2.1 Molecules to metabolism · 2018-04-20 · 2.1.U3 Life is based on carbon compounds including...

ByChrisPaine

h-ps://bioknowledgy.weebly.com/

2.1Moleculestometabolism

EssenAalidea:LivingorganismscontroltheircomposiAonbyacomplexwebofchemicalreacAons.

ThebackgroundisjustasmallpartoftheIUBMB-Sigma-NicholsonMetabolicPathwaysChartaimstoshowallthemetabolicpathwaysfoundineukaryotecells.Thechartinit'senAretyshowshowcomplexthechemicalsreacAonsneededtosupportlifeinasinglecellunit.

2.1.U1 Molecular biology explains living processes in terms of the chemical substances involved.

ThestructureofDNAwasdiscoveredin1953,sincethenmolecularBiologyhastransformedourunderstandingoflivingprocesses

TherelaAonshipbetweengenesandthepolypepAdestheygenerateisattheheartofthisscience.Thecentralideacanbesimplifiedto“DNAmakesRNAmakesprotein”.TheinformaAoninthisflowcannotbereversedandtheproteingeneratedcannotchangetheRNAorDNA.

h-ps://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg

2.1.U1 Molecular biology explains living processes in terms of the chemical substances involved.

TheapproachofamolecularBiologistisareducAonistone–theyidenAfythestepsinametabolicpathwayandbreakdowneachoneintoit’scomponentparts.ThisapproachhasbeenaveryproducAveone.OurunderstandingofrespiraAon(2.8)andphotosynthesis(2.9)aregoodexamplesofthesuccessofthisapproach.

Organicmolecules,especiallyproteins,areverycomplexandvaried.Henceorganiccompoundshaveahugelyvariedroleswithin(andoutsideof)cells.ThereisalotaboutorganicmoleculesincellswesAllhavenotdiscoveredorunderstood.

SomescienAststhinkthatthereducAonistapproachaloneisulAmatelylimited.Moleculescanhavedualroles(e.g.Melaninisthepigmentthatcoloursbothskinandeyes)andalsomayinteractwitheachotherinwaysthatareducAonistapproachoverlooks.

h-ps://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg

2.1.U2 Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.

Despiteonlybeingthe15thmostabundantelementontheplanetcarbonformsthebackboneofeverysingleorganicmolecule.

Covalentbondsarethestrongesttypeofbondbetweenatoms.Stablemoleculescanbeformed.

Becauseofthestabilityofcovalentbondslargemoleculeswithmanybondscanbeformed.TiAnisthelargestknownproteinanditcontains539,000atoms(chemicalformulaC169723H270464N45688O52243S912.).TheimagebelowshowasmallpartoftheTiAnmolecule.

h-p://www.ks.uiuc.edu/images/ofmonth/2002-11/AAn.jpg

CarbonatomscontainfourelectronsintheiroutershellallowingthemtoformfourcovalentbondswithpotenAalfourotherdifferentatoms,e.g.methane(CH4).

TheresultoftheseproperAesisanalmostinfinitenumberofdifferentpossiblemoleculesinvolvingcarbon.

h-p://commons.wikimedia.org/wiki/File:Carbon-atom.jpg

h-p://upload.wikimedia.org/wikipedia/commons/3/3e/Methane-2D-dot-cross.png

ClassifyingCarbonCompounds(notinSkeletonnotes)-refpg65textbook

NameofGroup FullStructure SimplifiedNota:on

hydroxyl

amine

carboxyl

methyl

2.1.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates•  Containcarbon,hydrogenandoxygen•  OrganiccompoundsconsisAngofoneormoresimplesugars•  Monomersfollowthegeneralbasicformulaof(CH2O)x•  Monomersarecommonlyringshapedmolecules

Note:ExcepAonstothisthebasicformulaandtheinclusionofotherelements(e.g.N)canoccur

Glucose–ahexose (6carbon)monomer

h-p://www.doctortee.com/dsu/Ahickjian/cse-img/biology/chemistry/polysaccharides.jpg

pentose(5carbon)monomers

2.1.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

Lipids •  Lipidsareagroupoforganicmoleculesthatareinsolubleinwaterbutsolubleinnon-

polarorganicsolvents•  Commonlipidsincludetriglycerides(fats–solidatroomtemperatureandoils–liquid

atroomtemperature),phospholipidsandsteroidsh-p://hyperphysics.phy-astr.gsu.edu/hbase/organic/imgorg/lipid.gif

2.1.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

Leucine–anaminoacid

Proteins •  Containcarbon,hydrogen,oxygenandnitrogen(addiAonallysulphuriscommoncomponent,butitisnotpresent

inallproteins) •  Proteinsarelargeorganiccompoundsmadeofaminoacidsarrangedintooneormorelinearchains

2.1.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

Nucleicacids •  Containcarbon,hydrogen,

oxygen,nitrogenandphosphorus

•  Chainsofsub-unitscallednucleoAdes

•  NucleoAdesconsistofbase,sugarandphosphategroupscovalentlybondedtogether

•  IfthesugarisribosethenthenucleicacidformedisRNAifthesugarisdeoxyribosethenDNAisformed

h-p://www.nature.com/scitable/topicpage/Chemical-Structure-of-RNA-348

phosphate

base

sugar

ArginineAlanine Leucine

h-p://commons.wikimedia.org/wiki/File:Alanine.pngh-p://commons.wikimedia.org/wiki/File:Arginine.pngh-p://commons.wikimedia.org/wiki/File:Leucine.png

Herearethreeofthetwenty-oneaminoacidsfoundineukaryotes.IdenAfywhatpartsoftheirstructuresareidenAcal.

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

ArginineAlanine Leucine

Yeah,thatbit…

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

h-p://commons.wikimedia.org/wiki/File:AminoAcidball.svg

DrawnslightlydifferentlyyoucanseethebitthatisalwaysthesameandtheRGroup. TheRgroupislikexinanequaAon.Itisavariablethatstandsinforabunchofdifferentsidechains

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Theaminegroup(NH2)

Thecarboxylgroup(COOH) n.b.thisisanacidicgroup

Lookoutforthisstructure

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Hmmm…anaminegroupandanacidgroup… Whatshallwe callthisclass

ofmolecule?

h-p://commons.wikimedia.org/wiki/File:Filos_tercer_logo.JPG

Theamineandacidgroupscouldbeatoppositeends,theRcouldbeontop,bo-omorsidedependingonorientaAon.

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Oritcouldberepresenteddifferently:

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

h-p://commons.wikimedia.org/wiki/File:Amino_Acids.svg

Don’tfreakout,youdon’tneedtoknowthemall,justthegeneralformula

H3C (CH2)n CO

OH

Generalstructuralformulaforafa-y*acid

*Iprefer“bigboned”

Carboxylicgroup

Chain(orring)ofcarbonandhydrogenatoms

h-p://www.eufic.org/arAcle/pt/nutricao/gorduras/expid/23/

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

2.1.S1 Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.

Trydrawingbyhand(oroneMolecules)thefollowingmolecules:•  Glucose•  Ribose•  Ageneralisedsaturatedfa-yacid•  Ageneralisedaminoacid•  Anexampleaminoacide.g.Alanine(the

simplest)n.b.youalsoneedtotestyourself15mins,1dayandoneweeklatertomakesureyouremember

eMoleculesonlinedrawingtool

http://www.emolecules.com/

2.1.U4 Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.

RevisittheessenAalideaofthistopic.ExploretheIUBMB-Sigma-NicholsonMetabolicPathwaysChartandrealisethatmostcellsusethemajorityofthepathwaysandthateverypathiscontrolledbyadifferentenzyme.ThemetabolismasaconceptisthesumofallthepathwaysusedinaparAcularcell.

2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions. 2.1.U5 Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions. 2.1.U5 Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.

Maltosesynthasecondensestwomoleculesofglucoseintomaltoseformingaglycosidicbond

AribosomecondensestwoaminoacidsintoadipepAdeformingapepAdebond

Examplesofanabolismbycondensa:on

h-p://commons.wikimedia.org/wiki/File:PepAdformaAonball.svg

Thebondsformedaretypesofcovalentbonds.

Bondingmonomerstogethercreatesapolymer(mono=one,poly=many)

2.1.U5 Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

LactasehydrolysesLactoseintoGlucoseandGalactosebreakingtheglycosidicbond

h-p://commons.wikimedia.org/wiki/File:Amino_acid4.png

h-p://commons.wikimedia.org/wiki/File:Lactose_hydrolysis.svg

AproteasehydrolysesadipepAdeintotwoaminoacidsbreakingthepepAdebond

Examplesofcatabolismbyhydrolysis

Youmightseetheterm“dehydra:onreac:on”menAonedinterchangeablywithcondensaAonreacAon.

TechnicallyadehydraAonreacAoniswhenthewater

moleculehascomefromoneofthereactants.

WhereasforacondensaAonreacAon,partofeachwatermoleculehascomefromeachreactant.

Inthecaseofthepreviousslide,OHfromoneglucose

andHfromtheother.

h-p://www.flickr.com/photos/zachd1_618/5738829330/

2.1.A1 Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.

Source:h-p://www.biog1445.org/demo/08/nitrogenouswastes.html

Vitalismnowadayshasnocreditasatheory,butabovestatementisseenbymanyfromahistoricalperspecAvetobeuntrue.ForanoutlineonvitalismreadthisarAclebyWilliamBetchel.TheapplicaAonstatementaboveimpliesthatthecentraltenetVitalismis‘onlyorganismscansynthesiseorganiccompounds’.Thisisnotaccurate,inessensevitalismproposesthatanunknowablefactorisessenAalinexplaininglife.VitalismonthispremiseisbothunscienAficandandunfalsifiable.

NatureofScience:Falsifica:onoftheories—thear:ficialsynthesisofureahelpedtofalsifyvitalism.(1.9)Wöhleraccidentallysynthesisedureain1828,whilsta-empAngtoprepareammoniumcyanate.Inale-ertoacolleaguehesays“Icannolonger,sotospeak,holdmychemicalwaterandmusttellyouthatIcanmakeureawithoutneedingakidney,whetherofmanordog".Thisissupposedtounderminevitalismasorganicchemicalswerepreviouslythoughttobesynthesisedonlybyorganisms.

Source:h-p://en.wikipedia.org/wiki/File:Friedrich_woehler.jpg

Bibliography/Acknowledgments

JasondeNys