Berkeley Biology 1A Spring 2016 Lecture Reader Part 1

Bio1A:Introduc/ontoBiologySpring2016

PartI:JenniferDoudna

Guestlecturer:RossWilson

DoudnaofficehoursMondays12-1pm

Fridays2:30-3:30pmVLSB2084

Text:BIO1A/BUC,Berkeley

•  Reading:Chapters1&2

•  Lectureoutline:– Thechemistryoflife– ProperTesofwaterareessenTalinbiology

Lecture#1:Biology&Water

•  BiologyisthescienTficstudyoflifeonEarth•  Evolu/onbynaturalselecTonistheprocessofchangethathasproducedthediverselifeweobserve

•  BiologistsaskquesTonssuchas:– Howdoesasinglecelldevelopintoanorganism?– Howdoesthehumanbrainwork?– HowdoorganismsinteractincommuniTes?

Overview:InquiringAbouttheWorldofLife DefiningLife

•  Compartmentaliza/on•  Hierarchicalcomplexity•  Sensi/vity•  Reproduc/on•  Energyu/liza/on•  Homeostasis•  Adapta/on

“WhyLifeDoesNotReallyExist”h]p://Tnyurl.com/on-defining-life

Evolu/on:theOverarchingThemeofBiology

•  EvoluTonmakessenseofeverythingweknowaboutlivingorganisms

•  OrganismslivingonEartharemodifieddescendentsofcommonancestors

•  Thenatureofthelastuniversalcommonancestor(LUCA)andtheoriginofliferepresentbiology’sgreatestunsolvedmysteries

ChemicalFounda/onsofLife

•  BiologyisamulTdisciplinaryscience

•  Livingorganismsaresubjecttobasiclawsofphysicsandchemistry

•  YoushouldknowbasicdefiniTonsofma]er;chemistryofwater;chemistryofcarbon

Elements,Compounds,Molecules•  Ma]erismadeupofelements•  AnelementisasubstancethatcannotbebrokendowntoothersubstancesbychemicalreacTons

•  AcompoundisasubstanceconsisTngoftwoormoreelementsinafixedraTo

•  AcompoundhascharacterisTcsdifferentfromthoseofitselements

•  Amoleculeistwoormoreatomsheldtogetherbychemicalbonds

Elements,Compounds,Molecules•  Ma]erismadeupofelements•  AnelementisasubstancethatcannotbebrokendowntoothersubstancesbychemicalreacTons

•  AcompoundisasubstanceconsisTngoftwoormoreelementsinafixedraTo

•  AcompoundhascharacterisTcsdifferentfromthoseofitselements

•  Amoleculeistwoormoreatomsheldtogetherbychemicalbonds

Isoxygenanelement?…compound?…molecule?Whataboutiron?Water?Carbondioxide?

Sodium Chlorine Sodiumchloride

Saltissaferthanthesumofitsparts… Essen/alElementsofLife

•  Onlyabout25ofthe~80stableelementsareessenTaltolife•  Carbon,hydrogen,oxygen,andnitrogenmakeup96%of

livingma]er•  Mostoftheremaining4%consistsofcalcium,phosphorus,

potassium,andsulfur•  Traceelementsarethoserequiredbyanorganisminminute

quanTTes

h]p://umbbd.ethz.ch/periodic/spiral.html

TheBiochemicalPeriodicTable

Nitrogendeficiency

EffectsofDeficienciesofEssen/alElements

Iodinedeficiency:Goiter!

The abundance of water on Earth's surface is a unique feature that distinguishes our "Blue Planet" from others in the Solar System.

Water:TheMoleculeThatSupportsAllofLife

•  Water is the biological solvent on Earth

•  All living organisms require water more than any other substance

•  Most cells are surrounded by water, and cells themselves are about 70–95% water

•  The abundance of water is the main reason the Earth is habitable

Thepolarityofwatermoleculesresultsinhydrogenbonding

•  The water molecule is a polar molecule: the opposite ends have opposite charges

•  Polarity allows water molecules to form hydrogen bonds with each other

•  Polarity also promotes interactions between water and polar molecules or dissolved ions

Hydrogen bond

δ –H

δ +

H

O

——

δ +δ +

δ +

δ –

δ –

δ –

Fourproper/esofwatercontributetoEarth’sfitnessforlife

–  Cohesive behavior

–  Ability to moderate temperature high specific heat high heat of vaporization

–  Expansion upon freezing

–  Versatility as a solvent acid/base properties dissolves many (but not all) molecules

CohesionandAdhesion

•  Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion

•  Cohesion helps the transport of water against gravity in plants

•  Adhesion is an attraction between different substances, for example, between water and plant cell walls

Protonsdissociatebetweenwatermoleculesinaprocesscalledautoioniza/on

hydroniumionor“proton”

hydroxideion

“H+” or

ThepHscaleislogarithmicanddescribestheconcentra/onofhydroniumions,[H+]

pH = −log[H+]

HCl à H+ & Cl−

NaOH à Na+ & OH− •  The Celsius scale is a measure of temperature using Celsius degrees (°C)

•  A calorie (cal) is the amount of heat required to raise the temperature of 1 g of water by 1°C

•  The “Calories” on food packaging are actually kilocalories (kcal), where 1 kcal = 1,000 cal

•  The joule (J) is another unit of energy where 1 J = 0.239 cal 1 cal = 4.184 J

Unitsoftemperatureandenergy

Biologicalbuildingblocks:covalentconnec/onsbetweenC,H,O,N

Biologicalbuildingblocks:covalentconnec/onsbetweenC,H,O,N

C N O H

single bond

double bond

N/A

available electrons

4 3 2 1

C C

N N

O

Lecture#2:Biologicalpolymers

•  Reading:Chapter3

•  Lectureoutline:Molecularbuildingblocksofthecell– Sugars/carbohydrates– Fats/lipids– Aminoacids/proteins– Nucleo>des/nucleicacids

Overview:TheMoleculesofLife

•  Alllivingthingsaremadeupoffourclassesoflargebiologicalmolecules:carbohydrates,lipids,proteins,andnucleicacids

•  Withincells,smallorganicmoleculesarejoinedtogethertoformlargermoleculesBuildingblocksofthecell: Largerunitsofthecell: Sugars Polysaccharides FaEyacids Lipids/membranes Aminoacids Proteins Nucleo>des Nucleicacids

BefamiliarwiththecontentsofFigure3.2inyourbook!

Dehydra>on/condensa>onvideo:hEp://>nyurl.com/Bio1A-vid1Hydrolysisvideo:hEp://>nyurl.com/Bio1A-vid2

Carbohydratesasfuelandbuildingmaterial

•  Carbohydratesincludesugarsandthepolymersofsugars

•  Thesimplestcarbohydratesaremonosaccharides,orsinglesugars

•  Carbohydratemacromoleculesarepolysaccharides,polymerscomposedofmanysugarbuildingblocks

Sugars

•  Monosaccharideshavemolecularformulasthatareusuallymul>plesofCH2O

•  Glucose(C6H12O6)isthemostcommonmonosaccharide

•  Monosaccharidesareclassifiedby– Theloca>onofthecarbonylgroup(asaldoseorketose)– Thenumberofcarbonsinthecarbonskeleton(pentoseorhexose)

Monosaccharidesserveasamajorfuelforcellsandasrawmaterialforbuildingmolecules

H

CH2OH

H

OH

OH H H

H

C C C

C C

C C

H

C H

HO OH H

OH H C

OH H C OH H C

H

O H

C H H OH

H OH

H O H

H

OH

H

OH H H

H

C C C

C C O

OH

OH H H

H

C C C

C O C

OH

OH

O H 2 3

5

1 4

6 5 4 3 2 1

2 3

5 6

1 4

2 3

5

1 4

α-glucose or

β-glucose

O O

CH2OH

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

α

β

Fischer projection

Haworth projection

C C

H

C

HO H

O H C

H C H C

H 6 5 4 3 2 1

H

O H O H O H

H O

Fructose Glucose Galactose

H OH

O

C

C

C

C

C

C

H

H

HO H

H OH

H OH

H OH

H

O C

C

C

C

C

H

H

HO H

OH

H OH

H OH

O C

C

C

C

C

C

H

H

H

HO H

OH

H OH

H OH

C H OH HO H

Stereo- isomer

Structural isomer


ketose hexose

ketohexose aldose hexose

aldohexose aldose hexose

aldohexose

Disaccharides •  2 monosaccharides linked together by

dehydration synthesis •  Used for sugar transport or energy storage •  Examples: sucrose, lactose, maltose OH

Sucrose Fructose α-glucose HO

CH2OH H

OH

H OH H H

H

O H OH H

H O HO

H

OH

H OH O H H

H

O H OH OH H

H O +

Maltose HO

H

OH

H OH O H H

H

O H

OH

H OH

OH H H

H

O OH

HO H2O

CH2OH CH2OH CH2OH CH2OH CH2OH

CH2OH CH2OH


ThisisanexampleofacondensaConreac>on,inwhichtwomoleculesbecomecovalentlylinkedwiththelossofawatermolecule(dehydra>on).Thereversereac>on,inwhichwaterisadded,iscalledhydrolysis.

Polysaccharides

•  Long chains of monosaccharides – Linked through dehydration synthesis

•  Energy storage – Plants use starch – Animals use glycogen

•  Structural support – Plants use cellulose – Arthropods and fungi use chitin

Glycogen

Amylose + Amylopectin

3.3 µm


α-glucose

HO

CH2OH H

OH

H OH H H

H

O OH 4 1

α-1à4 linkages

CH2OH

OH

H OH H H

O CH2OH

OH

H OH H H

O CH2OH

OH

H OH H H

O O O

H

α-1à4 linkage

α - 1à6 linkage

CH2OH

O H

OH

H OH H H

H

O

CH2 H

OH

H OH H H

H

O O

CH2OH H

OH

H OH H H

H

O

7.5 µm

Starch:

4 1

branched

unbranched

ThechemicalformulaforglucoseisC6H12O6.What’stheformulaforaglycogenpolymer

composedof10glucosemolecules?a.  C60H120O60

b.  C60H102O51

c.  C60H100O50

d.  C60H111O51

Lipids:adiversegroupofhydrophobicmolecules

•  Lipidsaretheoneclassoflargebiologicalmoleculesthatdonotincludetruepolymers

•  TheunifyingfeatureoflipidsishavingliEleornoaffinityforwater

•  Lipidsarehydrophobicbecausetheyconsistmostlyofhydrocarbons,whichformnonpolarcovalentbondselectronega;vity:carbon(2.5),hydrogen(2.1),oxygen(3.5)

•  Themostbiologicallyimportantlipidsarefats,phospholipids,andsteroids

Fats

•  Fatsareconstructedfromtwotypesofsmallermolecules:glycerolandfaEyacids

•  Glycerolisathree-carbonalcoholwithahydroxylgroupaEachedtoeachcarbon

•  AfaNyacidconsistsofacarboxylgroupaEachedtoalongcarbonskeleton

Structuralformulaofasaturatedfatmolecule

Stearicacid,asaturatedfaNyacid

Structuralformulaofanunsaturatedfatmolecule

Oleicacid,anunsaturatedfaNyacid

cisdoublebondcausesbending

triglyceride

faNyacid

triglyceride

faNyacid

glycerol

glycerol

Space-fillingmodelStructuralformula Phospholipidsymbol

FaNyacids

Hydrophilichead

Hydrophobictails

Choline

Phosphate

Glycerol

Hydrop

hobictails

Hydrop

hilichead

Phospholipids•  Inaphospholipid,two

faEyacidsandaphosphategroupareaEachedtoglycerol

•  ThetwofaEyacidtailsarehydrophobic,butthephosphategroupanditsaEachmentsformahydrophilichead

Phospholipidsareessen>alforcellsbecausetheymakeupcellmembranes

Steroids

•  Steroidsarelipidscharacterizedbyacarbonskeletonconsis>ngoffourfusedrings

•  Cholesterol,animportantsteroid,isacomponentinanimalcellmembranes

•  Althoughcholesterolisessen>alinanimals,highlevelsinthebloodmaycontributetocardiovasculardisease

Proteinshavemanystructures,resul>nginawiderangeoffunc>ons

•  Proteinsaccountformorethan50%ofthedrymassofmostcells

•  Proteinfunc>onsincludecatalyzingbiochemicalreac>ons,structuralsupport,storage,transport,cellularcommunica>ons,movement,anddefenseagainstforeignsubstances

•  PolypepCdesarepolymersbuiltfromthesamesetof20aminoacids

•  Aproteinconsistsofoneormorepolypep>des

•  Aminoacidsareorganicmoleculeswithcarboxylandaminogroups

•  Aminoacidsdifferintheirproper>esduetodifferingsidechains,calledRgroupsαcarbon

Proteinsadoptmanyfunc>onsviacombina>onsofdiverseaminoacids

PepCdebond

Aminoend(N-terminus)

PepCdebond

Sidechains

Backbone

Carboxylend(C-terminus)

ProteinStructureandFunc>on

•  Afunc>onalproteinconsistsofoneormorepolypep>destwisted,folded,andcoiledintoauniqueshape

Aribbonmodeloflysozyme Aspace-fillingmodeloflysozyme

Groove

PrimaryStructure

SecondaryStructure

TerCaryStructure

βpleatedsheet

examplesofaminoacidsubunits

+H3NAminoend

αhelix

QuaternaryStructure

FourLevelsofProteinStructure

notetheextensivehydrogenbondingobservedinsecondarystructures

Polypep>dechain

βChains

HemeIron

αChains

Collagen Hemoglobin

ExamplesofQuaternaryStructure

EXPERIMENT

RESULTS

X-raysource X-ray

beam

DiffractedX-rays

Crystal Digitaldetector X-raydiffracConpaNern

RNApolymeraseII

RNA

DNA

Nucleicacidsstoreandtransmithereditaryinforma>on

•  Therearetwotypesofnucleicacids:Deoxyribonucleicacid(DNA)Ribonucleicacid(RNA)

•  Theaminoacidsequenceofapolypep>deisprogrammedbyaunitofinheritancecalledagene

•  GenesarestoredasDNA,anucleicacid

mRNA

SynthesisofmRNAinthenucleus

DNA

NUCLEUS

mRNA

CYTOPLASM

MovementofmRNAintocytoplasmvianuclearpore

Ribosome

AminoacidsPolypepCde

Synthesisofprotein

1

2

3

TheCentralDogmaofMolecularBiology

TheStructureofNucleicAcids

•  NucleicacidsarepolymerscalledpolynucleoCdes

•  Eachpolynucleo>deismadeofmonomerscallednucleoCdes

•  Eachnucleo>deconsistsofanitrogenousbase,apentosesugar(RiboseorDeoxyribose),andaphosphategroup

•  Thepor>onofanucleo>dewithoutthephosphategroupiscalledanucleoside

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

5’end

NucleosideNitrogenous

base

Phosphategroup Sugar

(pentose)

NucleoCde

PolynucleoCde,ornucleicacid

3’end

3’C

3’C

5’C

5’C

NitrogenousbasesPyrimidines

Cytosine(C) Thymine(T) Uracil(U)

Purines(rhymeswith“tworings”)

Adenine(A) Guanine(G)

Sugars

Deoxyribose(inDNA) Ribose(inRNA)

Nucleosidecomponents:sugarsandbases

inDNA inRNA

pentose

DNA/RNAformedviacondensa>on

TheDNADoubleHelix

•  ADNAmoleculehastwopolynucleo>desspiralingaroundanimaginaryaxis,formingadoublehelix

•  IntheDNAdoublehelix,thetwobackbonesruninopposite5ʹ→3ʹdirec>onsfromeachother,anarrangementreferredtoasanCparallel

•  OneDNAmoleculeincludesmanygenes•  ThenitrogenousbasesinDNApairupandformhydrogenbonds:adenine(A)alwayswiththymine(T),andguanine(G)alwayswithcytosine(C)


Sugar-phosphatebackbones

3'end

3'end

3'end

3'end

5'end

5'end

5'end

5'end

Basepair(joinedbyhydrogenbonding)

Oldstrands

Newstrands

NucleoCdeabouttobeaddedtoanewstrand

TheDNADoubleHelix• ADNAmoleculehastwopolynucleo>desspiralingaroundanimaginaryaxis,formingadoublehelix

•  IntheDNAdoublehelix,thetwobackbonesruninopposite5ʹ→3ʹdirec>onsfromeachother,anarrangementreferredtoasanCparallel

• OneDNAmoleculeincludesmanygenes• ThenitrogenousbasesinDNApairupandformhydrogenbonds:adenine(A)alwayswiththymine(T),andguanine(G)alwayswithcytosine(C)

DNAandProteinsasTapeMeasuresofEvolu>on

•  Thelinearsequencesofnucleo>desinDNAmoleculesarepassedfromparentstooffspring

•  TwocloselyrelatedspeciesaremoresimilarinDNAthanaremoredistantlyrelatedspecies

•  Molecularbiologycanbeusedtoassessevolu>onarykinship

Youshouldnowbeableto:

1.  Listanddescribethefourmajorclassesofmolecules2.  Describetheforma>onofaglycosidiclinkageand

dis>nguishbetweenmonosaccharides,disaccharides,andpolysaccharides

3.  Dis>nguishbetweensaturatedandunsaturatedfatsandbetweencisandtransfatmolecules

4.  Describethefourlevelsofproteinstructure5.  Dis>nguishbetweenthefollowingpairs:pyrimidine

andpurine,nucleo>deandnucleoside,riboseanddeoxyribose,the5ʹendand3ʹendofanucleo>de

Lecture#3:Cellstructure•  Reading:Chapter4

•  Lectureoutline: -Methodstostudycells -Differencesbetweenprokaryo>cand eukaryo>ccells -Proteintrafficking-Organelles

Sugar-phosphatebackbones

3'end

3'end

3'end

3'end

5'end

5'end

5'end

5'end

Basepair(joinedbyhydrogenbonding)

Oldstrands

Newstrands

NucleoDdeabouttobeaddedtoanewstrand

TheDNADoubleHelix

•  ADNAmoleculehastwopolynucleo>desspiralingaroundanimaginaryaxis,formingadoublehelix

•  IntheDNAdoublehelix,thetwobackbonesruninopposite5ʹ→3ʹdirec>onsfromeachother,anarrangementreferredtoasanDparallel

•  OneDNAmoleculeincludesmanygenes•  ThenitrogenousbasesinDNApairupandform

hydrogenbonds:adenine(A)alwayswiththymine(T),andguanine(G)alwayswithcytosine(C)

Overview:TheFundamentalUnitsofLife

•  Allorganismsaremadeofcells•  Thecellisthesimplestcollec>onofmaSerthatcanlive

•  Cellstructureiscorrelatedtocellularfunc>on•  Allcellsarerelatedbytheirdescentfromearliercells

Howdowestudycells?

•  Thoughusuallytoosmalltobeseenbytheunaidedeye,cellsarecomplex

•  Microscopesandthetoolsofbiochemistryhaverevealedmanyaspectsofcellbiology

Microscopy

•  Scien>stsusemicroscopestovisualizecellstoosmalltoseewiththenakedeye

•  Inalightmicroscope(LM),visiblelightpassesthroughaspecimenandthenthroughglasslenses,whichmagnifytheimage

•  Thequalityofanimagedependson– Magnifica(on,thera>oofanobject’simagesizetoitsrealsize

–  Resolu(on,themeasureoftheclarityoftheimage,ortheminimumdistanceoftwodis>nguishablepoints

–  Contrast,visibledifferencesinpartsofthesample

10m

1m

0.1m

1cm

1mm

100µm

10µm

1µm

100nm

10nm

1nm

0.1nm Atoms

Smallmolecules

Lipids

Proteins

Ribosomes

VirusesSmallestbacteria

Mitochondrion

NucleusMostbacteria

Mostplantandanimalcells

Frogegg

Chickenegg

Lengthofsomenerveandmusclecells

Humanheight

Una

ided

eye

Lightm

icroscop

e

Electron

microscop

e

•  LMscanmagnifyeffec>velytoabout1,000>mesthesizeoftheactualspecimen

•  Varioustechniquesenhancecontrastandenablecellcomponentstobestainedorlabeled

•  Mostsubcellularstructures,includingorganelles(membrane-enclosedcompartments),aretoosmalltoberesolvedbyaLM–althoughtechniqueslikefluorescentlabelingcanmakethispossiblebyimprovingcontrast.

LightMicroscopy(a)BrighXield(unstainedspecimen)

(b)BrighXield(stainedspecimen)

TECHNIQUE RESULTS

50µm

•  Twobasictypesofelectronmicroscopes(EMs)areusedtostudysubcellularstructures

•  Scanningelectronmicroscopes(SEMs)focusabeamofelectronsontothesurfaceofaspecimen,providingimagesthatlook3-D

•  Transmissionelectronmicroscopes(TEMs)focusabeamofelectronsthroughaspecimen

•  TEMsareusedmainlytostudytheinternalstructureofcells

ElectronMicroscopy(a)Scanningelectronmicroscopy(SEM)

TECHNIQUE RESULTS

(b)Transmissionelectronmicroscopy(TEM)

Cilia

LongitudinalsecDonofcilium

CrosssecDonofcilium

1µm

1µm

Scanningelectronmicroscopeimageofpollen

hSp://en.wikipedia.org/wiki/Microscopy

SEMtypicallyprovidesgooddepth-of-fieldresolu>on,sothesurfaceofthesampleiswellresolved.~250>mesbeSerresolu>onthanlightmicroscope.Samplemustbedriedandfixed.

CellFrac>ona>on

•  CellfracDonaDontakescellsapartandseparatesthemajororganellesfromoneanother

•  Ultracentrifugesfrac>onatecellsintotheircomponentparts

•  Cellfrac>ona>onenablesscien>ststodeterminethefunc>onsoforganelles

•  Biochemistryandcytologyhelpcorrelatecellfunc>onwithstructure


HomogenizaDon

TECHNIQUE

HomogenateTissuecells

1,000g(1,000Dmestheforceofgravity)

10min DifferenDalcentrifugaDon

Supernatantpouredintonexttube

20,000g20min

80,000g60minPelletrichin

nucleiandcellulardebris

Pelletrichinmitochondria(andchloro-plastsifcellsarefromaplant)

Pelletrichin“microsomes”(piecesofplasmamembranesandcells’internalmembranes)

150,000g3hr

Pelletrichinribosomes

•  CellfracDonaDontakescellsapartandseparatesthemajororganellesfromoneanother

•  Ultracentrifugesfrac>onatecellsintotheircomponentparts

•  Cellfrac>ona>onenablesscien>ststodeterminethefunc>onsoforganelles

•  Biochemistryandcytologyhelpcorrelatecellfunc>onwithstructure

Biochemistry ComparingProkaryo>candEukaryo>cCells

•  Basicfeaturesofallcells:–  Plasmamembrane–  Semifluidsubstancecalledcytosol–  Chromosomes(carrygenes)–  Ribosomes(makeproteins)

•  Thestructuralandfunc>onalunitofeveryorganismisoneoftwotypesofcells:prokaryo>coreukaryo>c

•  OnlyorganismsofthedomainsBacteriaandArchaeaconsistofprokaryo>ccells

•  Pro>sts,fungi,animals,andplantsallconsistofeukaryo>ccells

phospholipids proteins

carbohydrates

ProkaryoDccellshave:–  Nonucleus–  DNAinanunboundregioncalledthenucleoid–  Nomembrane-boundorganelles–  Cytoplasmboundbytheplasmamembrane

Fimbriae

Nucleoid

Ribosomes

Plasmamembrane

Cellwall

Capsule

Flagella

Bacterialchromosome

(a) Atypicalrod-shapedbacterium

(b) AthinsecDonthroughthebacteriumBacilluscoagulans(TEM)

0.5µm

1-10μmdiameter

ENDOPLASMICRETICULUM(ER)

SmoothER

RoughERFlagellum

Centrosome

CYTOSKELETON:MicrofilamentsIntermediatefilamentsMicrotubules

Microvilli

PeroxisomeMitochondrion Lysosome

Golgiapparatus

Ribosomes

Plasmamembrane

NuclearenvelopeNucleolusChromaDn

NUCLEUS

EukaryoDccellshave:–  DNAinanucleusthatisboundedbyamembranousnuclearenvelope–  Membrane-boundorganelles–  Cytoplasmintheregionbetweentheplasmamembraneandnucleus

•  Eukaryo>ccellsaregenerallymuchlargerthanprokaryo>ccells

10-100μmdiameter

TheNucleus:Informa>onCentral

•  Thenucleuscontainsmostofthecell’sgenesandisusuallythemostconspicuousorganelle

•  Thenuclearenvelopeenclosesthenucleus,separa>ngitfromthecytoplasm

•  Thenuclearmembraneisadoublemembrane;eachmembraneconsistsofalipidbilayer

•  Poresregulatetheentryandexitofmoleculesfromthenucleus

•  Theshapeofthenucleusismaintainedbythenuclearlamina,whichiscomposedofprotein

NucleolusNucleus

RoughER

Nuclearlamina(TEM)

Close-upofnuclearenvelope

1µm

1µm

0.25µm

Ribosome

Porecomplex

Nuclearpore

OutermembraneInnermembraneNuclearenvelope:

ChromaDn

Surfaceofnuclearenvelope

Porecomplexes(TEM)

Ribosomes:ProteinFactories

•  Ribosomesarepar>clesmadeofribosomalRNAandprotein

•  Ribosomescarryoutproteinsynthesisintwoloca>ons:–  Inthecytosol(freeribosomes)– Ontheoutsideoftheendoplasmicre>culumorthenuclearenvelope(boundribosomes)


Cytosol

EndoplasmicreDculum(ER)

Freeribosomes

Boundribosomes

Structureofaribosome

TEMshowingERandribosomes

0.5µm

Largesubunit

Smallsubunit

Centralprotuberance

Theendomembranesystemregulatesproteintrafficandperformsmetabolic

func>onsinthecell•  Componentsoftheendomembranesystem:– Nuclearenvelope– Endoplasmicre>culum– Golgiapparatus– Lysosomes– Vacuoles– Plasmamembrane

•  Thesecomponentsareeithercon>nuousorconnectedviatransferbyvesicles

TheEndoplasmicRe>culum:Biosynthe>cFactory

•  TheendoplasmicreDculum(ER)accountsformorethanhalfofthetotalmembraneinmanyeukaryo>ccells

•  TheERmembraneiscon>nuouswiththenuclearenvelope

•  Therearetwodis>nctregionsofER:– SmoothER,whichlacksribosomes– RoughER,withribosomesstuddingitssurface


SmoothER

RoughER Nuclearenvelope

TransiDonalER

RoughERSmoothERTransportvesicle

RibosomesCisternaeERlumen

200nm

•  ThesmoothER–  Synthesizeslipids–  Metabolizes

carbohydrates–  Detoxifiespoison–  Storescalcium

•  TheroughER–  Hasbound

ribosomes,whichsecreteglycoproteins(proteinscovalentlybondedtocarbohydrates)

–  Distributestransportvesicles,proteinssurroundedbymembranes

–  Isamembranefactoryforthecell

cisface(“receiving”sideofGolgiapparatus) Cisternae

transface(“shipping”sideofGolgiapparatus)

TEMofGolgiapparatus

0.1µm

•  TheGolgiapparatusconsistsofflaSenedmembranoussacscalledcisternae•  Func>onsoftheGolgiapparatus:

–  ModifiesproductsoftheER–  Manufacturescertainmacromolecules–  Sortsandpackagesmaterialsintotransportvesicles

TheGolgiApparatus:ShippingandReceivingCenter

Membranetrafficking,vesicletransportvideos:hSps://www.youtube.com/watch?v=t7o--F02qdMhSps://www.youtube.com/watch?v=9uA-Toy-RRA

•  Sometypesofcellscanengulfothercellsbyphagocytosis;thisformsafoodvacuole

•  Alysosomefuseswiththefoodvacuoleanddigeststhemolecules

•  Lysosomesalsouseenzymestorecyclethecell’sownorganellesandmacromolecules,aprocesscalledautophagy

Vesiclecontainingtwodamagedorganelles

Mitochondrionfragment

Peroxisomefragment

Peroxisome

Lysosome

DigesDonMitochondrionVesicle

(b)Autophagy

1µmLysosomes:DigesDve

Compartments

Mitochondriaandchloroplastsconvertenergyfromoneformtoanother

•  Mitochondriaarethesitesofcellularrespira>on,ametabolicprocessthatgeneratesATP

•  Chloroplasts,foundinplantsandalgae,arethesitesofphotosynthesis

•  Peroxisomesareoxida>veorganelles

•  Mitochondriaandchloroplasts–  Arenotpartoftheendomembranesystem–  Haveadoublemembrane–  Haveproteinsmadebyfreeribosomes–  ContaintheirownDNA

Mitochondria:ChemicalEnergyConversion

•  Mitochondriaareinnearlyalleukaryo>ccells•  Theyhaveasmoothoutermembraneandaninnermembranefoldedintocristae

•  Theinnermembranecreatestwocompartments:intermembranespaceandmitochondrialmatrix

•  Somemetabolicstepsofcellularrespira>onarecatalyzedinthemitochondrialmatrix

•  CristaepresentalargesurfaceareaforenzymesthatsynthesizeATP


Freeribosomesinthemitochondrialmatrix

IntermembranespaceOutermembrane

InnermembraneCristae

Matrix

0.1µm

Chloroplasts:CaptureofLightEnergy

•  ThechloroplastisamemberofafamilyofplantorganellescalledplasDds

•  Chloroplastscontainthegreenpigmentchlorophyll,aswellasenzymesandothermoleculesthatfunc>oninphotosynthesis

•  Chloroplastsarefoundinleavesandothergreenorgansofplantsandinalgae


StructureofachloroplastPeroxisomes:Oxida>on

•  Peroxisomesarespecializedmetaboliccompartmentsboundedbyasinglemembrane

•  Peroxisomesproducehydrogenperoxideandconvertittowater

•  Oxygenisusedtobreakdowndifferenttypesofmolecules


1µm

Chloroplast

Peroxisome

Mitochondrion

INTENTIONAL BLANK PAGE

Lecture#4:Cellstructurept.2

• Reading:Chapter4

• Lectureoutline:-Cytoskeleton-Extracellularmatrix-Intercellularconnec=ons

Thecytoskeletonisanetworkoffibersthatorganizesstructuresandac@vi@esinthecell

Microtubule

Microfilaments0.25µm

• Thecytoskeletonextendsthroughoutthecytoplasm• Itorganizesthecell’sstructuresandac=vi=es,anchoringmany

organelles• Itiscomposedofthreetypesofmolecularstructures:

– Microtubules– Microfilaments(ac=nfilaments)– Intermediatefilaments

RolesoftheCytoskeleton:Support,Mo@lity,andRegula@on

• Thecytoskeletonhelpstosupportthecellandmaintainitsshape

• Itinteractswithmotorproteinstoproducemo=lity

• Insidethecell,vesiclescantravelalong“monorails”providedbythecytoskeleton

• Recentevidencesuggeststhatthecytoskeletonmayhelpregulatebiochemicalac=vi=es

VesicleATP

Receptorformotorprotein

Microtubuleofcytoskeleton

Motorprotein(ATPpowered)

(a)

Microtubule Vesicles

(b)

0.25µm

Giantsquidaxon

ComponentsoftheCytoskeleton

•  Threemaintypesoffibersmakeupthecytoskeleton:– Microtubulesarethethickestofthethreecomponentsofthecytoskeleton

– Microfilaments,alsocalledac=nfilaments,arethethinnestcomponents

–  Intermediatefilamentsarefiberswithdiametersinamiddlerange

10µm 10µm 10µm

Columnoftubulindimers

Tubulindimer

Ac@nsubunit

α β

25nm

7nm

Kera@nproteins

Fibroussubunit(kera@nscoiledtogether)

8–12nm

10µm 10µm 10µm

Columnoftubulindimers

Tubulindimer

Ac@nsubunit

α β

25nm

7nm

Kera@nproteins

Fibroussubunit(kera@nscoiledtogether)

8–12nm

Tubulindimersgiveriseto+and–endsofmicrotubules

Movieshowingmicrotubuleforma=on/depolymeriza=on:hQp://cryoem.berkeley.edu/movies/nogales_400x300_narrated.mov

Microtubules

•  Microtubulesarehollowrodsabout25nmindiameterandabout200nmto25micronslong

•  Func=onsofmicrotubules:– Shapingthecell– Guidingmovementoforganelles– Separa=ngchromosomesduringcelldivision

LiH,DeRosierDJ,NicholsonWV,NogalesE,DowningKH(2002)."Microtubulestructureat8Åresolu=on".Structure10:1317–28

CentrosomesandCentrioles•  Inmanycells,microtubulesgrowoutfromacentrosomenearthenucleus

•  Thecentrosomeisa“microtubule-organizingcenter”

•  Inanimalcells,thecentrosomehasapairofcentrioles,eachwithninetripletsofmicrotubulesarrangedinaring

Centrosome

Microtubule

Centrioles0.25µm

Longitudinalsec@onofonecentriole

Microtubules Crosssec@onoftheothercentriole

CiliaandFlagella

•  Microtubulescontrolthebea=ngofciliaandflagella,locomotorappendagesofsomecells

•  Ciliaandflagellashareacommonultrastructure:– Acoreofmicrotubulessheathedbytheplasmamembrane(9doubletsarrangedinaring@2singlets–seep.115)

– Abasalbodythatanchorstheciliumorflagellum– Amotorproteincalleddynein,whichdrivesthebendingmovementsofaciliumorflagellum

5µm

Direc@onofswimming

(a)Mo@onofflagella

Direc@onoforganism’smovement

Powerstroke Recoverystroke

(b)Mo@onofcilia15µm

MovieshowingdyneinwalkingalongmicrotubulehQps://www.youtube.com/watch?v=JX2MdZX6Bys

Microtubuledoublets

Dyneinprotein

ATP

ATP

(a)Effectofunrestraineddyneinmovement

Cross-linkingproteinsinsideouterdoublets

Anchorageincell

(b)Effectofcross-linkingproteins

1 3

2

(c)Wavelikemo@on

•  Howdynein“walking”movesflagellaandcilia:−  Dyneinarmsalternatelygrab,move,andreleasetheoutermicrotubules

–  Proteincross-linkslimitsliding

–  Forcesexertedbydyneinarmscausedoubletstocurve,bendingtheciliumorflagellum

Microvillus

Plasmamembrane

Microfilaments(ac@nfilaments)

Intermediatefilaments

0.25µm

•  Microfilamentsaresolidrodsabout7nmindiameter,builtasatwisteddoublechainofac@nsubunits

•  Thestructuralroleofmicrofilamentsistobeartension,resis=ngpullingforceswithinthecell

•  Theyforma3-Dnetworkcalledthecortexjustinsidetheplasmamembranetohelpsupportthecell’sshape

•  Bundlesofmicrofilamentsmakeupthecoreofmicrovilliofintes=nalcells

•  Microfilamentsthatfunc=onincellularmo=litycontaintheproteinmyosininaddi=ontoac=n

•  Inmusclecells,thousandsofac=nfilamentsarearrangedparalleltooneanother

•  Thickerfilamentscomposedofmyosininterdigitatewiththethinnerac=nfibers

Musclecell

Ac@nfilament

MyosinfilamentMyosinarm

(a)Myosinmotorsinmusclecellcontrac@on

IntermediateFilaments

•  Intermediatefilamentsrangeindiameterfrom8–12nanometers,largerthanmicrofilamentsbutsmallerthanmicrotubules

•  Theysupportcellshapeandfixorganellesinplace

•  Intermediatefilamentsaremorepermanentcytoskeletonfixturesthantheothertwoclasses

Extracellularcomponentshelpcoordinatecellularac=vi=es

•  Mostcellssynthesizeandsecretematerialsthatareexternaltotheplasmamembrane

•  Theseextracellularstructuresinclude:– Cellwallsofplants– Theextracellularmatrix(ECM)ofanimalcells–  Intercellularjunc=ons

CellWallsofPlants

•  Thecellwallisanextracellularstructurethatdis=nguishesplantcellsfromanimalcells

•  Prokaryotes,fungi,andsomepro=stsalsohavecellwalls

•  Thecellwallprotectstheplantcell,maintainsitsshape,andpreventsexcessiveuptakeofwater

•  Plantcellwallsaremadeofcellulosefibersembeddedinotherpolysaccharidesandprotein

SecondarycellwallPrimarycellwall

Middlelamella

CentralvacuoleCytosol

Plasmamembrane

Plantcellwalls

Plasmodesmata

1µm

•  Plantcellwallsmayhavemul=plelayers:–  Primarycellwall:

rela=velythinandflexible

–  Middlelamella:thinlayerbetweenprimarywallsofadjacentcells

–  Secondarycellwall(insomecells):addedbetweentheplasmamembraneandtheprimarycellwall

•  Plasmodesmataarechannelsbetweenadjacentplantcells

TheExtracellularMatrix(ECM)ofAnimalCells

•  Animalcellslackcellwallsbutarecoveredbyanelaborateextracellularmatrix(ECM)

•  TheECMismadeupofglycoproteinssuchascollagen,proteoglycans,andfibronec@n

•  ECMproteinsbindtoreceptorproteinsintheplasmamembranecalledintegrins

EXTRACELLULARFLUIDCollagen

Fibronec@n

Plasmamembrane

Micro-filaments

CYTOPLASM

Integrins

Proteoglycancomplex

Polysaccharidemolecule

Carbo-hydrates

Coreprotein

Proteoglycanmolecule

Proteoglycancomplex

•  Func=onsoftheECM:– Support– Adhesion– Movement– Regula=on

IntercellularJunc=ons

•  Neighboringcellsin=ssues,organs,ororgansystemsorenadhere,interact,andcommunicatethroughdirectphysicalcontact

•  Intercellularjunc=onsfacilitatethiscontact•  Thereareseveraltypesofintercellularjunc=ons– Plasmodesmata– Tightjunc=ons– Desmosomes– Gapjunc=ons

Interiorofcell

Interiorofcell

0.5µm Plasmodesmata Plasmamembranes

Cellwalls

PlasmodesmatainPlantCells

•  Plasmodesmataarechannelsthatperforateplantcellwalls

•  Throughplasmodesmata,waterandsmallsolutes(andsome=mesproteinsandRNA)canpassfromcelltocell

Tightjunc@on

0.5µm

1µmDesmosome

Gapjunc@on

Extracellularmatrix

0.1µm

Plasmamembranesofadjacentcells

Spacebetweencells

Gapjunc@ons

Desmosome

Intermediatefilaments

Tightjunc@on

Tightjunc@onspreventfluidfrommovingacrossalayerofcells

TightJunc;ons,Desmosomes,andGapJunc;onsinAnimalCells

•  At@ghtjunc@ons,membranesofneighboringcellsarepressedtogether,preven=ngleakageofextracellularfluid

•  Desmosomes(anchoringjunc=ons)fastencellstogetherintostrongsheets

•  Gapjunc@ons(communica=ngjunc=ons)providecytoplasmicchannelsbetweenadjacentcells

TheCell:ALivingUnitGreaterThantheSumofItsParts

Cellsrelyontheintegra=onofstructuresandorganellesinordertofunc=on

5µm

•  Forexample,amacrophage’sabilitytodestroybacteriainvolvesthewholecell,coordina=ngcomponentssuchasthecytoskeleton,lysosomes,andplasmamembrane

SUMMARYCellComponent Structure Func@on

Houseschromosomes,madeofchroma@n(DNA,thegene@cmaterial,andproteins);containsnucleoli,whereribosomalsubunitsaremade.Poresregulateentryandexitofmaterials.

Nucleus

(ER)

Concept6.3Theeukaryo@ccell’sgene@cinstruc@onsarehousedinthenucleusandcarriedoutbytheribosomes

Ribosome

Concept6.4 Endoplasmicre@culumTheendomembranesystemregulatesproteintrafficandperformsmetabolicfunc@onsinthecell

(Nuclearenvelope)

Concept6.5Mitochondriaandchloro-plastschangeenergyfromoneformtoanother

Golgiapparatus

Lysosome

Vacuole

Mitochondrion

Chloroplast

Peroxisome

Twosubunitsmadeofribo-somalRNAandproteins;canbefreeincytosolorboundtoER

Extensivenetworkofmembrane-boundtubulesandsacs;membraneseparateslumenfromcytosol;con@nuouswiththenuclearenvelope.

Membranoussacofhydroly@cenzymes(inanimalcells)

Largemembrane-boundedvesicleinplants

Boundedbydoublemembrane;innermembranehasinfoldings(cristae)

Typicallytwomembranesaroundfluidstroma,whichcontainsmembranousthylakoidsstackedintograna(inplants)

Specializedmetaboliccompartmentboundedbyasinglemembrane

Proteinsynthesis

SmoothER:synthesisoflipids,metabolismofcarbohy-drates,Ca2+storage,detoxifica-@onofdrugsandpoisons

RoughER:Aidsinsynthesisofsecretoryandotherproteinsfromboundribosomes;addscarbohydratestoglycoproteins;producesnewmembrane

Modifica@onofproteins,carbo-hydratesonproteins,andphos-pholipids;synthesisofmanypolysaccharides;sor@ngofGolgiproducts,whicharethenreleasedinvesicles.

Breakdownofingestedsubstances,cellmacromolecules,anddamagedorganellesforrecycling

Diges@on,storage,wastedisposal,waterbalance,cellgrowth,andprotec@on

Cellularrespira@on

Photosynthesis

Containsenzymesthattransferhydrogentowater,producinghydrogenperoxide(H2O2)asaby-product,whichisconvertedtowaterbyotherenzymesintheperoxisome

Stacksofflalenedmembranoussacs;haspolarity(cisandtransfaces)

Surroundedbynuclearenvelope(doublemembrane)perforatedbynuclearpores.Thenuclearenvelopeiscon@nuouswiththeendoplasmicre@culum(ER).

SUMMARY

CellComponent Structure Func@on

Concept6.3Theeukaryo@ccell’sgene@cinstruc@onsarehousedinthenucleusandcarriedoutbytheribosomes

Nucleus Surroundedbynuclearenvelope(doublemembrane)perforatedbynuclearpores.Thenuclearenvelopeiscon@nuouswiththeendoplasmicre@culum(ER).

(ER)

Houseschromosomes,madeofchroma@n(DNA,thegene@cmaterial,andproteins);containsnucleoli,whereribosomalsubunitsaremade.Poresregulateentryandexitosmaterials.

Ribosome Twosubunitsmadeofribo-somalRNAandproteins;canbefreeincytosolorboundtoER

Proteinsynthesis

SUMMARY

CellComponent Structure Func@on

Concept6.4Theendomembranesystemregulatesproteintrafficandperformsmetabolicfunc@onsinthecell

Endoplasmicre@culum

(Nuclearenvelope)

Golgiapparatus

Lysosome

Vacuole Largemembrane-boundedvesicleinplants

Membranoussacofhydroly@cenzymes(inanimalcells)

Stacksofflalenedmembranoussacs;haspolarity(cisandtransfaces)

Extensivenetworkofmembrane-boundtubulesandsacs;membraneseparateslumenfromcytosol;con@nuouswiththenuclearenvelope.

SmoothER:synthesisoflipids,metabolismofcarbohy-drates,Ca2+storage,detoxifica-@onofdrugsandpoisons

RoughER:Aidsinsythesisofsecretoryandotherproteinsfromboundribosomes;addscarbohydratestoglycoproteins;producesnewmembrane

Modifica@onofproteins,carbo-hydratesonproteins,andphos-pholipids;synthesisofmanypolysaccharides;sor@ngofGolgiproducts,whicharethenreleasedinvesicles.

Breakdownofingestedsub-stancescellmacromolecules,anddamagedorganellesforrecycling

Diges@on,storage,wastedisposal,waterbalance,cellgrowth,andprotec@on

SUMMARY

CellComponent

Concept6.5Mitochondriaandchloro-plastschangeenergyfromoneformtoanother

Mitochondrion

Chloroplast

Peroxisome

Structure Func@on

Boundedbydoublemembrane;innermembranehasinfoldings(cristae)

Typicallytwomembranesaroundfluidstroma,whichcontainsmembranousthylakoidsstackedintograna(inplants)

Specializedmetaboliccompartmentboundedbyasinglemembrane

Cellularrespira@on

Photosynthesis

Containsenzymesthattransferhydrogentowater,producinghydrogenperoxide(H2O2)asaby-product,whichisconvertedtowaterbyotherenzymesintheperoxisome

Basedonlectures3&4,youshouldnowbeableto:

1.  Dis=nguishbetweenthefollowingpairsofterms:prokaryo=candeukaryo=ccell;freeandboundribosomes;smoothandroughER

2.  Describethestructureandfunc=onofthecomponentsoftheendomembranesystem

3.  Brieflyexplaintheroleofmitochondria,chloroplasts,andperoxisomes

4.  Describethefunc=onsofthecytoskeleton

5.  Comparethestructuresandfunc=onsofmicrotubules,microfilaments,andintermediatefilaments

6.  Explainhowtheultrastructureofciliaandflagellarelatetotheirfunc=ons

7.  Describethestructureofaplantcellwall8.  Describethestructureandrolesofthe

extracellularmatrixinanimalcells9.  Describefourdifferentintercellularjunc=ons


Lecture#5:Biologicalmembranes


•  Lectureoutline:Membranestructureandfunc:on– Fluidmosaicmodel– Membraneproteins– Osmosis– Ac:vetransport

Overview:LifeattheEdge

•  Theplasmamembraneistheboundarythatseparatesthelivingcellfromitssurroundings

•  Theplasmamembraneexhibitsselec5vepermeability,allowingsomesubstancestocrossitmoreeasilythanothers

Hydrophilic head

WATER

Hydrophobic tail

WATER

Cellularmembranesarefluidmosaicsoflipidsandproteins

•  Phospholipidsarethemostabundantlipidintheplasmamembrane

•  Phospholipidsareamphipathicmolecules,containinghydrophobicandhydrophilicregions

•  Thefluidmosaicmodelstatesthatamembraneisafluidstructurewitha“mosaic”ofvariousproteinsembeddedinit

Phospholipid bilayer

Hydrophobic regions of protein

Hydrophilic regions of protein

Fluidmosaicmodelofmembranestructure

FluidmosaicvideohIps://www.youtube.com/watch?v=Qqsf_UJcfBc

TECHNIQUEExtracellular layer

KnifeProteins Inside of extracellular layer

RESULTS

Inside of cytoplasmic layerCytoplasmic layerPlasma membrane

•  Freeze-fracturestudiesoftheplasmamembranesupportedthefluidmosaicmodel

•  Freeze-fractureisaspecializedprepara:ontechniquethatsplitsamembranealongthemiddleofthephospholipidbilayer

Freeze-fractureexperiments

Freezefractureelectronmicroscopy

A.Fujita,J.Cheng&T.FujimotoNatureProtocols5,661-669(2010)

Lateral movement (~107 times per second)

Flip-flop (~ once per month)

(a) Movement of phospholipids

(b) Membrane fluidity

Fluid Viscous

Unsaturated hydrocarbon tails with kinks

Saturated hydrocarbon tails

(c) Cholesterol within the animal cell membrane

Cholesterol

TheFluidityofMembranes

•  Phospholipidsintheplasmamembranecanmovewithinthebilayer

•  Mostofthelipids,andsomeproteins,dri_laterally

•  Rarelydoesamoleculeflip-floptransverselyacrossthemembrane

RESULTS

Membrane proteins

Mouse cellHuman cell Hybrid cell

Mixed proteins after 1 hour

Experiment:aremembranesfluid?

FryeandEdidin(1970)Therapidintermixingofcellsurfacean:gensa_erforma:onofmouse-humanheterokaryons.JournalofCellScience7:319.

•  Peripheralproteinsareboundtothesurfaceofthemembrane

•  Integralproteinspenetratethehydrophobiccore

•  Integralproteinsthatspanthemembranearecalledtransmembraneproteins

•  Thehydrophobicregionsofanintegralproteinconsistofoneormorestretchesofnonpolaraminoacids,o_encoiledintoalphahelices

MembraneProteinsandTheirFunc5ons

Areintegralmembraneproteinsamphipathic?

GPCRvideo:hIps://www.youtube.com/watch?v=2r0GyTEimZM

N-terminus

C-terminus

α HelixCYTOPLASMIC SIDE

EXTRACELLULAR SIDE

Sixmajorfunc:onsofmembraneproteins:

–  Transport–  Enzyma:cac:vity–  Signaltransduc:on–  Cell-cell

recogni:on–  Intercellularjoining–  AIachmenttothe

cytoskeletonandextracellularmatrix(ECM)

(a) Transport

ATP

(b) Enzymatic activity

Enzymes

(c) Signal transduction

Signal transduction

Signaling molecule

Receptor

(d) Cell-cell recognition

Glyco- protein

(e) Intercellular joining (f) Attachment to the cytoskeleton and extracellular matrix (ECM) i.e.HIVco-receptor

Bloodtypes

SynthesisandSidednessofMembranes

•  Membraneshavedis:nctinsideandoutsidefaces

•  Theasymmetricaldistribu:onofproteins,lipids,andassociatedcarbohydratesintheplasmamembraneisdeterminedwhenthemembraneisbuiltbytheERandGolgiapparatus

ER1

Transmembrane glycoproteins

Secretory protein

Glycolipid

2Golgi apparatus

Vesicle

3

4

Secreted protein

Transmembrane glycoprotein

Plasma membrane:Cytoplasmic faceExtracellular face

Membrane glycolipid

SynthesisandSidednessofMembranes

•  Membraneshavedis:nctinsideandoutsidefaces

•  Theasymmetricaldistribu:onofproteins,lipids,andassociatedcarbohydratesintheplasmamembraneisdeterminedwhenthemembraneisbuiltbytheERandGolgiapparatus

Membranestructureresultsinselec5vepermeability

•  Acellmustexchangematerialswithitssurroundings,aprocesscontrolledbytheplasmamembrane

•  Plasmamembranesareselec:velypermeable,regula:ngthecell’smoleculartraffic

•  Hydrophobic(nonpolar)molecules,suchashydrocarbons,candissolveinthelipidbilayerandpassthroughthemembranerapidly

•  Polarmolecules,suchassugars,donotcrossthemembraneeasily

Passivetransport:diffusionacrossamembranewithnoenergyinvestment

•  Diffusionisthetendencyformoleculestospreadoutevenlyintotheavailablespace

•  Althougheachmoleculemovesrandomly,diffusionofapopula:onofmoleculesmayexhibitanetmovementinonedirec:on

•  Atdynamicequilibrium,asmanymoleculescrossonewayascrossintheotherdirec:on

Molecules of dye Membrane (cross section)

WATER

Net diffusion Net diffusion Equilibrium

(a) Diffusion of one solute

Net diffusion

Net diffusion

Net diffusion

Net diffusion

Equilibrium

Equilibrium

(b) Diffusion of two solutes

EffectsofOsmosisonWaterBalance

•  Osmosisisthediffusionofwateracrossaselec:velypermeablemembrane

•  Waterdiffusesacrossamembranefromtheregionoflowersoluteconcentra:ontotheregionofhighersoluteconcentra:on

Lower concentration of solute (sugar)

H2O

Higher concentration of sugar

Selectively permeable membrane

Same concentration of sugar

Osmosis

WaterBalanceofCellsWithoutWalls

•  Tonicityistheabilityofasolu:ontocauseacelltogainorlosewater

•  Isotonicsolu:on:Soluteconcentra:onisthesameasthatinsidethecell;nonetwatermovementacrosstheplasmamembrane

•  Hypertonicsolu:on:Soluteconcentra:onisgreaterthanthatinsidethecell;cellloseswater

•  Hypotonicsolu:on:Soluteconcentra:onislessthanthatinsidethecell;cellgainswater

Hypotonic solution

(a) Animal cell

(b) Plant cell

H2O

Lysed

H2O

Turgid (normal)

H2O

H2O

H2O

H2O

Normal

Isotonic solution

Flaccid

H2O

H2O

Shriveled

Plasmolyzed

Hypertonic solution TransportProteins

•  Transportproteinsallowpassageofhydrophilicsubstancesacrossthemembrane

•  Sometransportproteins,calledchannelproteins,haveahydrophilicchannelthatcertainmoleculesorionscanuseasatunnel

•  Channelproteinscalledaquaporinsfacilitatethepassageofwater

FacilitatedDiffusion:PassiveTransportAidedbyProteins

•  Infacilitateddiffusion,transportproteinsspeedthepassivemovementofmoleculesacrosstheplasmamembrane

•  Channelproteinsprovidecorridorsthatallowaspecificmoleculeoriontocrossthemembrane

•  Channelproteinsinclude– Aquaporins,forfacilitateddiffusionofwater–  Ionchannelsthatopenorcloseinresponsetoas:mulus(gatedchannels)

EXTRACELLULAR FLUID

Channel protein

(a) A channel protein

Solute CYTOPLASM

Solute Carrier protein

(b) A carrier protein

Ac5vetransportusesenergytomovesolutesagainsttheirgradients

•  Facilitateddiffusioniss:llpassivebecausethesolutemovesdownitsconcentra:ongradient

•  Sometransportproteins,however,canmovesolutesagainsttheirconcentra:ongradients

•  Ac5vetransportmovessubstancesagainsttheirconcentra:ongradient

•  Ac:vetransportrequiresenergy,usuallyintheformofATP

•  Ac:vetransportisperformedbyspecificproteinsembeddedinthemembranes

2

EXTRACELLULAR

FLUID [Na+] high [K+] low

[Na+] low [K+] high

Na+ Na+

Na+

Na+ Na+

Na+

CYTOPLASM ATP

ADP P

Na+ Na+

Na+

P 3

K+

K+ 6

K+

K+

5 4

K+

K+

P P

1

IonPumpsMaintainMembranePoten5al

•  Membranepoten5alisthevoltagedifferenceacrossamembrane(insideofcellisnega:velycharged)

•  Voltageiscreatedbydifferencesinthedistribu:onofposi:veandnega:veions

•  Twocombinedforces,collec:velycalledtheelectrochemicalgradient,drivethediffusionofionsacrossamembrane:– Achemicalforce(theion’sconcentra:ongradient)– Anelectricalforce(theeffectofthemembranepoten:alontheion’smovement)

•  Anelectrogenicpumpisatransportproteinthatgeneratesvoltageacrossamembrane

•  Thesodium-potassiumpumpisthemajorelectrogenicpumpofanimalcells

•  Themainelectrogenicpumpofplants,fungi,andbacteriaisaprotonpump

Proton pump

–

–

–

–

–

–

+

+

+

+

+

+

ATP

H+

H+

H+

H+

H+

H+

H+

H+

Diffusion of H+

Sucrose-H+ cotransporter

Sucrose

Sucrose

Bulktransportbyexocytosisandendocytosis

•  Smallmoleculesandwaterenterorleavethecellthroughthelipidbilayerorbytransportproteins

•  Largemolecules,suchaspolysaccharidesandproteins,crossthemembraneinbulkviavesicles

•  Bulktransportrequiresenergy•  Inexocytosis,transportvesiclesmigratetothemembrane,fusewithit,andreleasetheircontents

•  Inendocytosis,thecelltakesinmacromoleculesbyformingvesiclesfromtheplasmamembrane

PHAGOCYTOSIS

EXTRACELLULAR FLUID

CYTOPLASM

Pseudopodium

“Food”or other particle

Food vacuole

PINOCYTOSIS

1 µm

Pseudopodium of amoeba

Bacterium

Food vacuole

An amoeba engulfing a bacterium via phagocytosis (TEM)

Plasma membrane

Vesicle

0.5 µm

Pinocytosis vesicles forming (arrows) in a cell lining a small blood vessel (TEM)

RECEPTOR-MEDIATED ENDOCYTOSIS

Receptor Coat protein

Coated vesicle

Coated pit

Ligand

Coat protein

Plasma membrane

A coated pit and a coated vesicle formed during receptor- mediated endocytosis (TEMs)

0.25 µm

SUMMARY Passive transport

Diffusion Facilitated diffusion

Active transport

ATP


1.  Definethefollowingterms:amphipathicmolecules,aquaporins,diffusion

2.  Explainhowmembranefluidityisinfluencedbytemperatureandmembranecomposi:on

3.  Dis:nguishbetweenthefollowingpairsorsetsofterms:peripheralandintegralmembraneproteins;channelandcarrierproteins;osmosis,facilitateddiffusion,andac:vetransport;hypertonic,hypotonic,andisotonicsolu:ons

4.  Explainhowtransportproteinsfacilitatediffusion

5.  Explainhowanelectrogenicpumpcreatesvoltageacrossamembrane,andnametwoelectrogenicpumps

6.  Explainhowlargemoleculesaretransportedacrossacellmembrane


Lecture#6:Cellularmetabolism


•  Lectureoutline:Whyweneedenzymes

– Metabolicpathways– Thermodynamics– Freeenergy–  Introduc@ontoenzymes

Overview:TheEnergyofLife

•  Thelivingcellisaminiaturechemicalfactorywherethousandsofreac@onsoccur

•  Thecellextractsenergyandappliesenergytoperformwork

•  Someorganismsevenconvertenergytolight,asinbioluminescence

Anorganism’smetabolismtransformsma?erandenergy,subjecttothelawsofthermodynamics

•  Metabolismisthetotalityofanorganism’schemicalreac@ons

•  Metabolismisanemergentpropertyoflifethatarisesfrominterac@onsbetweenmoleculeswithinthecell

Metabolomics: thestudyofallthesmallmolecules–metabolites–inacell

OrganizaEonoftheChemistryofLifeintoMetabolicPathways

•  Ametabolicpathwaybeginswithaspecificmoleculeandendswithaproduct

•  Eachstepiscatalyzedbyaspecificenzyme

Enzyme 1 Enzyme 2 Enzyme 3 D C B A

Reaction 1 Reaction 3 Reaction 2 Starting molecule

Product

•  Catabolicpathwaysreleaseenergybybreakingdowncomplexmoleculesintosimplercompounds

•  Cellularrespira@on,thebreakdownofglucoseinthepresenceofoxygen,isanexampleofapathwayofcatabolism

Somemetabolicpathwaysbreakdownmolecules…

•  Anabolicpathwaysconsumeenergytobuildcomplexmoleculesfromsimplerones

•  Thesynthesisofproteinfromaminoacidsisanexampleofanabolism

•  BioenergeEcsisthestudyofhoworganismsmanagetheirenergyresources

Andsomemetabolicpathwayscreatemolecules

Energyisthecapacitytodowork

Energyexistsinvariousforms,someofwhichcanperformwork:•  KineEcenergyisenergyassociatedwithmo@on

•  Heat(thermalenergy)iskine@cenergyassociatedwithrandommovementofatomsormolecules

•  PotenEalenergyisenergythatmaLerpossessesbecauseofitsloca@onorstructure

•  Chemicalenergyispoten@alenergyavailableforreleaseinachemicalreac@on

•  Energycanbeconvertedfromoneformtoanother

Climbing up converts the kinetic energy of muscle movement to potential energy.

A diver has less potential energy in the water than on the platform.

Diving converts potential energy to kinetic energy.

A diver has more potential energy on the platform than in the water.

TheLawsofEnergyTransforma@on

•  Thermodynamicsisthestudyofenergytransforma@ons

•  Aclosedsystem,suchasthatapproximatedbyliquidinathermos,isisolatedfromitssurroundings

•  Inanopensystem,energyandmaLercanbetransferredbetweenthesystemanditssurroundings

•  OrganismsareopensystemsTwolawsofthermodynamicsgovernenergytransforma@onsinorganismsandothercollec@onsofmaLer

TheFirstLawofThermodynamics

•  Accordingtothefirstlawofthermodynamics,theenergyoftheuniverseisconstant:–Energycanbetransferredandtransformed,butitcannotbecreatedordestroyed

•  Thefirstlawisalsocalledtheprincipleofconserva@onofenergy

Wheredoestheenergythatsupportslifecomefrom?

TheSecondLawofThermodynamics

•  Duringeveryenergytransferortransforma@on,someenergyisunusable,andisoPenlostasheat

•  Accordingtothesecondlawofthermodynamics:–Everyenergytransferortransforma<onincreases

theentropy(disorder)oftheuniverse

(a) First law of thermodynamics (b) Second law of thermodynamics

Chemical energy

Heat CO2

H2O +

•  Livingcellsunavoidablyconvertorganizedformsofenergytoheat

•  Spontaneousprocessesoccurwithoutenergyinput;theycanhappenquicklyorslowly

•  Foraprocesstooccurwithoutenergyinput,itmustincreasetheentropyoftheuniverse(ΔSisposi@ve)oritstotalenergymustdecrease(ΔHisnega@ve)

ΔG=ΔH-TΔS

BiologicalOrderandDisorder

•  Cellscreateorderedstructuresfromlessorderedmaterials

•  OrganismsalsoreplaceorderedformsofmaLerandenergywithlessorderedforms

•  Energyflowsintoanecosystemintheformoflightandexitsintheformofheat

Whydoestheevolu@onofmorecomplexorganismsnotviolatethesecondlawofthermodynamics?

•  Entropy(disorder)maydecreaseinanorganism(anopensystem),butthe

universe’stotalentropyincreases

Equilibrium and Metabolism

•  Reactions in a closed system eventually reach equilibrium and then do no work

•  Cells are not in equilibrium; they are open systems experiencing a constant flow of materials

•  A defining feature of life is that metabolism is never at equilibrium

•  A catabolic pathway in a cell releases free energy in a series of reactions

The free-energy change of a reaction tells whether or not the reaction occurs spontaneously

•  Biologists want to know which reactions occur spontaneously and which require input of energy

•  To do so, they need to determine energy changes that occur in chemical reactions

•  A living system’s free energy is energy that is available to do work when temperature and pressure are uniform, as in a living cell

•  The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), change in entropy (∆S), and temperature in Kelvin (T): ∆G = ∆H – T∆S •  Only processes with a negative ∆G are

spontaneous •  Spontaneous processes can be harnessed

to perform work

Free-Energy Change, ΔG Reaction coordinate diagram Free energy, G, is plotted as a function of the reaction progress (the reaction coordinate). The starting point for the forward or reverse reaction is called the ground state. The free energy change that occurs during a reaction under a standard set of conditions (temperature 298 K; 1 atm pressure; 1 M solute concentrations) is denoted ΔG°. ΔG’° is the standard free-energy change at pH 7. (and remember the change in Gibbs free energy relationship: ΔG = ΔH - TΔS)

FreeEnergy,Stability,andEquilibrium

•  Free energy is a measure of a system’s instability, its tendency to change to a more stable state

•  During a spontaneous change, free energy decreases and the stability of a system increases

•  Equilibrium is a state of maximum stability •  A process is spontaneous and can perform

work only when it is moving toward equilibrium

EnzymesEnzymes (“in yeast”) are the chemical reaction catalysts of biological systems. Most enzymes are proteins, and they often use metal ions or prosthetic groups like vitamins to assist catalysis. Many inherited genetic disorders result from a defect or even a total absence of a particular enzyme, or excessive activity of an enzyme. Measurement of enzyme activities in body fluids is important in diagnosing various illnesses. Furthermore, many drugs act by altering the activities of enzymes. And enzymes are practical tools in the laboratory.

Video about enzymes https://www.youtube.com/watch?v=E2UNc5zBejc

LactoseintolerancePeople lacking the enzyme lactase can’t digest a sugar found in milk/dairy products:

Lactose: What’s the cause of lactose intolerance? How is lactose intolerance treated?

Discovery of enzymes

In 1897 it was discovered that yeast extracts could ferment sugar to alcohol: C6H12O6 → 2C2H5OH + 2CO2 + 2 ATP This finding showed that fermentation was promoted by molecules that continued to function when removed from cells.


In 1926, jack bean urease was isolated and crystallized. This enzyme catalyzes the reaction: CH4N2O + H2O → 2NH3 + CO2 The urease crystals contained only protein, leading to the idea that all enzymes are proteins.

Various intestinal-tract pathogens produce urease, enabling detection of urease to be used as a diagnostic. For example: Helicobacter pylori, which causes ulcers.


In 1926, jack bean urease was isolated and crystallized. This enzyme catalyzes the reaction: CH4N2O + H2O → 2NH3 + CO2 The urease crystals contained only protein, leading to the idea that all most enzymes are proteins.


In the 1930s, weak chemical bonding interactions between an enzyme and its substrate were hypothesized be used to catalyze a reaction. This key insight lies at the heart of our current understanding of enzyme catalysis.

Enzymes speed up the rates of biochemical reactions

The active site of an enzyme is usually a cleft or pocket where chemistry takes place. A molecule that binds in the active site and is acted upon by the enzyme is called a substrate. As simple equation for an enzyme-catalyzed reaction can be written:

E + S D ES D EP D E + P where E is enzyme, S is substrate and P is product. Enzymes do not alter the reaction equilibrium, but they alter the forward and reverse reaction rates. Enzymes remain unchanged after the reaction.

Someexamplesofenzyme-catalyzedrateenhancements

Note that enzyme names typically end in “ase”

Comparison of catalyzed vs. uncatalyzed reaction

The activation energy of the reaction is lower when catalyzed by an enzyme. One idea about how enzymes work is that they bind to the transition state better than to the substrate or product, stabilizing the transition state.

Free energy and equilibrium constant are related

K’°eq = [P]/[S] From thermodynamics, the equilibrium constant and the free energy are related by the expression

ΔG’° = -RTln K’°eq

= -2.3RTlog K’°eq If the equilibrium constant is 1, the energy released is zero. If the equilibrium constant is 1000, then the free energy released is -17 kJ/mole.

Binding energy, ΔGB, is a major source of free energy used by enzymes to lower the activation energy of a reaction.


Lecture#7:Enzymefunc1on


•  Lectureoutline:Howenzymeswork

– Freeenergy– Enzyme-catalyzedreac?ons– ATPpowersmuchofthecell’swork

•  Spontaneousprocessesoccurwithoutenergyinput;theycanhappenquicklyorslowly

•  Foraprocesstooccurwithoutenergyinput,itmustincreasetheentropyoftheuniverse(ΔSisposi?ve)oritstotalenergy(enthalpy)mustdecrease(ΔHisnega?ve)

ΔG=ΔH-TΔS

Enzymesspeeduptheratesofbiochemicalreac1ons

Theac1vesiteofanenzymeisusuallyacleMorpocketwherechemistrytakesplace.Amoleculethatbindsintheac?vesiteandisacteduponbytheenzymeiscalledasubstrate.Assimpleequa?onforanenzyme-catalyzedreac?oncanbewriPen:

E+SDESDEPDE+PwhereEisenzyme,SissubstrateandPisproduct.Enzymesdonotalterthereac?onequilibrium,buttheyaltertheforwardandreversereac?onrates.EnzymesremainunchangedaMerthereac?on.

Enzymesspeedupmetabolicreac1onsbyloweringenergybarriers

•  Acatalystisachemicalagentthatspeedsupareac?onwithoutbeingconsumedbythereac?on

•  Anenzymeisacataly?cprotein•  Hydrolysisofsucrosebytheenzymesucraseisanexampleofanenzyme-catalyzedreac?on

Sucrose (C12H22O11)

Glucose (C6H12O6) Fructose (C6H12O6)

Sucrase

TheAc1va1onEnergyBarrier

•  Everychemicalreac?onbetweenmoleculesinvolvesbondbreakingandbondforming

•  Theini?alenergyneededtostartachemicalreac?oniscalledthefreeenergyofac1va1on,orac1va1onenergy(EA)

•  Ac?va?onenergyisoMensuppliedintheformofheatfromthesurroundings

Progress of the reaction

Products

Reactants

∆G < O

Transition state

Free

ene

rgy EA

D C

B A

D

D

C

C

B

B

A

A

HowEnzymesLowertheEABarrier

•  Enzymescatalyzereac?onsbyloweringtheEAbarrier

•  Enzymesdonotaffectthechangeinfreeenergy(∆G);instead,theyincreasethereac?onrate

Progress of the reaction

Products

Reactants

∆G is unaffected by enzyme

Course of reaction without enzyme

Free

ene

rgy

EA without enzyme EA with

enzyme is lower

Course of reaction with enzyme

Bindingenergy,ΔGB,isamajorsourceoffreeenergyusedbyenzymestolowertheac?va?onenergyofareac?on.

E+SDESDEPDE+P

SubstrateSpecificityofEnzymes

•  Thereactantthatanenzymeactsoniscalledtheenzyme’ssubstrate

•  Theenzymebindstoitssubstrate,forminganenzyme-substratecomplex

•  Theac1vesiteistheregionontheenzymewherethesubstratebinds

•  Inducedfitofasubstratebringschemicalgroupsoftheac?vesiteintoposi?onsthatenhancetheirabilitytocatalyzethereac?on

Substrate

Active site

Enzyme Enzyme-substrate complex

(b) (a)

Videoonhexokinase:hPps://www.youtube.com/watch?v=2gZDHMQcgtQ

CatalysisintheEnzyme’sAc?veSite

•  Inanenzyma?creac?on,thesubstratebindstotheac?vesiteoftheenzyme

•  Theac?vesitecanloweranEAbarrierby– Orien?ngsubstratescorrectly– Strainingsubstratebonds– Providingafavorablemicroenvironment– Covalentlybondingtothesubstrate

EnzymesbindbeLertotransi1onstatesthantosubstrates

Chorismatemutaseexample:

hPp://en.wikipedia.org/wiki/Chorismate_mutase

hPp://en.wikipedia.org/wiki/Chorismate_mutase#mediaviewer/File:Chorismate_Mutase_Scheme.png

hPp://www.pnas.org/content/111/49/17516.abstract

hPp://www.pnas.org/content/95/25/14640/F2.large.jpg

Transi1onstateanalogsmimicthestructureinthetransi1onstate

TheHilvertLabhPp://www.protein.ethz.ch

An1bodiesthatbindtotransi1onstateanalogscansome1mesbecatalysts…

Bindingenergycontributestocatalysisinmul1pleways:

•  Entropyreduc?on

•  Substratedesolva?on

•  Inducedfit

Substrates

Enzyme

Products are released.

Products

Substrates are converted to products.

Active site can lower EA and speed up a reaction.

Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds.

Substrates enter active site; enzyme changes shape such that its active site enfolds the substrates (induced fit).

Active site is

available for two new

substrate molecules.

Enzyme-substrate complex

5

3

2 1

6

4

Specificcataly1cgroupscontributetocatalysis

•  Generalacid-basecatalysis

•  Covalentcatalysis

•  Metalioncatalysis

EffectsofLocalCondi?onsonEnzymeAc?vity

•  Anenzyme’sac?vitycanbeaffectedby– Generalenvironmentalfactors,suchastemperatureandpH

– Chemicalsthatspecificallyinfluencetheenzyme

EffectsofTemperature

andpH

•  Eachenzymehasanop?maltemperatureinwhichitcanfunc?on

•  Eachenzymehasanop?malpHinwhichitcanfunc?on

Rat

e of

reac

tion

Optimal temperature for enzyme of thermophilic

(heat-tolerant) bacteria

Optimal temperature for typical human enzyme

(a) Optimal temperature for two enzymes

(b) Optimal pH for two enzymes

Rat

e of

reac

tion

Optimal pH for pepsin (stomach enzyme)

Optimal pH for trypsin (intestinal enzyme)

Temperature (ºC)

pH 5 4 3 2 1 0 6 7 8 9 10

0 20 40 80 60 100

Exergonicvs.Endergonicreac1ons

•  Exergonicreac?onsreleaseenergytothesystem.

•  ΔG<0•  Exergonicreac?onsproceedspontaneously

•  Endergonicreac?onsabsorbenergyfromthesystem.

•  ΔG>0•  Endergonicreac?onsarenotspontaneous

ATPpowerscellularworkbycouplingexergonicreac?onstoendergonic

reac?ons•  Acelldoesthreemainkindsofwork:– Chemical– Transport– Mechanical

•  Todowork,cellsmanageenergyresourcesbyenergycoupling,theuseofanexergonicprocesstodriveanendergonicone

•  MostenergycouplingincellsismediatedbyATP Phosphate groups Ribose

Adenine

TheStructureandHydrolysisofATP

•  ATP(adenosinetriphosphate)isthecell’senergyshuPle•  ATPiscomposedofribose(asugar),adenine(anitrogenousbase),andthreephosphategroups

•  ThebondsbetweenthephosphategroupsofATPcanbebrokenbyhydrolysis

•  EnergyisreleasedfromATPwhentheterminalphosphatebondisbroken

•  Thisreleaseofenergycomesfromthechemicalchangetoastateoflowerfreeenergy,notfromthephosphatebondsthemselves

ATPhydrolysis

Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP) H2O

+

HowATPPerformsWork

•  Thethreetypesofcellularwork(mechanical,transport,andchemical)arepoweredbythehydrolysisofATP

•  Inthecell,theenergyfromtheexergonicreac?onofATPhydrolysiscanbeusedtodriveanendergonicreac?on

•  Overall,thecoupledreac?onsareexergonic

•  ATPdrivesendergonicreac?onsbyphosphoryla?on,transferringaphosphategrouptosomeothermolecule,suchasareactant

•  Therecipientmoleculeisnowphosphorylated

(b) Coupled with ATP hydrolysis, an exergonic reaction

Ammonia displaces the phosphate group, forming glutamine.

(a) Endergonic reaction

(c) Overall free-energy change

P P

Glu NH3

NH2

Glu i

Glu ADP +

P ATP +

+

Glu

ATP phosphorylates glutamic acid, making the amino acid less stable.

Glu NH3

NH2

Glu +

Glutamic acid

Glutamine Ammonia

∆G = +3.4 kcal/mol

+ 2

1 EnzymeA

EnzymeB

(b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzed

Membrane protein

P i

ADP +

P

Solute Solute transported

P i

Vesicle Cytoskeletal track

Motor protein Protein moved

(a) Transport work: ATP phosphorylates transport proteins

ATP

ATP

TheRegenera?onofATP

•  ATPisarenewableresourcethatisregeneratedbyaddi?onofaphosphategrouptoadenosinediphosphate(ADP)

•  TheenergytophosphorylateADPcomesfromcatabolicreac?onsinthecell

•  Thechemicalpoten?alenergytemporarilystoredinATPdrivesmostcellularwork P i ADP +

Energy from catabolism (exergonic, energy-releasing processes)

Energy for cellular work (endergonic, energy-consuming processes)

ATP + H2O

Free-energychangeofreac1on

•  ΔrG=ΔrG˚+RTlnQr;Qristhereac?onquo?ent.

•  Atequilibrium,ΔrG=0andQr=Keqsotheequa?onbecomesΔrG˚=−RTlnKeq;Keqistheequilibiumconstant.


Lecture#8:Enzymeregula3on


•  Lectureoutline:Howenzymesarecontrolled

– Enzymecofactors– Enzymeinhibitors– Allostericregula?on

Overview

•  Cofactorshelpenzymestofunc?onefficiently•  Enzymeinhibitorsblockac?vitythroughdifferentmechanisms:

•  Compe??ve•  Non-compe??ve•  Uncompe??ve

•  Enzymescanberegulatedbystructuralchanges

Inducedfitmodelofenzymecatalysis

hGp://en.wikipedia.org/wiki/File:Induced_fit_diagram.svg

Cofactors

•  Cofactorsarenonproteinenzymehelpers•  Cofactorsmaybeinorganic(suchasametalinionicform)ororganic

•  Anorganiccofactoriscalledacoenzyme•  Coenzymesincludevitamins

VitaminB12isanexampleofacoenzyme:

hGp://en.wikipedia.org/wiki/Vitamin_B12#Enzyme_func?on

Cofactors

•  Tightly-boundcofactorsarecalledprosthe3cgroups.Example:heme

•  Loosely-boundcofactorsarecalledcoenzymes.•  Aninac?veenzymelackingthecofactoriscalledanapo-enzyme;thecompleteenzymewithitscofactoriscalledaholoenzyme.

Cofactors

•  OrganiccofactorsoYenshareacommonchemicalfeature,canyouseeit?

CoenzymeA

FADNAD+

Cofactors

•  NADHisreversiblyoxidizedtoNAD+duringelectrontransportincells.

•  ManyenzymescontaincommonstructuralfeaturesthatbindNAD+/NADH

Rossmannfoldinlactatedehydrogenase

Regula3onofenzymeac3vityhelpscontrolmetabolism

•  Chemicalchaoswouldresultifacell’smetabolicpathwayswerenot?ghtlyregulated

•  Acelldoesthisbyswitchingonoroffthegenesthatencodespecificenzymesorbyregula?ngtheac?vityofenzymes

FeedbackInhibi3on

•  Infeedbackinhibi3on,theendproductofametabolicpathwayshutsdownthepathway

•  Feedbackinhibi?onpreventsacellfromwas?ngchemicalresourcesbysynthesizingmoreproductthanisneeded

Intermediate C

Feedback inhibition

Isoleucine used up by cell

Enzyme 1 (threonine deaminase)

End product (isoleucine)

Enzyme 5 Intermediate D

Intermediate B

Intermediate A

Enzyme 4

Enzyme 2

Enzyme 3

Initial substrate (threonine)

Threonine in active site

Active site available

Active site of enzyme 1 no longer binds threonine; pathway is switched off.

Isoleucine binds to Enzyme 1 and induces structure change

EnzymeInhibitors

•  Compe33veinhibitorsbindtotheac?vesiteofanenzyme,compe?ngwiththesubstrate

•  Noncompe33veinhibitorsbindtoanotherpartofanenzyme,causingtheenzymetochangeshapeandmakingtheac?vesitelesseffec?ve

•  Examplesofinhibitorsincludetoxins,poisons,pes?cides,andan?bio?cs

(a) Normal binding (c) Noncompetitive inhibition (b) Competitive inhibition

Noncompetitive inhibitor

Active site Competitive inhibitor

Substrate

Enzyme

Manyan?bio?cdrugsbindandinhibitthebacterialribosome.Inthisstructureofthesmallribosomalsubunit(30S)fromVenkiRamakrishnan’slab,theglowingmoleculeisthean?bio?cbindingnearthedecodingcenter.

Videoofchloramphenicolon70Sribosome:

hGps://www.youtube.com/watch?v=dY-hP8Wd4sA

4typesofHIV-1inhibitors

hGp://en.wikipedia.org/wiki/HAART

HIVproteaseinhibitorsblocktheviralenzymerequiredtoproduceindividualHIVproteins

ritonavir

hGp://en.wikipedia.org/wiki/Enzyme_inhibitor

AllostericRegula?onofEnzymes

•  Allostericregula3onmayeitherinhibitors?mulateanenzyme’sac?vity

•  Allostericregula?onoccurswhenaregulatorymoleculebindstoaproteinatonesiteandaffectstheprotein’sfunc?onatanothersite

Hemoglobinisaclassicexampleofanallostericallyregulatedprotein

AllostericAc3va3onandInhibi3on

•  Mostallostericallyregulatedenzymesaremadefrompolypep?desubunits

•  Eachenzymehasac?veandinac?veforms•  Thebindingofanac?vatorstabilizestheac?veformoftheenzyme

•  Thebindingofaninhibitorstabilizestheinac?veformoftheenzyme

Allosteric enyzme with four subunits

Active site (one of four)

Regulatory site (one of four)

Active form Activator

Stabilized active form

Oscillation

Non- functional active site

Inhibitor Inactive form Stabilized inactive form

(a) Allosteric activators and inhibitors

Substrate

Inactive form Stabilized active form

(b) Cooperativity: another type of allosteric activation

(a) Allosteric activators and inhibitors

Inhibitor Non- functional active site

Stabilized inactive form

Inactive form

Oscillation

Activator Active form Stabilized active form

Regulatory site (one of four)

Allosteric enzyme with four subunits

Active site (one of four)

TheHbtetramerincludestwoαandtwoβsubunits

Stronginterac?onsbetweentheα1andβ1(andα2/β2)subunitsholdthemtogethereveninthepresenceofurea(adenaturant).

Hbexistsin2majorconforma3ons

O2willbindHbineitherstate,buthasmuchhigheraffinityforHbintheRstate.Tstateisstabilizedbyagreaternumberofionpairsatthesubunitinterfaces.WhenO2binds,Hbconforma?onchangestotheRstate.

Movie:R-Tstatetransi?onforHb

hGp://biochem.web.utah.edu/iwasa/projects/hemoglobin.html

•  Coopera3vityisaformofallostericregula?onthatcanamplifyenzymeac?vity

•  Incoopera?vity,bindingbyasubstratetooneac?vesitestabilizesfavorableconforma?onalchangesatallothersubunits

(b) Cooperativity: another type of allosteric activation

Stabilized active form

Substrate

Inactive form

Iden3fica3onofAllostericRegulators

•  AllostericregulatorsareaGrac?vedrugcandidatesforenzymeregula?on

•  Inhibi?onofproteoly?cenzymescalledcaspasesmayhelpmanagementofinappropriateinflammatoryresponses

SH

Substrate

Hypothesis: allosteric inhibitor locks enzyme in inactive form

Active form can bind substrate

S–S SH

SH

Active site

Caspase 1

Known active form

Known inactive form

Allosteric binding site

Allosteric inhibitor

EXPERIMENT

Caspase 1

RESULTS

Active form Inhibitor

Allosterically inhibited form

Inactive form


1.  Dis?nguishbetweenthefollowingpairsofterms:catabolicandanabolicpathways;kine?candpoten?alenergy;openandclosedsystems;exergonicandendergonicreac?ons

2.  Inyourownwords,explainthesecondlawofthermodynamicsandexplainwhyitisnotviolatedbylivingorganisms

3.  Explainingeneraltermshowcellsobtaintheenergytodocellularwork

4.  ExplainhowATPperformscellularwork5.  Explainwhyaninvestmentofac?va?on

energyisnecessarytoini?ateaspontaneousreac?on

6.  Describethemechanismsbywhichenzymeslowerac?va?onenergy

7.  Describehowallostericregulatorsmayinhibitors?mulatetheac?vityofanenzyme

8.  Explainhowsomeenzymeinhibitorswork

Lecture#9:Energe.cs


•  Lectureoutline:Cellularrespira6on

– Redoxreac6ons– Electrontransportchain– Glycolysis

Overview:LifeIsWork

•  Livingcellsrequireenergyfromoutsidesources•  Someanimals,suchasthegiantpanda,obtainenergybyea6ngplants,andsomeanimalsfeedonotherorganismsthateatplants

Lightenergy

ECOSYSTEM

Photosynthesisinchloroplasts

CO2+H2O

Cellularrespira.oninmitochondria

Organicmolecules+O2

ATPpowersmostcellularwork

Heatenergy

ATP

•  Energyflowsintoanecosystemassunlightandleavesasheat

•  Photosynthesis

generatesO2andorganicmolecules,whichareusedincellularrespira6on

•  Cellsusechemical

energystoredinorganicmoleculestoregenerateATP,whichpowerswork

Video:Howcellsharvestenergy

hLps://www.youtube.com/watch?v=-Gb2EzF_XqA

CatabolicPathwaysandProduc.onofATP

•  Thebreakdownoforganicmoleculesisexergonic

•  Fermenta.onisapar6aldegrada6onofsugarsthatoccurswithoutO2

•  Aerobicrespira.onconsumesorganicmoleculesandO2andyieldsATP

•  Anaerobicrespira.onissimilartoaerobicrespira6onbutconsumescompoundsotherthanO2

RedoxReac.ons:Oxida.onandReduc.on

•  Thetransferofelectronsduringchemicalreac6onsreleasesenergystoredinorganicmolecules

•  Thisreleasedenergyisul6matelyusedtosynthesizeATP

ThePrincipleofRedox

•  Chemicalreac6onsthattransferelectronsbetweenreactantsarecalledoxida6on-reduc6onreac6ons,orredoxreac.ons

•  Inoxida.on,asubstanceloseselectrons,orisoxidized

•  Inreduc.on,asubstancegainselectrons,orisreduced(theamountofposi6vechargeisreduced)

becomesoxidized(loseselectron)

becomesreduced(gainselectron)

•  Theelectrondonoriscalledthereducingagent•  Theelectronreceptoriscalledtheoxidizingagent

•  Someredoxreac6onsdonottransferelectronsbutchangetheelectronsharingincovalentbonds

•  Anexampleisthereac6onbetweenmethaneandO2

Reactants

becomesoxidized

becomesreduced

Products

Methane(reducingagent)

Oxygen(oxidizingagent)

Carbondioxide Water

Oxida3onofOrganicFuelMoleculesDuringCellularRespira3on

•  Duringcellularrespira6on,thefuel(suchasglucose)isoxidized,andO2isreduced:

becomesoxidized

becomesreduced

StepwiseEnergyHarvestviaNAD+andtheElectronTransportChain

•  Incellularrespira.on,glucoseandotherorganicmoleculesarebrokendowninaseriesofsteps

•  ElectronsfromorganiccompoundsareusuallyfirsttransferredtoNAD+,acoenzyme

•  Asanelectronacceptor,NAD+func6onsasanoxidizingagentduringcellularrespira6on

•  EachNADH(thereducedformofNAD+)representsstoredenergythatistappedtosynthesizeATP

DehydrogenaseR

R

R

R

Dehydrogenase

Reduc.onofNAD+

Oxida.onofNADH

2e–+2H+ 2e–+H

+

NAD+ + 2[H]

NADH

+

H+

H+

Nico.namide(oxidizedform)

Nico.namide(reducedform)

Nico.namideAdenineDinucleo.de

•  NADHpassestheelectronstotheelectrontransportchain

•  Unlikeanuncontrolledreac6on,theelectrontransportchainpasseselectronsinaseriesofstepsinsteadofoneexplosivereac6on

•  O2pullselectronsdownthechaininanenergy-yieldingtumble

•  TheenergyyieldedisusedtoregenerateATP

Freeene

rgy,G

Freeene

rgy,G

(a)Uncontrolledreac.on

H2O

H2+1/2O2

Explosivereleaseof

heatandlightenergy

(b)Cellularrespira.on

Controlledreleaseofenergyforsynthesisof

ATP

2H++2e–

2H + 1/2O2

(fromfoodviaNADH)

ATP

ATP

ATP

1/2O22H+

2e–

Electrontransport

chain

H2O

TheStagesofCellularRespira6on:APreview

•  Cellularrespira6onhasthreestages:– Glycolysis(breaksdownglucoseintotwomoleculesofpyruvate)

– Thecitricacidcycle(completesthebreakdownofglucose)

– Oxida.vephosphoryla.on(accountsformostoftheATPsynthesis)

Substrate-levelphosphoryla.on

ATP

Cytosol

Glucose Pyruvate

Glycolysis

Electronscarried

viaNADH

Mitochondrion


ATP

Cytosol

Glucose Pyruvate

Glycolysis

Electronscarried

viaNADH


ATP

ElectronscarriedviaNADHand

FADH2

Citricacidcycle

Mitochondrion


ATP

Cytosol

Glucose Pyruvate

Glycolysis

Electronscarried

viaNADH


ATP

ElectronscarriedviaNADHand

FADH2

Oxida.vephosphoryla.on

ATP

Citricacidcycle

Oxida.vephosphoryla.on:electrontransport

andchemiosmosis

•  TheprocessthatgeneratesmostoftheATPiscalledoxida.vephosphoryla.onbecauseitispoweredbyredoxreac6ons

•  Oxida6vephosphoryla6onaccountsforalmost90%oftheATPgeneratedbycellularrespira6on

•  AsmalleramountofATPisformedinglycolysisandthecitricacidcyclebysubstrate-levelphosphoryla.on

Enzyme

ADP

PSubstrate

Enzyme

ATP+

Product

Glycolysisharvestschemicalenergybyoxidizingglucosetopyruvate

•  Glycolysis(“splibngofsugar”)breaksdownglucoseintotwomoleculesofpyruvate

•  Glycolysisoccursinthecytoplasmandhastwomajorphases:– Energyinvestmentphase– Energypayoffphase

Energyinvestmentphase

Glucose

2ADP+2 P 2ATP used

formed4ATP

Energypayoffphase

4ADP+4 P

2NAD++4e–+4H+ 2NADH +2H+

2Pyruvate+2H2O

2Pyruvate+2H2OGlucoseNet

4ATPformed–2ATPused 2ATP

2NAD++4e–+4H+ 2NADH+2H+

ATP

ADP

Hexokinase1

ATP

ADP

Hexokinase1

Glucose

Glucose-6-phosphate

Glucose

Glucose-6-phosphate

Phosphoryla6onmakessugarmorereac6ve;chargetrapssugarincell

Hexokinase

ATP

ADP

1

Phosphoglucoisomerase2

Phosphogluco-isomerase

2

Glucose

Glucose-6-phosphate

Fructose-6-phosphate

Glucose-6-phosphate


1

Fig.9-9-3

Hexokinase

ATP

ADP

Phosphoglucoisomerase

Phosphofructokinase

ATP

ADP

2

3

ATP

ADP

Phosphofructo-kinase

Fructose-1,6-bisphosphate

Glucose

Glucose-6-phosphate



1

2

3


3

Keystepinregula6ngglycolysis

Glucose

ATP

ADP

Hexokinase

Glucose-6-phosphate



ATP

ADP

Phosphofructokinase


Aldolase

Isomerase

Dihydroxyacetonephosphate

Glyceraldehyde-3-phosphate

1

2

3

4

5

Aldolase

Isomerase


Dihydroxyacetonephosphate


4

5

2NAD+

NADH2+2H+

2

2 P i

Triosephosphatedehydrogenase

1,3-Bisphosphoglycerate

6

2NAD+



NADH2+2H+

2 P i


6

2

2

2

Glyceraldehydephosphatedehydrogenase(GAPDH)

2NAD+

NADH2


+2H+

2 P i

2

2ADP


Phosphoglycerokinase2ATP

2 3-Phosphoglycerate

6

7

2

2ADP

2ATP


3-Phosphoglycerate

Phosphoglycero-kinase

2



2NAD+

2 NADH+2H+

2 P i

2

2ADP

Phosphoglycerokinase


2ATP

3-Phosphoglycerate2

Phosphoglyceromutase

2-Phosphoglycerate2

2-Phosphoglycerate2

2

Phosphoglycero-mutase

6

7

8

8

2NAD+

NADH2

2

2

2

2

+2H+


2 P i



2ADP

2ATP

3-Phosphoglycerate


Enolase

2-Phosphoglycerate

2H2O

Phosphoenolpyruvate

9

8

7

6


Enolase

2

2H2O

Phosphoenolpyruvate

9


2NAD+

NADH2

2

2

2

2

2

2ADP

2ATP

Pyruvate

Pyruvatekinase

Phosphoenolpyruvate

Enolase2H2O

2-Phosphoglycerate


3-Phosphoglycerate


2ATP

2ADP


+2H+

6

7

8

9

10

2

2ADP

2ATP

Phosphoenolpyruvate

Pyruvatekinase

2 Pyruvate

10

2 P i

Warburgeffect

•  Tumorcellshaveglycoly6cratesupto200Xhigherthanthoseofnormalcellsintheir6ssueoforigin.

•  Canbeusedtodiagnosetumors,usingan18F-labeledsubstrateofhexokinaseandPETscanning.

•  Reasons:low-oxygenenvironmentoftumors,tumor-associatedpyruvatekinaseenzyme,damageorshutdownofmitochondria


Lecture#10:Aerobicmetabolism


•  Lectureoutline:

– Citricacidcycle– Oxida8vephosphoryla8on

Thecitricacidcyclecompletestheenergy-yieldingoxida=onoforganicmolecules

•  InthepresenceofO2,pyruvateentersthemitochondrion

•  Beforethecitricacidcyclecanbegin,pyruvatemustbeconvertedtoacetylCoA,whichlinksthecycletoglycolysis

CYTOSOL MITOCHONDRION

NAD+ NADH +H+

2

1 3

Pyruvate

Transportprotein

CO2CoenzymeA

AcetylCoA

Mitochondria:ChemicalEnergyConversion

•  Mitochondriaareinnearlyalleukaryo8ccells•  Theyhaveasmoothoutermembraneandaninnermembranefoldedintocristae

•  Theinnermembranecreatestwocompartments:intermembranespaceandmitochondrialmatrix

•  Somemetabolicstepsofcellularrespira8onarecatalyzedinthemitochondrialmatrix

•  CristaepresentalargesurfaceareaforenzymesthatsynthesizeATP


Freeribosomesinthemitochondrialmatrix

IntermembranespaceOutermembrane

InnermembraneCristae

Matrix

0.1µm

•  Thecitricacidcycle,alsocalledtheKrebscycleorthetricarboxylicacid(TCA)cycle,takesplacewithinthemitochondrialmatrix

•  Thecycleoxidizesorganicfuelderivedfrompyruvate,genera8ng1ATP,3NADH,and1FADH2perturnRemember:NADH=reducedformofNico8namideAdenineDinucleo8deNew,butrelatedmolecule:FADH2=FlavinAdenineDinucleo8de

hUp://vcell.ndsu.nodak.edu/anima8ons/citricacid_overview/movie-flash.htm

Pyruvate

NAD+

NADH+H+

AcetylCoA

CO2

CoA

CoA

CoA

Citricacidcycle

FADH2

FAD

CO22

3

3NAD+

+3H+

ADP+ P i

ATP

NADH

•  Thecitricacidcyclehaseightsteps,eachcatalyzedbyaspecificenzyme

•  TheacetylgroupofacetylCoAjoinsthecyclebycombiningwithoxaloacetate,formingcitrate

•  Thenextsevenstepsdecomposethecitratebacktooxaloacetate,makingtheprocessacycle

•  TheNADHandFADH2producedbythecyclerelayelectronsextractedfromfoodtotheelectrontransportchain

AcetylCoA

Oxaloacetate

CoA—SH

1

Citrate

Citricacidcycle

AcetylCoA

Oxaloacetate

Citrate

CoA—SH

Citricacidcycle

1

2

H2O

Isocitrate

AcetylCoA

CoA—SH

Oxaloacetate

Citrate

H2O

Citricacidcycle

Isocitrate

1

2

3

NAD+

NADH+H+

α-Keto-glutarate

CO2

AcetylCoA

CoA—SH

Oxaloacetate

Citrate

H2O

IsocitrateNAD+

NADH+H+

Citricacidcycle

α-Keto-glutarate

CoA—SH

1

2

3

4

NAD+

NADH+H+Succinyl

CoA

CO2

CO2

AcetylCoA

CoA—SH

Oxaloacetate

Citrate

H2O

IsocitrateNAD+

NADH+H+

CO2

Citricacidcycle

CoA—SH

α-Keto-glutarate

CO2NAD+

NADH+H+Succinyl

CoA

1

2

3

4

5

CoA—SH

GTP GDP

ADP

P iSuccinate

ATP

AcetylCoA

CoA—SH

Oxaloacetate

H2O

CitrateIsocitrate

NAD+

NADH+H+

CO2

Citricacidcycle

CoA—SH

α-Keto-glutarate

CO2NAD+

NADH+H+

CoA—SH

P

SuccinylCoA

iGTP GDP

ADP

ATP

SuccinateFAD

FADH2

Fumarate

1

2

3

4

5

6

AcetylCoA

CoA—SH

Oxaloacetate

Citrate

H2O

IsocitrateNAD+

NADH+H+

CO2

α-Keto-glutarate

CoA—SH

NAD+

NADHSuccinylCoA

CoA—SH

PP

GDPGTP

ADP

ATP

SuccinateFAD

FADH2

Fumarate

CitricacidcycleH2O

Malate

1

2

5

6

7

i

CO2

+H+

3

4

AcetylCoA

CoA—SH

Citrate

H2O

IsocitrateNAD+

NADH+H+

CO2

α-Keto-glutarate

CoA—SH

CO2NAD+

NADH+H+Succinyl

CoA

CoA—SH

P iGTP GDP

ADP

ATP

SuccinateFAD

FADH2

Fumarate

CitricacidcycleH2O

Malate

Oxaloacetate

NADH+H+

NAD+

1

2

3

4

5

6

7

8

Duringoxida=vephosphoryla=on,chemiosmosiscoupleselectrontransporttoATPsynthesis

•  Followingglycolysisandthecitricacidcycle,NADHandFADH2accountformostoftheenergyextractedfromfood

•  Thesetwoelectroncarriersdonateelectronstotheelectrontransportchain,whichpowersATPsynthesisviaoxida8vephosphoryla8on

ThePathwayofElectronTransport

•  Theelectrontransportchainisinthecristaeofthemitochondrion

•  Mostofthechain’scomponentsareproteins,whichexistinmul8proteincomplexes

•  Thecarriersalternatereducedandoxidizedstatesastheyacceptanddonateelectrons

•  ElectronsdropinfreeenergyastheygodownthechainandarefinallypassedtoO2,formingH2O

NADH

NAD+2FADH2

2 FADMul=proteincomplexesFAD

Fe•SFMN

Fe•S

Q

Fe•S

Ι

Cytb

ΙΙ

ΙΙΙ

Cytc1Cytc

Cyta

Cyta3

IV

Freeene

rgy(G)rela=

veto

O2(kcal/m

ol)

50

40

30

20

10 2(fromNADHorFADH2)

0 2H++1/2 O2

H2O

e–

e–

e–

•  ElectronsaretransferredfromNADHorFADH2totheelectrontransportchain

•  Electronsarepassedthroughanumberofproteinsincludingcytochromes(eachwithanironatom)toO2

•  TheelectrontransportchaingeneratesnoATP•  Thechain’sfunc8onistobreakthelargefree-energydropfromfoodtoO2intosmallerstepsthatreleaseenergyinmanageableamounts

Chemiosmosis:TheEnergy-CouplingMechanism

•  ElectrontransferintheelectrontransportchaincausesproteinstopumpH+fromthemitochondrialmatrixtotheintermembranespace

•  H+thenmovesbackacrossthemembrane,passingthroughchannelsinATPsynthase

•  ATPsynthaseusestheexergonicflowofH+todrivephosphoryla8onofATP

•  Thisisanexampleofchemiosmosis,theuseofenergyinaH+gradienttodrivecellularwork

INTERMEMBRANESPACE

Rotor

H+

Stator

Internalrod

Cata-ly=cknob

ADP+P ATPi

MITOCHONDRIALMATRIX

ATPSynthase:ANanomachine1-H+ions(protons)enterchannelinstator2-Protonsbindspecificsitesintherotor,causingconforma8onalchangesthatacttospintherotorwithinthemembrane3-Eachprotonmakes1completeturnbeforeenteringthemitochondrialmatrixthroughanotherchannelinthestator4-rotorspinningcausestheinternalrodtospin.Therodextendsintothesta8onarycataly8cknob5-turningoftherodac8vatescataly8csitesintheknobthatproduceATPfromADPandPi

hUp://www.youtube.com/watch?v=PjdPTY1wHdQ

•  TheenergystoredinaH+gradientacrossamembranecouplestheredoxreac8onsoftheelectrontransportchaintoATPsynthesis

•  TheH+gradientisreferredtoasaproton-mo=veforce,emphasizingitscapacitytodowork

Proteincomplexofelectroncarriers

H+

H+H+

Cytc

Q

Ι

ΙΙ

ΙΙΙ

ΙV

FADH2 FAD

NAD+NADH(carryingelectronsfromfood)

Electrontransportchain

2H++1/2O2 H2O

ADP+ P i

Chemiosmosis

Oxida=vephosphoryla=on

H+

H+

ATPsynthase

ATP

21

AnAccoun8ngofATPProduc8onbyCellularRespira8on

•  Duringcellularrespira8on,mostenergyflowsinthissequence:glucose→NADH →electrontransportchain→proton-mo8veforce→ATP

•  About40%oftheenergyinaglucosemoleculeistransferredtoATPduringcellularrespira8on,makingabout38ATPmolecules

Maximumperglucose: About36-38ATP

+2ATP+2ATP +about32or34ATP

Oxida=vephosphoryla=on:electrontransport

andchemiosmosis

Citricacidcycle

2AcetylCoA

Glycolysis

Glucose2

Pyruvate

2NADH 2NADH 6NADH 2FADH2

2FADH2

2NADHCYTOSOL Electronshueles

spanmembraneor

MITOCHONDRION

26-28ATP

30-32ATP

3reasonsforinexactATPyieldes8mate:-phosphoryla8onandredoxrxnsnotdirectlycoupled, soNADH:ATPnotawholenumber -ATPyieldvariesdependingonelectrontransportsys -PMFusedtodriveotherkindsofwork

Overallrespira8onefficiencyis~35%,meaningthat35%ofenergystoredinglucoseisharvested

Howdobacteriadoit???

Theylackmembrane-boundorganelles(i.e.mitochondrion)…buthavetwocellularmembranes!

Lecture#11:Anaerobicmetabolism


•  Lectureoutline:

– Fermenta7on– Anaerobicrespira7on– Regula7onofcellularrespira7on

Fermenta5onandanaerobicrespira5onenablecellstoproduceATPwithout

usingoxygen

•  Mostcellularrespira7onrequiresO2toproduceATP

•  GlycolysiscanproduceATPwithorwithoutO2(inaerobicoranaerobiccondi7ons)

•  IntheabsenceofO2,glycolysiscoupleswithfermenta7onoranaerobicrespira7ontoproduceATP

•  Anaerobicrespira7onusesanelectrontransportchainwithanelectronacceptorotherthanO2,forexamplesulfate(SO4

2-)•  Fermenta7onusessubstrate-levelphosphoryla7oninsteadofanelectrontransportchaintogenerateATP

Enzyme

ADPP

Substrate

Enzyme

ATP

Product

HowdoProkaryotesdoit???

Theylackmembrane-boundorganelles(i.e.mitochondrion)…buthavetwocellularmembranes!

Sulfate-reducingbacteriaTypesofFermenta7on

•  Fermenta7onconsistsofglycolysisplusreac7onsthatregenerateNAD+,whichcanbereusedbyglycolysis

•  Twocommontypesarealcoholfermenta7onandlac7cacidfermenta7on

2NAD+ 2NADH+2H+

EthanolLac5cAcid

•  Inalcoholfermenta5on,pyruvateisconvertedtoethanolintwosteps,withthefirstreleasingCO2

•  Alcoholfermenta7onbyyeastisusedinbrewing,winemaking,andbaking

2ADP+2 P i 2ATP

Glucose Glycolysis

2Pyruvate

2NADH2NAD+

+2H+CO2

2Acetaldehyde2Ethanol

(a)Alcoholfermenta5on

2

•  Inlac5cacidfermenta5on,pyruvateisreducedbyNADH,forminglactateasanendproduct,withnoreleaseofCO2

•  Lac7cacidfermenta7onbysomefungiandbacteriaisusedtomakecheeseandyogurt

•  Humanmusclecellsuselac7cacidfermenta7ontogenerateATPwhenO2isscarce

Anaerobicfermenta5on

•  Fermenta7veanaerobicorganismsmostlyusethelac7cacidfermenta7onpathway

•  C6H12O6+2ADP+2phosphate2lac7cacid+2ATP•  Theenergyreleasedinthisequa7onisapproximately150kJpermole,whichisharvestedingenera7ng2ATPfromADP.

•  Thisisonly5%oftheenergypersugarmoleculethatthetypicalaerobicreac7ongenerates.

Glucose

2ADP+2 P i 2ATP

Glycolysis

2NAD+ 2NADH+2H+

2Pyruvate

2Lactate

(b)Lac5cacidfermenta5on

ComparingFermenta7ontoAerobicandAnaerobicRespira7on

•  All3processesuseglycolysistooxidizeglucoseandotherorganicfuelstopyruvate

•  Inall3pathways,NAD+isoxidizingagentthatacceptselectronsfromfoodduringglycolysis

•  Theprocesseshavedifferentfinalelectronacceptors:anorganicmolecule(suchaspyruvateoracetaldehyde)infermenta7on,O2inaerobicrespira7onandanothermolecule,i.e.SO4

2-,inanaerobicrespira7on

•  Respira7onproduces3832-34ATPperglucosemolecule;fermenta7onproduces2ATPperglucosemolecule

•  Obligateanaerobescarryoutfermenta7onoranaerobicrespira7onandcannotsurviveinthepresenceofO2

•  Yeastandmanybacteriaarefaculta5veanaerobes,meaningthattheycansurviveusingeitherfermenta7onorcellularrespira7on

•  Inafaculta7veanaerobe,pyruvateisaforkinthemetabolicroadthatleadstotwoalterna7vecatabolicroutes

Glucose

Glycolysis

Pyruvate

CYTOSOL

NoO2present:Fermenta5on

O2present:Aerobiccellularrespira5on

MITOCHONDRIONAcetylCoAEthanol

orlactate

Citricacidcycle

TheEvolu5onarySignificanceofGlycolysis

•  Glycolysisoccursinnearlyallorganisms•  Glycolysisprobablyevolvedinancientprokaryotesbeforetherewasoxygenintheatmosphere

Glycolysisandthecitricacidcycleconnecttomanyothermetabolicpathways

•  Glycolysisandthecitricacidcyclearemajorintersec7onstovariouscatabolicandanabolicpathways

TheVersa5lityofCatabolism

•  Catabolicpathwaysfunnelelectronsfrommanykindsoforganicmoleculesintocellularrespira7on

•  Glycolysisacceptsawiderangeofcarbohydrates

•  Proteinsmustbedigestedtoaminoacids;aminoacidscanfeedglycolysisorthecitricacidcycle

•  Fatsaredigestedtoglycerol(usedinglycolysis)andfabyacids(usedingenera7ngacetylCoA)

•  Fabyacidsarebrokendownbybetaoxida5onandyieldacetylCoA

•  AnoxidizedgramoffatproducesmorethantwiceasmuchATPasanoxidizedgramofcarbohydrate

hbps://www.youtube.com/watch?v=J5wGPHm-2og

Proteins Carbohydrates

Aminoacids

Sugars

Fats

Glycerol FaZyacids

Glycolysis

Glucose

Glyceraldehyde-3-

Pyruvate

P

NH3

AcetylCoA

Citricacidcycle

Oxida5vephosphoryla5on

Biosynthesis(AnabolicPathways)

•  Thebodyusessmallmoleculestobuildothersubstances•  Thesesmallmoleculesmaycomedirectlyfromfood,from

glycolysis,orfromthecitricacidcycle

Regula7onofCellularRespira7onviaFeedbackMechanisms

•  Feedbackinhibi7onisthemostcommonmechanismforcontrol

•  IfATPconcentra7onbeginstodrop,respira7onspeedsup;whenthereisplentyofATP,respira7onslowsdown

•  Controlofcatabolismisbasedmainlyonregula7ngtheac7vityofenzymesatstrategicpointsinthecatabolicpathway

Glucose

GlycolysisFructose-6-phosphate

Phosphofructokinase

Fructose-1,6-bisphosphateInhibits

AMP

S5mulates

Inhibits

Pyruvate

CitrateAcetylCoA

Citricacidcycle

Oxida5vephosphoryla5on

ATP

+

––

1Hexokinase

ATP

ADP


Phosphofructokinase

ATP

ADP

2

3

ATP

ADPPhosphofructo-kinase


Glucose

Glucose-6-phosphate



1

2

3


3

ATPisanaturalallostericinhibitorofPFK,inordertopreventunnecessaryproduc7onofATPthroughglycolysis.

Phosphofructokinase

Thereisaconcertedtransi7onfromanenzyma7callyinac7veT-statetotheac7veR-state.F6PbindswithahighaffinitytotheRstatebutnottheTstateenzyme.ForeverymoleculeofF6PthatbindstoPFK1,theenzymeprogressivelyshiisfromTstatetotheRstate.

hbps://www.youtube.com/watch?v=rb4jImee4NU

Electron shuttles span membrane

MITOCHONDRION 2 NADH

2 NADH 2 NADH 6 NADH

2 FADH2

2 FADH2

or

+ 2 ATP + 2 ATP + about 26 or 28 ATP

Glycolysis

Glucose 2 Pyruvate

Pyruvate oxidation

2 Acetyl CoA Citric acid cycle

Oxidative phosphorylation: electron transport

and chemiosmosis

CYTOSOL

Maximum per glucose: About 30 or 32 ATP

INTER-MEMBRANESPACE

H+

ATPsynthase

ATPADP+ P i

H+MITO-CHONDRIALMATRIX

Chemiosmosis

hbp://en.wikipedia.org/wiki/Chemiosmosis

Fermenta5onandAerobicRespira5onCompared

•  Bothprocessesuseglycolysistooxidizeglucoseandotherorganicfuelstopyruvate

•  Theprocesseshavedifferentfinalelectronacceptors:anorganicmolecule(suchaspyruvateoracetaldehyde)infermenta7onandO2incellularrespira7on

•  Cellularrespira7onproduces32ATPperglucosemolecule;fermenta7onproduces2ATPperglucosemolecule

Twoexamplesofuncouplingbetweenglycolysisandaerobicmetabolism

•  Hiberna7on

•  Warburgeffect

Hiberna5on

•  Animalsthathibernatehavelargenumbersofbrownfatcellspackedfullofmitochondria

•  ThesecellscanexpressamitochondrialuncouplerintheinnermitomembranethatallowsH+ionstoflowbackintothematrix

•  Uncouplersenableongoingoxida7onofstoredfuels(fats)withoutgenera7ngATPandinsteadproducingheat


1.  Explainingeneraltermshowredoxreac7onsareinvolvedinenergyexchanges

2.  Namethethreestagesofcellularrespira7on;foreach,statetheregionoftheeukaryo7ccellwhereitoccursandtheproductsthatresult

3.  Ingeneralterms,explaintheroleoftheelectrontransportchainincellularrespira7on

4.  Explainwhereandhowtherespiratoryelectrontransportchaincreatesaprotongradient

5.  Dis7nguishbetweenfermenta7onandanaerobicrespira7on

6.  Dis7nguishbetweenobligateandfaculta7veanaerobes


Lecture#12:PhotosynthesisI


•  Lectureoutline:IntrotoPhotosynthesis

– Lightenergytochemicalenergy– Lightreac:ons

Overview:TheProcessThatFeedstheBiosphere

•  Photosynthesisistheprocessthatconvertssolarenergyintochemicalenergy

•  Directlyorindirectly,photosynthesisnourishesthelivingworld

•  Autotrophssustainthemselveswithoutea:nganythingderivedfromotherorganisms

•  Autotrophsaretheproducersofthebiosphere,producingorganicmoleculesfromCO2andotherinorganicmolecules

•  Almostallplantsarephotoautotrophs,usingtheenergyofsunlighttomakeorganicmoleculesfromH2OandCO2

(a)Plants

(c)UnicellularproBst10µm

1.5µm

40µm(d)Cyanobacteria

(e)Purplesulfurbacteria

(b)MulBcellularalga

•  Photosynthesisoccursinplants,algae,certainotherpro:sts,andsomeprokaryotes

•  Theseorganismsfeednotonlythemselvesbutalsomostofthelivingworld

•  Heterotrophsobtaintheirorganicmaterialfromotherorganisms

•  Heterotrophsaretheconsumersofthebiosphere

•  Almostallheterotrophs,includinghumans,dependonphotoautotrophsforfoodandO2

Photosynthesisconvertslightenergytothechemicalenergyoffood

•  Chloroplastsarestructurallysimilartoandlikelyevolvedfromphotosynthe:cbacteria

•  Thestructuralorganiza:onofphotosynthe:ccellsallowsforthechemicalreac:onsofphotosynthesis

Chloroplasts:TheSitesofPhotosynthesisinPlants

•  Leavesarethemajorloca:onsofphotosynthesis

•  Theirgreencolorisfromchlorophyll,thegreenpigmentwithinchloroplasts

•  Lightenergyabsorbedbychlorophylldrivesthesynthesisoforganicmoleculesinthechloroplast

•  CO2entersandO2exitstheleafthroughmicroscopicporescalledstomata

LeafcrosssecBon

Vein

Mesophyll

StomataCO2 O2

ChloroplastMesophyllcell

Outermembrane

Intermembranespace

5µm

Innermembrane

Thylakoidspace

Thylakoid

Granum

Stroma

1µm

•  Chloroplastsarefoundmainlyincellsofthemesophyll,theinterior:ssueoftheleaf

•  Atypicalmesophyllcellhas30–40chloroplasts

•  Thechlorophyllisinthemembranesofthylakoids(connectedsacsinthechloroplast);thylakoidsmaybestackedincolumnscalledgrana

•  Chloroplastsalsocontainstroma,adensefluid

TrackingAtomsThroughPhotosynthesis:

•  Photosynthesiscanbesummarizedasthefollowingequa:on:

6CO2+12H2O+Lightenergy→C6H12O6+6O2+6H2O

•  ChloroplastssplitH2Ointohydrogenandoxygen,incorpora:ngtheelectronsofhydrogenintosugarmolecules

Reactants: 6CO2

Products:

12H2O

6O26H2OC6H12O6

PhotosynthesisasaRedoxProcess

•  PhotosynthesisisaredoxprocessinwhichH2OisoxidizedandCO2isreduced

Energy+6CO2+6H2O C6H12O6+6O2

Endergonicreac:on!

TheTwoStagesofPhotosynthesis:APreview

•  PhotosynthesisconsistsofthelightreacBons(thephotopart)andCalvincycle(thesynthesispart)

•  Thelightreac:ons(inthethylakoids):– SplitH2O– ReleaseO2– ReduceNADP+toNADPH– GenerateATPfromADPbyphotophosphorylaBon

•  TheCalvincycle(inthestroma)formssugarfromCO2,usingATPandNADPH

•  TheCalvincyclebeginswithcarbonfixaBon,incorpora:ngCO2intoorganicmolecules

NADP+

h[ps://www.youtube.com/watch?v=YeD9idmcX0w

Light

H2O

Chloroplast

LightReacBons

NADP+

PADP

i+

Light

H2O

Chloroplast

LightReacBons

NADP+

PADP

i+

ATP

NADPH

O2

Light

H2O

Chloroplast

LightReacBons

NADP+

PADP

i+

ATP

NADPH

O2

CalvinCycle

CO2

Light

H2O

Chloroplast

LightReacBons

NADP+

PADP

i+

ATP

NADPH

O2

CalvinCycle

CO2

[CH2O](sugar)

Thelightreac:onsconvertsolarenergytothechemicalenergyofATPand

NADPH•  Chloroplastsaresolar-poweredchemicalfactories

•  TheirthylakoidstransformlightenergyintothechemicalenergyofATPandNADPH

TheNatureofSunlight

•  Lightisaformofelectromagne:cenergy,alsocalledelectromagne:cradia:on

•  Likeotherelectromagne:cenergy,lighttravelsinrhythmicwaves

•  Wavelengthisthedistancebetweencrestsofwaves

•  Wavelengthdeterminesthetypeofelectromagne:cenergy

•  TheelectromagneBcspectrumistheen:rerangeofelectromagne:cenergy,orradia:on

•  Visiblelightconsistsofwavelengths(includingthosethatdrivephotosynthesis)thatproducecolorswecansee(380-750nm)

•  Lightalsobehavesasthoughitconsistsofdiscretepar:cles,calledphotons

UV

Visiblelight

InfraredMicro-waves

RadiowavesX-raysGamma

rays

103m1m

(109nm)106nm103nm1nm10–3nm10–5nm

380 450 500 550 600 650 700 750nm

LongerwavelengthLowerenergyHigherenergy

Shorterwavelength

Photosynthe:cPigments:TheLightReceptors

•  Pigmentsaresubstancesthatabsorbvisiblelight

•  Differentpigmentsabsorbdifferentwavelengths

•  Wavelengthsthatarenotabsorbedarereflectedortransmi[ed

•  Leavesappeargreenbecausechlorophyllreflectsandtransmitsgreenlight

Reflectedlight

Absorbedlight

Light

Chloroplast

Transmieedlight

Granum

•  Aspectrophotometermeasuresapigment’sabilitytoabsorbvariouswavelengths

•  Thismachinesendslightthroughpigmentsandmeasuresthefrac:onoflighttransmi[edateachwavelength

Galvanometer

Slitmovestopasslightofselectedwavelength

Whitelight

Greenlight

Bluelight

Thelowtransmieance(highabsorpBon)readingindicatesthatchlorophyllabsorbsmostbluelight.

Thehightransmieance(lowabsorpBon)readingindicatesthatchlorophyllabsorbsverylielegreenlight.

RefracBngprism

Photoelectrictube

ChlorophyllsoluBon

TECHNIQUE

1

2 3

4

•  AnabsorpBonspectrumisagraphploingapigment’slightabsorp:onversuswavelength

•  Theabsorp:onspectrumofchlorophyllasuggeststhatviolet-blueandredlightworkbestforphotosynthesis

•  AnacBonspectrumprofilestherela:veeffec:venessofdifferentwavelengthsofradia:onindrivingaprocess

3typesofpigmentsinchloroplasts:chlorophyllapar:cipatesdirectlyinthelightreac:ons chlorophyllbisanaccessorypigment carotenoidsareaccessorypigments

•  Theac:onspectrumofphotosynthesiswasfirstdemonstratedin1883byTheodorW.Engelmann

•  Inhisexperiment,heexposeddifferentsegmentsofafilamentousalgatodifferentwavelengths

•  AreasreceivingwavelengthsfavorabletophotosynthesisproducedexcessO2

•  HeusedthegrowthofaerobicbacteriaclusteredalongthealgaasameasureofO2produc:on

Wavelengthoflight(nm)

(b)AcBonspectrum

(a)AbsorpBonspectra

(c)Engelmann’sexperiment

Aerobicbacteria

RESULTS

Rateofp

hotosynthe

sis

(measuredbyO

2release)

AbsorpBo

noflightb

ychloroplastp

igmen

ts

Filamentofalga

Chloro-phylla Chlorophyllb

Carotenoids

500400 600 700

700600500400

•  Chlorophyllaisthemainphotosynthe:cpigment

•  Accessorypigments,suchaschlorophyllb,broadenthespectrumusedforphotosynthesis

•  Accessorypigmentscalledcarotenoidsabsorbexcessivelightthatwoulddamagechlorophyll

Porphyrinring:light-absorbing“head”ofmolecule;notemagnesiumatomatcenter

inchlorophyllaCH3

Hydrocarbontail:interactswithhydrophobicregionsofproteinsinsidethylakoidmembranesofchloroplasts;Hatomsnotshown

CHO inchlorophyllb

Excita:onofChlorophyllbyLight

•  Whenapigmentabsorbslight,itgoesfromagroundstatetoanexcitedstate,whichisunstable

•  Whenexcitedelectronsfallbacktothegroundstate,photonsaregivenoff,anakerglowcalledfluorescence

•  Ifilluminated,anisolatedsolu:onofchlorophyllwillfluoresce,givingofflightandheat


(a)ExcitaBonofisolatedchlorophyllmolecule

Heat

Excitedstate

(b)Fluorescence

Photon Groundstate

Photon(fluorescence)

Energyofe

lectron

e–

Chlorophyllmolecule

Lecture#13:PhotosynthesisII


•  Lectureoutline:Carbonfixa8on

– Photosystems– TheCalvincycle– C4andCAMplants

(a)Excita9onofisolatedchlorophyllmolecule

Heat

Excitedstate

(b)Fluorescence

Photon Groundstate

Photon(fluorescence)

Energyofe

lectron

e–

Chlorophyllmolecule

APhotosystem:AReac8on-CenterComplexAssociatedwithLight-

Harves8ngComplexes•  Aphotosystemconsistsofareac9on-centercomplex(atypeofproteincomplex)surroundedbylight-harves8ngcomplexes

•  Thelight-harves9ngcomplexes(pigmentmoleculesboundtoproteins)funneltheenergyofphotonstothereac8oncenter

•  Aprimaryelectronacceptorinthereac8oncenteracceptsanexcitedelectronfromchlorophylla

•  Solar-poweredtransferofanelectronfromachlorophyllamoleculetotheprimaryelectronacceptoristhefirststepofthelightreac8ons

CrystalstructureofPSII

Guskovetal(2009)NSMB

20proteins35chlorophyllamolecules12carotenoids25integrallipids

Plastoquinonesbindinspecificsites

Guskovetal(2009)NSMB

QBisaplastoquinone;isoprenoidtailextendstowardthethylakoidmembrane.

THYLAKOIDSPACE(INTERIOROFTHYLAKOID)

STROMA

e–

Pigmentmolecules

Photon

Transferofenergy

Specialpairofchlorophyllamolecules

Thylakoidmem

bran

e

Photosystem

Primaryelectronacceptor

Reac9on-centercomplex

Light-harves9ngcomplexes

hWp://vcell.ndsu.nodak.edu/anima8ons/photosystemII/movie-flash.htm

•  Therearetwotypesofphotosystemsinthethylakoidmembrane

•  PhotosystemII(PSII)func8onsfirst(thenumbersreflectorderofdiscovery)andisbestatabsorbingawavelengthof680nm

•  Thereac8on-centerchlorophyllaofPSIIiscalledP680

•  PhotosystemI(PSI)isbestatabsorbingawavelengthof700nm

•  Thereac8on-centerchlorophyllaofPSIiscalledP700

LinearElectronFlow

•  Duringthelightreac8ons,therearetwopossibleroutesforelectronflow:cyclicandlinear

•  Linearelectronflow,theprimarypathway,involvesbothphotosystemsandproducesATPandNADPHusinglightenergy

Pigmentmolecules

Light

P680

e–2

1

PhotosystemII(PSII)

Primaryacceptor

•  Aphotonhitsapigmentanditsenergyispassedamongpigmentmoleculesun8litexcitesP680

•  AnexcitedelectronfromP680istransferredtotheprimaryelectronacceptor

Pigmentmolecules

Light

P680

e–

Primaryacceptor

2

1

e–e–

2H+

O2

+3

H2O

1/2

PhotosystemII(PSII)

•  P680+(P680thatismissinganelectron)isaverystrongoxidizingagent

•  H2Oissplitbyenzymes,andtheelectronsaretransferredfromthehydrogenatomstoP680+,thusreducingittoP680

•  H+arereleasedintothethylakoidlumen

•  O2isreleasedasaby-productofthisreac8on Pigment

molecules

Light

P680

e–

Primaryacceptor

2

1

e–e–

2H+

O2

+3

H2O

1/2

4

Pq

Pc

Cytochromecomplex

5

ATP

PhotosystemII(PSII)

•  Eachelectron“falls”downanelectrontransportchainfromtheprimaryelectronacceptorofPSIItoPSI

•  Energyreleasedbythefalldrivesthecrea8onofaprotongradientacrossthethylakoidmembrane

•  DiffusionofH+(protons)acrossthemembranedrivesATPsynthesis

Pigmentmolecules

Light

P680

e–

Primaryacceptor

2

1

e–e–

2H+

O2

+3

H2O

1/2

4

Pq

Pc

Cytochromecomplex

5

ATP

PhotosystemI(PSI)

Light

Primaryacceptor

e–

P700

6

PhotosystemII(PSII)

•  InPSI(likePSII),transferredlightenergyexcitesP700,whichlosesanelectrontoanelectronacceptor

•  P700+(P700thatismissinganelectron)acceptsanelectronpasseddownfromPSIIviatheelectrontransportchain

•  Eachelectron“falls”downanelectrontransportchainfromtheprimaryelectronacceptorofPSItotheproteinferredoxin(Fd)–noprotongradientcreatedandhencenoATPgenerated

•  TheelectronsarethentransferredtoNADP+andreduceittoNADPH

•  TheelectronsofNADPHareavailableforthereac8onsoftheCalvincycle

Pigmentmolecules

Light

P680

e–

Primaryacceptor

2

1

e–e–

2H+

O2

+3

H2O

1/2

4

Pq

Pc

Cytochromecomplex

5

ATP

PhotosystemI(PSI)

Light

Primaryacceptor

e–

P700

6

Fd

NADP+reductase

NADP++H+

NADPH

8

7

e–e–

6

PhotosystemII(PSII)

ATPPhotosystemII

PhotosystemI

Primaryacceptor

Pq

Cytochromecomplex

Fd

Pc

Primaryacceptor

Fd

NADP+reductase

NADPH

NADP++H+

•  CyclicelectronflowusesonlyphotosystemIandproducesATP,butnotNADPH

•  CyclicelectronflowgeneratessurplusATP,sa8sfyingthehigherdemandintheCalvincycle

AComparisonofChemiosmosisinChloroplastsandMitochondria

•  ChloroplastsandmitochondriagenerateATPbychemiosmosis,butusedifferentsourcesofenergy

•  MitochondriatransferchemicalenergyfromfoodtoATP;chloroplaststransformlightenergyintothechemicalenergyofATP

•  Spa8alorganiza8onofchemiosmosisdiffersbetweenchloroplastsandmitochondriabutalsoshowssimilari8es

•  Inmitochondria,protonsarepumpedtotheintermembranespaceanddriveATPsynthesisastheydiffusebackintothemitochondrialmatrix

•  Inchloroplasts,protonsarepumpedintothethylakoidspaceanddriveATPsynthesisastheydiffusebackintothestroma

Key

Mitochondrion Chloroplast

CHLOROPLASTSTRUCTURE

MITOCHONDRIONSTRUCTURE

Intermembranespace

Innermembrane

Electrontransportchain

H+ Diffusion

Matrix

Higher[H+]Lower[H+]

Stroma

ATPsynthase

ADP+P iH+

ATP

Thylakoidspace

Thylakoidmembrane

Light

Fd

Cytochromecomplex

ADP+

i H+

ATPP

ATPsynthase

ToCalvinCycle

STROMA(lowH+concentra9on)

Thylakoidmembrane

THYLAKOIDSPACE(highH+concentra9on)

STROMA(lowH+concentra9on)

PhotosystemII PhotosystemI

4H+

4H+

Pq

Pc

LightNADP+

reductase

NADP++H+

NADPH

+2H+

H2OO2

e–e–1/21

2

3

•  ATPandNADPHareproducedonthesidefacingthestroma,wheretheCalvincycletakesplace

•  Insummary,lightreac8onsgenerateATPandincreasethepoten8alenergyofelectronsbymovingthemfromH2OtoNADPH

TheCalvincycleusesATPandNADPHtoconvertCO2tosugar

•  TheCalvincycle,likethecitricacidcycle,regeneratesitsstar8ngmaterialahermoleculesenterandleavethecycle

•  ThecyclebuildssugarfromsmallermoleculesbyusingATPandthereducingpowerofelectronscarriedbyNADPH

•  CarbonentersthecycleasCO2andleavesasasugarnamedglyceraldehyde-3-phosphate(G3P)

•  Fornetsynthesisof1G3P,thecyclemusttakeplacethree8mes,fixing3moleculesofCO2

•  TheCalvincyclehasthreephases:– Carbonfixa9on(catalyzedbyrubisco)– Reduc9on– Regenera9onoftheCO2acceptor(RuBP)

Ribulosebisphosphate(RuBP)

3-Phosphoglycerate

Short-livedintermediate

Phase1:Carbonfixa9on

(Enteringoneata9me)

Rubisco

Input

CO2

P

3 6

3

3

P

PPPRibulosebisphosphate

(RuBP)3-Phosphoglycerate



(Enteringoneata9me)

Rubisco

Input

CO2

P

3 6

3

3

P

PPP

ATP6

6ADP

P P61,3-Bisphosphoglycerate

6

P

P6

66NADP+

NADPH

i

Phase2:Reduc9on

Glyceraldehyde-3-phosphate(G3P)

1 POutput G3P

(asugar)

Glucoseandotherorganiccompounds

CalvinCycle

Ribulosebisphosphate(RuBP)

3-Phosphoglycerate



(Enteringoneata9me)

Rubisco

Input

CO2

P

3 6

3

3

P

PPP

ATP6

6ADP

P P61,3-Bisphosphoglycerate

6

P

P6

66NADP+

NADPH

i

Phase2:Reduc9on

Glyceraldehyde-3-phosphate(G3P)

1 POutput G3P

(asugar)

Glucoseandotherorganiccompounds

CalvinCycle

3

3ADP

ATP

5 P

Phase3:Regenera9onoftheCO2acceptor(RuBP)

G3P

Alterna8vemechanismsofcarbonfixa8onoccurinhot,dryclimates

•  Dehydra8onisaproblemforplants,some8mesrequiringtrade-offswithothermetabolicprocesses,especiallyphotosynthesis

•  Onhot,drydays,plantsclosestomata,whichconservesH2Obutalsolimitsphotosynthesis

•  TheclosingofstomatareducesaccesstoCO2andcausesO2tobuildup

•  Thesecondi8onsfavoraseeminglywastefulprocesscalledphotorespira8on

Photorespira8on:AnEvolu8onaryRelic?

•  Inmostplants(C3plants),ini8alfixa8onofCO2,viarubisco,formsathree-carboncompound

•  Inphotorespira9on,rubiscoaddsO2insteadofCO2intheCalvincycle

•  Photorespira8onconsumesO2andorganicfuelandreleasesCO2withoutproducingATPorsugar

•  Photorespira8onmaybeanevolu8onaryrelicbecauserubiscofirstevolvedata8mewhentheatmospherehadfarlessO2andmoreCO2

•  Photorespira8onlimitsdamagingproductsoflightreac8onsthatbuildupintheabsenceoftheCalvincycle

•  Inmanyplants,photorespira8onisaproblembecauseonahot,drydayitcandrainasmuchas50%ofthecarbonfixedbytheCalvincycle

C4Plants

•  C4plantsminimizethecostofphotorespira8onbyincorpora8ngCO2intofour-carboncompoundsinmesophyllcells

•  ThissteprequirestheenzymePEPcarboxylase•  PEPcarboxylasehasahigheraffinityforCO2thanrubiscodoes;itcanfixCO2evenwhenCO2concentra8onsarelow

•  Thesefour-carboncompoundsareexportedtobundle-sheathcells,wheretheyreleaseCO2thatisthenusedintheCalvincycle

C4leafanatomy

MesophyllcellPhotosynthe9ccellsofC4plantleaf

Bundle-sheathcell

Vein(vascular9ssue)

Stoma

TheC4pathway

Mesophyllcell CO2PEPcarboxylase

Oxaloacetate(4C)

Malate(4C)

PEP(3C)ADP

ATP

Pyruvate(3C)

CO2Bundle-sheathcell

CalvinCycle

Sugar

Vascular9ssue

CAMPlants

•  Someplants,includingsucculents,usecrassulaceanacidmetabolism(CAM)tofixcarbon

•  CAMplantsopentheirstomataatnight,incorpora8ngCO2intoorganicacids

•  Stomatacloseduringtheday,andCO2isreleasedfromorganicacidsandusedintheCalvincycle

CO2

Sugarcane

Mesophyllcell

CO2C4

Bundle-sheathcell Organicacids

releaseCO2toCalvincycle

CO2incorporatedintofour-carbonorganicacids(carbonfixa9on)

Pineapple

Night

Day

CAM

SugarSugar

CalvinCycle

CalvinCycle

Organicacid Organicacid

(a)Spa9alsepara9onofsteps (b)Temporalsepara9onofsteps

CO2 CO2

1

2

TheImportanceofPhotosynthesis:AReview

•  Theenergyenteringchloroplastsassunlightgetsstoredaschemicalenergyinorganiccompounds

•  Sugarmadeinthechloroplastssupplieschemicalenergyandcarbonskeletonstosynthesizetheorganicmoleculesofcells

•  Plantsstoreexcesssugarasstarchinstructuressuchasroots,tubers,seeds,andfruits

•  Inaddi8ontofoodproduc8on,photosynthesisproducestheO2inouratmosphere


1.  Describethestructureofachloroplast2.  Describetherela8onshipbetweenanac8on

spectrumandanabsorp8onspectrum3.  Tracethemovementofelectronsinlinear

electronflow4.  Tracethemovementofelectronsincyclic

electronflow

5.  Describethesimilari8esanddifferencesbetweenoxida8vephosphoryla8oninmitochondriaandphotophosphoryla8oninchloroplasts

6.  DescribetheroleofATPandNADPHintheCalvincycle

7.  Describethemajorconsequencesofphotorespira8on

8.  Describetwoimportantphotosynthe8cadapta8onsthatminimizephotorespira8on


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Berkeley Biology 1A Spring 2016 Lecture Reader Part 1