Review for Final Part 1.docx
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Review for Final Part 1.docx
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ReviewforFinalPart1
ReviewforFinal-Part1
Chapters2-7,21,and8-9
MolecularBiology
Lecture1:
NucleicAcids(Chapter2)
Whatarethe4basepairsfoundinDNA?
adenine(A)
guanine(G)
thymine(T)
cytosine(C)
Thereare2methodsscientistsusetostudybiology.
Whatarethey?
1.Discoveryscience
2.Hypothesis-drivenscience
DiscoveryScience
Whatisdiscoveryscience?
Discoveryscienceisrecordingobservationsandmeasurements.
Howishypothesis-drivensciencedifferentfromdiscoveryscience?
Itbeginswithaquestion.
Hypothesis-drivenscience
Whatisahypothesis?
Thehypothesisisaproposedanswertothisquestion.Itisaneducatedguess.
Whatarethestepsinhypothesis-drivenscience?
Thestepsinhypothesis-drivenscienceare:
1.observationsofphenomena
2.formationofaquestionabouttheobservations
3.formationofahypothesistoanswerthequestion
4.Makingapredictionthatallowsthehypothesistobetested
5.Testingthehypothesis
Basedontheresultsofthetestingthehypothesiswillbeacceptedorrejected.
SummaryofGriffithexperiment
Smoothbacteriaescapetheimmunesystemandkillmice.
Roughbacteriaaredestroyedbytheimmunesystem.
Treatingsmoothbacteriawithheatkillsthemandtheyarenolongerinfectious.
Addingheatkilledsmoothbacteriatoroughbacteriatransformssomeofthemintosmoothbacteria.
Thesubstanceiscalledthetransformingprinciple.
HowdidAvery,MacLeodandMcCartyshowtherewerenoproteinsintheirpurifiedDNA?
Theytreatedthesampleswithproteasesandshowedthatthisdidnotaffecttransformation.Proteaseswoulddegradetheproteins.
HowdidtheyshowtherewasnoRNAintheirpurifiedDNA?
TheytreatedthesampleswithRNases(ribonucleases).RNaseswoulddegradeanycontaminatingRNA.Againthisdidnotstoptransformation.
ThentheytreatedtheirsampleswithDNases.DNaseswoulddegradetheDNAintheirsamples.TreatmentofsamplesofthetransformingprinciplewithDNaseseliminateditsabilitytotransformbacteria.
SummaryofHershey-Chaseexperiment
WhatdidHersheyandChaseusetolabeltheDNA?
BacteriophageT2DNAwaslabeledwith32P.
WhatdidHersheyandChaseusetolabeltheprotein?
T2proteinwaslabeledwith35S.
E.coliwereinfectedwiththeT2samples.
HowdidtheystoptheinfectionandremovetheT2fromthesurfaceofthebacteria?
byspinningthesamplesinablender
HowdidtheyseparatetheT2bacteriophagefromtheE.colibacteria?
Thesampleswerecentrifuged.TheT2wasinthesupernatantandtheE.coliwasinthepellet.
The35SproteindidnotentertheE.coli,butthe32PDNAdidentertheE.coli.
HersheyandChaseconcluded:
DNAisthetransformingprincipleandthehereditaryorgeneticmaterial.
Whatisitcalledwhenscientistschangethewaytheythinkaboutanimportantaspectofscience?
DNAisadoublehelix
WatsonandCrickstudiedthex-raydiffractionpatternsandmadeseveralpotentialmodelsofDNA.Eventuallytheyproposedthedouble-strandedhelixstructureofDNA.
HowisRNAdifferentfromDNA?
1.itissinglestranded
2.ithasthesugarribose
3.ithasuracilinsteadofthymine
WhatiscalledwhenDNAiscopiedintoRNA?
Transcription
WhatisitcalledwhentheinformationinmRNAisusedtomakeproteins?
Translation
WhatisthenameforalloftheDNApresentinaspecies?
Itiscalledthegenome.
ThestudyofalltheDNAinaspeciesiscalledgenomics.
TheImportanceofWeakChemicalInteractions
Chapter3
Someofthemoleculesinacellareverylarge?
Whatarethesecalled?
Thesearecalledmacromolecules(macro=big).
Macromoleculesareproducedfromjoiningsmallmoleculestogetherinachain.
Whatisthenameforthesmallmolecules?
monomers
1.Covalentbonds
Achemicalbondisanattractiveforcethatholdsatomstogether.
When2atomsshareanelectron,achemicalbondisformed.Whatisthenameforthiskindofbond?
covalent
Chemicalbondsdifferintheirfreedomofrotation.Singlecovalentbondscanfreelyrotate.Doubleandtriplecovalentbondsdonotrotate,whichholdstheatomsinthesameplane.
Noncovalentbondsaregenerallymuchweakerthancovalentbonds.
Whatarethe4kindsofnoncovalentbonds?
1.Hydrogenbonds
2.hydrophobicbonds
3.ionicbonds
4.VanderWaalsbonds
b.FreeEnergy
Whatisthenamefortheenergythatisavailablefordoingwork?
Inspontaneousreactions,thereisadecreaseinfreeenergy(∆Gisanegativenumber).
Howmuchfreeenergyisthereatequilibrium?
thereisnofreeenergy(∆G=0)
a.PolarandNonpolarMolecules
Whatarethe2kindsofcovalentbonds?
a.polar
b.nonpolar
Whatisdifferentaboutapolarbond?
Inapolarbondtheelectronsarepulledmoretowardoneatomthantheother.
Whatisthenamefortheattractionthatanatomhasforsharedelectrons?
Atomsthatareveryelectronegativehaveaverystrongattractionforsharedelectrons.
Whatisthenameforatomsthathaveaweakattractionforsharedelectronsandtendtogivethemup?
d.AqueousSolutions
Whatisasolvent?
Asolventisaliquidinwhichasubstancecandissolve.
Innucleicacidshydrophobicinteractionscausethepoorlysolubleorganicringsofnucleicacidbasepairstoclusterawayfromwater.Whatisthemostefficientclustering?
Itisstacking.
B.Enzyme-Substratebinding
Whatisthenameforspecialproteinsthatcatalyzechemicalreactions?
Enzymes
Enzymesbindtotheirsubstratewithnoncovalentbonds.
Theenergyofbindingislow(5to10kcal/mol)whichallowstheenzyme-substratecomplextoformandthenbreakapartquickly.
TheImportanceofHighEnergyBonds
Chapter4
Whatisthenamefortheenergyrequiredtobreaktheoldcovalentbondsinachemicalreaction?
Generally,howdomoleculesreachanactivatedstate?
Acollisionbetween2reactingmoleculestemporarilyformsamolecularcomplexcalledanactivatedstate.
Thisisdescribedbytheformula:
(A-B)+(C-D)→(A-D)+(C-B)
Keq=concA-DxconcC-B
concA-BxconcC-D
Whichmoleculesarethereactants?
(A-B)and(C-D)
Whichmoleculesaretheproducts?
(A-D)and(C-B)
B.EnzymesLowerActivationEnergies
Whatdoenzymesdo?
Enzymesspeeduptherateofthebiochemicalreactionsbyloweringtheactivationenergiestoamountsthatcanbesuppliedbytheheatofmotion.
Whatbindsintheactivesiteofanenzyme?
Thesubstrate.
Thesubstrateischangedintotheproductandthenitisreleased,allowingtheenzymetobindanothersubstrateandrepeattheprocess.
Lockandkey
Whatisthenameforthemodelofenzymeactivityinwhichtheshapeoftheactivesiteorbindingsitesfitsthesubstrate?
inducedfit
Whatisthenameforthemodelofenzymeactivityinwhichtheenzymechangesshapetofitthesubstrate?
Intheinducedfitmodeltheenzymechangesshapetofitthesubstrate.
Whatisitcalledwhenmonomersarebrokenapartwithwater?
Thisiscalledhydrolysis.
Whatisthemostimportanthighenergymolecule?
ATP
Producinglargemoleculesbyjoiningtogethersmallermolecules,whichiscalledbiosynthesis,requiresenergy.Thisenergyisoftenprovidedbyahighenergybond.
CouplingofNegativewith
Positive∆G
Freeenergymustbeaddedtoaminoacidssotheycanbejoinedtoformproteins.ThisenergyisaddedbyATP.
ATPcanbebrokeninto3importantmolecules.Whatarethey?
1.aphosphategroup
2.apyrophosphategroup
3.adenosinemonophosphate(AMP)
P-PSplitsCharacterizeMostBiosyntheticReactions
Essentiallyallbiosyntheticreactionshaveoneormorestepsinwhichapyrophosphategroupisreleasedandbroken.
WeakandStrongBondsDetermineMacromolecularStructures
Chapter5
1.DNAStability
WhyisDNAverystable?
a.therearemanyhydrogenbondsholdingthe2strandstogether
b.basestackingexcludeswatermolecules
RNAStability
rRNAandtRNAarestabilizedbyhydrogenbondsandbasestacking.
Theyarealsostabilizedbytheassociationofmetalions.
3.ProteinStability
Proteinsarepolymersofaminoacidmonomers.Proteinsarealsocalledpolypeptides.
Whatareproteinsmadeof?
Proteinsaremadeof20differentaminoacids.
Whatisthenameforthevariablepartofanaminoacid?
TheRgroupisthevariablepartofanaminoacidwhichisalsoknownasthesidechain.Differentaminoacidshavedifferentelementsorgroupsofelementsboundhere.
a.Rgroups
Whatarethe4differentkindsofRgroups?
1.neutral-nonpolar
2.neutral-polar
3.acidic
4.basic
Whatisthenameforthebondthatconnects2aminoacids?
Theyareconnectedbyapeptidebond.
Inapeptidebondanaminogroupononeaminoacidbindstothecarboxylicacidgrouponanotheraminoacid.
Whatisitcalledwhenmovementislimitedbytheamountofspace?
Itiscalledstericinterference.
1.primary
Whatformstheprimarystructureofaprotein?
Thelinearsequenceofaminoacidsformstheprimarystructureoftheprotein.
2.secondary
Thereare2typesofsecondaryfolding.Whatarethey?
1.alpha(α)helix
2.betasheet(βsheet)orbetapleatedsheet
Whatkindsofbondsformsecondarystructures?
Secondarystructuresarecausedbyhydrogenbondingbetweenatomsintheaminoacidbackbone.
Whatcausestertiarystructure?
Tertiarystructureiscausedbycovalentandnoncovalentbondsbetweenaminoacidsidechains.
Cysteinescanformcovalentbonds.
Whatarethesecalled?
Thesearecalleddisulfidebonds.
Quaternarystructuresareproducedwhenpolypeptidesassociatenoncovalentlywithotherpolypeptidestoformproteins.
Whatisthenameforeachpolypeptidechain?
ProteinStructureIsDeterminedbyHydrogenBonds
Whilehydrophobicinteractionsareimportant,thespecificstructureofaproteinismainly
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