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11-2-09_chemnaturegeneB
Course: BIOL 230, Fall 2009School: Purdue
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survives,northemostintelligentthat Itisnotthestrongestofthespeciesthat survives.Itistheonethatisthemost adaptabletochange. CharlesDarwin Informationistheresolutionofuncertainty. ClaudeShannon Announcements Yoursecondwrittenassignmentwillusethesame formatasthefirst.Youmustincludeatleast2other referencesbesidestheoriginalarticle. ItwillbedueFriday,December4(Notemajorshiftindue date)....
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survives,northemostintelligentthat Itisnotthestrongestofthespeciesthat survives.Itistheonethatisthemost adaptabletochange. CharlesDarwin Informationistheresolutionofuncertainty. ClaudeShannon
Announcements
Yoursecondwrittenassignmentwillusethesame formatasthefirst.Youmustincludeatleast2other referencesbesidestheoriginalarticle. ItwillbedueFriday,December4(Notemajorshiftindue date). Quiz7willbemadeavailablesoonbuthasnotbeenyet.
NowWhat?
WehaveATPandNADPH Lightindependentreaction CanmakeacarbohydrateoutofCO2
CalvinBensonCycle
SixmoleculesofCO2are fixedbyRuBPcarboxylase (orRubisco)toa5carbon compound,RuBP Formsa6carbonunstable intermediate Rubiscoistheratelimiting stepofphotosynthesis,with aturnoverrateofonly3/s. Constitutes~1/2ofthe proteinmassinplantsandis themostabundantproteinon Earth.
CalvinCycle
Unstable6carbonintermediatesplits intotwoPGA(3phosphoglycerate) molecules TheATPfromthelightreactionis usedtophosphorylatePGAinto1,3 bisphosphoglycerate(BPG) Allofthisistakingplaceinthe chloroplaststroma
CalvinCycle
ThephosphorylatedBPGusesthe NADPHformedfromthelightdependent cycle BPGisreducedintoglyceraldehyde3 phosphate(GAP) Outofthe12GAPmoleculesthathave beenformedfromthe12PGA molecules,2GAPmoleculeswillgoon tomakecarbohydratesinoneof2ways 1)GAPcanbetransportedoutintothe cytosol,whereitwillbeconvertedto glucoseandsucrose 2)GAPcanalsobeusedtomakestarch inthestromaofchloroplasts Starchisgeneratedbyreversingthe reactionsofglycolysistomakeglucose 1phosphate,whichisaddedtothe starchgranule
WholeCalvinCycle
StartwithRuBP CO2andRubiscoareusedto convertRuBPintothesix carbonintermediate 6carbonintermed.splitsinto PGA UseATPtophosphorylateBPG UseNADPHtoreduceBPG intoGAP 2GAPcangoontosynthesize sucrose/starchmolecules Other10GAPisconvertedinto RuBPwiththehelpofATP Startthecyclealloveragain!
6 CO2+ 18 ATP + 12 NADPH +2 H20 2 GAP + 16 Pi + 18 ADP + 12 NADP+
RedoxcontroloftheCalvincycle
Asmall%ofelectronsgeneratedbyphotosystemIand carriedbyferredoxinendupreducingthioredoxin ReducedthioredoxinmaintainsmultipleCalvincycle enzymesinanactivestate Inthedark,thioredoxinisoxidizedandinactive,thereby inactivatingtheCalvincycleenzymes
Photorespiration
RubiscocanalsocatalyzeasecondreactionthatproducesPGAand2 phosphoglycoateusingO2insteadofCO2 Thisiscalledphotorespiration.Thisisnothelpfultotheplant becauseitonlycreatesone3PGAmoelculeinsteadoftwoandit releasesCO2. SomeplantscanlosealmostoftheirCO2bythisprocess AsatmosphericCO2levelsrise,cropgrowthbecomesmoreefficient becausethesecondaryphotorespirationreactionoccurslessfrequently.
C3Plants
PlantsthattakeCO2directlyfromtheatmosphereareC3 plants FixCO2fromairtoRuBP MostlyfoundinplaceswhereCO2isplentiful Temperateclimate Lotsofsunlight Lotsofwater
C4Plants
InMesophyllcell,CO2isfixedtoPEPthroughPEPcarboxylase NADPHisusedtoconvertoxaloacetateintomalatewhichistransportedinto thebundlesheathcell There,theCO2isreleasedandtheCalvincyclecanbegin PyruvateisformedfrommalateafterthereleaseofCO2 ATPisusedtoconvertpyruvatebackintoPEP CAMplants(cacti)aresimilartoC4plantsbutfixCO2atnightasmalicacid andgothroughCalvincycleinmorning.
Genesarethemainwaythatinformationis inheritedbetweenorganisms(theunitof inheritance)
Alternateformsofagenearecalledalleles Thegenesthatanorganismhasareitsgenotype.Theirobservable expression(e.g.greenvs.yellow)isthephenotypederivedfromthe genotype. Dominantallelesonlyneedonecopyofanalleletoproducetheir phenotype. Recessiveallelesneedacopyoneachchromosome Codominantalleleswillproduce3phenotypes;dominant,recessive,
ChromosomesandDNAarenotjust abstractsequencesofinformation. Theyarephysicalandchemicalobjects withphysicalandchemicalproperties.
Geneticlinkageanalysisdemonstrates physicalnatureofchromosomes
Studythecoinheritanceofaspecifichumanphenotype(herea marker.Ifindividualswhoinheritthediseasenearlyalwaysinherita geneticdisease)witha(singlenucleotidepolymorphism)SNP particularSNPmarker,thenthegenecausingthediseaseandthe SNParelikelytobeclosetogetheronthechromosome,asshown
ChromosomesarelongstrandsofDNAthat arefoundinhomologouspairs
Thechromosomepairsare notidenticalandoften containdifferentalleles. Thisistheembodimentof informationstorageand transmissionacross generations Bacterialgenomesconsistof asingledoublestranded chromosome
ChemicaltransformationexperimentsbyGriffithandlaterAvery demonstratedthatDNAcarriesheritableinformation
Nucleic Acid Structure
Phosphate, charged and hydrophilic
Phosphate and sugar form the backbone. The base carries the information.
Phosphates and sugars make up the nucleic acid backbone. Bases are linked to the sugars. The phosphate is normally linked to the 5'carbon of the sugar The nitrogenous base is attached to the sugar's 1'-carbon Monomers polymerize when sugar 3'-OH is linked by ester bond to 5'-phosphate of next nucleotide in chain (3' - 5' phosphodiester linkage); so nucleotides are joined by sugarphosphate linkages
Nitrogenous bases fall into two classes: purine and pyrimidines
Purines=2 rings, Pyrimidines=1 ring. Thymine found in DNA only. Uracil found in RNA only
DNApairings
P O Adenine Thymidine P P O Guanine Cytosine P O P O Thymidine Adenine P O P O Cytosine Guanine P O O
A-T are bonded by two H-bonds. G-C are bonded by three H-bonds. Sugar and phosphate play no role in information transmission. Only the nitrogenous bases do.
In RNA, uracil substitutes for thymidine (thymine). Bonds made between one purine and one pyrimidine
LevelsofDNAstructure
Primary:Sequence Secondary:Helix,NOTalphahelixasinproteins TertiaryStructure:supercoiling,other RubberBandanalogy
Structureofdoublehelix
34angstroms(3.4nm)length/10nucleotidesinahelix Thehumangenomeisabout3billionnucleotides So3.4x109mx3x108groupsof10nucleotidesgivesa totallengthof1.02meters!ofDNAineachhumancell, whichisusuallyabout1050micronsindiameter
Topoisomerasescontrolthecoilingand supercoilingofDNAstrands
Bycoilinganduncoilingthe DNA,theamountof compactionandaccesstothe DNAcanbecontrolled Topoisomerasescreate breaksinastrandofDNAto allowrotationofastrand Onetypeofsupercoiling (negativesupercoiling) controlledbytopoisomerasesis shownontheright
Genomesequencinghasbeenfacilitatedgreatly bythepolymerasechainreaction(PCR)
FindingthejunkDNA
Wehave40timesmoreDNA thanweneedinourcells basedsimplyonthenumber ofexpressedproteins! Methodsneededtobe devisedtodeterminehow complexourDNAwas Turnsoutthebestwaytodo thiswastotakeitapart(dont worry,weputitbacktogether eventually) Accomplishedbymonitoring theRENATURATION KINETICSofDNA
Howisthisuseful?
DNAfingerprinting Analyzeshowmany repeatedsequencesan individualhastoidentify familyrelationships CSIunitsandJerry Springerbothusethis Diseaseprevention Huntingtonsdisease iscausedbytoomany repeatswithinagenome Testscandetectthis
DNAfingerprinting
Variablenumbertandemrepeat (VNTR)sequencesareshort DNAsequenceswhosenumber willvarybetweenindividuals. ByanalyzingmultipleVNTR,a uniquefingerprintisfoundfor eachindividual. Thiscanbeusedtocompare biologicalsamplesobtainedata crimescenewiththose potentiallyinvolved
LargesegmentsofDNAorevenwhole genomescanbemodifiedorduplicated
Relatedplantssometimesundergogenomeduplication, withbothwholegenomespresentintheoffspringof matedplants Geneduplicationisthoughttoarisefromunequal crossingoverinmeiosis,wheremisalignmentbetween chromosomesallowsanextrasegmentofDNAtogoto onechromosomeandtheotherlosesasegment.
Manualtransmission: DNAistheinstruction manualforcellsandis transmittedacrosscell generations
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