Flashcards
Advanced Cell Biology
Cards in this deck (106)
- 1Cytoskeleton’s functions- Cell shape
- Cell migration
- Intracellular transport - 2Actin filaments- maintain cell shape and movement
- divide animals cells
- move cytoplasm and organelles - 3Intermediate filaments- maintain cell shape
- anchor nucleus and other organelles - 4Microtubules- maintain cell shape and movement
- move organelles and chromosomes
- provide tracks for intercellular transport - 5Barbed endplus end of filament assemble from ATP-actin monomers
- 6pointed endminus end of filament disassemble from ADP-actin
- 7myosin-based force productionATP-hydrolysis and ADP-release in myosin motor domain induce conformational changes, which generate myosin movement along the actin filament
Examples: cytokinesis - 8Actin filament treadmillingExamples: endocytosis, cell morphogenesis
- 9cell migrationBoth treadmilling and myosin-based force
- 10In vitro model to study actin filament treadmillingListeria bacteria on plus end of filament -> movement
- 11Arp2/3induces actin nucleation at the sides of pre-existing
actin filaments and thus promotes the formation of a branched actin filament network
activated by nucleation promoting factors (NPFs), WASP - 12ForminsFH2 domain forms a dimer that promotes
nucleation of unbranched actin filaments and
also functions as a ’leaky capper’ that allows
filament elongation
Activated by binding to regulators such as small GTPases - 13Heterodimeric capping protein- binds actin filament barbed ends
- Bind to nonproductive filaments preventing association and dissociation of actin monomers to/from capped filament ends - 14ADF/cofilin- prefer ADP-actin over ATP-actin
- severing ’old’ actin (ADP) filament in cells
- promotes disassembly
- fundamental role in rapid actin filament treadmilling - 15Cyclase-associated protein (CAP)- accelerates depolymerization of cofilin-decorated actin filaments
- promotes ADP-to-ATP nucleotide exchange in resulting monomers - 16Profilin- Inhibits spontaneous actin filament nucleation, and assemebly of actin monomers
- promotes actin polymerisation by bringing to site - 17Actin filament cross-linking proteinstwo independent actin-binding sites or they are dimers to interact with two actin filaments
Example: Ezrin and moesin -> actin- lipid-binding domains - plasma membrane - 18Rho family GTPases- shuttle between an active GTP- bound form and an inactive GDP-bound form
- activated by guanine nucleotide exchange factors (GEFs) and inactivated by GTPase activating proteins (GAPs) - 19PI(4,5)P2 –rich membranes- attracted by actin-binding proteins -> the positively charged surfaces of these proteins interact with the negatively charged headgroups of PIP2
- proteins disassembly or inhibit polymerization -> down-regulated by PIP2
- proteins assembly or promoting actin cytoskeleton –> upregulated by PIP2 - 20Functions of cell nucleus• Control center of the cell
• Stores the genetic material
• Maintains genomic integrity ->DNA repair & replication
• Gene expression→building blocks for the cells -> Transcription, mRNA processing - 21RNA pol Itranscribes ribosomal RNA genes (in nucleolus)
- 22RNA pol IItranscribes protein encoding genes to mRNA
- 23RNA pol IIItranscribes tRNA and other small RNAs
- 24Nuclear envelope- Lipid bi layer membrane (similar to endoplasmic reticulum)
Within membrane -> many embedded proteins -> some anchor chromatins to membrane
- Nuclear lamina -> underlining whole inner membrane
- 25Nuclear laminaFibrillar network composed of lamins and lamin-associated membrane proteins
• Functions in: Mechanical support, NPC anchorage, Chromatin organization and Etc. - 26Lamins- Types A and B
- Concentrate near INM
- Mechanical properties of nucleus and functins in transcription, replication, chromatin organisation, DNA damage and etc. - 27LINC complexConnects nuclear interior with cytoplasm and ECM
- KASH domain proteins -> cytoskeletal systems
- SUN domain proteins -> binds lamins/chromatin - 28Nuclear pore complexesPassive diffusion of small molecules
Active transport of larger cargo
• Energy (Ran-GTP gradient)
• Nuclear localization and export signals (NLS/NES)
• Soluble transport factors - 29ChromatinA disordered granular chain with varying diameters between 5 and 24 nm
• Chromatin is DNA complexed with proteins
• Chromatin is less condensed form of chromosomes - 30Regulators of gene organisation and gene expression- writers (histone acetyl transferases)
- erasers (histone deacetylates)
- readers (bromodomains)
- 31Lamina-associated domains (LADs)heterochromatin at the nuclear periphery with low gene density
- 32Chromosome territories- Regions of the nucleus preferentially occupied by particular chromosomes
- Intermingling between territories have been linked to chromosomal translocations - 33Radial distribution- Gene-rich chromosomes are found toward the nuclear center, and gene-poor toward to nuclear periphery.
- Gene can have a preferential positioning, but it can vary depending on activation status. But radial position does not predict activity status. - 34Topologically associated domainsA self-interacting genomic region, DNA sequences of which interact with each other more frequently than with sequences outside the TAD and their expression is usually correlated during development.
- 35Boundaries of TADs• CTCF and cohesin proteins are essential for TAD boundaries, and for creating loops between enhancers and promoters
• Enhancer-promoter interactions restricted to within TADs - 36Hi-C
- 37Nuclear bodiesdynamic structures, components constantly exchanged with the nucleoplasm
- concentrate substrates, enzymes and assembly intermediates within their confined space to accelerate enzymatic and assembly reactions
- Formation seeding event, depends on a biological process, & random and self-organizing assembly - 38liquid-liquid phase separated (LLPS) droplets or condensatesdistinct phases into which proteins and RNAs inside the cell nucleus are organized into
- 39Nucleoskeletonnetwork of network, involve actin and its binding partners, as well.
In the nucleus, actin has been linked to:
• All steps of gene expression
• DNA repair
• DNA replication
• Chromatin organization - 40Reasons for cell migration- Development
- immune cells
- communication
- regeneration
- pathological cell migration - 41First step of cell migrationExtension:
1) Forward - Actin polymerisation: Arp2/3 > lamellipodia vs Formins > filopodia
2) Middle and back - organization of actin filaments with myosin motor proteins and sliding of myosin along actin filaments, leading to contraction of actomyosin filament - 42Second step of cell migrationAdhesion
Integrin-based focal adhesion to ECM
Focal adhesions links actin cytoskeleton and ECM by integrins - 43Third step of cell migrationTranslocation
The branched actin network is remodeled to contractile actomyosin arrays, that translocate the cell body and help in tail retraction
contractility -> Myosin2 motors walking on anti-parallel actin filaments
- 44Fourth step of cell migrationDe-adhesion
Possible role of myosin 2. Integrins proposed that integrins are endocytosed and trafficked to front of cell for further attachment - 45Guidance of directional migration
- 46Receptors to detect ligandsProtein G-coupled transmembrane protein (cAMP)
Chemokine receptors (fish lateral line)
Receptor tyrosine receptor (EGFR/EGF) - 47Migration of dictyostelium cells
- 48Rho Small GTPases in migrationRac promotes nucleation of branched actin networks via activation of Arp2/3 - lamellipodial extensions in front
Rho promotes actomyosin contractility via Rho kinase -> Assembly of contractile actin-myosin filaments
- 49Mechanical properties of filopodia and lamellopodia
- 50Polarisation by Rac and Rho
- 51Eukaryotic chemotaxis1. Cells often exhibit intrinsic random motility
2. Exposure to a chemoattractant gradient leads to small spatial or temporal differences in receptor activation that are amplified within the cell to induce Rac-mediated actin polymerization and protrusion formation
3. cell polarity is stabilized by positive-feedback loops (at the cell front) combined with long-range inhibitory signals (in the rest of the cell) that restrict protrusion formation towards the cell front - 52Mesenchymal cell migration
- 53Amobeoid cell migration
- 54Epithelial-mesenchymal transitionpromotes enhanced migratory capasity
- 55Collective
- 56Zebrafish lateral line migrationLeading cells have guidance receptor Cxcr4 receptor that respond to SDF-1, but Trailing region expresses additional SDF-1 receptor Cxcr7, which is thought to function as a sink
- 57Vascular sproutingLeading tip cell
- specified, responds to VEGF
-> starts to express Notch-ligand delta
-> Notch signaling in following cells represses VEGFR transcription and maintains stalk cell fate - 58Migration of border cells to oocyte nucleusBorder cells (cluster of 8-9 cells, part of the epithelium)
- They delaminate, become a cluster, migrate towards oocyte through nurse cells, happens during the same stage of development
- Border cells make a small hole in the eggshell to allow sperm entry – defective migration of border cells results in infertility
- Use e-cadherin (not ECM) to migrate
- One leading cell pulling the rest of the cluster – initially, later migratory behaviour changes (forward extensions not as persistent, migrations seems less determined)
- The oocyte nucleus is the final destination - 59Epithelium morphogenesisEx. gastrulation -> from column-shaped to bottle-shaped
Myosin motor become apically enriched forming a supracellular meshwork across the tissue that promotes tissue bending - 60Dendritic spines
- 61Developmental changesprogressive replacement of the thin, elongated, and highly motile filopodia with more stable dendritic spines with a distinct neck and head.
- 62LearningThe maintenance of new spines correlates with the maintenance of the learned skill and the extent of new spine formation with the quality of the skill acquisition.
- 63Actin dynamics in dendritic spines- Arp2/3 complex is required for the formation of spine heads
- Reduction in cofilin1 expression levels induces branching of spines. - 64Phosphorylation of actinTHERE ARE DYNAMIC AND STABLE ACTIN POOLS IN SPINES. DYNAMIC POOL IS IMPORTANT FOR SURFACE DYNAMCS AND STABLE POOL IS IMPORTANT FOR STABILIZATION.
LTP - long term potentiation
- 65Spines formationPLASMAMEMBRANE CURVING PROTEINS RECRUIT ACTIN POLYMERIZING FACTORS TO SITES OF CURVED MEMBRANE
- 66Types of cellular membranesI) Single membrane: Plasma membrane, Endoplasmic reticulum (ER), Golgi apparatus, Lysosome
endosome
ii) Double membranes: Mitochondria, nucleus, Leucoplast
iii) Membrane contact sites:
For example: Mitochondria- associated membrane (MAM) iv) Extracellular Vesicles - 67Membrane contact sitesclose appositions between two membranes. They transmit signals and exchange material between compartments.
Ex. between the endoplasmic reticulum and a second organelle - 68Roles of membrane contact sites- transfer of cellular components between different organelles
- important cellular processes such as apoptosis, cell growth, organelle division and biogenesis - 69Membrane Properties- Membrane Fluidity
- Membrane Compressibility and Elasticity
- Membrane Permeability
- Membrane Potential
- Membrane Asymmetry
- Membrane Curvature - 70AsymmetryControlled by enzymes
(1) flippases (including phospholipid translocases), which catalyze the ATP-dependent transport into the cytoplasmic leaflet, (2) floppases, which catalyze the ATP-dependent transport towards the exoplasmic leaflet, and (3) scramblases, which catalyze bidirectional lipid movement in an energy-independent fashion
- 71Roles of membrane asymmetryMembrane curvature
Regulation of protein-membrane interactions and activities
Signaling - 72Membrane Phase transitions
- 73Factors Affect the Physical State of MembranesHydrocarbon length
Unsaturation of acyl chains
Charge, and headgroup species
Sterols, cholesterol (hydrophobic)
Protein concentrations: - 74Lipids in a biological membrane can be divided
- 75Lipid Polymorphism
- 76Membrane dynamics1. Membrane Fluidity: lateral movement, lipid and proteins diffuse laterally within the plane of the membrane.
2. Lipid sorting: vesicle and non-vesicles trafficking
3. Transbilayer movement: Flip-Flop
4. Lateral segregation: lipid microdomain, such as the lipid rafts, not dissolve and cell signaling
5. Membrane structural remodeling: membrane curvature - 77Ratio of volume to areaV/A maximal:
Emphasis on soluble content: lysosomes, peroxisomes, nucleus
V/A minimal:
Abundant with membrane proteins: ER, Golgi, Mitochondria inner cristae - 78ER• entry site for secretory pathway
• protein and lipid synthesis
- Soluble secreted proteins hormones, growth factors etc.
- Plasma membrane proteins receptors etc.
- Proteins residing in organelles of the secretory pathway - 79ER hosts- protein biosynthesis
- protein secretion
- unfolded protein response
- ER associated degradation
- Calcium homeostasis
- lipid biosynthesis - 80ER structure- Sheets - can be intact or fenestrated, and they are decorated with ribosomes. Average size varies between cell types, but thickness is constant - equals to the diameter of tubules
- Tubules: the diameter of COP-vesicles - 81ER's contact with other organelle allows to- transmit exterior signals
- transmit signals between organelles
- share functions - 82ER dynamics- Movement of individual structures the network
- Reorganization of the network
- Transformation of structures - 83Depolymerization of microtubules and cytoskeleton• Depolymerization of microtubules increases the amount of sheets
• Depolymerization of dynamic actin cytoskeleton induces transformation of sheets to tubules and unevenly distributed ER network - 84Golgi• oligosaccharide processing
• protein sorting
• interphase between endo- and exocytic pathways - 85Asymmetric cell division1. Establishment of cell polarity
2. Segregation of cell fate determinants according to the polarity axis
3. Orienting the mitotic spindle and cell division plane along the polarity axis - 86Establishment of cell polarity in C.elagansBreak symmetry -> entrance of sperm cells posterior site -> inhibit RhoA -> contractile elements of myosin towards anterior -> more contractile end and flow of contractile elements
Maintenance of state -> mutual exclusion ->
Posterior end : PAR1 induces phosphorylation in PAR3 -> prevents PAR3 to bind to membrane
Anterior end : aPKC phosphorylates PAR-1/2 (causing membrane detachment) - 87Segrageation of P granulesPar1 induced release of mRNA -> PGL-3 creates network meshwork of protein-mRNA networks -> visible as P granules
- 88Endocytosis• Membrane
• Receptor
• Cargo
• Force (Cytoskeleton) • Coat protein
• Curvature effectors
• Scission (fusion!)
• Timekeeping - 89MacropinocytosisNon-specific uptake of extracellular material regulated by growth factors - “Cell drinking”
ARP2/3 dependent membrane protrusions - 90phagocytosisUptake of pathogens and dead cells
1) Initial cup formation: Receptor recognition of particle and actin activation by PI(3,4)P2 -> WASP
2) Initial pseudopod extension: Actin forward and myosin traction as extend around
3) Maximal pseudopod extension - forward thrust limited and delivery of vesicles for membrane
4) Closure - membrane fuse and actin stops
- 91Caveolae endocytosisMuscle and epithelial cells
higher membrane surface - 92CLathrin Independent Carriers/GPI-AP enriched Early Endosomal Compartments CLIC/GEEC endocytosis• Activation of cdc42
• Cdc42 !N-WASP !ARP2/3 !
Actin polymerisation
• GRAF1 coats the tubulated
membrane and keeps the GTP
cycle of cdc42 - 93Fast Endophilin Mediated Endocytosis FEMEAt leading edge
GTPases -> WASP -> ARP2/3 -> actin - 94Clathrin Mediated Endocytosis1. Coat formation: AP2 and clathrin and cargo
2. Bending of coat by FCHO1/2
3. Membrane bending -> ball formation
4. Pinch vesicle by dynamin
5. Uncoating mechanical force and PI(4,5)P2 hydrolysis - 95FSHSD2Recruited to Clathrin Coated Pits
- 96Role of osmosis1) p38 MAP kinase inhibits Na+ channels 2) Cellular stress inhibits p38,
which results in Na+ influx 3) Water enters the cell and
cell size increases
- 97Hippo pathway
- 98mTOR
- 99Cells can regulate division speed and growth by dilutinga cell division inhibitor (Whi5, RB, KRP4) against a constant cell division driver (Cln3, Cdk)
- 100Budding yeast• During aging, budding yeast enlarge in size
• Upon enlargement, DNA becomes limiting and cannot ensure functional concentrations in cell • Large budding yeast are diluted and lose function - 101Human cells in vitro• When human cells in vitro enlarge, they become senescent (state of irreversible cell cycle arrest) which
is associated with aging - 102Blood stem cells (HSCs) in vivo of mice• HSCs can become DNA-damaged as they divide
• During the damage, they arrest in the cell cycle to repair the damage, and enlarge in size due to contin-
ued growth
• This larger size causes their dysfunction and they fail to build new blood cells - 103SRPRecognises signal peptides on secretory
Targeted to translocon
Cleavage and across membrane - 104Experiment with partial mRNA for proteinsSRP54 recognizes signal peptide
Translocon component - Sec61 (near SR)
Across and in membrane (if hydrophobic sequence is met) - 105SRP-signal interactionClaw to hydrophobic signal sufficient to move lif
1. Amphipathic lid
2. Signal - 106Translocon-signal interactionSec61
Quiescent -> lateral gate with plug
Primed -> lateral gate cracked and plug is still there
Engaged -> helix of signal -> replace one placeholder by a more stable signal
Information
- Description
- Biology Flashcards on Advanced Cell Biology, created by Alexandra Shabanova on 26/11/2022.
- Created by
- Alexandra Shabanova
- Views
- 4
- Rating