Where does growth factor have its effect in cell? (aka where does it bind?)
surface receptor that is a transmembrane protein
Where do steroid hormones bind?
Binds a nuclear receptor in cytoplasm and activate changes in gene transcription inside nucleus
cell sends signal to itself
cell sends signal to adjacent/contacting cell from membrane to membrane
cell sends signal over some distance
Receptor Tyrosine Kinase, Growth factor receptor
Makeup of a growth factor receptor
extracellular ligand binding domain and an intracellular tyrosine kinase domain
What forces dimerization
ligands of receptor tyrosine kinases
Epidermal Growth factor receptor (Receptor Tyrosine Kinase Receptor)
Phosphorylation equation for a EGFR receptor
phosphorylation = k[EGFR]^2 - second order, requires 2 receptors per ligand, double concentration of receptor quadruple phosphorylation
How do RTK's phosphorylate?
By forming dimers and trans phosphorylating each other
domains that bind to phosphorylated RTK dimers and begins a signaling cascade
What is happening in the Figure?
Shows trans-phosphorylation as you mutate one that can't phosphorylate, but can still be phosphorylated.
RTK Kinase Cascade
SH2 domain binds phosphorylated RTK, SOS binds SH2, activates Ras, activated protein scaffold
Why is a signal complex necessary?
It makes signaling more efficient and prevents uncontrolled diverging of signaling pathways
plasma protein involved in RTK Kinase cascade. Always located at membrane
attaches to SH2 domain in RTK cascade
Cytokine cross links adjacent receptors, JAK's on receptor trans-phosphorylate each other, activated JAK's phosphorylate receptors on tyrosines, SH2 and STAT proteins dock on receptor and is phosphorylated, then transported directly to nucleus with no signaling cascade
Difference between JAK-STAT and RTK curves? Cellular response is Y axis, receptor ligand is x axis
high levels ligand required to activate JAK-STAT pathway.
Large Hill Coefficient
RTK pathway. On or off signaling pathway, generally no half-on state. More feedback loop possibilities
Small Hill Coefficient
JAK-STAT pathway. More direct pathway, more graded response
The above images are taken from cultures of cells treated with increasing amounts of a growth factor that induces cells to make a protein that turns the cell dark (melanin). Based on the response you predict that the factor's receptor signals to the nucleus by
D. D. Becoming proteolytically cleaved and the fragment going into the nucleus. Gradual like the JAK-STAT pathway
Activated G protein
ligand binds, G protein complex breaks up, G alpha (GDP to GTP), G Beta, and G Gamma, any of three can activate phospholipase C, cleaves PIP2 to IP3, binds to receptor and releases Ca2+, binds and activates Protein Kinase C, also attached to lipid tail diacylglycerol, initiates further signaling
G protein complex. Converted from GDP to GTP when ligand binds
G protein complex. It is a GEF protein
when activated by G alpha or Ggamma/Beta cleaves specific lipids into the lipid tail and head group, which have secondary signaling roles (ex cleaves PIP2 to IP3 and diacylglycerol)
Protein Kinase C
initiates further cell signaling when bound to diacylglycerol (lipid tail from PIP2), and calcium (released by binding of IP3 lipid head from PIP2 to IP3 receptors)
turns ATP into cyclic AMP, activated by G Alpha
Protein Kinase A (PKA)
activated by cAMP which binds to regulatory subunit receptors and releases/activates the inactive catalytic subunit, which then can enter the nucleus and phosphorylate proteins that alter transcription such as CREB
regulation by a post-translational modification in the protein or using another molecule to bind or release it. This causes a conformational change
Regulation by Localization
proteins are always active but are only brought to the right location to exert their effect at the right time.
A B -| C D E
A goes up, B goes up causing C to go down, which causes D to go up and E up.
Arrows in PKA system
Between cAMP and PKA blunt arrow (cAMP deactivates PKA subunit), between PKA reg. subunit and PKA cat subunit blunt arrow (reg deactivates cat). Between PKA (cat) and target, pointed arrow
NF kB signaling
NF kB bound to IkB, IKK breaks apart complex by allosterically changing IkB, NF kB enters nucleus
Notch protein binds transcription factors, transmembrane protein Delta (juxtacrine) binds to notch and cleaves it, cleaved portion can go into nucleus and exert effects on transcription
The above images are taken from cultures of cells treated with increasing amounts of a growth factor that induces cells to make a protein that runs the cell dark (melanin). Based on the response you predict that the factor's receptor signals to the nucleus by
Cells have growth or none (black or white no gray) aka stepwise response by activating a multi-step kinase cascade
Signaling downstream of G-protein coupled receptors occurs through
B.Small molecules C. Generation of specific lipids D. Ion concentration changes (B-D are all correct)
individual actin monomers
Actin plus end/minus end
Actin graph shape
starts slow because it's hard to begin making the chain, then depolymerization occurs as rapidly as polymerization where graph levels off (only in vitro)
Nucleation of actin filaments
monomers brought together to form the shortest possible filament, a tetramer (slow process), cannot occur spontaneously
occurs exclusively at barbed end
polymerization occurring at barbed end while depolarization occurring at pointed end simultaneously (does not occur in muscle cells)
stabalizes pointed end (prevents depolymerization)
stabalizes barbed end and prevents addition of monomers
prevents spontaneous polymerization
Where does barbed end point
always towards outside of cell
How can cell make more barbed ends?
Nucleation cannot occur spontaneously, the cell can make more barbed ends by simply cutting existing actin filaments or uncapping barbed ends that are "inactive."
Formins, SPIRE, VASP
forces monomers into a barbed end. These machines remain stuck to the barbed end to facilitate further monomer addition and to prevent capping
binds to the side of a existing filament and mimics a barbed end, allowing monomers to be added onto this false barbed end to generate a new filament that branches from the original
You assemble actin in vitro in the presence of Arp2/3 complex and tropomodulin, then examine the resulting filaments by fluorescence. You expect to see . . .
Alpha and Beta tubulin graph
Shows they form dimers
individual pieces that are assembled to make microtubules (made of Alpha and Beta tubulin)
Where does Polymerization/depolymerization occur in cells and in vitro?
at either end in vitro. In cells, polymerization occurs only at the plus end (they are polarized)
a couple of alpha and beta tubulin dimers put together side by side
plus ends can both depolymerize or polymerize, depending on conditions in the cell. This makes it harder to control microtubule length
Why are microtubules less rigid than actin?
Microtubules are made by assembling tubulin dimers into a filament that winds together into a helix with an empty centrol core, the microtubule. These have less elasticity than actin, and are less rigid.
Why does microtubule graph plateau?
Equal number of plus ends polymerizing/depolymerizing
protein that drives microtubule nucleation, but is not required for polymerization.
The location of microtubule nucleation and extension in the cell
microtubules all emanate from a single point in most cells, the microtubule organizing center. Microtubules are captured there by their minus ends and with their plus ends pointing away from the organizing center
Centrosome of microtubule, contains gamma tubulin protein which initiates mictrotubule nucleation and tethers microtubules to the MTOC. AKA centrioles
stabilizes and allows for polymerization (No Gap proteins needed to hydrolyze GTP to GDP - process occurs spontaneously)
depolymerize and destabilizes
You microinject cells with GFP-tagged gamma-tubulin and then observe where this tubulin localizes after only 2 minutes. Assuming you get no nucleation and only polymerization from existing filaments, you would expect to see GFP fluorescence at...
the centrosome only
In order to flip a lipid head from one side of membrane to another
Integral Membrane proteins
which means embedded into the membrane itself, have either transmembrane domains or a lipid modification
Peripheral Membrane Proteins
proteins that interact with either lipid heads or with other membrane proteins
Cytosolic Lipid modifications
several varieties including lipid tail can be masked by another protein, allowing shuttling of these proteins on and off the membrane
Outer/luminal Lipid modifications
GPI anchor only
Lipids move laterally throughout membrane (ex. can fill a hole blasted by a laser)
Membrane Protein Tracking
A barely moves, B moves all over, C moves far, D has a lot of movement, but limited to a certain distance
proteins are constrained to a specific type of membrane with specific types of lipid composition.
act as fences blocking a protein from diffusing past the boundary. Such structural boundaries can also bind and retain proteins in place (includes membrane skeletons)
Lipid raft formation
results in the sequestration of certain types of proteins (particularly lipid-modified proteins) into those areas of membrane. The lipid raft can act as a phase boundary that limits the diffusion of those proteins.
Membrane elastic or inelastic?
Elastic - when membrane stretched and then released, it goes back to its original shape
Simple Membrane Skeletal System
Beta 2 AR (transmembrane protein), EBP 50 and ERM's (Adaptor proteins), Actin (Cytoskeletal elements)
Beta 2 AR
transmembrane protein in membrane skeletal system
EBP 50 and ERM's
Adaptor proteins in membrane skeletal system
Protein Protein Interaction Genetics
You attach the bait and prey to other proteins. If they interact and DNA transcription occurs, gene expression will increase
Complex Membrane Skeletal System (most membranes)
Spectrin form alpha and beta dimers (red) that connect the points of the triangles. The points are held together by very short actin filaments and adducin. All of this is connected to the membrane through adaptor proteins (band 4.1 and ankyrin), which in turn bind membrane proteins
made up of alpha and beta dimers that connect the points of the triangles, held together by short actin filaments. Forms long roid structures
short actin filaments that hold spectrin dimers together
adaptor proteins that connects skeletal system to membrane (ankyrin is another adaptor)
adaptor protein that connects skeletal system to membrane (Band 4.1 is another adaptor). C shape that can act as a spring. Note that ankyrins can interact with many membrane proteins along the length of this spring.
Lattice systems (including cytoskeletons)
provide 2D structure to the inner surface of the membrane.
You monitor the lateral diffusion of a membrane protein in cells and find that its movement is restricted to a certain distance. This might result from...
A. Association with other diffusive binding partners, B. Structural boundaries, C. Phase boundaries (B and C not A)
dynein, kinesin (smaller, esp head group), both "walk"
Heavy and Light chains of Kinesin/Dynein
Heavy chain attached to head, light chain more like a tail
ATP effect on actin motor head
Hydrolysis effect on actin motor head
like moving leg forward
Phosphate release effect on actin motor head
binds again to myosin, and a "stroke" occurs
Actin motor head power stroke steps
ATP releases binding, Hydrolysis of ATP to ADP moves leg forward, phosphate release allows head to bind again and cause a power stroke
Direction of Kinesin
towards plus end
Direction of Dynein
towards minus end
2 legs - can move things over a long distance but not as efficiently as non-processive
1 leg - work in unison. Motors allow the cargo to move a small distance. It is another motor that carries the cargo further. Many motors are required for movement. More efficient, but genearally move shorter distances compared to processive motors
Function of microtubule-based motors
transport of vesicles
The cargo can be moved to the plus end of microfilaments (actin) by the action of only one motor molecule. What type is it?
the myosin has two heads and is processive - kinesin likely
What type of cell adhesion is B-Cell and T-Cell?
Blood cell adhesion
no-adherant, solitary cell
cell-substrate, integrin based adhesion
neurons, epithelia, cardiomyocytes adhesion
Cell-substrate and cell-cell adhesion
Cadherin based cell adhesion
Cadherin extracellular domains bind the extracellular domains of cadherins on adjacent cells in a calcium-dependent manner. On the inside, the cytoplasmic tails of cadherins bind catenin adaptor proteins, ultimately linking cadherin-based adhesion to actin
Different Cadherins in a cell, what occurs?
Ex. Red clumps with red, green with green. If red can interact with green we might see a big yellow clump
Totipotent cancer cell that can become N, E, or M cadherins, which then become neurons, Epithelia, or Muscle cells
Similar to Cadherin adhesion system, binds to afadin and ponsin. Different adhesion systems allow for specialization of membranes
Non-adherent cells treated with cadherin
Non-adherent cells treated with nectin
spans membrane 4 times (tetra). Loops interact with adaptor proteins and actin
Cadherin extracellular domains bind . . .
A. calcium B. extracellular domains of cadherins of different types C. extracellular domains of cadherins of the same type (A and C)
Sites of integrin-based adhesion occur as points
actin cables emanating from focal adhesions
transmembrane porteins that bind ECM on the outside and adaptor protein on the inside. The adaptor proteins link the integrins to the actin cytoskeleton of the stress fiber.
proteinaceous network built outside the cell and to which integrins can bind.
Alpha and beta dimers work like scissors
Inside-out integrin signaling
Alpha and beta dimers can be closed, binding more tightly to ECM, as a result of intracellular signaling or actin-based tension inside the cell
Outside-in integrin signaling
ECM binding can force the integrin to close, in turn activating signaling and actin rearrangements inside the cell
an adhesion system that anchors z lines in muscle cells. Binds to sarcolemma
dystrophin-associated glycoprotein complex - ECM, receptors, adaptors, cytoskeletal networks
How is DGC related to disease?
Myscular dystrophy, defects in adhesion systems, lack of costamere sites, membrane does not fold properly during contraction, tearing and damage can occur
Cell migration, where is actin concentrated?
Leading edge, actin polymerization and barbed ends push membrane, or act as a ratchet forming perpendicular to membrane causing net movement
activated GTPase that initiates assembly of branched, dendritic actin structure at leading edge
branched, dendritic actin structure including cell membrane, made through Arp2/3 complex
it is a relative of Rac1, forms actin-based protrusions called filopodia, without Arp2/3, but activates formin proteins
actin-based protrusions made by cdc42 without Arp2/3
lamellipodia (Rac1) in center, Filopodia (cdc42) protrusions
drives integrin-based adhesions to be linked to thick stress fibers and for myosin-based tension to be put on those stress fibers, thus causing the cells to pull on the focal adhesion and move the cell body forward.
Where Rac1 and cdc42 are active
Breakdown of focal adhesions
No more tension and exit the zone of rhoA activity, eventually broken down
Focal adhesion - Rho A activated (GTP state) activates Rho kinase, activates MLC kinase, activates myosin light chain. Creates tension in myosin
What happens in cell once focal adhesions are broken down?
integrins are endocytosed and recycled via vesicle trafficking back to the front of the cell. Vesicles at back hooked up to dyneins to bring them up to front
What brings integrins to front of cell?
Vesicle transport via dyneins
Picture - which one is rac1, cdc42, and rhoA
A.RhoA, B. rac1, C. cdc42
directional migration, divide plasma membranes into regions with different functions and proteins
lipid located at front of a membrane, generated from PIP2 by PI-2 kinase
peripheral membrane protein, converts PIP3 back to PIP2, activated globally and levels are same throughout cell. Sets a global threshold that PI3 Kinase is only able to overcome at the front of the cell.
How does G-Protein coupled Receptor affect cell movement?
Activated by chemoattractant (ex cAMP) and activates both PTEN and PI3 Kinase
activates PIP3 at front of cell, overcomes PTEN threshold when activated by chemoattractant
How is PTEN recruited to the membrane?
PIP2. At rear of cell, PIP3 is converted quickly back to PIP2 so PTEN accumulates at rear of cell
How is PTEN excluded from the membrane?
As PIP2 level decrease at the front of the cells when PIP3 is produced by high PI-3 kinase activity, PTEN is excluded from the membrane
This occurs in sheets of cells, particularly epithelial, that can tell the difference from the 'top' and the 'bottom,' thus allowing these cells to form direction, vectorial barriers between compartments
Basal region (cell polarity)
defined by regions of integrin-based adhesion (contact with the Extra Cellular Matrix)
Lateral region (cell polarity)
cell-cell contact cadherin based adhesion
Apical region (cell polarity)
tetraspanin proteins of several types, which bind to ZO adaptor proteins, linking the adhesion system to the actin cytoskeleton. Occludins and claudins are 2 main types of proteins
one of main protein types of tetrospanins in tight junctions (also claudins)
one of main protein types of tetrospanins in tight junctions (also occludins)
Planar cell polarity
occurs in layers of cells that all have oriented in a particular direction within the plane of the layer of cells. Bristles all point same direction. Ex - in class we are all facing the front of the classroom
Cells already undergoing directional migration are forced to reverse by introducing a new, stronger gradient in the opposite direction. The result at the global level is...
increases in both PI-3 kinase and PTEN output
What phase is DNA replication?
What phase are neurons found in?
Go phase - quiescient cells not actively proliferation (little division)
How would you determine machinery for cell cycle?
Use temp sensitive mutants. At higher temp, gene is replicated, but protein does not work at higher temp. If you don't see the colony growing on the right plate you can see that that colony does not divide
Cyclin Dependent Kinase, initiates events of cell cycle. Inactive until bound by a cyclin
How does cyclin affect cell cycle?
Different cyclins bind CDK to initiate different events of cell cycle
What happens when cyclin levels are high?
the CDK activates machinery that results in expression of the next cyclin and the degradation of the current cyclin.
S Phase, G2 phase, M phase, G1 phase/Go phase, S Phase
What is checkpoint for G2 phase?
Has DNA damage been repaired
What is checkpoint for M phase?
Are chromosomes aligned and bound to microtubules
What is checkpoint for Go phase?
Will conditions support cell division
What is checkpoint for S phase?
Has replication been completed
What happens when checkpoint for certain cell cycle phase is not achieved?
Cell cycle may pause to allow for events to be completed
Rb (cell cycle)
must be inactivated to start cell cycle, or deactivated for cell to enter Go phase. Normally sequesters E2F transcription factors
How is cell cycle started?
Phosphorylation of Rb releases E2F transcription factors which makes cyclins and CDK's for cell cycle to commence.
What is time of cell cycle when Rb is bound to E2F?
activated when DNA is damaged, released from MDM2, binds to damaged DNA and transcribes genes (p21) that inactivate CDK, or causes cell to undergo apoptosis
p53 inhibitor, released when DNA damage recognized
gene that is transcribed by P53 to inactivate CDK during DNA damage
What is the most likely mutation for hereditary retinoblastoma, a result of inability of cells to enter the quiescent state?
A. deletion of the Rb gene B. overexression of the Rb protein C. a mutation that prevents Rb Phosphorylation D. a mutation that mimics Rb phosphorylation (A and D)
Phosphorylation (S) histone modification
hold sister chromatids together
semi-conservative like DNA duplication, one mother centriole is paired with a daughter centriole (always paired together at 90 degrees)
How do chromosomes line up in middle on metaphase plate?
Tension, Minus ends are on poles - kinesins are used (motor proteins)
inactivates cohesion, sequestered by securing
sequesters separin, degraded at point of anaphase initiation
What degrades securing and when?
At point of anaphase initiation, degraded by E2/E3 proteins (ubiquitylation)
What moves sister chromatids to poles?
Separase degrades cohesion, then dynein moves them to poles
site of attachment of sister chromatids
site of microtubule attachment to the centromeric region.
How is new nucleus formed after chromosome separation?
nuclear envelope fragment bind to the DNA of the separated chromsomes and then fuse to make a new nuclear envelope enclosing the DNA. This is done via BAF proteins of the LINC complex
Which protein(s), involved in preventing sister chromatids from separating until anaphase, is activated at the onset of anaphase?
A. securin, B. separase C. Cohesion (B, the others are deactivated)
Epithelial mesenchyme transitions, epithelial cell receives signal to invade other cells and differentiate into proper tissue type
cells from the ectoderm are triggered to undergo EMT. They detach, migrate over the ectoderm surface, invade through the primitive streak, and differentiate into non-epithelial mesodermal cells. This event is triggered by signaling from the endodermal cells.
occurs when a single parent cell gives rise to two different daughter cells. This occurs when the contents of the cell (proteins, and particularly transcription factors) are inherited differently. One cell receives all of one or two factors, while the other cell receives none
Par 3/6 and Par 1/2, never found together, always on opposite ends of cell
What par complex does cdc42 and PKC bind to?
What happens to polarity when sperm/egg fuse?
RhoGAP pyk1 is dumped into the resulting cell. causing more active RhoA on the opposite side of the cell and little near the site of sperm-egg fusion. RhoA, in its active state, drives myosin-dependent contraction of a cortical membrane skeleton system at the inner cell surface (tension). The result is asymmetric contraction of this membrane skeleton away from the site of sperm-egg fusion
How is membrane coated prior to fusion of egg and sperm?
Par3/6 coats entire membrane and Par 1/2 is in cytosol.
How is membrane coated following fusion of egg and sperm?
Contraction of membrane skeletal system drags par3/6 to one side of cell and Par1/2 can translocate to vacated part of membrane. This is also thought to generate cytosolic currents
Par protein function during divisions
bind to astral microtubules to ensure that the spindle apparatus is organized so that cytokinesis occurs to split the cell between the two different par protein complexes and generate two different resulting cell types
used in development to get rid of cells that are no longer needed or are specifically unwanted. Also programmed cell death
following extensive DNA damage
cell shrinkage and chromatin condensation, membrane blebbind and nuclear collapse, apoptotic body formation, lysis of apoptotic bodies, phagocytosis of fragments
extrusion of apoptotic cells from epithelial tissues, extrude the dying cell from the tissue while maintaining tissue integrity.
Where does anoikis commonly occur?
Intestines where cells only last about 5 days
Fas binds 3 fas receptors, FADD binds to fas, recruits ProCapsase to complex, cleaved, and capsase signals apoptosis in cell
signal from immune cells to trigger apoptosis
adaptor protein that binds to Fas trimer that recruits ProCapsase
cleaved from ProCapsase complex bound to FADD and Fas trimer, signals apoptosis in cell. activates more and more capsases with different targets (inactivate or deactivate), driving events of apoptosis
induced by conditions within apoptotic cell, pro apoptotic bcl proteins
Pro-apoptotic bcl proteins, form channel on membrane of mitochondria that allows cytochrome C to pass through
inner mitochondrial protein that passes through pro apoptotic membrane proteins and complexes with Apaf1that activates procapsases to capsases and drives apoptosis
complexes with Cytochrome C in cytoplasm, then activates procapsases to capsases to drive apoptosis