Sunday, May 15, 2011

Book Notes: Signaling Part 2

  • even prior to multicellular organisms, it was important for unicellular things to sense signals from each other
    • quorum sensing: receive chemical signals from neighbor bacteria to coordinate motility, antibiotic production, and conjugation (bacteria sex)
    • yeast cells secrete mating factor to get neighbors to stop cloning and make a haploid cell for sexual fusion (communication is important in a relationship!)
  • general multicellular signaling process
    1. signaling molecule released into ECM (amino acid, peptide, protein, steroid, fatty acid, dissolved gas, etc, etc)
    2. target cell binds the signal with a receptor protein on its surface
    3. binding causes cytoplasmic domain of receptor to activate or act on other proteins and molecules within the cell
    4. intracellular signaling pathway involves many molecules activating/binding to each other
    5. effector proteins are expressed/activated to cause the effect that the signal was going for
  • 2 types of short distance signaling:
    • contact-dependent: cells must be touching each other (i.e. signal molecule is attached to the source cell, and the receptor is attached to the target cell, so signal-receptor binding can only happen if the two cells are right next to each other)
    • paracrine signaling: secreted signal only hangs around in the ECM near the source cell, affecting only locals
      • how do you keep the signal from flowing too far away?  The neighbor target cells take up the signal or ECM enzymes destroy the signal, or the ECM itself traps the signal like superglue
      • autocrine signaling: similar to paracrine, except secreted signal only affects itself and other neighbors of the same cell type
  • 2 types of long distance signaling:
    • synaptic signaling: neurons emit chemical signals at a synapse right next to the target cel (however, the axon can extend literally from your head to your toes!)
    • endocrine signaling: source cells spit out hormones who travel by bloodstream to find target cells all over the body (usually one kind of hormone causes different effects to different cell types for a coordinated response between multiple tissues and organ systems)
    • compare & contrast: synaptic is targeted precisely and super fast (electric zap!), while endocrine is targeted generally and pretty slow (diffusion and blood flow)
  • in general, response time also depends on effect
    • causing an effect with existing proteins is fast
    • causing an effect that requires synthesis/gene expression is slow
  • remember gap junctions?  They help with "the most intimate of all forms of cell communication"
    • they equalize cytoplasmic conditions between connected cells
    • they allow sharing of second messengers, especially important where some cells of a tissue cannot be reached by nerve impulses, so the signal is passed on through sharing second messengers (cAMP, calcium ions, etc, etc)
  • cells, based on cell type, respond to specific combos of signals (if every single signal molecule meant something different, cells would get so confused if they happened to receive both a DEATH signal and a KEEP LIVING signal)
    • combinations prevent confusion and accidental wrong signals (maybe you sometimes get half the molecules necessary to spell DEATH but you always get all the letters of KEEP LIVING)
  • different cells types produce different response to the same signal molecule
    • response based on receptor type, intracellular signaling molecules (they serve as the signal interpreter), and which effectors are activated
  • what happens when the signal is removed?
    • in some cases, the changes caused by the signal are permanent, so removing the signal does nothing
    • in other cases, the changes caused by the signal are temporary, so removing the signal removes the effect it caused
      • how does this work?  usually by having second messengers/proteins that are quickly destroyed (very short half lives)
      • having a continuous signal causes continuous production to maintain concentration of the second messenger/protein
      • no signals means no production means the existing messengers get degraded quickly and the cell stops producing the response
  • some signals skip the outside receptor and go directly into the cell to cause response
    • gases like nitric oxide pass through the plasma membrane and bind to proteins to cause effects (is short-lived and local, through, because it can only diffuse)
      • nerve signals endothelial cells to make NO, NO diffuses out and into neighbor cells, binds guanylyl cyclase to make cGMP that relaxes muscle to increase blood flow
    • steroid hormones also pass through the plasma membrane: they bind to intracellular nuclear receptors
      • the nuclear receptors are either free-floating in the cytoplasms or already bound to DNA
      • normally the receptors are bound by inhibitors, and binding of the steroid causes release of the inhibitors
      • the receptors then go ahead and activate DNA transcription (all receptors bind as dimers)
      • some receptors are not inhibited normally, but get inhibited by the steroid
      • these receptors cause the primary response: transcription of a few genes
      • the products of those genes go and activate transcription of a lot of effector genes to make the delayed secondary response
    • many cell types use the same receptors: it's the combination of other molecules who join forces with the receptor to cause different effects (for example, activation of gene transcription requires a whole slew of factors, activators, removal of repressors, etc, etc)
  • most signals meet up with surface receptors, who act as signal transducers (because they convert outside signal to internal signaling pathway without actually going in)
  • 3 main types of surface receptors:
    1. ion-channel-coupled receptors (ICCR) : rapid signaling, usually with synapses
      • signal attaching to receptor causes ion channels to open, which alter the concentration of ions on either side of the membrane, depolarizing the membrane and passing on the electrical signal
    2. G-protein-coupled receptors (GPCR) : acts by regulating a neighbor membrane-bound trimeric GTP-binding protein (G protein)
      • the G protein then activates a free target protein that initiates the signaling pathway
      • all GPCRs are multipass transmembrane proteins of one superfamily
    3. enzyme-coupled receptors (EZCR) : are enzymes of target molecules and/or activators of other enzymes
      • usually single pass transmembrane, kinases or kinase activators
  • signals are usually relayed from cell surface to internal organelles/proteins/genes by both small secondary messengers (mediators) and large intracellular signaling proteins
    • they are small molecules, normally not present or only in low concentrations, that get mass-produced in response to signal
    • their high concentration allows rapid diffusion throughout cell (or membrane, in the case of diacylglycerol)
    • they bind to specific signaling and effector proteins to pass on the message by altering function and/or conformation in the molecules they bind to
  • the large signaling proteins have multiple functions
    1. receive signal and pass it on
    2. serve as scaffold for multiple signaling guys to dock and efficiently trade messages
    3. transduce signal (i.e. from kinase cascade to secondary messenger diffusion)
    4. amplify signal (produce lots of messengers or activate lots of downstream proteins)
    5. integrate/receive 2 signals and pass only 1 signal
    6. spread to other pathways (activate proteins in this pathway and other pathways)
    7. anchor proteins to a specific location to attract molecules or create a localized response
    8. regulate other signaling proteins (regulates signal strength within cell)
  • usually these large signaling proteins are like ON-OFF switches: activated/deactivated with phosphorylation and/or GTP hydrolysis
    • with phosphorylation, a protein is active or inactive depending on balance of kinase and phosphatase activities  (kinase and phosphotases are also coordinated to either be all kinase active at one time or all phosphatase active at one time)
      • phosphorylation cascade: kinase activates a kinase that activates a kinase that activates a kinase and so on.
      • kinases phosphorylate either serine/threonine or tyrosine residues
    • with GTP binding domains, they turn on with GEF making them get GTP and turn off when GAP forces them to hydrolyze it into GDP
  • because so many proteins are also part of other pathways, how can a cell avoid cross talk (activation of another pathway through proteins from a signaled pathway)?
    • form complexes of all the correct signaling molecules on pre-formed scaffolds or temporarily on the tail of a receptor with multiple docking sites
    • having all the right ones in close proximity makes signaling fast, efficient, and specific
  • the complex can be induced to form by signals and by interaction domains
    • the domains are small binding pockets and complementary motifs on the receiving protein that don't interfere with shape or function
    • examples are SH2, SH3, PTB, and PH domains
    • complexing can also be structurally important: the way the complex is built can form a protein "trail" that leads to a specific location
    • adaptor proteins are important in complexing (protein whose job is to connect protein A and protein B)
  • cell response can either be ON/OFF (all-or-none) or gradual increase/decrease based on signal concentration (gradient)
    • a lot of gradient response can look ON/OFF if the concentration is high enough
      • e.g. 4 cAMP binds to PKA in order to activate it: a lot of cAMP will suddenly turn on all the PKA in the cell, a slowly growing concentration of cAMP will gradually turn on the PKA one by one as they grab up 4 (the 4 must bind simultaneously)
      • the slope of the graded response looks steeper (more on-off) as the number of required cooperative molecules increase
    • another way a graded response appears ON-OFF is if enzyme A that activates enzyme B also deactivates the inhibitor of enzyme B
    • a true all-or-none response needs a positive feedback loop
      • enzyme A activates enzyme B, who comes back around to further activate enzyme A (as well as doing its other functions)
      • because 1 enzyme A can activate, say, 15 enzyme B, all 15 enzyme B can come back and activate 15 enzyme A's each (totaling up to 225+1 enzyme A's) who can now activate 15 more enzyme B's each (totaling up to 3390 + 15 enzyme B's).
      • essentially, a small response very quickly EXPLODES into a huge response
      • even if the original signal fades, the response can keep going until another signal comes by to stop it (through another pathway)
      • this form of signal memory can be passed on to daughter cells (epigenetics)
  • negative feedback can provide 2 different effects:
    • a quick acting negative feedback shuts down a response as soon as the signal is gone and the cell goes back to normal (adaptive)
    • a slow acting negative feedback doesn't shut down a response until later, when the signal might reappear again, causing the cell to oscillate (go back and forth) between response and no response (some oscillating pathways continue without new signal)
  • desensitization: even if signal sticks around for a while, cell returns back to normal by not being able to continue sensing the signal
    • prevents uncontrolled response (i.e. EGF causing growth continuously)
    • cells sense change in signal concentration, not presence of signal
    • five ways of desensitizing:
      1. ligand binding causes response and causes endocytosis of the receptor, so cell no longer has receptors to sense signal until receptors get returned by exocytosis
      2. endocytosis of receptor leads to destruction of receptor (even longer delay until cell can re-synthesize receptors)
      3. activated receptors get quickly modified (i.e. phosphorylated) and become inactive
      4. downstream signaling protein is inhibited: so active receptor doesn't lead to response because the signal is interrupted somewhere along the line
      5. part of the response is to synthesize an inhibitor of signaling protein

pg. 879 - 903 (from Chapter 15)

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