Monday, September 6, 2010

Molecular Crowding

After looking at Figure 7.2 I wondered how on earth could anything move within a cell that crowded. Even with ATP powering the movements of vesicles and the like, with something so densely packed surely no movement was possible. Furthermore specific reactants would never be able to find each other. It would be like trying to push to the front of a mosh pit at an epic concert.

However, a great explanation followed this picture. Nelson was able to explain that movement of larger molecules was possible due to the entropic forces of smaller molecules. By removing the depletion layer surrounding large molecules the entropy of the smaller ones could increase. This was achieved by sheparding the larger molecules together.
The depletion layer is a result of the smaller particles not being able to occupy (or concentrate in) the space directly surrounding the larger particles i.e they cannot occupy the maximum number of states, they're not at the maximum entropy. The entropy is maximised by decreasing the size of the depletion layer. Where the biggest decrease is seen when the large molecules are 'matching'. That is the larger molecule reactants are pushed toward the recognition sites of their specific enzymes speeding up the reaction. It's more like crowd surfing in a mosh pit, with everyones hands (the smaller molecules) propelling your body (the larger molecule).
It is amazing how so many processes, that at first seems backward, happen because of entropy.

It also made me wonder. Is this how bacteria are able to feed in laminar fluid? Do these 'sheepdogs' herd the food particles for the bacteria to eat?


  1. While the image is good at describing how crowded the inside of a molecule is, I think the image fails to show the whole picture, as it is only a static image. We have to remember that thermal motion is a large force on this size scale. So while it is very crowded here, it is reasonable to believe that at any time interval, due to thermal motion, the picture could be very differnt. The same level of complexity and disorder would be present, but the molecules would be in some different order. So it does seem reasonable that reactants would find each other in this environment. However, I agree, the depletion layer theory explains why it is likely, not merely probable, that these reactions would occur.

  2. At what point would a cell become so dense that thermal motion would stop? And do cells that survive in colder temperatures have a less crowded system or just different constituents? I know that the membrane of cells at colder temperatures have a higher percentage of cholesterols, but wouldn't there also have to be less crowding within the cell for things to move.

  3. At what point would a cell become so dense that thermal motion couldn't occur? Do cells at colder temperatures have less crowding or just different constituents? I know that the cell membrane at colder temperatures has a greater percentage of cholesterol, but do the cells also require less crowding within them for movement to occur?

  4. Not necessarility I don't believe. The higher percentage of cholesterols is so that it's harder to freeze the membrane, due to the specific internal energy of the cholesterols.
    I would likely also say that cells which survive at different temperatures have different constituents.

  5. Also, in light of your crowd surfing analogy, or the sheepdog and sheep one, have a think about lipids or oils or other hydrophobic substances dropped in water. All the hydrophobic molecules are hustled together to form a complex such as micelles, bilayers, vesicles etc so as to decrease the overall energy of they system.