Ch 15, 16, 19 (signaling, cytoskeleton, ECM) Flashcards
5 basic types of signaling (endocrine, paracrine, neuronal, contact-dependent, and autocrine)
contact-dependent: cell-cell specific; membrane-bound signal molecule
paracrine: short distane, local distribution; local mediator
autocrine: short distance, local distribution; local mediator (signaling cell = target cell)
synaptic: long distance, cell specific; neurotransmitter
endocrine: long distance, wide distribution; hormone
Describe the formation of signaling complexes by scaffolding proteins
Bring singaling proteins into close proximity, enhancing specificity and efficiency of the signal transmission by preventing unnecessary interactions between signaling molecules
so that their transient interactions in a crowded and heterogeneous environment of cytosol can be greatly facilitated
describe phosphorylation of receptor to allow docking of intracellular signals
phosphorylated tyrosine residues act as docking sites for intracellular signaling molecules, which in turn activate kinases and initiate signaling cascades
describe phospholipid modification to recruit intracellular signaling molecules
What are molecular switches and how do they work?
- kinases and phosphatases
- GTP-binding proteins
- GEFs and GAPs
Kinase vs phosphatase
kinase- enzyme-adding phosphatate group (2 types: serine/threonine; tyrosine)
phosphatase- enzyme-removing phosphatase group
Ion channel- vs G-protein vs. enzyme-linked receptors
Ion channel : Ligand binding directly opens the ion channel, causing rapid changes in membrane potential.
G-protein coupled: Ligand binding activates a G protein which then interacts with downstream effector molecules to produce intracellular responses.
Enzyme-linked : Ligand binding activates the intrinsic enzymatic activity of the receptor or associated enzyme, leading to phosphorylation cascades.
what do enzymes activated by G-proteins trigger?
synthesis or release of second-messenger molecules that relay and amply the signal- cAMP/IP3/DAG/Ca2+
what do G-protein coupled receptors (Gas) activate?
adenylyl cyclase, which produces cAMP
What does cAMP do?
diffuses easily throughout the cell to interact with proteins in the cytosol, nucelus, and other organelles
What enzyme makes cAMP? what is a target of cAMP?
adenylyl cyclase
cAMP-dependent PKA
what is cAMP made of?
ATP
Order of GPCRs signaling leading to transcription of genes
- Activation of adenylyl cyclace
- binding of cAMP to PKA
- dissociation of PKA into catalytic and regulatory subunits
- binding of CREB to PKA
Explain what caffeine does
blocks cAMP phosphodiesterase –> levels of cAMP increase and accumulate, so keeps affecting pathway
phospholipase C reaction, products, and effects on a cell
products:
diacylglycerol activates protein kinase C
IP3 releases Ca2+ from ER
Diagram the structure and function of PKA, explain how mutations in different subunits affect its function
Describe calmodulin
When it binds to Ca2+, undergoes conformational change that allows it to bind CaM-kinase
What is CaMKII activated by?
calcium
what do CamKIIB knockout mice have?
memory impairment and fail to build nests
what do receptor tyrosine kinases activate?
Ras (active when GTP-bound; inactive when GDP-bound)
Why do cells use scaffolding proteins?
to ensure signal specificity between parallel pathways
Illustrate a Ras pathway and a MAP kinase cascade
Ways by which signal adaptation occurs and examples
- negative feedback
- delayed feed-forward
- receptor inactivation
- receptor sequestration (cholesterol)
- receptor destruction (receptor degraded in lysosome)
Describe the different signaling pathways that can lead to target specific gene transcription
- NFkB: stress and inflammatory stimulated pathways
- Wnt
- MAPK pathway
- PI3K/Akt/mTOR
- Notch pathway
how do cytokine receptors signal?
by associating with cytosolic tyrosine kinases
STAT (signal transducer and activators of transcription)
TGFB and Smad
TGFB- secreted signaling proteins
Smad- latent transcription regulators
wnt pathway proteins
Wnt- extracellular ligand
LRP- transmembrane receptor that binds wnt
Frizzled- transmembrane receptor that binds wnt
Dishevelled- cytosolic protein, recruited to activated frizzled
Axin, APC in complex with GSK3 and CK1- promote degradation of B-catenin
Groucho- transcriptional repressor
what does activation of frizzled and LRP do?
activates dishevelled and dismantles the axin-APC complex to stabilize B-catenin –> B-catenin enters nucleus and activates transcription by removing Groucho from DNA
Hedgehog signaling cascade pathway
primary cilium- membrane protrusion present in each vertebrate cell - senses env. and mediates signaling pathways
hedgehog- extracellular ligand
smoothened- transmembrane receptor present outside the cilium and enters the cilium upon pathway activation
patched- transmembrane receptor. inhibits smoothened
Gli 2- transcription factor inhibited by SuFu in absence of hedgehog
GLi3- transcription repressor modulated by Gpr161 in absence of hedgehog
SuFu- inhibits Gli2 and Gli3
receptors in plants vs animal cells
- plants mainly have enzyme-coupled receptors
- plant cells DONT use RTKs, steroid-hormone receptors, cAMP, and have few GPCRs
- ethylene- gaseous hormone that regulates seed germination and fruit ripening
- photochrome- light sensitive cytosolic serine/threonine kinase; mediates plant growth in response to light
ethylene signaling in plants
ethylene deactivates receptor –> deactivates CTR1 –> no degradation of EIN3 –> allows transcription
pathway turns on genes by relieving inhibition
What does binding of delta to Notch promote?
cleaves off Notch cytosolic tail –> moves into nucleus and regulates gene expression
what type of receptors do steroid hormones use?
intracellular receptors
nuclear receptor- bind steroid hormones and enter the nucleus to regulate gene transcription
cytoskeleton
network of protein filaments that extends throughout the cytoplasm
main functions:
support large cytoplasm volume
highly dynamic continously reorganized to fit the needs of the cell
large scale movement
muscle contraction
cell shape during development
Describe the role of the 3 types of cytoskeletal systems
actin filaments: cell motility, contraction
microtubules: mitotic spindles, cell polarity, intracellular transport
intermediate filaments: provide mechanical strength to cells; strongest of the 3; most abundant in an animal cell nucleus
proteins of the cytoskeletal system and their structure
actin filaments: protein actin, thin, 2-stranded helix
microtubules: tubulin; protein rigid hollow cylinder
intermediate filaments: fibrous intermediate filament protein; strong ropelike fibers
Describe, compare, and contrast the 3 types of cytoskeletal systems and how the filaments grow
actin filaments:
microtubules:
Explain what nucleation is
process of forming the actin oligomer needed for filmanet growth. Rate limiting step
(the time it takes to make the first short cluster. Need 3-monomer cluster)
Explain how the concentrations of cytoskeletal components monomers (for example actin) are maintained within the cell
Explain one simple way to generate cell polarity
proteins such as partitioning defective (PAR), and complexes such as Scribble, and Crumbs are responsible for polarity in epithelial cells
Why does so little of the actin polymerize into filaments?
cells keep sequestered to enable polarization as needed
cofilin
- promotes actin depolymerization by introducing mechanical stress to the filament
- binds actin-ADP preferentially (the one that is less stable)
myosin 2
- present in muscles
- dimer with 2 globular ATPase heads
- one coiled-coil tail
- binds actin to allow for skeletal muscle contraction
actin filaments
myosin filaments
actin filaments- (thin filaments) are anchored to Z disc
myosin filaments (thick filaments)- overlap with minus end of actin
Myofibrils
Contractile elements of muscle cells; extend the length of the cell
What does Z disk do?
attaches 2 sarcomeres
Sarcomere
- Contractile unit of myofibril that shortens during muscle contraction
- organized assemblies of actin and myosin filaments
Diagram the myosin cycle, with ATP and ATP hydrolysis
Explain muscle structure and how a muscle contracts
simultaneous shortening of all the cell’s sarcomeres due to sliding of actin filaments past the myosin filaments without change in length
ADD MORE??
Explain how Ca2+ causes a muscle to contract, naming the key components
neurotransmitter signal causes release of Ca2+ from sarcoplasmic reticulum (specialized region of ER)
Ca2+ triggers actin-myosin contraction through binding of actin-associated proteins
tropomyosin vs troponin
tropomyosin- rod-shaped protein that prevents binding of myosin to actin
troponin- calcium-sensitive complex that binds to tropomyosin. When Ca2+ levels rise, it moves tropomyosin so that myosin can bind to actin
what happens when calcium binds to calmodulin?
activates myosin light chain kinase, which phosphorylates myosin, which allows interaction with actin and contraction
Microtubules assembly
- assembly and disassembly occurs only at the + end
- dynamic instability- driven by GTP hydrolysis
- catastrophe- microtobule shrinking when GTP hydrolysis is faster than addition of new tubulin subunits
- rescue- adition of GTP-containing subunits to the shrinking end to resume growth
Microtubule nucleation site
y-tubulin ring complex of the centrosome
microtubules only form out of these complexes
centrosome vs centriole
centrosome: where microtubules are organized (a type of MTOC)
centriole- component of centrosome matrix (2 in centrosome)
Why do cells need MTOC sites?
- organization, efficiency
- separate gamma ring from centrioles
- make sure microtubules dont spontaneously assemble
- not much free-tubulin in cell- when you need it, it will be ready to be made
microtubule-organizing center
MAPs
- bind microtubules and regulate their dynamics in cells
- structure determines the spacing of microtubules within the cell
- when bound to microtubule ends, can promote growth or disassembly
- Kinesin-13, XMAP215
microtubule associated proteins
Augmin
- binds the side of an existing microtubule and recruits g-tubulin ring complex to nucleate a new microtubule branch (to branch microtubule off)
- nucleates microtubule binding
a type of MAP
Kinesin-13
XMAP215
Kinesin-13: binds to microtubule ends and pries them apart to increase catastrophe events (promotes disassembly)
XMAP215: binds free tubulin and delivers them to + end of microtubule, increasing polymerization rates (promotes microtubule assembly)
types of MAPs
what can motor proteins do?
- interact with microtubules to move cargo like organelles and macromolecules across long distances in cells
- promote sliding microtubules one over another to generate specific microtubule arrengements
- regulate microtubule dynamics
kinesins
- with microtubules, move cargo from - to + end (forward, with the growth of microtubules)
- when ATP-bound: tightly bound; ADP-bound: loose
what “drives” motor protein movement?
ATP hydrolysis
dyneins
- move from + to - end (back to the source)
- movement occurs by linker swing, dynein-winch mechanism
cilia vs flagella
cilia- can propel cells or sweep layers of liquid and particles along
flagella- enable cells to swim in liquid media
axoneme
- core structure of cilia/flagella
- composed of microtubules and their associated proteins arranged in a distinct pattern
what generates motion in cilia and flagella?
ciliary dynein bending
keratins
- most diverse intermediate filament family
- found in skin, hair, nails, claws, and scales
desmosome
cell-cell contact sites where intermediate filaments are anchored
effect of mutated kertain expressed in the skin
epidermolysis bullosa simplex- causes blisters in response to slight mechanical stress
amyotropic lateral sclerosis (ALS)
effect of abnormal accumulation of neurofilaments in soma and axons of motor neurons
what happens when lamin is phosphorylated?
weakens the interaction between filmanets, causes the lamina to fall apart- important during cell division
defect in lamin vs plectin
lamin- progeria: premature aging disorders
plectin: disease-combining features of epudermyosis bullosa simplex, ALS, and neurodegeneration
plectin
an accessory protein that crosslinks filaments into bundles/connects them to microtubules, actin filaments
Explain how Rho and Rac are involved in promoting cell movement
Rac activation- actin polymerization at cell periphery
Rho activation- stress fibers and focal adhesion formation
Rac and Rho regulating cell movement
Rac dominates polymerization (protrusions)
Rho dominates actin-myosin contractions
they are antagonist to each other
chemotaxis
movement of cells towards or away from a source of diffusible chemical
Treadmilling
constant movement of actin monomers through the filament from + to - end
why are intermediate filmanets not polar, but actin and microtubules are?
polarity: allows to have directionality. There is meaning to where it is headed. Made and dissassembled quickly- need to know where it starts
no polarity: just conntects to itself. No real meaning to being polar
what drives extension of the actin protrusion?
Arp2/3
Rac vs Rho, which is front and back of cell movement?
Rac: front
Rho: back
what stimulates extension of filopodia?
Cdc42 polarization –> Par-3 –> Rac-GTP –> wave proteins –> Arp2/3
How do cells have less contractility and stress fibers?
Rac-GTP –> PAK inhibits MHC and MLCK –> decreased myosin activity
how are cells held together?
by interactions with ECM or cell-cell junctions
Define cadherins and explain their role in cell-cell interactions
- mediate cell-cell interactions (link cytoskeletons)
- present in animal cells only
- homophilic binding: adjacent cells bind to same or closely related type (more homo than hetero)
- heterophilic binding: adjacent cells bind to different types
how are cadherin intracellular domains linked to cytoskeleton?
at adherens junctions and desmosomes via adaptor proteins- including catenin
(cadherins link to actin through adaptor proteins)
why are cells with cadherin mutations thought to be malignant?
cells become more motile, break off form original, and start tumor somewhere else
how are transient cell-cell adhesions in bloodstream mediated?
by selectins
how is calcium independent cell-cell adhesion mediated?
by members of immunoglobulin superfamily (IG)
what do tight junctions do?
- allow epithelial cells to limit solute diffusion (seals gaps between tissues to prevent leakage)
- prevents proteins from migrating along side of the cell
- claudins and occudins form the tight junctions
Compare and contrast tight junctions and gap junctions
- tight: create a watertight seal that prevents the movement of water and ions between cells.
- Gap: allow the exchange of small molecules, ions, and second messengers between cells; couple cells both electrically and metabolically (gated channels); made from connexins
how are astrocytes interconnected?
by gap junctions
plasmodesmata and how they compare to tight or gap junctions
- intercellular junctions in plants
- perform similar roles as gap junctions: connecting adjacent cells to allow exchange of ions, small molecules BUT pass through the cell wall
types of molecules that make up mammalian ECM
- proteoglycans and GAGs- large highly charged polysaccharides that can be linked to proteins (hyaluronan, perlecan; decorin, aggrecan)
- fibrous proteins- proteins of the collagen family (type 4 collagen; fibrillar collagen)
- glycoproteins- gp with conventional Asp-linked saccharides (laminin, nidogen, fibronectin)
Proteoglycans vs GAGs
proteoglycans: proteins covalently linked to GAG chains
GAGs: glycosaminoglycans; unbranched polysaccharide disaccharide; negatively charged; form hydrated gels, resistant high compression pressures
difference between proteoglycans and collagen
collagen assemble into long-triple stranded helical struces a-chains; resist stretch pressure
ADD MORE
basal lamina & components
- beneath epithelial cells, surrounds muscle, fat, and Schwann cells
- role is to separate cells from the environment
- nidogen, perlecan, laminin, type 4 collagen, integrin
Explain the role of integrins in the cell and define their interacting partners
- transmembrane laminin receptors that organize assembly of basal lamina
- cells interact with ECM via transmembrane integrins
- recruit intracellular signaling proteins at sites of cell-matrix to regulate cell division, growth, and survival
molecular composition of the plant cell wall and compare to mammalian cell
- a type of cellular matix (much stronger than animal cell ECM)
- made of cellulose microfibrils and pectic polysaccharides
NFKB IKK complex and Ikb
IKK: includes NEMO and is activated when TNFa binds to receptor
Ikb: binds NFkb and marks for degradation in absence of signal. Activated IKK promotes NFkb separation from Ikb
Collagens are extremely rich in which amino acids?
glycine, proline
In actin filmanet polymerization, what does the “lag phase” correspond to?
Nucleation
Gq function
activates phospholipase C-B –> release of Ca2+
what do arrestins do?
bind to phosphorylatd GPCRs to prevent GPCRs from interacting with G proteins
how are enzyme-coupled receptors activated?
dimerization of 2 receptors from the binding of a signal
what do tyrosine phosphatases do?
inactivate RTK receptors
mTOR1 vs mTOR2
mTOR1: includes protein raptor; activated by Akt
mTOR2: helps activate Akt
