Proteins II PDF Lecture Notes

PROTEINS Biochemistry-I Shumyila Nasir Lecturer Department of Biomedical & Biological Sciences Learning Objectives Structures of Protein Properties of Protein Classification of Protein 2 LO: Structure of Protein...

PROTEINS Biochemistry-I Shumyila Nasir Lecturer Department of Biomedical & Biological Sciences Learning Objectives Structures of Protein Properties of Protein Classification of Protein 2 LO: Structure of Protein FOUR ORDERS OF PROTEIN STRUCTURE Four orders of Protein Structure – Primary structure: linking amino acid residues in polypeptide chain. – Secondary structure: stable arrangements of amino acid residues giving rise to recurring structural patterns into geometrically ordered units; twisting resulting in α-helix or pleated – Tertiary structure: the three-dimensional assembly of secondary structural units to form larger functionalunits – Quaternary structure: It’s the arrangement in spaceof protein having two or more polypeptide subunits 3 LO: Structure of Protein 4 LO: Structure of Protein PRIMARY STRUCTURE Primary (1°) structure Each protein has a distinctive number and sequence of amino acid residues These determines how it folds up into a unique three-dimensional structure This in turn determines the function of the protein Bovine Pancreatic RibonucleaseA 5 LO: Structure of Protein SECONDARY STRUCTURE 2° structures Polypeptide chain can arrange itself into characteristic helical or pleated segments – Given by Pauling and Corey – hydrogen bonding interactions between adjacent amino acid residues Free rotation is possible about only two of thethree Phi (Φ)angle Psi (Ψ)angle covalent bonds of the polypeptide backbone α-carbon (Cα) to the carbonyl carbon (Co) bond Cα to nitrogen bond 6 LO: Structure of Protein SECONDARY STRUCTURE (α-helix) α helix is twisted by an equal amount about each α- carbon With a phi angle of approx. −570 and a psi angle of approx − 470 Complete turn of the helix contains an average of 3.6 aminoacyl residues distance it rises per turn (pitch) is 0.54 nm R groups of each aminoacyl residue in an α helix faceoutward α-helix is the most common type of secondary structure. 7 LO: Structure of Protein SECONDARY STRUCTURE (α-helix) Viewdown the axisof anα helix 8 LO: Structure of Protein SECONDARY STRUCTURE (α-helix) Stability of an α helixarises primarily from hydrogen bonds Between the oxygen of carbonyl and the hydrogen atom of nitrogen of the 4th residue down the polypeptide chain Supplemented by van der Waals interactions 9 LO: Structure of Protein SECONDARY STRUCTURE (α-helix) 10 LO: Structure of Protein SECONDARY STRUCTURE (β-sheets) Extended conformation of polypeptide chains Viewed edge-on, form a zigzag or pleated pattern in which the R groups of adjacent residues point in opposite directions Stability from hydrogen bonds between the carbonyl oxygens and amide hydrogens of peptide bonds - adjacent segments of βsheet 11 LO: Structure of Protein SECONDARY STRUCTURE (β-sheets) Parallel: polypeptide chain proceed Antiparallel: they proceed in in the same direction amino to opposite directions carboxyl 12 LO: Structure of Protein Loops & Bends Short segments of amino acids that join two units of secondary structure –3-4 units Globular proteins - compact foldedstructure Nearly one-third of the amino acid residues are in turns or loops where the polypeptide chain reverses direction The structure is a 1800 turn involving four amino acid residues 13 LO: Structure of Protein Loops & Bends Carbonyl oxygen of the first residue forms a hydrogen bond with the amino- group hydrogen of the fourth residue The peptide groups of the central two residues do not participate in any hydrogen bonding Gly (small and flexible) and Pro (readily assume the cis configuration) residues often occur in turns. 14 LO: Structure of Protein Loops & Bends Generally found on the surface of a protein γ-turn - less common is the, a three residue turn with a hydrogen bond between the first and third residues. 15 LO: Structure of Protein Tertiary Structure Entire 3-dimensional conformation of a polypeptide Beside H bond, sulfide bond (-S-S), ionic interaction and hydrophobic bond Consists of helices, sheets, bends, turns, and loops— assemble to form domains Domain is a section of protein structure - perform a particular chemical or physical task – binding of a substrate or other ligand – anchor a protein to a membrane – interact with a regulatory molecules 16 LO: Structure of Protein 17 LO: Structure of Protein Single domain:triose phosphate isomerase Enzyme triose phosphate isomerase complexed with the substrate analog 2- phosphoglycerate (red) Elegant and symmetrical arrangement of alternating β sheets(light blue) and a helices (green), with the βsheets forming a β-barrel core surrounded by the helices 18 LO: Structure of Protein Tertiary Structure Single domain - triose phosphate isomerase, myoglobin Two domains - lactate dehydrogenase, quinone oxidoreductase A polypeptides with 200 amino acids normally consists of two or more domains Tetrameric enzyme lactate dehydrogenase with the substrates NADH(red) and pyruvate (blue) bound 19 LO: Structure ofQuaternary Protein Structures Majority of proteins are composed of single polypeptide chains Some of protein consists of 2 or more polypeptide chain which may be identical or different Such protein are termed as oligomers and poses quaternary structures. When it consists of 2 polypeptides - dimers Homodimers contain two copies of the same polypeptide chain, while in a heterodimer the polypeptides differ 20 LO: Properties of Protein Solublity: forms colloidal solution instead of true solutions in water – large size of protein Molecular Weight: depends on number of amino acid Shape: there is wide variety in shape – globular(insulin), oval(albumin), fibrous or elongated (fibrinogen) Acidic and basic: depends on ratio of (lysine + arginine) : (Glut + Asp). Ratios greater than 1 is basic and vice-versa 21 LO: Properties of Protein Protein are isoelectric Nature of amino acids determines the pH of a protein At isoelectric pH, the protein exist as Zwitter-ions and dipolar ions – Electrically neutral – Minimum solubility – Maximum precipitability – Least buffering capacity 22 LO: Classification ofClassification Protein Proteins are classified on the basis of – Chemical nature and solubility Simple Conjugates Derived – Nutritional Importance – Function Complete Structural Partially incomplete Enzyme or catalytic Incomplete Transport Hormonal Contractile Storage Genetic Defense Receptor 23 LO: Classification of Protein Chemical nature and solubility: Simple They are composed of only amino acid residues They are again classified as – Globular Protein : spherical or oval in shape, soluble in water or other solvent and digestible Globulin: soluble in neutral and salt solution.Ex: serum globulin Albumin: soluble in water and dilute salt solutions and cogulated by heat. Ex: serum albumin, ova albumin, lactalbumin 24 LO: Classification of Protein Chemical nature and solubility: Simple GlobularProtein(Cont)… – Glutelins : soluble in dilute acids, alkalies and mostly found in plants. Ex: Glutelin (wheat), oryzenin (rice) – Prolamines: soluble in alcohol. Ex: gliadin(wheat), zein (maize) – Histones: strongly basic proteins, soluble in water and dilute acids but insoluble in dilute ammonium hydroxide. Ex: thymus histone 25 LO: Classification of Protein Chemical nature and solubility: Simple Fibrous Protein: fiber like in shape, insoluble in water and resistant to digestion. It again of 3 types – Collagen: connective tissue protein lacking tryptophan. On heating with boiling water or acids it turns to soluble gelatin – Elastin: elastic tissues such as tendons andateries – Keratin: present in the exoskeleton structures. Ex: hair, nails, horns 26 LO: Classification of Protein Chemical nature and solubility: Conjugate Protein Beside amino acid, it contains a non-protein moiety known as prosthetic group or conjugating group. Its again of 6 types – Nucleoprotein: nucleic acid (DNA or RNA) – Glycoprotein: prosthetic group is carbohydrate which is less than 4 % and when it exceeds 4% its called mucoprotein. Ex: mucin (saliva), ovamucid (egg white) – Lipoprotein: found in the conjugation with lipids. Ex: serum lipoprotein, membrane lipoprotein 27 LO: Classification of Protein Chemical nature and solubility: Conjugate Protein Phosphoprotein: phosphoric acid as conjugate. Ex: casein(milk), vitelline (egg yolk) Chromoprotein: prosthetic group is colored in nature. Ex: Hemoglobins, cytochromes Metalloprotein: it contains metal ions such as Fe, Co, Zn, Cu, Mg, 28 LO: Classification of Protein Chemical nature and solubility: Derived Protein Denatured or degraded product of simple or conjugated protein Its of 2 types – Primary derived protein: denatured or cogulated or first hydrolyzed product of proteins. They are Cogulated proteins Proteans Metaprotein – Secondary derived protein: progressive hydrolytic product of protein hydrolysis. Ex: proteoses, peptones, polypeptides and peptides 29 LO: Classification of Protein 30 LO: Denaturation ofDenaturation Protein The phenomenon of disorganization of native protein structure It results in the loss of secondary, tertiary and quaternary structure of proteins. It involves the change of physical, chemical and biological properties Agents of Denaturation – Physical agents: Heat, UVradiation, X-rays and violent shaking (centrifuge) – Chemical Agents: Acids, alkalies, organic solvents (ether, alcohol), salts of heavy metals, urea, salicylate 31 LO: Denaturation ofDenaturation Protein Primary structures remains intact i.e peptide linkage are not broken Loses its biological activity Insoluble in solvent which was previously soluble Its more easily digestible Its usually irreversible, but careful denaturation (renaturation) is reversible. Ex: Hemoglobin is renatured on removal of salicylates 32 LO: Denaturation of Protein Coagulation – Irreversible denaturation of protein to semi-solid viscous precipitate – Albumins and globulins – coagulable proteins Flocculation – Precipitation is known as flocculum – Casein – milk protein, prepared by adjusting isoelectric pH by dilute acetic acid – Its reversible, but on heating it turns to be irreversible 33  Refrences Nelson, D. L., Lehninger, A. L., & Cox, M. M. (2008). Lehninger principles of biochemistry. Macmillan. Murray, R. K., Granner, D. K., Mayes, P. A., & Rodwell, V. W. (2014). Harper’s illustrated biochemistry. Mcgraw-hill. Biochemistry - Garrett And Grisham 2008 [email protected] 34