Understanding Biological Macromolecules: Types and Structures

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University of Prince Edward Island**We aren't endorsed by this school

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BIOLOGY 1010

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Biology

Date

Dec 12, 2024

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Uploaded by DeaconSalamanderPerson1258

Introduction to Biological Macromolecules (00:00-00:28)Definition: Large molecular structures fundamental to biological systemsFour Primary Types of Biological Macromolecules:1.Carbohydrates2.Lipids3.Proteins4.Nucleic AcidsPolymers and Monomers Concept (00:28-01:47)Polymer StructureAnalogy: Like "beads on a string"Key Terminology:oMonomer: Individual, unconnected unitsoPolymer: Connected units (subunits)oSubunits: Individual components within a polymerExamples of PolymersPolypeptides:oComposed of amino acid monomersoPrecursors to proteinsCarbohydrate Polymers:oMade from monosaccharide unitsNucleic Acid Polymers:oConstructed from nucleotide subunitsPolymer Formation: Dehydration Synthesis (02:13-04:28)Polymer Creation ProcessMechanism: Adding monomers sequentiallyReaction Type: Dehydration (Condensation) ReactionKey Requirements:oAt least one hydroxyl groupoEnzymatic catalysisPolymer Breakdown: Hydrolysis (03:47-04:28)Reverse of dehydration synthesisProcess:oEnzymes break bonds between subunits

oWater molecule is splitoHydroxyls and hydrogens reinstatedCarbohydrates: Saccharides (05:36-08:53)Classification by Carbon CountSaccharide TypeCarbon CountExampleTrioses3 carbonsGlyceraldehydePentoses5 carbons-Hexoses6 carbonsGlucoseSaccharide LevelsMonosaccharides: Single sugar unitsoGlucose: Most important saccharideoPrimary product of photosynthesisDisaccharides: Two linked monosaccharidesoExamples: Sucrose, LactosePolysaccharides: Multiple sugar unitsoExamples: Starch, CelluloseStructural CharacteristicsNearly every carbon contains a hydroxyl groupCan exist in linear and ring formsPolymer Formation DiagramKey TakeawaysMacromolecules are essential biological structuresPolymers form through systematic monomer connectionsEnzymatic processes control molecular transformationsSaccharides have diverse structural configurationsNomenclature Notes-ose suffix indicates sugar/saccharideMono-: One unitDi-: Two unitsPoly-: Multiple unitsSaccharides (Carbohydrates) Study Notes

Monosaccharide ClassificationCarbonyl Group PositioningAldehyde Sugars (Aldoses):oCarbonyl group at the terminal (end) carbonoExample: Glucose (a hexose)oIdentified by "-ose" suffixKetone Sugars (Ketoses):oCarbonyl group interior to the molecular structureoExample: FructoseoIdentified by "-ulose" suffixCarbon Number ClassificationTrioses: 3-carbon sugarsPentoses: 5-carbon sugarsHexoses: 6-carbon sugarsMolecular Structure VariationsLinear vs. Ring FormsLinear Form:oUsed during initial synthesisoUnstable in cellular environmentsRing Form:oPredominant in living systemsoFormed through nucleophilic attackoMore stable in waterRing Formation MechanismInvolves bonding between carbon #1 and hydroxyl group on carbon #5Electron interactions cause structural shiftCarbons maintain original numberingStereochemistry of GlucoseAlpha and Beta GlucoseAlpha Glucose:oHydroxyl group points downwardoPrimarily produced by animal cells

Beta Glucose:oHydroxyl group points upwardoProduced by plant cellsStereoisomer CharacteristicsConsidered cis-trans stereoisomersSlight structural differences impact molecular behaviorDisaccharide FormationExamples of DisaccharidesDisaccharideCompositionSourceSucroseGlucose + FructoseTable sugar, plant sapLactoseGalactose + GlucoseMilkMaltoseTwo glucose moleculesStarch digestionFormation MechanismCreated through dehydration reactionJoined by 1-2 glycosidic linkagesRequires specific enzymatic breakdown for digestionPolysaccharidesStarch CharacteristicsComposed of alpha glucose monomersConnected by 1-4 glycosidic linkagesVariations in branching structureTypes include:oAmylose (simple, unbranched)oMore complex branched variantsStructural ConsiderationsHydroxyl groups on #2 carbons typically point in same directionMolecular arrangement impacts functionalityKey Molecular InsightsStructural variations significantly impact:oMetabolic processesoCellular interactionsoChemical properties

Mermaid Diagram of Ring FormationIndustrial and Biological SignificanceDifferent sugar forms vary in:oSweetnessoStabilityoMetabolic pathwaysPractical ApplicationsFood industry sugar manipulationUnderstanding metabolic processesNutritional science researchCarbohydrate Macromolecules: Advanced Study NotesGlucose Polymers: Structure and MetabolismAlpha Glucose Polymers (Starch and Glycogen)Composition: Hexagonal glucose units forming helical structures (17:56-18:10)Storage Function:oStored in cells as energy reserveoUsed when organism needs energyGlycogen Characteristics (18:10-18:34):oPrimary storage molecule in animal cellsoFirst to be metabolized during energy shortageoMore highly branched compared to amyloseoEnables quick metabolism due to complex structureBranching SignificanceMetabolic Advantage (18:34-18:48):oMore branched structureoSupports variable and intense energy requirements in animalsoFaster metabolic processing compared to plant storage moleculesBeta Glucose Polymers: CelluloseStructural Unique Features (18:58-19:26)

Glycosidic Bond Orientation:oAlternating up and down patternoHydroxyl groups on #2 carbon alternate orientationGlucose Unit Arrangement:oUnits positioned "upside down" relative to each otheroConsequence of hydroxyl orientation on carbon #1Cellulose in Plant Cell Walls (19:38-20:14)Structural Characteristics:oLong, extended polysaccharide chainsoNumerous hydrogen bonds between adjacent strandsHydrogen Bonding:oWeak individual bondsoStrong collective molecular interactionoCritical for structural integrityEnzymatic Breakdown Limitations (20:40-21:26)Enzyme Incompatibility:oAmylases (starch-breaking enzymes) ineffective on celluloseoDifferent glycosidic bond orientation prevents efficient breakdownDigestive Implications:oHumans cannot metabolize cellulose effectivelyoConsumed cellulose passes through digestive system as "roughage"oEssential for digestive tract bulk but provides no direct energyAmino Sugars: Structural SignificanceN-Acetylglucosamine (21:26-22:48)Unique Structural Feature:oModified amino group on #2 carbonBiological Importance:oConstituent of peptidoglycan and pseudopeptidoglycanoKey component in bacterial and archaeal cell wallsoPrimary material in arthropod exoskeletonsEvolutionary Impact:oEnabled unprecedented animal life diversificationoCritical in early evolutionary development (Cambrian period)Comparative Polymer Characteristics

Polymer TypeGlucose OrientationMetabolic EfficiencyBiological RoleStarch (Alpha)UniformModeratePlant Energy StorageGlycogen (Alpha)BranchedHighAnimal Energy StorageCellulose (Beta)AlternatingLowStructural SupportKey TakeawaysMolecular orientation critically determines metabolic potentialHydrogen bonding plays crucial role in molecular stabilityStructural variations enable diverse biological functionsTriacylglycerols (Fats): Comprehensive Study NotesFormation of Fatty Acids and Fats (26:24-27:29)Key Process: Body converts 2-carbon intermediates into fatty acidsComposition:oRequires three fatty acidsoEach fatty acid has a carboxyl groupoGlycerol has hydroxyl groups at each carbonBonding Mechanism:oLinked via dehydration/condensation reactionoForms an ester bondStructural Characteristics:oGlycerol backboneoThree long-chain fatty acidsoEnergy stored in non-polar carbon-carbon and carbon-hydrogen bondsFunctions of Triacylglycerols (27:44-28:26)Primary Purposes:1.Energy StorageCan be broken down during low energy intakeEnters cellular metabolism2.Organ ProtectionCushions vital organsActs as a shock absorber3.Thermal InsulationHelps maintain body temperatureEspecially crucial for animals in cold environments (e.g., polar bears, seals)

Fatty Acid Structural Variations (28:26-30:48)Saturated Fats (Animal Cells)Characteristics:oNo double bonds between carbonsoStraight fatty acid chainsoTwo hydrogens per carbonoSolid at room temperatureExamples: Mammalian milk, butterUnsaturated Fats (Plant Cells)Characteristics:oOne or more double bonds in fatty acid chainoCreates "kinks" in molecular structureoMore fluid at room temperatureExamples: Olive oil, corn oilDouble Bond Configurations (31:00-32:18)Cis and Trans ConfigurationsCis Configuration:oCarbon chains on same side of double bondoMost naturally occurring fatty acidsoLess likely to cause heart diseaseoMore susceptible to breakdownTrans Configuration:oCarbon chains on opposite sides of double bondoProduced through hydrogenation processoStacks more easily in arteriesoIncreases heart disease riskPolyunsaturated Fatty Acids (33:11-34:34)Omega-3 Fatty AcidsStructure:oMultiple cis double bondsoFirst double bond at third carbon from omega endPotential Health Benefits:oReported prevention of heart diseaseoPotential cancer prevention

oScientific evidence remains inconclusiveFatty Acid NomenclatureCarbon Numbering:oAlpha Carbon: First carbon from carboxyl groupoOmega Carbon: Last carbon in fatty acid chainIdentification: Characterized by:oNumber of double bondsoCarbon chain lengthoDouble bond positionsFatty Acid Classification TableFatty Acid TypeDouble BondsChain LengthCharacteristicsSaturated0VariesSolid at room tempMonounsaturated1VariesSlight fluidityPolyunsaturated2+VariesHighly fluidOmega-33VariesPotential health benefitsKey TakeawaysFats are complex molecules with diverse structures and functionsMolecular configuration significantly impacts physiological effectsUnderstanding fatty acid types is crucial for comprehending nutrition and metabolismLipids: Comprehensive Study NotesFatty Acids (First Category of Lipids) (35:01-35:15)Essential Fatty AcidsoLinoleic acidoAlpha-linoleic acidoCritical Nutrients: Must be obtained through dietoCharacterized by first double bond from omega endPhospholipids (Second Category of Lipids) (35:15-38:19)Structural CharacteristicsKey Components of Cellular MembranesSimilar to fats with critical differencesComposition:oTwo fatty acid chains on glycerol backboneoUnique polar group on third carbon

Membrane Structure (36:57-38:05)Bilayer ConfigurationoTwo phospholipid layersoHydrophilic heads oriented toward wateroHydrophobic tails pointed inwardHydrophilic vs Hydrophobic PropertiesHydrophilic HeadoPolaroContains electronegative atomsoInteracts with water inside/outside cellHydrophobic TailsoNon-polaroExcludes wateroCreates selective membrane barrierSpecial Formations (38:19-38:59)Micelles and LiposomesoSpherical structuresoHydrophobic tails point inwardoUsed in laboratory for:Nutrient deliveryPharmaceutical transportSphingolipids (39:15-39:38)Similar to phospholipidsUnique roles in:oCellular signalingoCellular raftsSteroids (Third Category of Lipids) (39:38-43:24)Fundamental CharacteristicsStructural FeaturesoFour-ring structureoVirtually water-insolubleoHighly non-polar and hydrophobicNumbering Convention

Rings designated A, B, C, DNumbering starts on ring AAllows precise description of functional groupsHormone ExamplesEstradioloFemale hormone precursoroSpecific molecular configurationTestosteroneoMale hormoneoSubtle molecular differences from estradiolUnique Steroid: 7-DehydrocholesterolPrecursor to serum cholesterolConverts to Vitamin D3 when exposed to sunlightUltraviolet rays trigger molecular transformationMermaid Diagram: Lipid StructureKey TakeawaysLipids are diverse molecular structuresCritical for cellular functionVary in polarity and interaction with waterPlay crucial roles in biological processes

Biological Macromolecules: Proteins Deep DiveProtein Overview (00:37-00:58)Cellular Significance: Arguably the most important cellular constituentUnique Characteristics:oPerform a vast variety of cellular functionsoEspecially critical as enzymesoEnable and accelerate specific biochemical reactionsProtein Structure (01:11-01:38)Visualization Techniques:oRibbon model commonly used in scientific representationoPurple line represents protein backboneoYellow lines indicate disulfide bridgesKey Insight: Protein's twisty shape is crucial to its functionalityProtein Functions (05:50-08:54)Diverse Protein Roles1.Enzymatic ProteinsoAccelerate chemical reactionsoExample: Sucrase breaking down sucrose2.Defensive ProteinsoAntibodies protect against:VirusesFungal sporesToxinsBacteria3.Storage ProteinsoProvide materials for developing embryosoExample: Egg whites4.Transport ProteinsoHelp molecules pass through cell membranesoFacilitate selective cellular entry/exit5.Hormone/Signaling ProteinsoEnable inter-cellular communication

oTrigger gene expressionoExample: Insulin6.Receptor ProteinsoEmbedded in cellular membranesoReceive signaling moleculesoFacilitate nerve impulse propagation7.Motor ProteinsoCause cellular structural movementoCritical for muscle cell action8.Structural ProteinsoProvide strength and textureoExamples:Keratin (in hair)Collagen (binds cells in tissues)Amino Acids: Protein Building Blocks (09:10-10:53)Basic Amino Acid StructureComponents:oCentral alpha carbonoHydrogen atomoAmino group (gives "amino" in name)oCarboxyl group (gives "acid" in name)Amino Acid CharacteristicsVariation: 20 different amino acids in human systemsDistinguishing Feature: R-group (side chain)State Changes:oNon-ionized state: Chemical shelf conditionoAqueous solution: Zwitterion (positive and negative charges)Amino Acid Classification1.Non-Polar/Hydrophobic Amino Acidso9 total typesoExamples: Glycine, Alanine, ValineNaming ConventionsThree-Letter Codes:oGLY (Glycine)oALA (Alanine)One-Letter Codes:

oUsed in advanced biochemistryEnzyme Specificity (02:36-03:29)Active Site:oSpecific pocket in enzymatic proteinsoAccepts particular substrateNaming Convention:oSuffix "-ase" indicates enzymeoSuffix "-ose" indicates sugarFunctional Process:oSubstrate enters active siteoEnzyme facilitates specific chemical reactionoEnzyme can repeat process multiple timesEnzyme Example: SucraseSubstrate: SucroseReaction: Hydrolyzes glycosidic bondResult: Breaks sucrose into glucose and fructoseMnemonic for Enzyme NamingSuffix Rule:- Ends in "-ose" → Sugar- Ends in "-ase" → EnzymeAmino Acids and Protein Structure Study NotesAmino Acid Backbone Structure (12:07-12:33)Core Components:oAlpha carbonoHydrogenoAmino groupoCarboxyl groupIonization in Aqueous Solution:oAmino group picks up hydrogen ionoCarboxyl group loses hydrogen ionAmino Acid Categories Based on R-Groups1. Non-Polar Amino Acids (12:33-13:27)

Characteristics:oComposed primarily of carbon and hydrogen atomsoLack electronegative atomsoDo not attract wateroNon-soluble in waterExample: Methionine (sulfur atom is minimally impactful)2. Polar Amino Acids (13:28-14:30)Key Features:oContain prominent electronegative atoms in R-groupoIncludes oxygen, sulfur, and nitrogenoOften part of functional groups like amidesControversy: Cysteine classificationoSome consider it polaroOthers classify as non-polar3. Charged Amino Acids (14:53-15:45)Acidic Amino AcidsCharacteristics:oCarboxyl group at endoIonizes by losing hydrogen ionoBecomes negatively chargedoHydrophilicBasic Amino AcidsCharacteristics:oAmino group at endoIonizes by taking up hydrogen ionoBecomes positively chargedoHydrophilicPolypeptide Formation (17:40-19:56)Peptide Bond:oConnects amino acidsoFormed through dehydration reactionPolypeptide Growth:oAlways adds new amino acids to C-terminusoInvolves removing water moleculeTerminology:oN-terminus: First amino acid

oC-terminus: Last amino acid addedProtein Structure Levels (20:20-24:09)1. Primary Structure (20:32-23:30)Definition: Sequence of amino acids from N-terminus to C-terminusExample: Transthyretin protein (127 amino acids)Case Study: Sickle Cell AnemiaoMutation in hemoglobin beta chainoSingle amino acid change impacts protein function2. Secondary Structure (23:31-24:09)Characteristics:oProtein shape determined by hydrogen bondsoOccurs between amino acid backbonesoInvolves common structural elements (alpha carbon, hydrogen, amino/carboxyl groups)Exam Preparation Tips (15:45-17:15)What to Know:oBasic amino acid structureoR-group characteristicsoAbility to identify amino acid categoriesExam Expectations:oDraw representative amino acidsoExplain R-group propertiesoDemonstrate understanding of structural variationsMermaid Diagram: Amino Acid ClassificationKey TakeawaysAmino acid properties depend on R-group compositionProtein structure is hierarchical and complexSmall changes can significantly impact protein functionProtein Structure: A Comprehensive Guide

Primary Structure (29:50-30:01)Definition: Sequence of amino acids in a polypeptide chainFundamental building block of protein structureSecondary Structure (24:21-25:24)Beta-Pleated SheetCharacterized by hydrogen bonds running parallelCommon in fibrous proteins like:oSilkoKeratinoCollagenInvolves waviness in protein structureAlpha HelixHelical arrangement of polypeptideHeld together by hydrogen bondsFound in globular proteins like enzymesKey Point: Involves backbone hydrogen bonding, NOT R-group interactionsTertiary Structure (25:24-28:33)Interactions Determining Protein Shape1.Hydrogen BondsoWeak but significant when multiple bonds formoPolar amino acids interact via electronegative atoms2.Hydrophobic InteractionsoNon-polar amino acids cluster togetheroSimilar to phospholipid tail interactionsoForce non-polar groups inward, polar groups outward3.Ionic BondsoAttraction between positively and negatively charged amino acidsoWeak but contributory to protein structure4.Disulfide BridgesoFormed by cysteine amino acidsoStrong covalent bonds between sulfur groupsoCritically stabilize protein shapeQuaternary Structure (28:58-30:24)

Occurs when multiple polypeptide chains form a complete proteinExample: HemoglobinoComposed of 4 polypeptideso2 alpha chainso2 beta chainsRequires correct assembly of subunit chainsProtein Folding and FunctionalityImportance of Protein ShapeShape determines protein functionIncorrect folding can lead to:oReduced efficiencyoComplete loss of functionDenaturation (34:26-36:38)Causes:pH changesTemperature shiftsIon concentration variationsEffects:Weak bonds breakProtein loses native structurePotential for renaturation under mild conditionsExtreme conditions can permanently alter proteinClinical Example: Sickle Cell AnemiaCaused by single amino acid changeGlutamic acid → Valine mutationAlters protein shapePrevents proper hemoglobin functionLeads to misshapen red blood cellsProtein Structure HierarchyKey TakeawaysProtein structure is hierarchical

Each level contributes to overall protein functionSmall changes can have significant consequencesEnvironmental conditions critically impact protein structureNucleic Acids: The Cellular Information MoleculesOverview of Nucleic Acids (37:16-37:43)Fundamental Role: Primary information storage and transmission system for cellular composition and functioningMetaphorically considered the "blueprint of the cell"Primary function: Encoding information for protein productionTypes of Nucleic Acids (38:22-38:49)1. DNA (Deoxyribonucleic Acid)Contains protein information for every cellTransmitted during cell divisionBasis of heredity2. RNA (Ribonucleic Acid)Multiple functional typesKey role in protein information transferNucleotide Structure (40:36-41:46)Nucleotide ComponentsPentose SugarPhosphate group (attached to #5 carbon)Nitrogenous base (attached to #1 carbon)Bonding CharacteristicsPhosphodiester BondConnects nucleotide subunitsLinks #3 carbon of one nucleotide to #5 carbon of nextNucleic Acid Differences: DNA vs RNA

Sugar CompositionFeatureDNARNASugar TypeDeoxyriboseRibose#2 CarbonNo hydroxyl groupHydroxyl group presentNitrogenous BasesPurines (2):Adenine (A)Guanine (G)Pyrimidines (3):Cytosine (C)Thymine (T) - DNA onlyUracil (U) - RNA onlyDNA Structure (47:45-48:42)Typically double-strandedBases paired via hydrogen bondsSpecific pairing rules:oA always pairs with T (2 hydrogen bonds)oG always pairs with C (3 hydrogen bonds)Information Flow (39:02-40:22)Transcription ProcessDNA section (gene) copied to RNAMessenger RNA (mRNA) createdmRNA leaves nucleus to ribosomesTranslation ProcessRibosomes read mRNA informationAssemble polypeptides by combining amino acidsResulting polypeptide folds into functional proteinKey Terminological Highlights5' End: Last free carbon is #5 carbon3' End: Last free carbon is #3 carbon

Base sequence determines nucleic acid identityStructural VisualizationImportant ConsiderationsNucleic acid length variesRNA: 20-1000s nucleotidesPrecise base orientation critical for hydrogen bondingStructural complementarity essential for functionDNA Structure and Genetic Information TransmissionDNA Complementarity and Base Pairing (49:52 - 51:23)Key Pairing Rules:oA always pairs with ToC always pairs with GStrands are complementary, like a chemical mirror imageComplementarity ensures accurate genetic information transmissionDNA Strand Orientation (51:39 - 52:53)Strands are antiparallel5' and 3' ends are opposite on each strandAnalogy: Like a two-lane road with opposite directionsStrand Orientation VisualizationDNA Double Helix Structure (53:08 - 53:40)Characteristics:oTwisted corkscrew configurationoStrands held together by hydrogen bondsoNo covalent bonds between strandsDNA Structural Parameters (53:53 - 54:50)

Key Measurements:oOne full helix turn = 10 base pairsoHelix turn length = 3.4 nmoHelix radius = 1 nmoHelix diameter = 2 nmBase Size DifferencesBase TypeSizePurines (G, A)LargePyrimidines (C, T)SmallRNA vs DNA Differences (54:50 - 55:18)RNA Characteristics:oPolymer of ribonucleotidesoNot double-strandedoNot hereditary materialoUses uracil instead of thymineGene Transcription and Translation (55:18 - 56:26)Transcription Process:oTemplate strand copied into messenger RNAomRNA is complementary and antiparalleloA pairs with UoC pairs with GMutations and Genetic Variation (57:26 - 59:52)Mutation Characteristics:oOccasional errors during DNA replicationoCan be corrected by proofreadingoSource of genetic variationoCan produce beneficial or harmful protein variantsMolecular Clock ConceptSelectively neutral mutations accumulate at steady rateUsed to estimate evolutionary relationships between speciesEvolutionary Protein Analysis (59:52 - 60:41)Protein primary structure differencesCan reconstruct evolutionary relationshipsFirst evidence of using protein variants as molecular clock

Mutation Impact ExampleSickle-cell anemia mutationoGlutamic acid replaced by valineoDemonstrates how single nucleotide change affects protein functionKey TakeawaysDNA structure is crucial for genetic information transmissionComplementarity and precise base pairing are fundamentalMutations drive genetic diversityMolecular techniques allow tracking evolutionary relationships