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Gravity and the cell

  1. Oct 28, 2015 #1
    I ran across a term called 'isothermal settling' where you have an exponential distribution of particles - with more at the bottom and fewer at the top and how it relates to the cellular environment.

    My question is to what degree does isothermal settling (and the overall effect of gravity) occur inside the cell with regard to soluble proteins/DNA/molecules? I know that proteins/enzymes/DNA/molecules do not settle in the cell even though they are more dense due to Brownian motion, but are they 'closer to the bottom' in the cell than the top - such as in isothermal settling? I thought the cytosol would be a 'homogenous solution', however if isothermal settling happens inside the cell - which I believe it does but am not sure, then having more of everything skewed towards the bottom due to gravity doesn't seem very homogenous to me. Wouldn't this have negative effects on cellular processes? I always thought that gravity was negligible at the molecular level in the cell. Is this true? What about intercellular transport and diffusion at the synapse, is that negatively 'hindered' by gravity at all since more dense/heavier molecules would 'sediment'?

    This may seem obsessive but it's something I'm very confused about and I appreciate it if anyone here can help me.
     
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  3. Oct 28, 2015 #2

    Ygggdrasil

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    Let's say a typical cell has a height of ~10µm. Ignoring buoyancy, what would be the difference in gravitational potential energy of a 100 kDa molecule being at the bottom of the cell versus the top of the cell? How does that energy difference compare with thermal energy (kT), which tends to mix the contents of the cell via diffusion. How massive a particle would you need for the energy difference to be on the order of kT?
     
  4. Oct 28, 2015 #3
    you would need a 6 million kDa sized particle to be close to KbT (310 for body temperature).

    So what you're saying is that the thermal energy (Brownian Motion) is much much stronger than the difference in gravitational potential energy from the top to the bottom of the cell. Thus, the difference in particle position from top to bottom is negligible. That makes sense.
     
  5. Oct 29, 2015 #4
    I've attached screenshots showing this isothermal/barometric distribution does occur. However, I think given the particles in their example were a lot larger than 5nm proteins (and usually in these experiments these are insoluble particles) that this distribution would be much smaller with a small (5nm) water soluble protein.

    Perhaps this distribution does exist in cells (more towards the bottom than the top) but maybe it's to a very small degree, due to smaller diameter solute size of proteins/DNA and the fact that these are water-soluble. So being in a water solvent should give these particles more kinetic energy (and thus less sedimenting/distribution).

    It's all still very confusing to me. We just calculated that the difference in gravitation potential energy should be negligible. Why then are these small particles in this example that I attached showing a distribution in location with more towards the bottom of a small container/cell?
     

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  6. Oct 29, 2015 #5

    Ygggdrasil

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    According to your file 1*, Brownian motion counterbalances sedimentation for particles < 0.5 µm in diameter. Remember that volume (and hence mass) scales with length^3, so these particles, which are 100 times larger than 5 nm proteins, will be 100^3 = 1,000,000 times as massive (which, not coincidentally, gets you to the mass range where gravitational potential energies are comparable to kBT, as you calculated above).
     
  7. Oct 29, 2015 #6
    I understand now. So, on the graph in file 3* - If we had a particle with a radius the size of a protein (like 2.5nm... or even 25nm like for a virus) that would be just about 1.0 for concentration at top vs bottom, correct?

    What about file 3 (look at figure 8, letter B) there it says a = 0.29 um - these are showing a clear asymmetry in distribution with more towards the bottom .... not sure whether this is radius (in which case would be fine because that would be 580 nm diameter which is huge), but if it's talking about diameter, then that's starting to get pretty small (290nm) and that would contradict our reasoning.
     
  8. Oct 31, 2015 #7

    Ygggdrasil

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    Even if it's a 0.29 µm diameter, that's still ~200,000 times more massive than a typical protein.
     
  9. Nov 2, 2015 #8

    ogg

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    Of course, it isn't as simple as that. No "live" cell is a closed system. There are all sorts of pumps changing the cell's contents. And whether or not you should assume that the VISCOSITY of a cell is water-like, or gel-like depends (among other things) on the size of the molecule (particle) as well as its configuration and polarity. The cell is a colloidal, structured system of fluids, and semi-solids. That said, a larger particle will TEND to find its way to the bottom of a non-mixed solution. But lets see, sedimentation is (for simple particles) proportional to the 4th or 6th power of radius (sorry, I've forgotten which). On the other hand, there's still (last I heard) a lot of debate on how long it takes water - AFTER it reaches isothermality - to cease all mass flow (in isothermal and vibration free environment). Typically experimenters wait many hours or days after they disturb the water before assuming no "eddy currents" exist. The implication is that in "real world" conditions, there will be currents and concerted movement.
     
  10. Nov 2, 2015 #9
    So what you're saying is that even if small particles do happen to form a stratification (where there's slightly more particles at the bottom compared to the top) it won't be much because of all the other cellular reactions mixing things up. Do you think this is all negligible for small particles... wouldn't this cause problems if enzymes were straddled towards the bottom of our cells.

    Let me just throw an example out... do you think that for a typical enzyme (10 - 100kDa) that there would be say, 10% less in the top of a cell compared to the bottom?

    Thanks,
     
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