Lecture 3: Chemistry of Life Part 3 of 2Slide 2Amino Acid StructureProperties of Amino AcidsPowerPoint PresentationProtein SynthesisSlide 7Slide 8We need a vocabulary for describing proteinsProtein ShapesProtein StructurePrimary StructureSecondary StructureExamples of Secondary StructureTertiary StructureQuaternary StructurePolypeptides With Attached Organic CompoundsDenaturationProtein RestorationA Permanent WaveQUIZ 1Slide 22Slide 23A brief survey of a some protein typesSlide 25Slide 26Slide 27Types of proteinSlide 29Slide 30Slide 31SignalingSlide 33Slide 34StorageSlide 36Protein for DefenseSlide 38TransportationConcepts in Transportation The Basic TermsCell Membranes And Selective Permeability (Think Grapefruit!)Mechanisms of Crossing Over (the membrane)Transport Proteins General CharacteristicsPassive TransportActive TransportBulk TransportSlide 47Enzyme Structure and FunctionFeatures of EnzymesActivation EnergyInduced-Fit ModelPulling it all togetherWhy is Cholesterol Important?DisclaimerBasic Cholesterol MetabolismSlide 56Cholesterol and HealthStatinsSlide 59Cholesterol SynthesisStatins on the MarketToo Much of a Good ThingSlide 63Slide 64Slide 65Slide 66Nucleic acids = MacromoleculesNucleotide StructureSlide 69Slide 70Slide 71Slide 72Nucleotide FunctionsNucleic AcidsNucleotidesDNARNANatural ToxinsSynthetic ToxinsAtmospheric Carbon DioxideCO2 and Global WarmingHumans and Global WarmingProducers Capture CarbonBioremediationNegative Effects of PesticidesPolyunsaturated Fatty AcidsSlide 87Slide 88Lecture 3: Chemistry of LifeLecture 3: Chemistry of LifePart 3 of 2Part 3 of 2Same songSecond verseA little bit louder And a whole lot worseLecture 3: Chemistry of LifeLecture 3: Chemistry of LifePart 3 of 2Part 3 of 2Goals:•Finish with biochemistry•Understand: 1.)What protein is, 2.)What protein does, and 3.) how make one•Relate concepts of protein structure and function to real events and issuesKey Terms: Amino acid, R-group, polypeptide, protein types, Key Terms: Amino acid, R-group, polypeptide, protein types, protein structure (1protein structure (1°°,2,2°°,3,3°°,4,4°°), peptide bond, lipoprotein, ), peptide bond, lipoprotein, glycoprotein, diffusion, permeability, transport, gradientglycoprotein, diffusion, permeability, transport, gradientAssingment:Assingment:For Tuesday, read Ch 12 and 13For Tuesday, read Ch 12 and 13For Thursday, read Ch 8 and 14For Thursday, read Ch 8 and 14Amino Acid StructureAmino Acid StructureaminogroupcarboxylgroupR groupProperties of Amino Acids•Determined by the “R group”•Amino acids may be: –Non-polar –Uncharged, polar –Positively charged, polar–Negatively charged, polarAmino acidsAmino acidsNH2CHOCH2CH2CH2NHNHNH2OHNH2CHOCH3OHNH2CHOCH2ONH2OHNH2CHOCH2OOHOHNH2CHOCH2SHCH3AlanineArginineAsparagineAspartic AcidCysteineNH2CHOCH2CH2ONH2OHNH2CHOCH2CH2OOHOHNH2CH2OOHGlutamineGlutamic AcidGlycineNH2CHOCH2NCHCHNHOHNH2CHCHCH2OCH3CH3OHHistidineIsoleucineNH2CHCH2CHOCH3CH3OHNH2CHOCH2CH2CH2CH2NH2OHLysineLeucineNH2CHOCH2CH2SCH3OHNH2CHCH2OCHCHCHCHCHOHNHCHCH2CH2CH2OOHNH2CHCH2OHOOHMethioninePhenylalanineProlineSerineCHCHNH2CH3OHOOHNH2CHCH2OCHNHCHCHCHCHOHNH2CHCH2OCHCHCHCHOHOHNH2CHCHCH3OCH3OHThreonineTryptophanTyrosineValineIf you memorize the single and three letterabreviations, the chemical structure, the pKa and the relative hydrophobicity for each amino acid, then you are a student of biochemistry and do not belong in this class.•The R-groups are different•R-groups help to determine the intramolecular arrangement of a proteinProtein Synthesis•Protein is a chain of amino acids linked by peptide bonds•Peptide bond–Type of covalent bond–Links amino group of one amino acid with carboxyl group of next–Forms through condensation reactionProtein = chain of amino acidsCondensation of Amino Acids is the formation of a peptide bondChemical ReactionChemical ReactionForming Peptide BondsWe need a vocabulary for We need a vocabulary for describing proteins describing proteins 1. General shape2. Level of detail we are talking aboutIdentityHomology3D Structure1. General function of the proteinProtein ShapesProtein Shapes •Fibrous proteins–Polypeptide chains arranged as strands or sheets•Globular proteins –Polypeptide chains folded into compact, rounded shapesProtein StructureProtein Structure•Primary- just the sequence (1D)•Secondary- interactions on the chain (2D)•Tertiary- interactions between parts of the chain the chain. (3D)•Quaternary- interactions with other chainsPrimary StructurePrimary Structure•Sequence of amino acids•Unique for each protein•Three or more = polypeptide•Backbone of polypeptide has nitrogen atoms (not just a hydrocarbon):–-N-C-C-N-C-C-N-C-C-N-Secondary StructureSecondary Structure•Hydrogen bonds form between different parts of polypeptide chain•These bonds give rise to coiled or extended pattern•Helix or pleated sheetExamples of Secondary Examples of Secondary StructureStructure-helix-helix-sheet-sheetTertiary StructureTertiary StructureFolding as a result of interactions between R groupsheme groupcoiled and twisted polypeptide chain of one globin moleculeQuaternary StructureQuaternary StructureSome proteins are made up of more than one polypeptide chainHemoglobinPolypeptides With Attached Polypeptides With Attached Organic CompoundsOrganic CompoundsNothing new! Just more combinations of Tuesday’s vocabulary•Lipoproteins–Proteins combined with cholesterol, triglycerides, phospholipids•Glycoproteins –Proteins combined with oligosaccharidesDenaturationDenaturation•Disruption of three-dimensional shape•Breakage of weak bonds•Causes of denaturation:–pH–Temperature•Destroying protein shape disrupts functionProtein RestorationRenaturing proteinsRefolding ?A Permanent WaveA Permanent Wavehair wrapped around cuticlesdifferentbridges formbridgesbrokenhair’scuticlekeratinmacrofibrilone hair cellmicrofibril (threechains coiled into one strand)coiled keratinpolypeptidechainQUIZ 1Quiz ISB-202 1- Is it always wrong to kill another human being? A. It is always wrong to kill another human being (Morally wrong). B. It is OK if one is defending one’s family or property (Self-defense). C. It is OK if the majority of Americans vote for it (Voters say its “OK”). D. It is OK if it does not break the Law (Supreme Court say its “OK”). E. Since all life is related and descendant from more primitive forms, killing a human is not different than
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