Note Oct 15, 2024 9_12_26 AM - Cell Biology Notes PDF

Lysosomes synagggmotaxis optimum pH prawAtp ATP drivenH pumpcreates pH degradeallmacromoleculestaken Ifmf...

Lysosomes synagggmotaxis optimum pH prawAtp ATP drivenH pumpcreates pH degradeallmacromoleculestaken Ifmf ho matrix cytosol byendocytosis Phagocytosis Autophagy atttifin assemorosslink ÑEsbd hjjipia.gg gopoe cell actin locomotion myosin useclathrinindependent particles maturate fuse whysosome pathway pg which release binding stois stroke power Odorsanelles orcytosolisenclosed byinternalmenprangaumo.name stuff visualallmuscle centrosome structures Estense Time functionoftubulin necea feetmovement selfrenewalofcellularcomponents kinesin5 goalstructure justdistinguishAnaphases Mitochondria 2 membranes inner outer verydistinctnotconnected 2 spaces matrix intermembrane space Inner membrane 1 has Electrontransportsystem to make gradient across inner membrane ATPsynthase FFo ATPase Transporters to incorporatemetabolites AppfAF etc ItPi 2 Inner is full of proteins but not rigid is flexible continuouslymovingdividing fusing 3 Inner needs large surface area to fold into Cristae Matrix 4 inside of inner membrane contains enzymes for citricacid cycle replication oxidation mitochondrialDNAribosome Ees growthdivision functions Outer 5 has porin freepass forsmallmolecules aminoacidpyruvatefattyacid glyterol Proteinscan't go out throughporin  NADH NAD is converted to NADH During conversion 2 e Nbecomes neutral add acovalentbond a NAPT seedNADH NADH in cytosolneed extra energy NADH is highenergy 60 energyyield Glycolysis In cytosol Glucose 2 pyruvates 2 ATP Produced per glucose 2 NADH After Glycolysis In mitochondrial matrix Acetylgroupof Pyruvate is transferred to CoA to form Acetyl CoA CitricAcidCyle oxidizes all carbonto CO2 8NADH 2 FADH 2GTP producedper one glucose ElectronTransport Chain Complex 1 recognizesNADH oxidizes it toNADT transfersze from NADHto ubiquinone pumps 4H into intermembrane space Complex 2 recognizesFADH2 FADH Doesn't pump H Ubiquinone electron carrier transfers e to Complex3 Complex3 transfers é to CytochromeC oxygen é receiver needed for process pumps H into intermembrane space 4 tocontinue CytochromeC passesté to complex 4 Complex 42 e is used to make 20 Pumps 4 H into intermembrane space Redoxpotential NADH FADH2 Ubiquinone cytochromeC oxidized energy 12H per NADH reduced energy hashydrogens 8H per FADH 2 Ubiquinone double bonded Oxygens become OH reduced energy Note Cytochrome C can only bind to 1 é ATP Synthase Convert electrochemical gradient of H into ATP F Fo separate domains components connected F is exposed to matrix Catalytic component of ATP F has synthesis 3 units alternate to make spherical 3 Bunits structure 2 unit rotor stalk a stalk Fo is embedded in membrane transmembrane H Fo 10 14 subunits Cring carrier  1 a subunit a ch ed or bunits 2lb subunits anchor stalk CAB holds stalls β head green parts are fixed cring is fixed but slides relative to a energy H gradient is converted to rotation of rotor rotation causesstructuralchangeof protein inside the vessel to perform chemicalreaction rotorstalks rotate ATPsynthesis qgsdnf How it rotates 1 a subunit has 2 half channels for H 2 Each sub unit has a proton acceptorwhich receives proton from a half channel 3 After accepting proton c ring slides by 1 subunit Then next H comes through the half channel binds next subunit 4 After 1 round of rotation H is transferred from sub unit to another half channel that is open to the opposite side of the membrane Note 1 c ring has 12 c subunits  happens onlywhen protongradient is large enough How8 stalk makes ATP in F 8 stalk rotates w o ring B 3 complex in F1 is fixedbystatorstalk b subunit so it does not rotate with 8 stalk As 8 stalk rotates in F1 ATPase 3 8 subunits change conformation drivenbygradient 209 Open low tight Open conformation has affinity to ATP can exchange ATP ADP usuallybindsADP 8 Tight conformation can bind only ATP never releaseit Low conformation binds to ADP Pi but theycan'tescape from the protein can'texchangeadpto atp 120 turn O conformation releasesATPthenbinds ADP Pi T conformation can convert ADP P 20ATP 120 turn Every 120 turn 1 ATP is produced make 3ATP are produced per 1 complete turnthffon ATP Note 12 H are consumed perturn ETCpumps 12HNADH 8H FAPH2 Booth ATPsynthaseisreversible f Ér.citFao 1171g canhydrolyzeATPtoproduceH gradient p byreversereactionofATPsynthesis  Protein Import majority of MTproteins are translatedby cytosolic ribosome transported to MT after translation is done N terminal 20 to 55 aa seauence presequence serves as a signal for matrix inner membrane 4destinations Matrix 4distinct destinations Inner membrane have adistinctmechanisms Intermembranespace membranes have own distincttransmembrane Outermembrane protein channel translocators providechannel for 2 Translocators Polypeptide topassthrough Outer membrane translocator TOM Inner membrane translocator TIM Protein Import steps 1 CytosolicHsp70 unfolds protein 2 TOM complex recognizes signal presequences 3 ATPhydrolysis by hsp70 pushesprotein in TOM 4TOM TIM interact 5 Negative charge attractsthe presequence 6 Some are released as inner membraneproteins Presequence is cleaved MT Hsp70 pull the proteininto 7 matrix 8 ATPhydrolysis releaseof MTHsp70 NoteHSP 70 is required binds pulls MT Evolution Genome structure  2Aerobicprokaryotemightbeengulfedtoearlyanaerobiceukaryote tobecome 1stmito 2ThensomeMTgenes weretransferred tonucleusduringevolutionofeukaryotes usuallynot connected wcytoskeleton Lipid delivered from ER toMTby protein is MT doesn't have ability to synthesize itsmembranelipid phospholipids are synthesized in the ER carried to mito by phospholipidtransfer proteinsnot by vesicular traffic outermembrane inner membrane has small contact site where ipid is exchanged Ocassionally MT ER interact to transfer lipids Peroxisome human cells 500 metabolicenzymes Containoxidation detoxification enzymes some other some fatty acid oxidation occurs in peroxisome can replicateby division but doesn'tgrowby itself Peroxisome Assembly derivedfrom ER butmoststatesizedoffoosomes Sometransmembrane proteins ofperoxisomes are synthes ed rough ER NO Golgi involved Internal proteins are synthesized on free ribosomes ther imported by Pex proteins ATP dependent peroxisome grows by fusion can divideinto 2 Notesomeproteins are embedded in peroxisome some are imported cytoskeleton Chemotaxis Protein Filaments mm Actin Filament very thin plasma membrane Microtubule Thickest 25mm Intermediate Filament 10mm Action Overview Actin can exist as bundle or network no clear organizing Actinfilament has polarity shows dynamic assembly disassembly involved w cell movement crawling of non flagellar cell during mitosis Actin forms contractile ring Biochemically distinct ends 7hm diameter Plus minus ends made by non covalent binding of globularproteins G actin ATP required for actin to assembleinto filaments canbind to ATP ADP made exclusivelyfromone d ATP actin is active for filamentformation  Assembly Disassembly of actin filaments Plus minus end ATP actin monomer assembles on filament mainly at plus end ATP ishydrolyzed in the filament ADP actin dissociates from filament mainly from minus end ADP minus ATP plus Bothassembly disassemblyarecrucialforactin functions Inhibitionof eitherpolymerization ordepolymerization uses quickstopof cellmovement certainshapes proteins forcertain Filament Actin Binding Proteins controls the behavior of ARP 2 3 binds to minus end iniatesbranch Tropomyosin mediatesactinmyosin interaction Formin bindstoplusend extendinggrowth Cofilin disassembly 1 minusendintomonomers 2splitinto2piecesfromcenter Profilin facilitatesexchangeforATP ADP CrosslinkingProtein Ex Need to know Villin Microvilli Fimbrin Filopodia Filamin Lamellipodia X actin ContractileBundle motorproteins Myosin11 mainlymuscle Regulators Myosin V I non muscle Troponins Spectrin Dystrophin α actinin required for myosin sliding_activatement regulatorforsomething Rhofamilyproteins purposelocation recruitsformin Integrin bind drag cell in movement ARP talin helps α actinin bind Cadherin How cell crawls 1 ell extends protrusions at leadingedge 2 The protrusions adhere to the surface 3The rest of cell is draggedtowards adhesion point 1 a Two types of protrusions 1 Lamellipodia thin sheetlike protrusionwhichcontainsnetwork ofactin filaments Plusend of actin filamentis facingtotheleadingedge 2Filopodia thin stiff fingerlike protrusionwhichcontainsbundleofactinfilaments 210 ARP Complex CreatesBranch 1 Actin relatedproteins APR2 3 complexcan assembleat actin ATP neargrowingend of filament 2 ARP2 3bothhavesimilarstructuretoactin 3 ARP binds toactinfilamentatfixedangle diniatesbranch 1C ActinNetwork at leadingedgepushes cell forward ARPcontinuouslymakesbranches on preexistingfilament Plusendsarecappedto preventpolymerization depolymerization  some requency Networkgrows towardstheleadingedgeto extendlamellipodium Cross linking Proteins are involved in actinnetwork bundle 1 Actinbundlingproteins Fimbrin maketightbundleof actinfilament in filopodia 2 Otheractincrosslinking proteins filamin makes much moreflexiblenetwork with randomlyrunningfilaments Ld Molecular structures of bundling cross linkingproteins 1 Fimbrin bundling has 2 tightlyarranged actin binding domains ABD 2 Cross linking protein filamin is homodimer oflong subunits 3 α actin headto tail dimer is abundlingprotein in contractile bundle stress fiber muscle at 2 disk Note actinimportant if you consider frm Hing myosin required 1 eFormin iniates de novo filament formation 1 Formin can start filament formation from G actins undercontrol of intracellular signaling via Rho GTP 2Whenactivated formin can assemble ATP actin monomer into a filament 3 Formin can stay at growing plus end of the filament Basically assembles ATP actin monomers actin attaches changes conformation more actin 1 FMicrovillihavebundledactin filaments Intestinal epithelial cells have microvilli surface for absorption Interacting with myosin 1 on plasmamembrane that can bend the vilus  2 a Cellcrawl Cellattachment involves actin bundles the contactsites 1 Integrins bind to the surface or extracellular matrix 2 Integrinsbundles actin filaments make anchor to drag other part of cell stress fiber Contact integrinactivation talin α activationbinding stress fiber formation at adhesionpoint 3A Rest of cell is pulledby actin myosinsliding myosin 1 muscle myosin actinin is required forpulling myosin11 contracts bottom myosin l shortenprotrusionbyslidingactin filament edge pushesittowardsleading plusendsoverlappingmyosinmakesthe ringsmaller extensionadhesionpulling prob3distinctmechanismsinto1 singlemotion also note where to move Attractant for neutrophils f MetLeuPhe Local activation of Rho GEF Local Production of Rho GTP  recruits formin ARP Formin starts actin filament ARP makes branch Local lamellipodia formation move towards the attractant Rho Ras superfamily member cytoskeleton cellularmovement 1 Rho GTP is associatedw membrane 2 Formin associate w Rho GTP 3 Formin iniates Actin Polymer Association of actin filaments w plasma membrane action other filaments from networks underlyingplasma membrane cell cortex 1 Determine tell shape 2 well demonstrated by RBC studies 3 Shortactinfilament is anchored to plasmamembrane with glycophorin 4 Actin filament is connected to spectrinfilament spectrinishomologousto otheractinbinding proteins likedystrophin majoraetoskeleton associatingproteinwhichbinds to actinring majorityis underneath plasmamembrane Duchenne Muscular Dystrophy X linkedrecessive genedystrophin onXchromosome Dystrophinanchorsactinfilamentw plasmamembraneofmuscletissue  Adherensjunction adhesion belt epithelialsheet is enforcedbyseveral cell celljunctions 1adhesionbeltcancontracttochangetheshapeofeachcell 2 actinfilamentoftheadhesionbelt is associatedwithcadherinthatconnects adjacentcells adherensjunction SkeletalMuscle motorproteins Musclefiber is onelongmultinuclear cellcontainingbunch of miofiblils Each myofibril cylindricalbundles of actin myosin I 1 Sarcomere is a 2.5 m unit of contraction 2 Myosin 1protein is made by 2 heavychains 2 2 lightchains 3 Heavy chains dimerized by coiled coil tail 4 Several 100s of myosin l proteins form a bipolar stack 5 Large bipolar filament of myosin 11 slide in actinfilaments 6 Heads of heavychain has ATPase domain that can bindattainment 7 ATPhydrolysis heads allows actin by myosin sliding a what are these steps for 1 No ATPformstaysboundon actinfilament 2Binding to ATP causes dissociation ofhead from actinfilament 3 ATPhydrolysischanges conformation of neckboth ADP phosphate arestill boundto myosinhead 4 Head ADP binds to actinfilament releasephosphate 5 ADPisreleased neck bends powerstroke 6Headstays on actinfilament untilnextATPcomes  cart aceteichaineincreasescytosolic a controlsactin myosin contact in skeletalt.ggigitt 1 Actinfilament in skeletalmuscle are associatedwithtropomyosin troponin complex troponinC I T 2 W o castmyosinhead can't bindactin becausetropomyosin is blocking myosin binding site on actinfilament 3 Lastbindsto troponin changethestructure oftropomyosin sothat the myosinbinding site is exposed for myosin 4 Because lastchanges rapidly myosinsliding occurs very quicklyto generat trongforce of contraction smoothmusclecontraction Lastactivates protein kinase 2 differences Notraponins in smoothmuscle actinfilament isready for contact withmyosin myosincan'tmake bipolar filament w out stimulus Cart nosarcomere in smoothmuscle  ᵗ Calmodulin a dependentmodulatorof proteinkinases 1 smoothmuscle Castbindscalmodulin 2 Lastcalmodulincomplexbinds activatesmyosinlightchainkinase phosphorylates alightchain ofmyosin 3Thisphosphorylationchanges structure ofheavychains allowthemto make oipolarfilament y 4 Bipolarfilament canslideon actinfilament contractilering celldivisionismediatedby Contractile ring in Cytokinesis 1 Rho activation occurs in the mid cell at elophase formin 2 Actinfilament is assembledunderneaththe plasmamembrane by 3 Rhoalsoactivates myosinlight chain phosphorylation indirectly 4 Myosin11bipolar filamentcontracts the ring plasmamembrane is pulledwiththering myosin vs basics Myosin I can move membrane vesicle 1 Myosin I has singlehead short tail monomer 2 Tail canbindmembrane 3Involved in somevesiculartraffic endocytosis of yeast transporting organelles 4 Alsoinvolved in microvillimovement MyosinV involved in membrane traffic organelle traffic in neurons NoteMitority ofvesiculartraffic depends on microtubule bitsmotor Microtubule MT Overview Typical non dividing cellhas 1 centrosome nearnucleus enter MTorganizing motorproteinsmove on MT to transport ofvesicles for cilia flagellatobeat or vend forchromosomemovement celldivision MT is made bytubulins microtubule is made by 2tubulinmonomers α B tubulin Both are globularproteinwhichhaveGTPbindingsites tubulin alwayshas GTP tubulin has GTPase activity filamentformation dissociation is controlledby GTPGDPformof_tubulin NoteTubulinDimer isbuildingunitofmicrotuble MTstructure α B tubulinheterodimerworks as a buildingunit diameter 25mm α B stackalterativelyto form protofilament 13protofilamentsÉhollowfilament MT Allprotein proteininteraction are non covalent Mothas InpurifiedMTplusendgrowsfasterthanminusend polarity tubulin endisboundtothecentrosome In vivominus  tubulin Polarity of Microtublegrowth GTPtubulindimersassociatewgrowing endswhilethey're in a flatsheetthenstreetzips up intothematuremicrotuble Shortlyafterpolymerization the_tubulin hydrolyzesGTPtoGDP GDPtubulin is stable in microtubule dissociates fromtheminus end Notubulincan dissociatefromthemiddle ofthemicrotuble NoteInvivo most ends areanchoredtocentrosome centrosomecontains apool of tubulins pair of centrioles alsohas motorproteins manyother MTassociating proteins Centrosome start site of microtubulegrowth MTstartgrowingfromthefixedpoint Centrosome major MT organizing center Centrosomesurface has multiple ring like assembly site of MT eachof theringsare madeby_tubulin otherfactors tubulinbinds to_tubulin ofdimer starts MT fromthe centrosome Assembly disassemblyof end areblocked by_tubulin normally tendsarepointing outward association dissociationof tubulinsubunits occur at mostly the tend DyamicInstabilityof MT 1 OnlyGTP form oftubulindimer canassembleinto filament butafter assembly GTPis hydrolyzed toGDP 2GDP form ofthefilament stable but candisassembleonlyfromthe  freeend 3Whenfilamentisgrowingnewly assembled tubulins are GTPforms sothat thefilamentis stable it can keepgrowing 4 Onceitstopsgrowing tabulins end becomeGDP form easily disassembled 5 Growingandgrows fast shrinkingendshrinks fast dynamicinstability Note Dynamicinstability MT rapidly Growing grows butonceitstops itstartsshrinkingrapidly thenstop thenagainstartgrowing forrandomseeking idealmechanism Dynamicinstabilityis Microtubule associatedproteins MAPS regulatethedynamicbehavior of microtubules manyMAPScontrolMTstructure stability Organizationof MTw inneuron Axonstructureis supportedby MT intermediate filament 1 MTinaxoniscrucialtotransportvesiclestonerveterminal 2 AllMTinaxonarepointing endoutwardbutnotconnectedtocentrosome 3They'renotcontinuous capped bothends 4Taustabilizesmicrotubules inaxon axonspecificMAP involvedin the Alzheimerdisease Dendrites 1 MTsareorientedtobothdirections exceptional 2DendritecontainsotherMAPS Normalcells 1 MTofordinallycell is stemmedfromthe centrosome stabilizedby MAP1,2 tau MAP 1,2 y tubulin stabilizers  Dynein Kinesin Overview Motors Dynein walks on MTtoend v14 msec Kinesin walks on MT to tend 2.3 m sec Bothhave at least 2heavy chains 82 or more lightchains Eachheavy chain has MTbindingsite ATPbindingsitein large globulardomain head In both cases ATPbinding hydrolysis release are coupledwith structural change humanhas 40 Kinesins 2dyneins Vesicles are transported to nerve terminal by kinesin I Vesicleswhich are moving back to cellbody are connected to dynei cytoplasmicdynein MicrotubuleMotors Movement ATPbindinghydrolysis release head domains are coupled w structural change Howkinesin1 moves on MT Note Eachhead can bindtoATPhydrolyzeit thenreleaseADP in 1step ofwalking 1 ATPbinding of 1head makes anotherhead ADPform thrown forward to facilitatewalking 2 ADP formbinds MTat new position 3 ADP formreleasesADP ATP formhydrolyzes intoADP 4 WhenATP freeformbinds ATPanotherhead w ADP isthrown forward  9 generates power stroke Motors move vesides 145diffkinesinshavebeenfoundinnumans found least2cytoplasmicdyneinare 2At diffcargos gotodiffdestinations regulation carry Kinesins extends ER Dynein pulls Golgi Smith ER is extended to near plasmamembrane Golgi islocated near centrosome ERmembrane is linkedto kinesin Golgimembraneislinked to dynein IfsuchcellistreatedbycolchicineERcollapseGolgiisfragmented Lysosome is alsolinked w kinesin dynein mitochondria hasbothdynein kinesin Cilia flagella are attached to basal body 9 doublets of cilium are directextensionofbasalbodytriplets Basalbodylookssimilarto a single centriole atripletstructure There's not y tubulin sing on thebasalbody  Cilium flagellum have identicalstructure 9 doubletMT are arranged in central pair of MT 9 2 a ring with protein Nexin Adjacent doublet is is permanently connected Dynein tail is attached to one doublet headis facingto adjacent doublet Dyneinin flagellum AxonemalDynein Dynein makes doublets slide Axonemal Dynein locates btwn 2 doublets Dynein is fixed to 1 doublet by the energy of ATPhydrolysis However doublets can'tslide freely because they are connected by other protein nexin Note Local slidingof doublets makes flagellum band Note Local slidingof doublets makes flagellumband Flagella motion is coordinated sliding is coordinated to enable organized action of flagellumbut the mechanism of the coordination is not well understood Recognition of microtubles during mitosis 1 Mitoticspindleis derived from microtubules Mphase 2 In S phase centrosomeduplicates but remain together until 3 In prophase a 2 centrosomes pusheach other to separate b microtubules become shorter more dynamic 4 Centrosomes move to opposite poles to create spindle 5 In metaphase some MTs catchkinetochores of condensedchromosomes Kinetochore microtubule Some MTS overlap with oppositely oriented MTs Overlapping mtg have kinesin like proteins interpolar microtubule Some MTs reach cell periphery to connect cell cortex Astral microtubule Mechanism of centrosome separation role of interpolarmicrotubules bipolar kinesin is loaded on the interpolar MT Kinetochoremicrotubule bond at end Interpolar MTpush centrosomes away tend can extend sisterchromatidconnection is cut atthebeginning of anaphase