Molekulare Zellbiologie (Subject) / - (Lesson)

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• Three changes that most proteins undergo during maturation in ER. peptide fold oligomerization glycosylation formation of disulfide bridges
• Which are the 3 sensors in the ER membrane, that signal the protein folding state in ER to the unfolding protein response? PERK IRE1 ATF6
• What enzymatic activity of IRE1 directly triggers expression of Xbp1? ribonuclease activity
• What is the ER-export signal for secretory membrane proteins and what does it bind to for export? the di-acidic signal that binds to the B-site of Sec24
• EEA1 or HRS bind PI3P. What is the name that mediates this binding? the FYVE domain
• Name two advantages for the fact that many transcription factors function as dimers. 1) Heterodimers allow generation of many different dimeric factors from few monomers (each with specific recognition sites). 2) Transcription factor can be negatively regulated by binding of an inhibitory partner 3) Coordinated binding as dimer allows much more specific and stronger binding to DNA
• What are the main steps of signaling through the Notch receptor? - (Binding of the ligand) - Proteolytic cleavage of the intracellular part of the receptor - Translocation of the intracellular part (Notch-IC) into the nucleus - Assembly with cofactors and function as transcription factor
• State the main (architectural) structures of the nucleus - nuclear envelope/membrane - nuclear pores - nuclear lamina - chromatin - nucleoli - subnuclear bodies
• What is Haptotaxis? Directed migration on a gradient of ECM component.
• Which Rho GTPase pathway induces contractility of stress fibers? RhoA/ROCK pathway
• Name the enzyme that keeps Cdk1-Cyclin B inactive at G2/M before entry into mitosis. Explain how. Wee1 --> via phosphorylation at T14 and Y15
• How do microtubules localize signaling proteins to distinct places within the cell? -transport of vesicles as cargo via motor proteins -Depolymerization
• Which part of microtubules protects them from depolymerization? GTP-Cap --> loss of GTP-Cap leads to faster depolymerisation
• What is rapid deplolymerization of microtubules called when GTP-cap is lost? Catastrophy
• What is the direction of growth of microtubule filaments? „polymerisation predominantly at + End“
• What is the rate limiting step during actin polymerization? Generation of the stable trimer / nucleus limits the step.
• What is the formula describing actin polymerization in solution? v = kon * cmonomer
• Which function of actin molecules is switched on, when they are incorporated into filament? ATPase activity of Actin
• An actin filament end grows as long as … An actin filament end grows as long as the concentration of monomers is higher than ATP-hydrolysis
• How does the actin nucleator complex Arp2/3 overcome the kinetic barrier to initiate actin polymerization? Arp2/3 structure is similar to the trimeric complex. --> Docking is easy. NPFs (nucleation promoting factors) accelerate nucleation.
• How do formin actin nucleators overcome the kinetic barrier to initiate actin polymerization? - Formin stay dynamically attached to the growing + End. „Processive caps“ - increase of local concentration (catch & pull)
• Which nucleator(s) generate(s) branched filaments? Arp2/3 complex
• Which nucleator(s) generate(s) linear filaments? - Spire and Formins - 4 Actin Monomers
• Why are „older“ actin filaments more susceptible for breakage by ADF/Cofilin? Cofilin binds better ADP-Actin
• How does Profilin „re-generate“ actin monomers? Profilin catalyzes ADP/ATP exchange
• Which Rho GTPase pathway induces contractility of stress fibers? RhoA
• Which molecular mechanism drives Myosin movement on individual actin filaments? ATP-Hydrolysis driven structural change defines cycles of attachment / deattachment from the filament --> 2 structural switches
• Why can the motor protein Myosin pull anti-parallel actin filaments towards each other and thus generate contractation? Dimerisation in head-to-tail fassion
• Which Rho GTPase and its two effectors induce lamellipodia? RhoGTPase --> Rac1 Effector NPF --> Scar, Wave
• How does the Rho GTPase Cdc42 induce the actin elongations called filopodia? What promote the two effectors promote specifically? -mDia2 -Ena/VASP
• What determines the effect of signaling proteins during directional cell migration? - Amount of signaling protein - Activation dynamics --> Localization Duration
• What is chemotaxis? Recruitement of migrating cells by soluble factors --> gradient
• Specify a microtuble associated motor protein and its direction of movement Kinesin (+) Dynein (-)
• Specify an actin bound motor protein and its direction of movement Myosin (+)
• What are the requirements for a stress-fiber to exert force via contractility? minimum two adhesion points, one stress fiber
• Which are the two possible outcomes of ER stress response depending on the strength and duration of ER stress? - Cell protection - Apoptose
• What specific posttranslational modification regulates entry into and exit from Calnexin/Calreticulin cycle? glycosylation of mannose/glucose
• Name one enzyme that mediates disulfide-bond formation or isomerization in ER. Thiol-disulfid oxidoreductase (e.g. PDI -> Protein disulfid isomerase)
• Name the two GTPases that trigger a) COP I coat assembly b) COP II coat assembly Cop I  --> ARF Cop II --> Sar1
• Name two components whithin COP II that deform the membrane and specify how Component: Sar1p, Mechanism: wedging Component: Sec23/24, Mechanism: scaffolding
• Name two components whithin COP I that deform the membrane and specify how: Component: ARF, Mechanism: wedging Component: coatamer-complex, Mechanism: scaffolding
• Name two components whithin Clathrin that deform the membrane and specify how: Component: Clathrin, Mechanism: scaffolding
• Which factor retrieves ER-resident proteins from the ERGIC and cis-Golgi and brings them back to the ER? KDEL receptor
• How many alpha-helices make up a SNARE-pin during synaptic vesicles fusion? How can these vesicles/helices?? be classified on the structural basis? - 4 alpha helices (3 t-SNAREs +1 v-SNARE) - structural classification -> Q- and R- SNAREs - localization classification -> v- and t- SNAREs
• Which class of protein mediates specificity of membrane fusion on the level of vesicle tethering. What is their catalytic activity? Rab proteins (bring the SNAREs together); catalytic activity = Rab-GTPase
• Which GTPase are mostly associated with a) the early endosome? b) the late endosome? a) early endosome = Rab5 b) late endosome = Rab7 (Rab9 -> Transgolgi-Network) --> Lipidmodifikation: (Pi45p2 Membranmodifikation, Pi3p early endosome, Pi35p2 late endosome)
• State the two posttranslational modifications that trigger EGF receptor endocytosis and degradation. -autophosphorylation  -then mono-ubiquitination
• Which is the name of the domain in EEA1 or HRS/VPS27 that binds PI(3)P? Fyve
• Which is the name of the domain in Epsin that binds PI(4,5)P: ENTH
• Which is the name of the domain in GGA that binds PI(3)P: VHS

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