Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19UNIT III:AMINO ACIDS, PROTEINS, & ENZYMESLecture 2: Protein Structure & FunctionStructure and function of proteinsHow do proteins go from this:long chain of amino acidsTo this:a specific, stable, and functional3-D functional shapeH2N CH CCH2OCH2SCH3NHCH CCH2OHN CH CCHOCH3CH2CH3HNCHCCH2OCNH2OHN CH CCH2OCH2CH2CH2NH2........4 “levels” of protein structurePrimary (1º) structure - amino acid sequence – determines all else! - common peptide-bond backbone - 20 different “R” groups1ºSecondary (2º) structure - H-bonds between backbone elements give specific basic “common” structures1. -helix2. -pleated sheet3. random coil (exactly what it sounds like)2ºQuaternary (4º) structure - multiple subunit polypeptides associated to give functional protein form4ºTertiary (3º) structure - specific 3-D structure of a single peptide chain - determined by 1º and 2º structures and more3ºSecondaryStructure4 “levels” of protein structure - some specific detailsProtein chains fold into defined, ordered3-D structures held together by various chemical interactions.Interactions of “R” side-chains with eachother and with water are major determinants-helix – every carbonyl C=O isH-bonded to amide-H 4 aa away;H-bonds parallel to axis of helix -pleated sheet – all carbonyl C=O andamide-H involved in H-bonds, perpendicularto axis of chains, which are “extended” – parallel or anti-parallel sheets“random coils tooSecondary structures folded/arranged togive tertiary (3-D) structureMultiple subunits often associated togive quaternary structure– backbone interactionslSH lSH S S[OX]Disulfide bridges – covalent bonds involved in protein structureH Ol llN―C―Cl lH CH2lSHSHlH CH2l lN―C―Cl llH O cysteine residues ina polypeptide chain(same or different chain)H Ol llN―C―Cl lH CH2lSSlH CH2l lN―C―Cl llH O DisulfidebridgeDisulfide “bridge” linkingpolypeptide chains(or parts of the same chain)2H2H3-D “backbone” structures of 4 real proteinsChymotrypsinDNA PhotolyaseMyoglobinArrows denote -pleated sheets-helixes look like helixesRandom coils everywhere elseDeadenylasePeptide bonds are very stableMetabolic energy (ATP) and enzymes/ribozymes (biological catalysts) are required to make them (in Biochem 108)Enzymes (proteases) are required to break peptide bonds in living organisms (later this semester)Very harsh conditions are required for chemical hydrolysis of peptide bonds - 6 M HCl - 110º C - 16 hrs+HOHAmino acid 1 Amino acid 2, H+Amino a-helix polypeptide assembledacids (or b-sheet) chain monomersCACGCAGUGCUUGGGGGUAAAAAGGTGCGTCAC GAACCC CCATTTTTCDNA RNAPrimarystructureSecondarystructureTertiarystructureQuaternarystructureAminoacids-helixor-sheetPolypeptidechainAssembledmonomers Base sequence of the gene (DNA) determines the amino acid sequence (1° structure). The 3-dimensional shape of the protein (2°, 3°, and 4° structure) is determined by the 1° structure. The function of the protein is determined by its 3-dimensional shape. Changes in shape lead to changes in function. - binding of regulatory molecules - phosphorylation/dephosphorylation“Form Forever Follows Function” Louis H. SullivanProtein structure and function-pleated sheetdisulfidebondsSSSS-helixhydrogenbondsCH2-OHO-CH2 lHhydrogen bondHydrophobicinteractionCH2 l lCH2CH3CH3OH lCH2NH2 lC=O lCH2Hydrophilicattraction(HOH)NH3+ O ll-O-Cionic bondNH2 lC=O lH-O-CH2hydrogen bondMany types of interactions stabilizethe 3-D structure of proteinsMostly non-covalent - individually weak and transientBut collectively strong and stable;Water is a major playerhydrogenbondsCombination allows for: - stability - flexibility (plastic) - both critical to functionDenaturation of proteins – loss of 3-D structure and functionOrganized 3-D structure of a protein becomes completely disorganizedUsually an irreversible event – complete loss of functionMany factors can denature proteins: pH (altered [H+])Organic solvents & detergentsSalts of heavy metals - Hg, Ag, Pb, &c Amino acid sequence - genetic mutationsIntracellular environment must becarefully controlled!Life literally depends upon it.Why whip egg whites in copper bowls?McGee et al., Nature 308:667-668 (1984)Physical agitationHeat (increased thermal energy)Relationship between protein structure & function:Fibrous vs Globular ProteinsFibrous proteins: - have mostly one type of secondary structure - adopt an extended fiber-like structure that makes them strong & elastic - important structural building blocks - insoluble in water - hair, hooves, horns, nails (keratins) - silk (fibroin) - muscle (actin, myosin), connective tissue (collagen) - cytoskeleton (tubulins, neurofilaments)Globular proteins: - most cellular proteins (enzymes &c) - soluble in water - usually roughly spherical - usually have more than one type of secondary structure - all “non-structural” proteins are globularCollagen – an important fibrous proteinCollagens: - most abundant protein in body (~ 1/3 total) - connective tissues skin bone blood vessels ligaments tendons cartilage - supports and holds together tissues & organs - very strong and resilient (resists stretching) - elastic (springs back)Repeating amino acid sequence of collagen: Gly-X-Pro-Gly-X-Pro-Gly-X-Pro . . . . . . The presence of proline &glycine allows collagen chains to form a very tightly coiledhelix; it also allows adjacentchains to pack together tightly (superhelix).A single amino acid replacement at a Gly orPro is sufficient to disrupt the structureand function of collagen.42 collagen genes in humans. Mutations in the COL1Agene most serious and cause two devastating disorders: - osteogenesis imperfecta – usually AD (bones do not form properly and are very brittle) sometimes confused with child abuseand - Ehlers-Danlos Syndrome - AD or AR (hyper-extensible skin, internal organs tear easily, joints easily dislocated). Ehlers-Danlos SyndromeMyoglobinHemoglobin & Myoglobin – Oxygen-binding globular proteinsMyoglobin has 1 polypeptide chain and is mostly -helical. Heme: O2-binding“prosthetic