Cell Biology Exam #2 Comprehensive Study Guide
∙ What are the key players for import to Mitochondria? What are these similar to? Key players in the import into the mitochondria are some signal sequence/presequence, translocators (some sort of channel for the proteins to go through, chaperones (some proteins to keep the proteins unfolded enough so it can get through the translator), energy (in the form of ATP and a proton gradient).
This is very similar to import to the ER.
∙ Are proteins post or co-translationally directed to the mitochondria? Proteins are post-translationally directed to the mitochondria. The protein is translated on ribosomes in the cytosol and brought over and imported post translationally into the mitochondria.
∙ What are the major steps of import of matrix protein into mitochondria? “Translation in cytosol, bound by chaperones to keep from folding and aggregation, presequence recognized by receptor in TOM complex, unfolded peptide fed (presequence first) through TIM23, presequence cleaved by signal peptidase” We also discuss several other topics like Monopoly means what?
You have a protein and a signal sequence/presequence and it binds to a receptor in the membrane. It’s interacting with the outer membrane translocons (TOM complex). The protein is brought through the TOM complex and the TIM complex (especially if it’s a matrix protein – it’ll be brought through both membranes with two different translocators). The signal peptidase cleaves the signal sequence/presequence. The protein will fold and be in the matrix. Recognition of the signal sequence ???? translocation through two different pores in the membrane ???? cleavage of signal sequence ???? release of protein into the matrix ∙ Describe import into inner membrane or intermembrane space.
Don't forget about the age old question of What is expletive infixation?
There is a signal sequence and stop transfer sequences are involved (a parallel with the ER). The stop transfer sequence with the ER is the transmembrane domain. There will be import through the TOM complex into the inner membrane complex, and then the signal sequence will get cleaved and then once the stop transfer sequence is in the translocator it will be pushed into the inner membrane. We also discuss several other topics like What is gametes?
OXA is another translocator that is involved in targeting a membrane protein into the inner membrane. Here there is import through TOM and TIM, signal sequence is cleaved, the whole thing is brought into the matrix and then there is a second signal sequence that allows it to be fed into another complex and then it is put into the membrane. If you want to learn more check out A problem-solving strategy that involves following a specific rule, procedure, or method that inevitably produces the correct situation, is what?
Proteins in the intermembrane space will have cleavage by the protease and it will be soluble in the intermembrane space. If you want to learn more check out What is social loafing?
Proteins that are multi-pass-transmembrane proteins will have multiple stop transfer sequences, the protein will be imported through the TOM complex, chaperones will bind to keep the protein from folding or aggregating and then it will go through the TIM complex. Each stop transfer sequence is going to interact and move into the inner membrane. This is how there will be multi-pass-transmembrane proteins into the inner membrane of the mitochondria.
∙ What drives transport across the mitochondrial membranes into the matrix? What are the steps of this process?
“ATP hydrolysis and a membrane potential drive transport across the mitochondrial membranes into the matrix.”
Energy is needed, and it comes in two forms: ATP and membrane potential. The membrane potential comes from electron transport.
1. HSP 70 chaperone release requires ATP hydrolysis ???? chaperones bind to the protein, help keep it unfolded a little bit but not aggregating with other proteins so it can be brought through the translocator into the mitochondria. HSP 70 plays this role. The binding and release is regulated through ATP hydrolysis. If you want to learn more check out Where does the energy come from?
2. Energy from membrane potential drives protein across intermembrane space and through TIM23 (inner membrane translocator)
3. Mitochondrial Hsp70 requires ATP to import protein into Matrix ???? there are chaperones in the mitochondria HSP 70 – interacts with the protein coming through the TIM complex, and through the binding and release of HSP 70 helps pull the protein in through the matrix)
Example signaling pathways, types of ligands
∙ Describe the generic signaling pathway. What does it do? What is the end result? Does it need to be turned on or off? How is it involved with cancer?
The generic signaling pathway facilitates cell-cell communication because these signaling molecules are being secreted by other cells. They relay a message from outside the cell to the nucleus, and the end result is to effect cell response to stimulus. This involved gene expression and motility. Signaling pathways must be turned on or off and when things go wrong, cancer can form.
All signaling pathways are essentially same. There is some sort of receptor protein in the plasma membrane and a signaling molecule, which turns it on. There are many different proteins that act to relay the signal to the messenger protein that will do whatever it needs to do. A target protein will be activated (transcription factor) and you’ll get gene expression. ∙ Describe the Jak-Stat signaling pathway? What is being regulated?
The Jak-Stat signaling pathway is activated by viral infections. It’s part of the antiviral response. It regulates a conformational change allowing a transcription factor to enter the nucleus. Receptors are activated by alpha-interferons (signaling molecule). When the signaling molecule binds, the receptors dimerize which activates the kinase associated with the receptor. Kinases activate phosphorylation. Phosphorylation activates even more phosphorylation which creates binding sites/docking sites for other proteins (STAT1 and STAT2- the transcription factors). Transcription factors aren’t active until they’re phosphorylated, released from the receptor, dimerized, and now they’re in the proper confirmation where they can go in the nucleus and activate gene expression by binding to a promoter.
Take Home ???? there are different kinds of pathways. Some of them are regulated by enzyme linked receptors. A conformational change allows the transcription factors to get into the nucleus.
∙ Describe the NFkB pathway. What does it regulate? What kind of pathway is it? The NFkB pathway is a regulator in the inflammatory response and immune response. It is an example of a pathway dependent on regulated proteolysis (of an inhibitor) and is similar to Wnt signaling and B-catenin. Activation results in recruitment of these different signaling proteins, and you’ll get activation of different kinases through the cytoplasm. The end result is phosphorylation of IkB which is an inhibitor. When that inhibitor is phosphorylated it is recognized by the ubiquitin proteasome system, its ubiquinated and degraded. The transcription factor NFkB has a NLS. It goes into the nucleus to activate gene expression and interacts with importins. Normally the inhibitor binds to and masks NLS. This is how its kept out of the nucleus. Activation of this pathway send that inhibitor to the trash and the NLS is exposed and the protein can be imported into the nucleus and activate gene expression. When the ligand binds to the receptor, the proteins assemble and there is activation of a kinase cascade. The end part is activation of the IKK complex, a kinase complex. The complex phosphorylates IkB and will then be recognized by ubiquitin proteasome system and degraded. This allows NfkB to go into the nucleus to activate gene expression.
Regulated degradation of an inhibitor.
∙ Describe the Wnt signaling pathway.
There is a protein that is constantly being degraded, that’s its normal off switch. When the pathway is activated, the complex usually associated with degradation of the protein is disabled. This allows the transcription factor to be stabilized.
No signal ???? In the absence of the signaling molecule the receptor is just hanging out on the cell surface. The protein beta-catenin is the transcription factor. That protein is normally
phosphorylated and interacting with this complex (the destruction complex because it destroys beta-catenin). Because its constantly being degraded it is not available to go into the nucleus. With signal ???? When there is signaling the whole complex of proteins is being recruited to the receptors and then it is no longer binding to beta-catenin. The GSK3 protein (which is a kinase) is no longer able to phosphorylate beta-catenin, so it is no longer degraded. It is stable and able to go into the nucleus, bind to a promoter, kicks off an inhibitor (Groucho protein), and activate gene expression
Nuclear receptors, concept of protein domains
∙ Where are nuclear receptors?
Nuclear receptors are not on the cell surfaces or nuclear envelope. They are intracellular proteins. They are receptors because they bind to a ligand, but they are not a cell surface protein. They are transcription factors that are inactive in cytosol and enter nucleus after ligand binding induces conformational change.
∙ What do nuclear receptors do upon ligand binding?
Upon ligand binding, nuclear receptors change conformation, which releases inhibitory proteins, recruit’s coactivator proteins, allows for binding to the DNA and activates transcription.
When the ligand diffuses into the cell it binds to the ligand binding domain, that kicks off the inhibitory protein, and then you get a conformational change which allows the protein to enter the nucleus (presumably exposing a NLS) and the DNA binding domain binds to the DNA and it acts as transcription factor. This activates gene expression and recruits co-activator proteins and RNA polymerase. You get transcription of the target gene (how hormones work). ∙ Describe the concept of domains in proteins.
There are different parts of proteins that do different things:
A transcription activating domain ???? the part of the protein that interacts with the coactivator proteins and activate transcription. If it is cut off, then you couldn’t activate transcription. DNA binding domain ???? the part of the protein that binds to the DNA. If there was a mutation you couldn’t bind to DNA and you couldn’t activate transcription.
Ligand binding domain ???? the part of the protein that binds to the ligand. ∙ What are the three classes of cell surface receptors?
Ion-channel coupled receptors
G-protein coupled receptors (GPCRs)
Enzyme coupled receptors
Note: nuclear receptors are not cell surface receptors
Types of receptors – ion channel coupled, GPCR, kinase associated
∙ Ion-channel-coupled receptors: What does signaling induce? What can it be regulated by? What can it be involved with?
Signaling induces conformational change which effects the ion channel (whether or not it’s open). It can be regulated by GPCRs and is involved in rapid synaptic signaling between nerve cells and electrically excitable target cells.
∙ What are G-Protein Coupled Receptors [GPCRs]? What do they regulate? GPCRs regulate other membrane proteins indirectly. They have three main parts: receptor that binds to the ligand, the G-protein (another GTP binding protein), and another protein. When they’re activated they activate another protein nearby (in this case it’s an enzyme). GPCRs regulate other proteins and are often associated with second messenger release.
∙ What are Enzyme Coupled Receptors (ECRs]? Describe their activity. Enzyme coupled receptors have intrinsic or associated enzyme (usually kinase) activity. They either have a domain within the receptor that has kinase activity, the ability to phosphorylate things or they will be bound to an enzyme such as a kinase. Ex: Jak-Stat pathway
Types of intracellular signaling complexes
∙ What are the three kinds of signaling complexes?
1. Preformed signaling complex on a scaffold – becomes activated by ligand binding 2. Assembly of a signaling complex on a activated receptor
3. Assembly of a signaling complex on hyperphosphorylated phospholipids ∙ Describe preformed signaling complex on a scaffold protein.
Even in the absence of a signaling molecule there will be a scaffolding protein. It will have and support inactive intracellular signaling proteins. It is a preformed signaling complex and is just waiting. When the receptor is activated, the conformation of the receptor will change due to ligand binding, and there will be activation of the signaling molecules by phosphorylation. This sends the signal downstream.
∙ Describe assembly of signaling complex on an activated receptor.
Here the inactive receptor does not have any intracellular signaling molecules bound to it. Only when the signaling molecule binds to the receptor is when phosphorylation occurs. These phosphate groups that were added (probably by the activated receptor which probably has kinase activity) will phosphorylate itself and create binding sites. When binding sites are there signaling molecules can bind to it.
The kinase domain is down at the bottom of the receptor. The proteins all have SH2 domains. The kinase phosphorylates itself and the receptor, and then you'll get binding sites for recruitment of proteins 1, 2, and 3, and they have SH2 domains. This is how they're able to bind. ∙ Describe assembly of signaling complex on phosphoinositide docking sites. The inactive receptor is just hanging out on the plasma membrane. There are phosphoinositides on some of the phospholipids. When the ligand binds to the receptor it gets hyperphosphorylated which creates binding sites so other molecules can bind, and this activates the signaling pathway. Recruits signaling molecules, more kinase activity phosphorylates a phospholipid and this creates a docking site at the plasma membrane, which recruits other proteins that have specific binding sites for these phosphate groups. When this binds there is a conformational change in those proteins.
Molecular switches, GTP, phosphorylation
∙ Describe molecular switches. What are two examples?
GTP binding proteins → (GTP is on, GDP is off – the on/off switch regulates the proteins) ATP binding proteins → (phosphorylation – a kinase can phosphorylate things and turn it on, and a phosphatase can remove a phosphate group and turn it off – phosphorylation doesn't always mean on or off. Phosphorylation changes the shape of a protein and that can activate or inactivate things depending on the protein)
∙ Describe signaling by phosphorylation.
A kinase with phosphorylate something and that will affect its activity. A phosphatase will remove the phosphate group, and this can turn off or on something.
∙ Describe signaling by GTP-binding.
GAP and GEF activity regulates GTP binding.
∙ How is a response activated?
A response is often activated by multicellular signals – signals are integrated by a class of proteins that are only activated when both signals are present.
It won't always be only one receptor and ligand. Things will be signaling at the same time. Signaling is combinatorial. There can be multiple ligands and multiple receptors. GPCRs – how they work, example pathways, PKA, PKC, desensitization
∙ Describe G protein Coupled Receptors (GPCRs)
G protein Coupled Receptors are receptors that are couples to GTP binding proteins. They usually have multipass transmembrane domains.
∙ What are the results of activating GPRCs?
Activation of GCPRs result in a conformational change and activation of a trimeric GTP binding protein (G-protein).
Receptors interact with G proteins. G proteins have alpha, beta, and gamma domains. When the ligand binds to the receptor there is a conformational change and this results in activation of the G protein. This causes GDP to be released and GTP to bind.
∙ What does GPCR act like?
GCPRs act like a GEF. Ligand binding has the same function as a GEF. Release GDP, GTP binds and now the G protein is activated.
∙ Describe activation of a cAMP dependent signaling pathway via GPCR. Describe gene transcription. (How GPCR activates a signaling pathway through the second messenger cAMP)
Signaling molecule binds to GPCR and this activates G-protein, and this activates some other membrane bound enzyme (ex: adenylyl cyclase – the enzyme that makes cAMP). This activates the PKA by releasing the regulatory subunits.
Kinases are on, go into the nucleus and activate things. There is a transcription regulator protein that is usually inactive, and then it can be phosphorylated, and now it can bind to a promoter/enhancer region and recruit other gene regulatory proteins and recruit RNA polymerase. You can get expression of these specific genes.
∙ What do some GPCRs do? [GPCRs activate an inositol phospholipid signaling pathway] Some GPCRs activate an inositol phospholipid signaling pathway through cleavage if PIP2 tolP3 and diacylglycerol by phospholipase C-beta.
There are two products of this cleavage – one activates protein kinase C (another kinase), one release will release calcium from the ER (a second messenger).
Phospholipase C is analogous to adenylyl cyclase. It is what is being activated by the Gprotein. GPCR → ligand binds → G-protein on → activate enzyme (adenylyl cyclase for cAMP, phospholipase C for this)
You can have diacylglycerol which activates protein kinase C, or you can have IP3 which will release calcium from the ER.
∙ What is the result of GPCRs activating phospholipase C-B?
GPCRs activate phospholipase C-B and this result in the release of Calcium from the ER. IP3 binds to a gated channel and will open the channel in the ER membrane, and calcium will release. Calcium will bind to protein kinase C, and now there is another active kinase that can go on and phosphorylate things.
Take home ???? PI 4, 5-bisphosphate gets cleaved by the activity of phospholipase C-B in the membrane
∙ What is desensitization? Describe receptor sequestration, downregulation, and inactivation.
Desensitization is turning off signaling.
degradation through the lysosome -- through clathrin – receptor mediated endocytosis downregulated through endocytosis – two ways of it happening (hanging out in an endosome and having it recycle, or downregulation and degradation where you will end up in the lysosome)
Inactivation ???? preventing signaling from happening by having some inhibitor protein being recruited and binding to the cytoplasmic tail-- when an active receptor is desensitized, signaling is turned off, there could be recruitment of other proteins that can block signaling
∙ What does GPCR desensitization depend on? Describe this mechanism. GPCR desensitization depends on phosphorylation and binding of the receptor by arrestin. Arrestin arrests signaling. Activating a GPCR will activate a lot of things. One of the substrates of the kinases is the receptor itself. There will be phosphorylation of the receptor and binding sites will be created for arrestin. Arrestin will bind and inhibit signaling by inhibiting interaction of a G-protein and it is also involved in endocytosis. Arrestin behaves like adaptin, an adapter protein that binds to clathrin. It is a nice mechanism to recruit an adaptin like protein that can interact with clathrin.
Enzyme linked receptors – RTKS, kinase associated receptors, how activated, role of phosphorylation
∙ Describe signaling through kinase associated cell surface receptors. (Ex: JAK-STAT & NFkB) Receptors on the cell surface that either bind to a kinase or have intrinsic kinase as a domain in their receptor
∙ Describe RTK subfamilies.
RTK subfamilies have common domains. These are receptors that have kinase domains, and are not bound to kinase. Part of the receptor itself can phosphorylate things. They have a transmembrane domain and kinase domains. They have other parts that are involved in interacting with ligands or other receptors
∙ What does ligand binding activate? What does crosslinking mean?
Ligand binding activates the intracellular kinase domain of RTKs by inducing receptor crosslinking. Crosslinking means binding two things and linking them together. ∙ What does ligand binding cause?
Ligand binding causes receptor chains to dimerize, bringing kinase domains in close proximity so they can phosphorylate each other. There is changing conformation, and doing something to activate kinase activity.
∙ What is the purpose of phosphorylating the cytoplasmic tails?
This creates docking sites for other proteins.
Intracellular signaling molecules - RAS, MAPK, Rho, PI3-Kinase, PTEN, Akt ∙ What can intracellular signaling proteins bind to?
Intracellular signaling proteins can bind phosphorylated tyrosine through their SH2 domain. The receptor gets phosphorylated on the tyrosine, and the different proteins involved in signaling that have SH2 domains can bind. We’re creating binding sites for SH2 domain containing proteins.
∙ Describe how Ras is a molecular switch?
Ras is a molecular switch (GTP binding protein) – relays the signal from the cell surface to different signaling pathways. It is a molecule that spreads the signal.
∙ How is the activity of Ras regulated?
A GAP or a GEF
∙ What is the effect of a mutated Ras?
If Ras is always bound to GTP, the outcome in terms of signaling will be signaling will always be on. ∙ What kind of mutations might be associated with cancer? How is Ras activity activated?
Ras activity is activated through recruitment of Ras GEF to the RTK signaling complex. Ras is always interacting with the plasma membrane on the cytoplasmic side. When signaling comes through a receptor, and you get phosphorylation, a binding site for an adaptor protein is created (Grb-2). It has an SH2 domain so it binds to the signaling and that recruits the Ras GEF. This is how Ras is activated.
∙ How is Ras activity regulated? Why isn't Ras active all the time?
Ras GEF is the regulator. If Ras GEF isn’t there it isn’t on. It is going to be off because it is normally in the GDP bound state through GAP activity.
∙ How does Ras-MAP Kinase signaling pathway continue to relay the signal downstream?
The Ras-MAP Kinase signaling pathway continues to relay the signal downstream by phosphorylating gene regulatory proteins and activating other kinases – MAP kinases. Map Kinases are a series of 3 kinases held together by a large scaffolding protein and they transmit the signal through the cytoplasm to activate the effector protein which is often a gene regulatory but it could also be another protein changing its function through phosphorylatio ∙ Describe the MAPK signaling pathway?
There are a lot of different receptors and a lot of then will activate Ras which will often result in activation in MAP Kinases. Map Kinases are a series of kinases that are held together by a scaffold protein and function in helping to relay the signal from the receptor to the effector protein through phosphorylation.
∙ Describe Ras activation? How is it quickly reversed?
Ras activation is brief and transient – quickly reversed by the activity of phosphatases. Ras is involved in spreading the signal to multiple pathways. If you wanted to turn off signaling you could add a phosphatase to dephosphorylate the receptor to lose the GEF. You’ll get shut off and hydrolysis of GTP and shut off of Ras
∙ What do Rho GTPases couple?
Rho is another GTP binding protein (like an on/off switch for something). Rho GTPases couple cell surface receptors to the cytoskeleton.
∙ What does Rho A do?
Rho A stimulates myosin dependent contraction of actin cytoskeleton. There is actin polymerization and there is myosin-mediated-filament-contraction.
∙ What do PI 3-kinase phosphorylates inositol phospholipids do? What can activate it? PI 3-Kinase phosphorylates inositol phospholipids creating docking sites for intracellular signaling proteins. This can be activated by RTSs, GPCRs, or Ras.
PI 3-Kinase is a kinase that can be activated by many different receptors. It phosphorylates inositol phospholipids in the plasma membrane and creates docking sites for other proteins. It activates another signaling pathway. PI 3-Kinase regulates different pathways. ∙ What is the outcome of a mutated PTEN?
associated with cell growth and survival = PTEN shuts this off
If PTEN was mutated, the pathway will always be turned on because you will never have the removal for phosphate groups. PI 3-Kinase adds all sorts of phosphate groups there, and PTEN removes them. Those phosphate groups are binding sites for different proteins associated with signaling
∙ What is PI3-K involved in?
PI 3-Kinase is involved in cell growth and survival
∙ What does signaling through PI3K-Akt pathway promote?
Signaling through PI3K-At pathway promotes growth and survival.
There is phosphorylation and dissociation of an AKt protein, a kinase. It is active and phosphorylates things. One of the targets that it phosphorylates is a Bad protein. Bad normally binds to and keeps the inhibitor of apoptosis inactive. When Bad is phosphorylated it goes and binds to something else and now there is an inhibitor of apoptosis that is active. It goes on and inhibits apoptosis. Apoptosis, from the perspective of the cancer patient, is good because you want to kill the cancer cells.
Latent gene regulatory proteins – how they are regulated – conformational change, proteolysis, degradation
∙ What is a latent gene regulatory protein?
A latent gene regulatory protein is a protein in the cytoplasm that is inactive in the form that it is in and gets activated somehow.
Genes are regulated through signal transduction and proteolysis of a regulatory protein. Phosphorylation might result in a conformational change. They could also be regulated through some kind of competitive inhibition and binding to another protein (maybe an inhibitor)
∙ Give 3 examples of latent gene regulatory proteins and explain how they are regulated.
B-catenin ???? [Pathway = Wnt] B-catenin is regulated through endocytosis of GSK3. GSK3 endocytosis is what controls degradation of B-catenin. B-catenin is usually being degraded, and activation of the Wnt pathway causes it to be stabilized. Regulating stability. Cytoplasmic Tail of Notch ???? [Pathway = Notch] the cytoplasmic tail is regulated through cleavage. Once Delta binds Notch and the pathway is stimulated, you get cleavage of the cytoplasmic tail of Notch and that is what turns it on and allows it to go to the nucleus. NFkB ???? [Pathway = NFkB] degradation of the inhibitor, NFkB is the latent gene regulatory protein and it is regulated through controlling the stability of the inhibitor
Turning off signaling – phosphatases
∙ When does signaling need to be turned off?
Signaling needs to turn off once the goal of the signaling pathway is accomplished. Signaling that is unregulated is bad.
∙ What are some ways you can inhibit a receptor?
Endocytosis ???? Downregulation through receptor mediated endocytosis and it goes into a MVB Endocytosis & Degradation ???? you can have endocytosis that eventually will be recycling, and then you can have endocytosis going to the lysosome – both are downregulation that are pulling the receptor off the cell surface
Inactivation???? through interaction of an inhibitor with the cytoplasmic tail – blocking intracellular signaling molecule
Modification of the receptor ???? a phosphorylation that is inhibitory can be useful in recruiting an inhibitor or you can have a signaling protein that gets shut off (ex: Ras turns off signaling)
an inhibitor ∙ Describe deactivation of G-proteins
“Deactivating the G-protein through GTP hydrolysis – induced by binding the target protein or interacting with an RGS protein which acts as a GAP”
Activated G-protein will activate another protein. The GPCR will actually activate this GAP activity which results in GTP hydrolysis, loss of the phosphate, and this turns off the GPCR ∙ How is signaling turned off?
Signaling is turned off when phosphatases remove phosphate groups. If a receptor or a signaling molecule in the middle of the pathway, or even the latent gene regulatory protein is phosphorylated to activate it – removal of phosphatases can shut it off.