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131 Cards in this Set

  • Front
  • Back
What are the 2 types of cell signalling molecules?
What are examples of intracellular signalling molecules? Where do they bind? Domains of homology w/in the receptor?
steroid hormones...bind to cytoplasmic receptors.
Explain/diagram how the hormone exerts an effect.
What are the 3 main motifs seen with signaling of membrane impermanent molecules?
a) Bind to a receptor which goes through a conformational change which changes the inside conformation, which affects downstream molecules. (e.g. G protein coupled receptors)
b) Bind to receptor which opens an ion channel. Ions enter cell and affect downstream molecules. (e.g. nicotinic acetyl choline receptor, NMDA receptor- most important signaling ion is Calcium)
c) Bind to receptor which cross-links the receptor. Cross-linking of receptors results in activation of downstream molecules. (e.g. receptor tyrosine kinases, TGFβ family receptors).
Describe Ras.
What is MAP kinase?
A major cytoplasmic protein that becomes phosphorylated following growth factor or mitogen stimulation; also phosphorylates microtubule assoc. proteins MAP2 and tau. Thus, it's both a major pro kinase and a major pro kinase substrate.
Where is MAP kinase phosphorylated?
On both a Y (185) and a T (183) residue.
Describe the classical mammalian MAP kinase cascade.
MAP kinase is a major protein kinase activated by phosphorylation on two residues by Map-Erk kinase (MEK).
o
MEK is activated by phosphorylation by c-Raf kinase.
o
c-Raf is activated by phosphorylation by other protein kinases, but only after it is membrane localized as a result of binding to p21-Ras, which only happens if p21-Ras is in the GTP bound form, and is itself membrane localized- to be functional p21-Ras needs to be isoprenylated.
Compare and contrast viral (v-) src to c-src.
pp-60-Src was the first Tyrosine kinase identified- but EGF, NGF and other growth factor receptors are also tyrosine kinases.
What is the evolutionarily conserved pathway involved in tyrosine kinase receptor signaling?
Describe the EGF signaling cascade.
Model the activation of a simple Tyr kinase.
What is a Ptb domain?
Found in adapters IRS-1 and 2, 3 and 4, Shc and relatives, DOC-1 and relatives- binds NPXY-PO4 sequences, (not, for example, Y-PO4EEI type sequences like SH2 domains).
Describe/diagram how adapter molecules can amplify a signal.
Describe the EGF receptors.
Group of receptors that form heterodimers upon activation. RTK's
Name some adapter and effector molecules of the EGFr family.
Describe the activation of cytokine/interleukin receptors.
The kinase and receptor are in different molecules, but otherwise quite similar to RTKs…
What are the effector molecules in the cytokine/interleukin receptor pathway? How do they work?
The STAT's dimerize when activated and interact directly with DNA.
How are cytokine receptors regulated?
Describe how non-receptor tyrosine kinases work.
Src associates with Fak and regulates its activation. Activation of Src family kinases often by CD45, a membrane spanning tyrosine phosphatase. Src family kinase are all inactivated by c-Src kinase (CSK) on a C-terminal tyrosine residue (remember c-Src versus v-Src and Tyr 527?).
Scr and Jak assoc. with receptors and are activated upon dimerization (autophosphorylate one another). Once Src and Jak are activated, they also phophorylate the receptor they're bound to allowing mol. with SH2 domains several binding sites.
How do B and T cell receptors work?
ITAM's contain conserved Y domains
How do protein phosphatases work and what do they do?
Turning off the kinases… Protein phosphatases; Human genome has 518 kinases, including 90 tyrosine kinases. More than 130 protein phosphatases are encoded in the human genome, including 107 tyrosine phosphatases. There are receptor and non-receptor tyrosine phosphatases….
Give a summary of tyrosine kinase signalling.
What are some notable features of the structure of p21 Ras (and other small G proteins)?
***have the same core structure as G alpha subunit***
Where does Ras bind and what are some notable domains of the molecules involved in the Ras signalling cascade?
Contrast the Rap and Ras pathways.
What are some similarities of the domains of molecules in the Rap and Ras pathways? Differences?
What are the main domains in the Rac/Rho/Cdc42 family?
PH domain=membrane bound
Describe the Map Kinase signaling cascade.
Describe the Map kinase cascade in terms of the Map kinase kinase kinase, Map kinase kinase, etc.
What are the 2 conserved residues of the activation loop of Map kinases?
Threonine and Tyrosine
What molecules feed into the Jnk pathway?
small GTPases (Rac, Rho, cdc42), cytokines, growth factors/RTK's,
What is adenylate cyclase?
2nd messenger; coverts ATP to cAMP
What mediates G-pro independent signalling?
beta-arrestin signalling to MAPK
What are the main players in G-pro coupled receptor signalling?
What are some key features of aa conservation among the 7 TM of GPCRs?
-hydrophobic alpha-helices span membrane
-extracellular N-term and intracellular C-term
-N-linked glycosolation=Asn (extracellular)
-S-S stabilize packing of TM helices
-black aa’s are conserved among receptors
mostly in TM spanning domains
variation in extra- and intracellular domains, loops connecting helices, and N- and C-termini
Explain how ligands bind differently to GPCR's based on size and other factors.
B) Binder of small molecules
tend to interact with residues in TM-spanning domains (which form a pocket)
C)Binds small peptides; rxn with extracellular loops
D) Subclass of family A; binds to N-term and cleaves it to reveal neo-N-terminus which then becomes the ligand (autolytic, irreversible process)
E) Regulates lg glycoproteins; react with N-terminal regions (too lg to react with extracellular loops)
F) Binds to extracellular domains
Describe the binding of retinal to Rhodopsin.
-Some TM-spanning domains are kinked (due to conserved Pro)
additional C-term alpha-helix that runs parallel to membrance
TM domains form pocket
-Rhodopsin-retinal covalently linked to helix in TM domain
How does Rhodopsin's basal activity differ from the adrenergic receptors?
Rhodopsin has no basal activity (on/off switch) whereas the adrenergic receptors have differing levels of basal activity (more like a dimmer).
What controls open vs. closed conformations of GPCRs?
highly conserved DRY seq in TM 3; R participates in ionic rxn’s with Y
Describe the G pro cycle.
Preassociation of heterotrimeric G-pro to GPCR
34 receptor catalyzes exchange of GDP for GTP (via disocciating GDP from alpha subunit))
5. Alpha has decreased affinity for beta subunit when bound to GTP
56 irreversible step (cleavage of GTPGDP)
alpha now has increased affinity for beta when bound to GDP
***receptors promote dissocciation of GDP***
-beta/gamma subunits can regulate ion channels
What are some effectors that G pro regulate?
adenylyl cyclase, Ca channels, c-Src Tyr kinases, RhoGEF, phospholipases, PI3K
Describe the G pro subunits.
-alpha subunits contain 2 domains- GTP/GDP binding and helical
-easy to separate alpha from gamma, but not gamma from beta
-lipid modifications on alpha and gamma help anchor the protein to the subsurface of the plasma mem.
-I, II, and III yellow regions are ‘switch’ regions that undergo conformational change (to activate or inactivate)
Describe the interaction between the G-pro and its GPCR.
Describe the active vs. the inactive conformation of GPCRs.
Cz=carazold; overlaid image
-no consensus seq among GPCR’s=no way to predict what ligands they bind
-an activated receptor can activate >1G-pro
Describe the role of RGS.
-GTPase activity rate too slow to explain rapidity of inactivation
-RGS binds GTP-bound alpha
RGS have GAP activity and stimulate hydrolysis (terminate signal)
-G alpha 12 and 13 subfamilies are esp. activated by RGS (as well as terminated)
RGS acts diff on diff families of G pro
What is the RGS domain responsible for?
GAP activity
Describe G pro-independent signaling of GPCRs.
-Desensitization=less responsibe to agonist
-ser/thr domains become substrates for phosphorylation by GRK
beta arrestins bind the phosphorylation sites to prevent activation
can also act as scaffolds to couple GPCR’s to other signalling pathways (like MAPK)
G pro independent pathway (but beta arrestin dependent)
Describe desensitization as it pertains to GPCRs.
A: G-pro activation of MAPK pathway and desensitization by beta-arrestin
B: G-pro-independent, beta-arrestin dependent activation of MAPK/ERK
class A arrestin=scaffold for MEK, etc transient ERK released rapidly once phosphorylated to nucleus and regulates transcription
class B arrestin binding of MEK etc. is tight leads to phosphorylation of cytoplasmic elements (for migration, etc.)
What family of molecules are TGFbeta receptors?
Ser/Thr kinases
Describe the SMAD proteins and what each does.
Inhibitory SMAD’s prevent R-SMAD from entering nucleus
activated by TGFbeta
Describe how dorsoventral polarity is regulated in Drosophilia.
-dorsal expressed in nucleus (at bottom) and in cytoplasm (at top)
-the Toll ligand (Spatzle) forms morphogenetic gradient
How is the mesoderm in Drosophilia regulated?
Need dorsal to have Twist expressed
What is the dorsal homolog in mammals?
-NF kappa=nuclear factor kappa (kappa=lt. chain)
dorsal in humans
Describe the NFkappa-B pathway and function.
-p65 and p50 are Nfkappa-like proteins
Ikappa=inhibitoryubiquitinated when phosphorylated
Compare and contrast Toll-like receptors and NFkappa-B.
-Dif=dorsal
-Spaetzle=ligand responsible for gradient
-defects in pathway=inability to fight infection
pathway of innate immune system
-receptors for specific bacterial ag’s (like lipopolysacc., flagellin, and unmethylated CpG <usually methylated in humans>)
What pathway(s) is/are TNF alpha receptors involved?
Nfkappa also acts in TNF pathway
Where do phospholipase A, C, and D cleave?
Phospholipase C involved in the release of ER Ca into the cell. Cleaves IP3 from the DAG in the membrane, IP3 acts as a 2nd messenger that opens a ligand-gated Ca channel in the ER.
Describe the membrane lipid cycle.
Describe the phospholipase C domains and what they do.
-PIP2 and DAG produced by phospholipase C
-PH domain=membrane binding
-PLCgamma activated directly by RTK’s due to SH2 and SH3
substrate w/in membrane
Efh=Ca binder
PLCdelta=Ca activated
-PLCbeta activated by GPCR
Describe Ca regulation in terms of the receptor and mediator.
-beta version of phospholipase C
-DAG stays in membrane due to lipid tail
-IP3=diffusible 2nd messenger
stimulate Ca to enter cells via IP3-gated Ca-channel
PKC pathway activated directly by Ca
localized to membrane by DAG
Describe the domains of protein kinase C family proteins.
-similar Set/Thr kinase domains
-C1 binds DAG
-C2 binds Ca and phospholipids
Describe the C1 and C2 domains.
C1 domain is ~50 amino acids
which binds diacylglycerol (DAG),
or phorbol esters. Found in PKC
family enzymes, chimearins, c-Raf1, B-Raf and many other molecules.
C2 is ~130 residues involved in
binding phospholipids in a calcium
dependent manner. Found in PKC
family enzymes, synaptotagmin,
perforin, phospholipase C and many other calcium regulated proteins.
Describe calmodulin.
-Gly flanked by acidic residue (EF hand)
How does calmodulin work?
-EF hand titrates level of Ca in cells
as [Ca] increases, conformation of EF hand changes (due to Ca binding)
activates other proteins in this conformation
Describe Cam Kinase II.
multifunctional Calcium/calmodulin dependent protein kinase- involved in learning and memory…

12-16 enzymes clumped together- once Calcium has activated this complex, each enzyme can keep the others activated- molecular memory!
-has a kinase domain and assoc. domain
Describe the different conc. patterns of PI(3,4), (4,5), and (3,4, 5) bis- and triphosphates.
-PIP2 usually=PI(4.5) bisphosphate
-PDGF=growth factor
PIP2 stayed pretty constant while other membrane lipids rapidly increased
-how PI3K were discovered (phosphorylate at the 3 position of inositol)
Describe the diff. pathways of the 3 diff classes of PI3 kinases.
-PI3K puts phosphate on portion 3 of inositol
class I PI3k’s not in yeasts (involved in cell signaling of multi-cellular organisms)
-
What are the diff subunits of the PI3 kinase enzymes? What do they do?
-catalytic and regulatory domains
-4 enzymes of PI3k in humans
catalytic domain forms heterodimer with regulatory domain
activated by RTK
p110gamma activated by GPCR [activation by RTK and GPC common theme among families]
How is PKB (protein kinase B) activated?
-PH domain usually involved in membrane binding
require PI3 phosphorylation on the membrane lipid
PH binds the 3-phos
Describe the PH domain.
PH domain binds many ligands -the one in Akt/PKB specifically
binds PI-3,4,5-P3 and PI-3,4-P2 but not PI-4,5-P2. PH domains of PDK1, Btk and several other proteins do this also, anchoring proteins to membranes in a fashion dependent on activation of PI-3 kinases.
Others bind PI-4,5-P2 such as those in GRK2 and GRK3, PLC enzymes, spectrin, all Dbl family members, many other small G protein regulators and many other proteins - more common in the human genome than SH2 domains.
Name what activates the diff kinases (Tyr or Ser/Thr).
What are some second messengers and what rxn's are they involved in?
Describe the different cytoskeletal networks.
-major cytoskeletal networks
-actin has diff. polymerization states
-microtubules are easily broken
-polarized1 end differs from the other
-IF provide structural integrity
sig. variation
What is the structural basis for chemotaxis?
-polarized placement of certain signaling molecules
PI3K, PTEN, PIP3, actin, myosin, etc.
Describe the general theme of cytoskeletal regulation.
****often on exams****
-general theme of cytoskeletal regulation
-active=GTP-bound
Rhonot an efficient GTPase by itself
GAP’s help hydrolyze GTP
**Rho activates WaSP and formins
GEF’s help exchange GDP for GTP
GDP-bound Rho can interact w/GDI that take Rho off membrane (GDI also regulated)
Squiggle is prenylation that anchors Rho to membran
What are the major classes of intermed. filaments in mammals and what do they do?
Which cytoskeletal element is the least dynamic?
IF's
What is the soluble subunit of IF's?
tetramer
What triggers disassembly of IF's?
phosphorylation
What forms specificity of cross-linking of IF's?
the termini
How are IF's packaged?
Describe the final 10nm IF.
The final 10 nm filament consists of a helical array with 16
Dimers in cross-section. Half of the dimers are pointed in each direction
Plot the different cytoskeletal elements as a function of deforming force vs. deformation.
***often on exams***
“light bulbs” signal breaks
Doesn’t take much force to deform and break MT’s
IF are flexible but don’t break
How do IF's contribute to structural integrity of sheets of cells?
Keratin filaments in epithelial cells.The filaments in adjacent cells are indirectly connected through desmosomes. Thus intermediate filaments contribute to the structural integrity not only of individual cells, but also sheets of cells.
What are some diseases with defective IF's?
ALS (neurofilaments), epidermolysis bullosa simplex (keratins)
Describe actin kinetics in vitro.
-actin in buffer that promotes polymerization
nuclei stabilize interaction with actin monomers (which otherwise don’t stick- limiting factor)
more actin in sol’n=more nuclei=faster polymerization
adding nuclei speeds up this process
-polymerized=fast-growing and slow-growing ends
Describe/graph critical conc. (Cc).
Cc=critical conc.
no filaments up until the Cc
at steady-state of Cc, filament conc. Filament conc. Increases as more actin is added
Cc=0.2 uM
~50% of actin is polymerized
conc. Of actin in cells is ~50-100uM
vastly above Cc
Describe the Cc's of the pos. and neg. ends of actin. What is treadmilling?
-actin is an ATPase
hydrolyzed when incorporated into filament
causes conformational change
-Each end has diff Cc
Cc+=0.12 uM, Cc- = 0.60 uM
-actin shown coming off – end and being added to + end
“treadmilling”
Cc in cell is always above each end
can experimentally fool w/Cc to facilitate additive properties
What are some regulatory pathways that prevent actin subunits from binding to a growing microfilament?
-1, 2, 3 bind to actin and prevent binding (accounts for high conc.)
-cofilin bind ADP actin
can break up filaments
-profilin increases nucleotide exchange (ADPATP)
-Thymosinbinds ATP actin to prevent polymerization
What are some ways microfilaments are modified to prevent polymerization?
-modulation of filament ends to prevent polymerization
What are 2 theories of how Listeria travels within a cell?
-ActA recruits endogenous actin machinery
binds actin sides and triggers polymerization
branching mediated by Arp 2/3

-Brownian-Ratchett hypothesis=Listeria moves by Brownian motion and says actin not attached to Listeria
What factors mediate actin branching?
-Arp2/3 forms a potent nuclei that promotes extension of filaments
can be inactivated and this is regulated
How is WASp activated?
-Wiscott-Aldrich syn. Protein (WASp) interact w/diff small GTPases
mediates actin activation/polymerization
WASP can also be inactivated
-RBD=Rho binding domain
What regulates monomer addition to a growing actin filament?
-formins assoc. w/barbed ends/nuclei
stays assoc. w/barbed end
allows regulated addition of new monomer via conformational change
How are formins activated?
-formins assoc. w/Rho GTPases and are thus activated
WASP and formins bind profilin
actually Profil-actin being added
Describe tubulin.
Tubulin array of fibrils
Soluble alpha beta tubulin dimer
Interactions along seam allow modulation
Only beta-tubulin hydrolyzes the GTP to GDP (alpha always GTP-bound)
What are some qualities of the tubulin seam?
Allows for different formations (singlets, doublets, triplets) that lead to specialized structures (cilia, flagella, etc.). Interactions along seam allow modulation.
Describe the orientation and localization of microtubules in a cell.
-Pos ends point away from nucleus
-Polymerized from specific locations (vs. diffuse like IF)
What is gamma TURC?
-gamma TURC associates w/- end of tubulin
-gamma TURC=site for initiation of new MT’s
>similar to ARP2/3
What does the graph of the assembly and disassembly of MT's look like in real time?
Describe the disassembly of microtubules.
-GDP-beta-tubulin causes ends to fray which is destabilizing and causes disassembly (this is regulated)
What are the role of MAP's in the neuron?
-MT’s in axons organize in a crystalline-like array
>MAP’s assist in this process
What is EB1?
-EB1 binds to seam at ends of MT's
>may contribute to stability of end
-used experimentally as a + end tracker
What are 2 molecules that play a role in MT disassembly?
-Kinesin are molecular motors that assoc. w/MT’s
>Kinesin-13 destabilize the ends of MT’s
-Stathmin is analogous to cofilin and profilin
>prevents units from being added back to filament
Describe the conformation of myosin. What enzymes cleave it? What do they yield? What molecule does myosin use to exert force on actin?
-coil is the C-term of myosin
>coil is reminiscent of IF’s
>head hydrolyzes ATP and converts it into physical motion
-papain cleavage=2 free head regions
What determines the functional properties of myosins?
-diff myosins have diff tails and # of heads
>same motif but diff. functions
Describe the mechanics of myosin.
-3 states: ATP, ADP+Pi, ADP
>use ATP to cock the motor
>power stroke results from Pi release from GDP+Pi
Describe the graphs of the 2 processivity schemes of myosin.
-processibity of diff myosins
-Myosin II releases the filament but B doesn’t (b/c it has 2 heads and one is bound at any given time)
What are the 2 routes of locomotion utilized by processive myosins?
How do non-processive motors work to move a vesicle?
-org. array of non-processive myosins allow movements
>some will be bound while others aren’t
Describe the polarity of different molecular motors.
-kinesins=(-) to (+)
-dyneins= (+) to (-)
-myosins= (-) to (+) <usually>
-dyneins and kinesins use MT’s but move on diff. tracks
What gives specificity of function to kinesins?
-diff coiled coils lend specificity of function
Describe the mechanics of kinesin and contrast it to myosin.
Motors work in tandem (vs. mysoin)
How do dyneins differ from kinesins?
-bigger than kinesins
>don’t attach directly to cargo
>uses dynactin complex
How does dynein link to cargo?
-dynactin complex
***a lot of regulation associated with small GTPases (Rho class)
What types of molecular messengers are associated with the ECM?
-many growth factors, cytokines, and chemokines are assoc. with the extracellular matrix
Describe the different cellular junctions.
What are the different functions of the cell junctions?
Describe the components of adherens junctions.
-CAM’s of adherens junction=cadherins
>extracellular and cytosolic domains
>allows interaction with environment
>conformational changes upon binding to ligand (like another cadherin)
>specific protein (adapters) interact with cytosolic domain
>trigger polymerization of cytoskeleton, activate kinases, attract scaffold proteins, etc.
>interaction extracellularly leads to intracellular effects
>info can flow from within to extracellular domain also
>adapters allow you to use same adhesion molecule in different ways in different cells
Define homo- and heterotypic (as they pertain to cell-cell adhesion molecules).
-homotypic interactions=the same type of molecule from different cells interact
-heterotypic=adhesion molecules interacting with different molecules
What are some of the adapter proteins in adherens junctions? What does the arrangement of adapter proteins determine?
-filaments=microfilament
-arrangement of adapter proteins dictate arrangement of cytoskeletal structure
What element stimulates cell adhesion via cadherins?
Ca
Describe desmosomes.
-desmosome
-desmoglein and desmocolin interact with intermed. Filaments
>provide structural strength to cell layer
-plaques are adapters
-there is still a space between cells where small molecules can diffuse
Describe the components that regulate tight junctions.
-extracellular domains of claudins and occludins zip up
>longer cytoplasmic tail
Describe claudins and occludins.
-extracellular domains of claudins and occludins zip up
>longer cytoplasmic tail
-involved in tight junctions
What dictates how "leaky" a tight junction will be?
-mix of occludins and claudins in junction dictates how leaky the junction will be
>can be regulated based on organism’s needs
Describe an experimental model that allows you to see transcellular transport.
-dye put on one side of cell
>allows visualization of whether transcellular transport is occuring
Describe gap junctions.
-gap junctions are a good way to recruit actin to allow contraction of cell
>direct connection between cytosol of different cells
-gap junctions only allow the passage of small molecules between cells
What determines the diversity of gap junctions?
-combo’s of connexins allow for different varieties of gap junctions
Give an overview of junctional and nonjunctional cell adhesion.