contain extra carboxyl group with a dissociable proton. And renders electrochemical behaviour to proteins e.g: Aspartic acid and Glutamic acid e Reaction with Ninhydrin: The a—amino group of amino acids reacts with ninhydrin to produce aldehydes. e Reaction with Alkalis’ (Salt formation): The carboxyl group of amino acids can release a H* ion with the formation of Carboxylate (COO-) ions. Reaction with Alcohols (Esterification): Amino acids react with alcohol to form, “Ester”. The esters are volatile in contrast to the form amino acids. Reaction with dansyl Chloride: Dansyl chloride means “Dimethyl Amino Naptha Sulphonyl Chloride”. When the amino acid reacts with dansyl chloride reagent, it gives a “Flourescent dansyl derivative Reaction with acylating agents (Acylation): When the amino acids react with “Acid _ chloride” and acid anhydride in alkaline medium it gives “pthaloyl amino acid. Reaction with Sanger’s reagent: 1-flouro-2, 4-dinitrobenzene is called Sanger’s reagent (FDNB). Sanger’s reagent reacts with a-amino acid to produce Yellow coloured derivative, DNB-amino acid. Reaction with Edmann’s reagent: Edmann’s reagent is “phenyl-isothiocyanate”. When amino acids react with Edmann’s reagent it gives “phenyl thiohydantoic acid” finally it turns into cyclized form “Phenyl thiohydantoin” (Edmann’s derivative) Types of Proteins Proteins are large, complex molecules that are required for the structure, function and regulation of body tissues. Proteins are made up of large numbers of amino acids linked into chains by peptide bonds, which joins the carboxyl group of one amino acid to the amino group of the next. The number of amino acids present varies from about a hundred to several thousands in different proteins. Some proteins are composed of only one polypeptide chain while others are composed of two or more polypeptide chains (multi-subunit proteins) held together by non-covalent bonds. This bond is otherwise an amide linkage. H,N-CH— COOH + H,N— a COOH “ao” H,N—CH>- CO — NH+ CH— COOH cH, Peptide CH, bond when peptide bonds are established among more than ten amino acids, they together form a polypeptide chain. Very often, when a polypeptide chain has a mass exceeding 10,000u and when the number of amino acids in the chain exceeds 100, a protein is obtained. Classification of Proteins: Proteins can be classified according to the following three different criteria: A) Based on their chemical composition. B) Based on their shape C) Based on their biological function. a) Classification according to their chemical composition: Proteins can be classified on the basis of their chemical composition into two main classes: Simple proteins and conjugated proteins Simple proteins: are those proteins which upon hydrolysis give only amino acids. Example: ribonuclease A, chymotrypsin. Conjugated proteins: are proteins which yield upon hydrolysis amino acids and non-protein part called the prosthetic group. Conjugated proteins are classified on the basis of the chemical nature of their prosthetic groups: i) nucleoproteins, ii) Glycoproteins (contains carbohydrate part), iii) Lipoproteins (contains lipid part), iv) Hemoproteins (contains heme), v) Metalloproteins (contains metal) b) Classification according to their shape: Proteins can be classified on the basis of their shape into two main classes: Globular proteins and Fibrous proteins Globular proteins: - They are generally soluble in water. The polypeptide chains are tightly folded into a globular shape (coiled around to give a spherical shape). Example: enzymes, hemoglobin, myoglobin, insulin, albumin. Fibrous proteins: - They are insoluble in water. Their polypeptide chains are arranged in long strands (elongated in the form of fibers). Example: Collagen, elastin, keratin (present in hair, wool and silk), myosin (present in muscles). C) Classification according to their biological functions: Proteins can be classified on the basis of their biological function into: * Catalytic function (enzymes) + Transport function (hemoglobin, albumin, transferrin) + Nutrient and storage proteins [e.g., casein & ferritin] contractile or mobile proteins [e.g,, actin, myosin] + Structural function [Keratin, elastin, collagen] Defense proteins [e.g., immunoglobulins, fibrinogen and thrombin] « Regulatory function, some hormones are proteins (Growth hormone somatotropin]) (GH, Some toxins are proteins Defense (Antibodies and coagulating factors) Protein Structure and forces involved in their stabilization Protein structure is defined as a polymer of amino acids joined by peptide bonds to form the linear polypeptide chain. Protein structures are made by condensation of amino acids forming peptide bonds. The amount and type of amino acids found in a protein and the sequence in which they are arranged in the polypeptide chains is a unique characteristic of each protein. The amino acid sequence in proteins is the force that determines the protein conformation, which in turn is responsible for the biological function of proteins. Configuration is the arrangement in space of substituent groups in steroisomers; such structures cannot be interconverted without breaking one or more covalent bond. Conformation refers to the spatial arrangement of substituent groups that are free to assume many different positions, without breakin g bonds, because of rotation about single bonds in the molecule. Each protein has a unique amino acid sequence and a well-defined three-dimensional structure known as the conformation. The need for multiple stable conformations reflects the changes that must take place in most proteins as they bind to other molecules or catalyze reactiors- Proteins in any of their functional, folded conformations are called native proteins. Proteins can have four levels of structural conformations or structures, which are: 1) Primary structure 2) Secondary structure 3) Tertiary structure 4) Quaternary structure. The sequence of amino acids in a protein is called its primary structure. The secondary structure is determined by the dihedral angles of the peptide bonds, the tertiary structure is determined by the folding of protein chains in space. Association of folded polypeptide molecules to complex functional proteins results in quaternary structure. The secondary, tertiary and quaternary structures are together called the three-dimensional (3D) structure of protein. Not all proteins have all the 4 levels of structures but some do. The bonds responsible for the stability of secondary structure are hydrogen bonds between peptide bond groups (ie. between NH group of one amino acid residue and the carbonyl oxygen (C=O) of other amino acid). The secondary structure is of three types: a) The a-helix b) B-pleated sheets c) Collagen helix a) a-helix: - It is a spiral structure. - The polypeptide backbone is tightly wound around the long axis of the molecule and the R-groups of amino acid residues protrude outward from the helical backbone. In all proteins, the helical twist of the a-helix is right handed. The a-helix is the most common secondary structure and it is the simplest arrangement of a polypeptide chain. The bonds responsible for stability of achelix are the hydrogen bonds between peptide bond groups. An ochelix permits the formation of intra-chain hydrogen bonds between successive coils of the helix, parallel to the long axis of the helix. Each successive turn of the a-helix is held to the adjacent turns by three to four hydrogen bonds, conferring significant stability in the overall structure. Hydrogen bonds are individually weak but collectively serve to stabilize the helix. Examples include © ackeratin: - it is a fibrous protein whose structure is entirely a-helix. Keratin is the major component of tissues such as hair and skin. © Hemoglobin: - it is a globular protein. About 80% of hemoglobin structure is a-helix. Factors that affect the stability of a-helix: a) Electrostatic repulsion (or attraction) between amino acid residues with charged R-groups. [ e.g., if there is a large numbers of charged amino acids, they disrupt the helix by forming ionic bonds, or by electrostatically repelling each other. b) The bulkiness of adjacent R-groups. Amino acids that branch at the B-carbon can interfere with formation of the a-helix if they are present in large numbers and close to each other. c) The interaction between amino acid side chains spaced three (or four) residues apart d) The occurrence of proline residues: In proline the nitrogen atom is part of a rigid ring and the rotation around N-a Carbon bond is not possible. In addition, the nitrogen atom of a proline residue in peptide linkage has no substituent hydrogen to form hydrogen bond with other residues so, it inserts a kink in the chain that disrupts the smooth, helical structure. 10 (b) B- pleated sheet: In the B-conformation, the backbone of the polypeptide chain is extended into a zigzag rather than a helical structure. - The zigzag polypeptide chains can be arranged side by side to form a structure resembling a series of pleats, hence the structure is called a B-pleated sheet. The R- groups of adjacent amino acids protrude from the zigzag structure in opposite directions, creating the alternating pattern. In this structure, all peptide chains are stretched out to nearly maximum extension and then laid side by side which is held together by intermolecular hydrogen bonds. Hydrogen bonds form between adjacent segments of polypeptide chain. The adjacent polypeptide chains in a B sheet can be either Parallel OR antiparallel (having the same amino to (having the opposite carboxyl orientations) carboxyl orientations. The bonds responsible for stability of B-pleated sheet,the hydrogen bonds between peptide bond groups. Example of B- pleated sheet includes f-keratins (such as silk fibroin). c) B-turns B-turns occur frequently whenever strands in B sheets change the direction. In globular proteins, nearly one-third of the amino acid residues are in B-turns. The turn is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence. The 180° turn is accomplished over four amino acids. There are two types of B-turns: type | and II. Type | occurs more than twice as frequently as type Il. Type II B-turns usually has Glycine as the third residue. 3. Tertiary Structure of Protein The tertiary structure refers to the spatial arrangement of amino acid residues that are far apart in the linear sequence (i.e. in the primary structure), so the polypeptide chain is folded into three dimensions. This structure arises from further folding of the secondary structure of the protein. Tertiary structure is three-dimensional conformation of a polymer in its native folded state. It gives rise to two major molecular shapes called fibrous and globular. interactions of the amino acid side chains guide the folding of the polypeptide chain to form a compact structure. In this structure the hydrophobic side chains are buried in the interior whereas hydrophilic groups are generally found on the surface of the molecule. Bonds that stabilize tertiary structure are the non-covalent bonds between R-groups (i.e. between groups 11 in the side chains). a) Hydrophobic interaction b) Hydrogen bonds c) lonic interaction d) Disulphide bonds. Hydrophobic interactions: is the association between non-polar groups (hydrophobic groups) in the side chains of amino acids. s: is a type of attractive interaction between an electronegative atom (such as Hydrogen bond gen) and a hydrogen atom bonded covalently to another electronegative atom. oxygen or nitro lonic interaction (electrostatic interaction): Interaction between opposite charged groups of the side chains of amino acids. It is small globular protein Example of tertiary structure is the structure of Myoglobin: h as a reservoir for oxygen (hemoprotein), present in heart and skeletal muscle. It functions bot! and as an oxygen carrier that increases the rate of transport of oxygen within the muscle cell. 4 Quaternary Structure of Protein Proteins that are composed of more than one polypeptide chain (subunits) show a fourth level of protein structure which is the quaternary structure. The spatial arrangement of various tertiary structures gives rise to the quaternary structure. Some of the proteins are composed of two or more polypeptide chains referred to as sub-units. The spatial arrangement of these subunits with respect to each other is known as quaternary structure. Quaternary structure is the three-dimensional structure of a multi-subunit protein, particularly the manner in which the subunits fit together. Subunits may either function independently of each other or may work cooperatively, as in hemoglobin. The interaction between subunits is stabilized by the same forces that stabilize tertiary structure (non-covalent bonds). Bonds that stabilize quaternary structure are a) Hydrophobic interaction b) Hydrogen bonds Non-covalent bonds c) lonic interaction between R-groups (i.e between groups in the side chains). Example of quaternary structure of protein is the structure of Hemoglobin. Hemoglobin is a simple oligomeric protein, found in red blood cells (RBC), where its main function is to transport oxygen from the lungs to the capillaries of the tissues. Hemoglobin is hemoprotein, composed of four polypeptide chains and four heme groups. 12