Biochemistry PowerPoint BIOL 2220
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This 10 page Class Notes was uploaded by Victoria Hills on Wednesday August 31, 2016. The Class Notes belongs to BIOL 2220 at Clemson University taught by John Cummings in Fall 2016. Since its upload, it has received 10 views. For similar materials see Human Anatomy and Physiology I in Biology at Clemson University.
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Date Created: 08/31/16
ClemsonUniversity Fall 2016 Biochemistry PowerPoint Slide 2: Definition of Biochemistry Chemical composition andreactionsofliving matter Lookingat biologicalcompounds(Compoundsoflivingorganisms) Slide 3-4: Bio-compounds Inorganic: - Doesn’tcontaincarbon - Includeswater, salts, acids, and bases - Whensalts, acids, andbasesdissolvein water theydissociate into charged particles called ions - Chargedparticlesin the humanbodyarecalledelectrolytes (Again, coming from the dissolvingofsalts suchasNaCl, KCl, etc.) Organic: - Do containcarbon - Carbonhasthepotential for 4covalentbonds,which meansit won’tdissociate into electrolytes(NOT ionic) - Focusisoncarbohydrates,proteins,lipids, andnucleic acids *Relatedto thelowest level of organizationwherebio-compoundsareusedto assemble cells that is usedto build andmake higher levels oforganizationoftissues, organsetc. Slides 5-15:ImportantInorganic Compounds Water: - 60-80% ofthemassofthe humanbodyis madeupofwater - Propertiesofwater: a) High heatcapacity: o Water is resistant to changesin temperature o This is important becauseofthebodyhavingahomeostatic body temperature Water makes it easier to maintain this homeostatic body temperature b) High heatof vaporization: o Water requiresalotofheat (Andthereforeenergy)inorder for itto turn fromaliquid into a gas o Allowing water to evaporatefromour bodiesmeansthatit also has coolingpowers(Regulator ofbodytemperature) c) Universal solvent: o Solution: Createdwhena solutedissolvesinto asolvent Solute: Substancebeingdissolved Solvent: Whatthe substanceisbeing dissolvedin Ex: Thesolute in asaline solutionis salt o Ionic molecules(Moleculesmade throughionicbonds)areableto dissolvein water o Polar compoundscandissolvein water, which meansthey havethe ability to createions which areableto then betransportedbywater (Since solventsalso act astransportmediums) Important becausefor anything to bebiologically active, it hasto bein solution o Ex: ConsumptionofFood Foodismoistenedinthe mouthin order to put it into solutionandhaveenzymes breaksomecomponentsdown Foodmovesto thestomachwheregastric juice is secretedin order to allow differentenzymes to work ondifferent components Main idea:Foodandits componentsareputinto solutionfor these breakdownmechanismsto happen d) Hydrolysis/condensation: o Water allows thebodyto engagein hydrolysisandcondensation reactions o Reminder: All ofthemetabolic activities ofthe bodyareeither anabolic (Build up)or catabolic (Breakdown) Therefore,everythingin our bodygoesthroughasynthesis(Anabolic)or decomposition(Breakdown) reaction o Condensation/Dehydration synthesis reaction:H O rem2ved If thereare2reactants goingthroughananabolicreactionin order to build something up,water is removed o Hydrolysis reaction:H O added 2 If thereisa substancethat is to bebrokendown,water is split and addedso that theOH goesto oneside andtheH goesto the other side e) Cushion o Water hastremendouscushioningpotential that canbefoundbetween bonesandjoints (Sacoffluid is presentso thatbonedon’tcrushinto each other,for example) o Cerebralspinalfluid surroundsthebrainandthewater actsa cushionto protectfromheadtrauma Salts: - Substancesthat dissociate to formcations(+) andanions(-) which are electrolytes o AKA: Salts createelectrolyteswhen theydissociate into solution - Important becausethemovementofchargedparticles produceselectrical energy - Movementofchargedparticles arespecifically necessaryfor electricalenergy usein nervepulsesthat transfer throughoutthebodyandthatalso act assignals that causemuscles to contract - Again: Electrical energyis usedfor lifeprocesses - Salts canalso bedepositedinto a matrix andbuildtissue suchas boneandteeth (Createhardtissue substances) o Ex: Ifmorediet is consumedfromthediet than for whatis neededatthe time, it is put into bonesandwhenit’sneededlater it will bereleased frombone - Salt balancein our bodyiscritical for life There isa verynarrowhomeostatic optimum for salt balance o Kidneys areresponsiblefor regulatingtheionicbalance o If onewereto go into renalfailure,death canfollowveryquickly sinceit is veryhardto re-establish saltbalance after it is lost Acids: - Substancesthat dissociate - Whenacidsdissociate, they increasethe hydrogenionconcentration - Hydrogenionshaveapositive chargeso theyhavemoreprotons Thismeans that anacid is a proton donor sinceit givesup ahydrogenionsomewherein another chemical reaction o AKA: Acids dissociateto produceH(+) - Acids throughdissociationcanalso createelectrical currentsandproduce electrical energy Bases: - Substancesthat increasethehydroxylion(OH) concentration-Typical chemistry definition - In termsofanatomy/physiology:Abaseis asubstancethat reducesthe hydrogenionconcentration,making bases proton acceptors pH: - Descriptionofthe levelofacidity or alkalinity ofasolution - Expressedonascalefrom0-14 o Basedonconcentrationofhydrogenionsinsolutionin moles/liter (Dissociation ofhydrogenionsinwater) o p= negative logandH= hydrogenionconcentration o <7 Acidic o >7 Basic(Basesremovehydrogenionsso theyshift thescale higher) o 7= Neutral - Is homeostatic: o Differentpartsofour bodyhavedifferentoptimal pH’s Ex: MouthpHis differentthan thestomach’spH All partshaveto haveahomeostatic pHthoughin order to work properly o HomeostasisofpHis maintained by: a) Neutralization: Addition ofanacid andbase Water +Salt Water aneutral pHof7 Summary: Combinationofwater andasalt results ina neutral solution b) Buffering: Processinwhich the addition ofsmall amountsofacid or basedo notresult in apHchange Resists pHchangesbyeither accepting or liberatinghydrogenions *Mechanismsareimportant becausehumansconstantly floodtheboywith acidic or basicfoods(Predominantlyacidic foodssuchascokethatis acidic dueto its ingredientsand carbonation,for example;Ex:Overindulgencein alcohol Acidosis Death) Slides 16-43:ImportantOrganic Compounds Carbohydrates: - Include sugarsandstarches - Bodyis composedof60-80%water,which means that the cell is madeup of1- 2% carbohydrates - Main functionofcarbohydratesisto beasourceofenergy - Glucoseactsas themajor player in energyproductionsinceit mosteasily enters glycolysis whereit is then brokendownto pyruvate TCA cycle Electron transportchain Ultimately making ATP for energy - Energycancome fromsourcesother thanglucoseaswell - Monosaccharides: o Smallest formofsugar;Individual units = simple sugars o Taste verysweet o Canbeabsorbedimmediately acrossthewall of the digestive tract o Canbeimmediately usedto provideenergydirectly fromtheblood stream o Simple sugarsarenamedbasedonthenumber ofcarbonstheycontain: Pentose:Have5 carbons Hexose:Have6carbons o Monosaccharideswill always haveaC:H:O ratio of1:2:1 Ex: C6H12 6 Glucose - Disaccharides: o 1monosaccharide+1monosaccharideviaadehydrationsynthesis reaction Polymerization to produceadisaccharide o Ex: Sucroseis1glucose+1 glucose=table sugar o Ex: Lactoseis1 galactose+1glucose= milk sugar Manyindividuals suffer fromlactoseintolerancebecauseas newbornsweproducelactasethat is theenzyme that breaksdown lactosebut asoneagesandespecially onceoneisweaned, the enzyme is usuallyno longer produced Issueswhen consuming dairyproductscontaining lactose o Must bedigestedand brokendowninto monosaccharidesbeforetheycan beabsorbed acrossthewallofthedigestive tractvia hydrolysisreaction - Polysaccharides: o Additions ofmonosaccharidesanddisaccharidesto produce polysaccharides viadehydrationsynthesis reactions o Must bedigestedand brokendowninto ultimately monosaccharides beforetheycanbeabsorbedacrossthewallofthedigestive tract via hydrolysisreactions o Unique characteristic: Don’ttastesweet like monosaccharides+NOT water soluble o Longchainpolysaccharidesarestoredasstarchinplants andasglycogen in animals o Glycogen: Createdin animals whenthereis extrasugar notneededfor energyyet Storedin liver and muscle Keyto understandthatglycogen consumedfromanimalsources must bebrokendowninto their monosaccharidecomponentsand berebuilt asglycogenin the humanbody Lipids: - Canexist in 1of2 statesofmatter Liquid or solidat roomtemperature - Solid =fat - Liquid= oil - NOT water soluble - Will dissolve in other lipids andorganicsolventssuchasacetoneandbenzene - NeutralFats(Triglycerides): o Atriglyceride contains 1glycerol +3fatty acids (FA) o Non-polar so won’tdissolvein water o Functionprimarily as energystoragemolecules Storageprocess: After the consumptionofameal, glycogenstoresfill upfirst with glucose Excessglucoseis storedasfatin adiposetissue Althoughglucose is usedthemost for energysinceit is easiest and in simplest form, moreenergycan beobtainedfromlipids thanout ofsugar (20x morethanoutofglycogen) Whenenergyisneeded: Glucosefromglycogenisbrokendownandusedup first Then breakdowntriglycerides in storagefor energy o Lipids functionin insulation: Ex: Pack kidneys infat that arelocatedonthe backside in order to preventmajor lossofbodytemperature o Lipids also protectorgansviaworking asacushion - Classes of Triglycerides: a) Saturated: o 1glycerol +3FAthat haveall singlebonds(NO doublebondsbetween2 carbons) o Solid atroomtemperature o Predominantly foundinanimal fat o Saturatedfat consumptiontendsto increasecholesterollevelsin the body o Cantell fromanevolutionaryperspectivethat humansaresupposedto havemeat in thediet Vegetarianshaveanadvantagethoughsincethey won’tconsume asmuch saturatedfat, which meansthat cholesterolwon’tbeas big ofanissue b) Unsaturated: o Containsa single bondin1 ofthe3FA’sthat areesterifiedto theglycerol backbone o Oils atroomtemperature o Do notcauseanyincreasein cholesterolbecausetheydon’thaveany effectoncholesterol c) Polyunsaturated: o Atriglyceride that has 2or morebondsinthe3 FA’sesterifiedto the glycerolbackbone d) Trans-fats: o Comesfromafat this is anoil that is composedofpredominantly polyunsaturatedtriglycerides This oil formissolidified in a lab by simply floodingit with hydrogens Breaksthedoublebondsofthe polyunsaturatedtriglyceride o This synthetic creationoftransfatwas originally done inorder to add moreflavor insnack foodssincelotsofsaturatedfat tendsto give more flavor Peopledid notwant the incorporationoflardasthesourceof addedsaturatedfatso trans-fat was synthetically createdto addthe sourceofsaturatedfatfor flavor o Trans-fat is aconcernbecauseitgrosslyincreasescholesteroland thereforeincreasesheartdisease o Trans-fat canalso benaturally foundinanimal sourcessuchasground beef e) Omega-3 FattyAcids: o PolyunsaturatedFA o Omega: Meansat thefar endofthe FAchain Namingcomesfromstarting at the endoftheFAchain and counting thecarbonsbackwardsuntil youmeet wherethedouble bondislocated rd Ex: Omega-3 FAhaveadoublebondatthe 3 carbonfromthetail Ex: Omega-6 FAhaveadouble bondatthe 6 carbonfromthetail o Shownto reducecholesterol(Samewith omega-6FA—Shownlater in research) o Predominantly foundinfish oils: (Extra) The stomachis acts asastoragetank so theproblemwith pills is that it will sit in thestomach for awhile beforethereisasignal for the stomachto empty into the small intestine so theoil will sit on topofthe stomach Nowother omega-3FAsourcesinpill formarecomingfromkrill - Phospholipids: o Structure:Take 1 FAawayfromthe glycerolbackboneonatriglyceride and substitute it with a phosphateresultsina phospholipid In summary:2 FA+phosphateonaglyceryl backbone o Havea non-polar componentthroughthe2FAthatdoesn’tlike water o Havea polar componentthroughthephosphatethatlikes water o Whenphospholipidsareinsolution Geta doublelayer of phospholipidsbecausethepolar/water lovingcomponentofthe phosphatefacestheoutsidetowardsthe water and thenon-polar/water opposingFAcomponentsfacetheinside away fromthewater Phospholipidbilayer makes upcellular membranes Amphipathic molecule Meaningmoleculehaspolar andnon- polar parts - Steroids: o Madefrom4interlocking hydrocarbonrings o Fatbased Fat soluble o Ex: Testosteroneandprogesterone Differene betweenthetwo hormonesis1doublebondand1hydrogen o Steroidsareaformofsignaling molecule(1 class ofhormones) o Nervoussystemandendocrinesystem areinvolvedin regulation Steroidsarepartofthe endocrinesystem o Long-distancesignaling molecules that areproducedinonepartand affectanother partsomewhereelse - Eicosanoids: o Localsignaling molecules Producedinonepartofthebodyandaffect that sameplace o Fatbased o Triglyceride structureis what getsmodified to produceeicosanoids Proteins: - 10-30% ofthemassofa cell is madeupofprotein Therefore,cellsare predominantly water andprotein - Proteinsarecomposedofamino acids(AA) - WhenAAarelinked together Results in apolypeptide - AA+ AAarebondedtogether viapeptide bonds—Functionthroughanitrogen - Proteinsin the humanbodyaremadeupof20AA - SomeofthoseAAareonly availablefromanimal sources - Someproteinscan’tbe madein thebodyif apersonisa strict vegetarian - Protein Structure: a) Primary Structure: o Linear sequenceofallthe AAthat make upa protein Review: Linear AAchains make upapolypeptide b) Secondary Structure: o BecausetheseAAhavedifferentchargesassociatedwith them(Positive or negative), all oftheseprimarystructureswill twist as aresult o 2possiblesecondarystructures: 1. Beta pleated sheet: For example-Foundinstraight hair 2. Alpha helix: For example-Foundincurlyhair c) Tertiary Structure: o Secondarystructurecoilsenoughso thatthe AAget closeenoughto each other andthey twist even moreto give a3D shape o Possessactive sites wherespecificsubstratescan fit Makes upa functional protein,for example(One typeofprotein) d) Quaternary Structure: o If thereismorethan 1peptide chainlinked together Complex protein >1polypeptide chain=Quaternarystructure o Ex: Hemoglobin Consistsof4 peptidechains =complex protein with 4 subunits that all wraparound=quaternarystructure - Types ofProteins: o Structural/Fibrous: Give formto bodyparts Mostabundantproteinin the bodyis collagenthat givesform o Regulatory: Regulateprocessesgenerallyasahormone(Inaddition to the steroid-basedhormonesaswell) o Contractile: Ex: Myosinandactin in muscle o Immunological: Antibodies that fight infectionor disease o Transport: Carrier moleculesknown astransportproteins Ex: Hemoglobincarriesoxygen o Catalytic: Enzymes that areproteinsthat functionasbiological catalysts and speedupchemical reactions 3D shapecausestheenzyme to havean active site that will bindto andonly certain substrates Whenasubstratebinds to the active site Inducesthe activation energyto allow that reactionto occur Enzymes do notget consumedin thereaction(Still havethe reactionwhen thereactionis complete) Overall Process:Enzyme bindswith specific substrate Forms enzymes- substratecomplex Substrateto formproduct+ enzyme availableto beusedagain Ex: Pictureshows adecompositionreaction - Denaturation: o Lossofaprotein’s3D shape o ChangepHor temperaturetoo muchoutside oftheoptimal range Denaturation Lossoffunctionoftheprotein o Structuralproteinsarerelatively stableanddon’tdenatureveryoften while functional proteinstend to denaturemoreeasily Nucleic Acids: - Largestmoleculesin thebody - Comprisedofnucleotides(ATCG that areeither a purineor pyrimidine) that are boundto apentosesugar viaphosphatebonds - Summary: Nucleic acidis made upofaphosphate group,5carbonsugar,and nucleotides(Nitrogenousbases) - DNA: o Genetic material locatedin the nucleusofthecell o Nuclear material contains codesegmentscalled genesthatindirectly code for theproductionofproteins o Sugar =Deoxyribose o Double-strandedmolecule o AT andGCcomplementary nucleotidepairing that areheldtogether by hydrogenbonds - RNA: o Ribonucleic acid o Sugar =Ribose o Single-strandedmolecule o T (Thiamine) is replacedbyU (Uracil) MeansRNA will haveadifferent nucleotide configuration AU andGCcomplementary nucleotidepairing o DNAcodesfor theproductionofproteinsindirectly via codingfor RNA o Process: DNAstays inthe nucleusbut sendsamessenger to ribosomestht make RND Adenosine Triphosphate(ATP): - Adenineis boundto aphosphatein which 2additional phosphatesareattached - Important becauseATPis the currencyofenergyinour bodies - Energyis releasewhenabondis broken: o Whenaphosphateiscleaved offATP Produceenergy(Typically 1 phosphateisbrokenoffandthena phosphateisaddedbackonto use ATP molecule over again)
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