Key termsProkaryotic – “before a nucleus” bacteriaEukaryoticOrganelleIn vivo – “in life” – real lifeIn vitro – “in glass” – experimental situationIn silico – “in the computer” – dataProperties of live cellsPossess a genetic program and the means to use itAsexual reproductionAcquire & use energyCarry out chemical reaction (metabolism)Engage in mechanical activities – move aroundRespond to stimuliSelf-regulateEvolutionBased on these properties viruses are not cellsBacteriaProkaryoticHave plasma membrane but no nucleus.Has a nucleoidNot all bacteria have a flagellum or a cell wallPlant cellEukaryoticSome plants can have both mitochondria & chloroplastAnimal cellEukaryoticexceptionsMature red blood cells don’t have a nucleus, ER, golgi, or mitochondriaTheoriesEndosymbiont theory - Eukaryotic cells ingest prokaryotic cells which lead to the formation of the organelles.Eukaryotic cells lost chloroplastsTypes of bonds and interactionsCovalent bondsNon-covalent bondsIonic/electrostatic bonds – fully chargesHydrogen bonds – partial chargesVan der Waals interactionsHydrophobic aggregationsThey are hydrophobic exclusions from water. Not bonds, interactions, or forces between moleculesLecture 4Four main types of organic macromoleculesCarbohydrates (sugars) – polar structuresMetabolic sugars – mainly used for energyGlucose, starchGlycogen – storage form of glucose. Metabolic sugar polymerStructural carbs – make up cell wall/membranesPolysaccharides, complex carbs.Cell walls of plants – celluloseSugars on glycoprotein (sugars covalently attached) and glycolipids in membranesProteinAmino acids are identified by their side chainsPolar & fully charged @ pH=7, hydrophilicPolar but uncharged @ pH=7, hydrophilicNonpolar @ pH=7, hydrophobic – non water soluble.Not lipidsFree amino acids all have both an amino & carboxyl groupAmino acids are covalently attached by peptide bonds between amino & carboxyl groupsCharge depends on pHpH = 7, free amino acid - amino = (+) and carbonyl = (-)LipidsMetabolic lipidsStructural lipidsPhospholipidsSterols – in plants cellsterminologyFree fatty acid – not covalently attached to anythingFatty acyl side chain - covalently attached to somethingSaturated fatty acids – no double bondUnsaturated – at least one double bondPolyunsaturated – a lot of double bonds (2 or more)Lye soapLard + high pH base -> glycerol + lye soap ( free fatty acid)Free fatty acids become amphotericMelting pointMore double bond = more fluid = increasing unsaturation = lower melting pointFatty acid above its melting point = more fluidPhospholipidPolar head groupPCNet charge = 0 at pH 7Head group = cholinePSNet charge = -1Head group serinePENet charge = 0Head group = ethanolaminePINet charge = -1Head group = inositolCLNet charge = -2Head group = glycerolGlycerol backboneFatty acid side chainsNo net charge at pH 7Sterol – none in prokaryotesCholesterolNone in plantsAmphipathicTestosteroneCholesterol made into more amphipathic, water soluble (more polar)EstrogenPhospholipid -> lysolipid + free fatty acids (strong detergents)How macromolecules are broken down1. Break macromolecules into its building blocks (mostly by hydrolysis) occurs at the lysosome and cytoplasm2. Break down further to acetyl-CoA by glycolysis – occurs at the cytoplasm3. Conversion of acetyl-CoA into TCA cycle components and high energy products like NADH. Occurs in mitochondriaNADH used for electon transport in mitochondriaDNA and RNAReplication – DNA -> DNATranscription – DNA -> RNATranslation – RNA -> ProteinReverse Transcriptase – RNA -> DNA3 main parts of Nucleotides – determines if something is RNA or DNA1. Base – tells you what it base pairs with2. Sugar – tells you if it is RNA or DNA3. Phosphate – negative charge at pH 7.0SugarDifferent in RNA and DNADeoxyribose (has a H instead of OH on 2nd Carbon) – on DNA onlyBase pairs – Hydrogen bonding between base pairsA-T = DNAA-U = RNAC-G = bothDNA – polymer of deoxyribonucleotidesPolypeptide – polymer of amino acids = proteinPolysaccharide – polymer of sugars = complex carbohydrate or oligosaccharidePolynucleotide – polymer of nucleotide = DNA or RNA3 major types of RNA – all made in nucleusRibosomal RNA (rRNA) – make up 80-90% of RNA, not translatedTransfer RNA (tRNA) – required for translationMessenger RNA (mRNA) – required for translationCentral Dogma – DNA -> mRNA -> ProteinDNA transcription to mRNAmRNA translation (needs rRNA and tRNA) to protein2 ways to cut RNA1. add a ribonuclease (RNAse), ending in ase = destroying. This is an enzyme and protein. Use protein to cut RNA2. Add a ribozyme. Different enzyme / catalytic RNA. Could use RNA to cut RNAMembranesExperiments to determine what membranes are1. E. Overton used hypertonic shrinkage to estimate the composition of plasma membranesHypothesis – like dissolves like – so if membrane is hydrophobic then it should be permeable (allows liquid/gas to pass through) and prevent hypertonic shrinkingHypertonic shrinkageOutside – high solute concentration, low water concentrationSemi-permeable membraneInside – lower solute concentration, high water concentration (things tend to move from high to low)Adding any solute to water lowers the water concentrationIn a hypertonic solution, water moves down its concentration from high water concentration to lowSince the water concentration is lower outside, water moves out = cell shrinkageWater moves toward the highest solute concentrationHypotonic solutionSwelling, water moves in the cellIsotonic solutionHypertonic solutionShrinking, water moves out of the cellOverton’s conclusion1. Hydrophobic compounds (fatty oils) prevented hypertonic shrinking of plant cells – permeable compounds2. Hydrophobic membranesTypical membrane structuresGorter and Grendel’s experiment – proposed that membranes are lipid bilayers1. Used red blood cells(RBC) because the only membrane in RBC is the plasma membrane2. Determined the surface area3. Extracted the lipids and measured the surface area of it on a monolayer to see if it matched with the calculated surface areaExtracting lipids from cells1. Add RBC to hexane (dissolves lipid)2. Add water to the hexane (interacts like oil and water)3. Take off the hexane layer – has all the lipidsmeasuring the area on monolayer1. Spread lipid on top of water2. Monolayer of phospholipid forms spontaneouslyresultsmeasured surface area was 2x the calculated