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How to picture the cell?

  1. Aug 23, 2012 #1
    I'm a biology dilettante who is trying to get a correct picture of the cell. From this web page http://www.arcfn.com/2011/07/cells-are-very-fast-and-crowded-places.html one gets a very chaotic impression. Small molecules are racing around with 250 miles per hour.
    Ken Shirrif: "In addition, a typical protein is tumbling around, a million times per second. Imagine proteins crammed together, each rotating at 60 million RPM, with molecules slamming into them billions of times a second. This is what's going on inside a cell."
    I was wondering if this is a commonly held view here or that someone is willing to dispute this.
     
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  3. Aug 23, 2012 #2

    Simon Bridge

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    Welcome to PF;
    That would appear to be pretty standard - to put it in perspective, though, geologists commonly talk about continents wizzing around and crashing into each other. Your understanding should be tempered with the scale of these events. The constituents of the cell are very small against everyday scales so the chaotic jumble is normal.

    The cell is certainly not the structured and ordered factory/machine that used to be portrayed when I was a kid.
     
  4. Aug 23, 2012 #3

    Pythagorean

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    Here's what it might look like inside a insulin-producing pancreas cell if we color code it:

    http://learn.genetics.utah.edu/content/begin/cells/membranes/images/tomography.jpg [Broken]

    from:
    http://learn.genetics.utah.edu/content/begin/cells/membranes/ [Broken]

    Of course, understanding the cartoon picture is the first step to understanding the major functioning parts:

    http://web.jjay.cuny.edu/~acarpi/NSC/images/cell.gif
     
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  5. Aug 24, 2012 #4
    That isn't really strange at the molecular scale. It's not just the cell, any fluid mixture is like that. All the molecules in a glass of water are whizzing around at those very 'phenomenal' speeds. So are the air molecules around you. The only molecular systems where you could say that molecules aren't moving that much would be perfect crystals at nearly absolute zero temperatures.
     
  6. Aug 24, 2012 #5

    Ryan_m_b

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    The link you posted had a very good video from Harvard, here is it in full





    The usual way that cell biology is taught is to work up in detail and complexity which may explain your surprise. First very simple fried egg-like pictures are shown to young kids at school.


    9fquxc.png


    Older students then use more detailed diagrams that show organelles


    1eb02w.jpg


    And beyond that more detailed diagrams of metabolic pathways and organelle structures are used. This is just one simple summary of one small pathway;


    35he8hl.jpg


    Cells are very complicated organisms with tens of thousands of different molecules interacting in metabolic webs all the time. This is what allows them to engage in all the complex behaviours that they need to in order to react to environmental conditions and survive (as well as cooperate).
     
    Last edited by a moderator: Sep 25, 2014
  7. Aug 24, 2012 #6
    Thank you all for answering my question. Thanks to you I understand that these speeds are 'perfectly normal' at the molecular scale.
    Now I'm trying to incorporate these speeds in my understanding of the cell. According to Ken Shirrif these speeds explain a lot: “Watching the video, you might wonder how the different pieces just happen to move to the right place. In reality, they are covering so much ground in the cell so fast that they will be in the ‘right place’ very frequently just by chance.”
    This seems debatable to me. If in a workshop all the parts of a car are floating around it’s hard to imagine that a car will be assembled. So there has to be some sort of guidance for all those parts?
     
  8. Aug 24, 2012 #7

    Ryan_m_b

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    It's not really debatable, it's well studied. I'd advise you to try not to think in analogies to human technology. I know it's hard not to but honestly it will mislead you because the similarities are few. Simply put all molecules act in accordance to thermodynamics and their chemical properties. Biology is fundamentally a collection of continuous chemical reactions that give rise to homeostatic phenomena. Proteins for example will fold into the most energetically favourable configuration through molecular interaction with the environment and themselves (e.g. sulpher bonds between amino acids).



    The scope of behaviour available is due to the incredible complexity and redundancy born from billions of years of evolutionary history.
     
    Last edited by a moderator: Sep 25, 2014
  9. Aug 24, 2012 #8

    Andy Resnick

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    Trafficking of proteins is an active area of research- some proteins, after being expressed, are then modified (acetylated, methylated, etc). Others are sent to specific locations in the cell (e.g. ciliary membrane), and others (cytoskeletal proteins) undergo polymerization/depolymerization cycles and are stored in 'pools'. "bad"- misfolded or damaged proteins- are sent to special organelles to be recycled. Proteins are inserted and removed from membranes, and as Ryan_m_b posted, there's coordinated motion of multiple proteins as well (signalling pathways). Much research is oriented towards understanding and controlling these dynamics.

    I wouldn't say there's 'guidance', tho. For example, simple hydrophobic/hydrophilic considerations allow for a wide range of organized stable structures.
     
  10. Aug 24, 2012 #9
    Do you mean by ‘are sent to’ anything other than that proteins happen to arrive at the right location by chance; because by their speed and rotation they cover so much ground?
    For instance: the correct protein 'happen' to slam into a receptor of the correct organelle?
     
  11. Aug 24, 2012 #10

    Ryan_m_b

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    In some cases it is due to diffusion in others due to transport via the cytoskeleton (as shown in the "inner life of the cell" video embedded about).
     
  12. Aug 24, 2012 #11

    Simon Bridge

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    I'd add here:
    Another way of looking at it is to consider that you are constantly moving, often at whole meters per second, and yet you can still have meaningful interactions with other humans also in constant motion ... you manage to get into the right position to do so. It does not always work - see how many people you have to ask out before you get a date for instance.

    The reason you can do this is that the interactions are on a time-scale that is small enough that the motions of you and others do not matter so much. (They still hinder you - just not fatally.) On top of this, you are not entirely passive in the process - you don't just, for instance, just ask everyone you see for a date: you try to ask people who you are attracted to and who appear attracted to you.

    It is the same in the cell - though everything is moving fast, the interactions are even faster. On top of that, the different bits have a range of ways they attract and repel other bits.

    To use your analogy of car assembly - it's like the situation where different workers and parts arrive at different times ... when someone sees the right part, they put it in the car. You can build a car that way - in fact, hobby auto-mechanics (restoring a car for eg) often works like that.

    -----------------
    Aside: scientists, particularly evolutionists, often talk about things happening by "chance". It is easy to confuse this with ideas about "randomness". This is not the case - the processes in the cell are not random. Bits don't "happen" to arrive in "just the right place" to do something. What they mean by "chance" is that the exact motion at any time cannot be anticipated.

    To get a picture of the difference - you may drive home after work and end up stuck behind a bus in slow traffic. That is a chance event in that you could not have anticipated the bus being right there. Yet this was not random - you left work at the time you did for a reason, the bus follows a route and tries to follow a timetable. Each of you got various delays and breaks in your travel which ended up with you stuck behind the bus.

    Now with all the traffic and the amount of driving you do in your lifetime - it is actually inevitable that you will get stuck behind a bus sometime (unless you don't drive...). This is certain, even though it is entirely a chance occurence.
     
    Last edited: Aug 24, 2012
  13. Aug 24, 2012 #12
    Which mechanism is dominant in the cell 'diffusion' or 'transport'?

    I'm not willing to discuss this. But seriously, your analogies are very helpful. Thank you.
     
  14. Aug 24, 2012 #13

    atyy

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    "A small molecule such as glucose is cruising around a cell at about 250 miles per hour"
    250 miles/hour = (250*1609 meters)/(60 *60 seconds) = 100 meters/second.

    "A small molecule can get from one side of a cell to the other in 1/5 of a second."
    If a cell is 0.000100 meters in across, then to get from one side to the other in 1/5 of a second, the speed is 0.00002 meters/second.

    Is the speed of 250 miles/hour always in a particular direction? If it is not, the net speed along a particular path over larger time scales might be slower.
     
  15. Aug 24, 2012 #14
    You should have pointed out that the picture that you posted is of a eukaryote cell, not a prokaryote cell. Prokaryotes don't have a nucleus or cytoplasm. Furthermore, prokaryotes don't have the cytoskeleton, the protein network that fills up the cytoplasm of eukaryotes.
    Prokaryotes include bacteria and other cells without nuclei. Eukaryotes include protozoa, fungi, plants and animals.
    The earliest fossils appear to be from prokaryotes, not eukaryotes. So it is a little misleading to refer to the eukaryote cell as "the first step". There are still more prokaryote cells on earth than eukaryotes.
    Maybe the "first step" should be in understanding the prokaryote cell. A eukaryote cell can be thought of as a "house" for a few prokaryote cells (i.e., nucleus, mitochondria, chloroplasts).
     
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  16. Aug 24, 2012 #15

    Andy Resnick

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    I mean that there is both directed transport along cytoskeletal elements such as tubulin and actin in addition to diffusive transport.

    Consider a neuron- a long one such as in your arm or leg. If I scaled the axon diameter to 6 feet, the length would be about 200 miles. Diffusive transport is not sufficient to get enough 'stuff' down the pipe.
     
  17. Aug 25, 2012 #16
    Prokaryotes (e.g., bacteria) don't have a cytoskeleton. Therefore, they don't have cytoskeletal elements.
    There are components of bacterial cells that may have these elements. Examples would be the cilia and pillai of some Gram-negative bacteria. However, these do no serve the same purpose as the cytoskeleton in eukaryotes.
    Bacteria have a lot of enzymes attached directly to their membranes. Thus, the reactions are mediated by the right molecule hitting the right enzyme in the right position.
    The prokaryote cell fits the description of the OP very well. The eukaryote cell fits the description a little less well because of the cytoskeleton. Eukaryotes have evolved a cytoskeleton that channels some of the molecular motions, selecting those that are more productive. However, the prokaryote ancestors of eukaryotes probably didin't have a cytoskeleton.
    Apparently, a cell doesn't need a cytoskeleton to survive. A cell needs a cytoskeleton to compete with other cells. The first eukaryote found the extra efficiency provided by the cytoskeleton useful in competing with prokaryotes. However, the full machinery of the cytoskeleton probably didn't develop in one step.
    So most of the collisions are nonproductive. The probability per collision with the cell membrane that the molecule hits the right enzyme in the right state is small. However, millions of such collisions occur every second. So the probability that a right collisions occurs after a few seconds is very high.
    However, diffusive transport gets "stuff" across the pipe. Material 'stuff' is not transmitted down the pipe. Electrochemical signals are sent down the pipe.
    Diffusive transport is characteristic of Markovian motion. Many of the calculations of probability that evolution skeptics give are based on Markovian motion. However, the motion of molecules in a cell are not completely Markovian. The concentration of molecules in a cell membrane are too high for Markovian motion.
     
  18. Aug 25, 2012 #17
     
  19. Aug 25, 2012 #18

    Pythagorean

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    particularly, the type of diffusion being considered recently is anamolous diffusion (as opposed to the classical diffusion usually considered). The basic idea is analogous to the perfumed room:

    Using passive/classical diffusion, in a "standard" sized classroom, if you squirted a little perfume in one corner, it would take about ten minutes for the smell to reach the opposite side of the room via passive diffusion.

    In the real world, we observe that it actually takes much less time because of all the convective currents in the room that actively transport the perfume particles much faster than passive diffusion would. So we expect in a cell, where there's a lot of action (interaction and reaction) going on that transport woud actually be much more anamolous than we have classically considered.

    Mathematically, this is represented by fractal derivatives. Classical diffusion utilizes the integer derivative (n=1) but anamolous diffusion comes in two varieties where n can now be a decimal (the significance of this is that coupling is no longer nearest-neighbor, but global). If n>1, we have superdiffusion, if n<1, we have subdiffusion.

    Much evidence lately has shown that diffusion processes in the cell could be super-diffusive. But some computer simulations show that subdiffusion might be better for target delivery:

    http://biocomplexity.indiana.edu/jglazier/docs/papers/54_Anomalous_Diffusion.pdf
    http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=TRD&recid=14419441SO [Broken]
     
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  20. Aug 25, 2012 #19
    So small molecules are moving and rotating really fast and larger molecules relatively slower. But how about the nuclear membrane, the cytoskeleton and the cell membrane? Should one consider these elements as static?
    And how about the cell membrane of prokaryotes?
     
  21. Aug 25, 2012 #20
    I can add another citation, although I can't provide an active link.
    There is an article in the most recent Physics Today that discusses many of these topics. The article is:
    "Strange Kinetics of Single molecules in Living Cells" by Eli Barai, Yuval Garini and Ralf Meltzer. Physics Today Volume 65 Number 8, page 29-35 (August 2012).
    It points out that most of the diffusion going on in the cell is anomalous diffusion. The diffusion is not governed by standard Markovian walks.
    For instance, ergodicity is not always satisfied by the motions of a molecule in a single cell. Furthermore, diffusion is not always stationary. The conditions in the cell change so rapidly that the environment at the beginning of a molecules trajectory is not the same as the environment later in the trajectory.
    So there is a separate process, called "subdiffusion", riding on the "normal" diffusion of a molecule. Thus, time averaged observables are not always reproducible. Since time averaging of handling most "random" variables, other mathematical approaches have to be developed to analyze the data.
    The real question is whether this addresses the questions of the OP. If he asks whether the molecules are really moving randomly, then he has to tell us what he means by "random". Maybe by "random" is talking only about observables that are ergodic. In other words, he will only accept as random situations where the ensemble average equals the time average. Then in all probability the motion of a single molecule in the cell is not always ergodic. By his definition, it is not random.
    The motion of big molecules in the cell are often anomalous, meaning that it doesn't precisely follow the rules of Brownian motion. The probabilities are weighted in a certain way that isn't exactly the same as would occur if the molecules moved like Einstein predicted for Brownian particles.
    My suspicion is that he and the person he talked to are thinking about a more teological definition of random. The motion of the molecules is not directed by any intelligence, so far as we can tell. So far, the molecules seem to be governed by the same rules of physics as is the case in nonliving organisms.
    The statistics may be a skewed in the sense that they are not Gaussian distributed. The Bell shaped curve doesn't seem to govern the probabilities of the important events. However, there is nothing unnatural in this. Gaussian statistics are not as universal as many statisticians think. In the most general sense, the statistics of the molecules in a cell are random and fast. There are millions of collisions of a molecule with the cell wall per second, and there is no fixed path that governs the trajectory of the motion.
    If the OP wants a more specific answer, then he should provide a more specific definition of "random" as he understands it. The word "random" is used in many different ways. There are many random distributions that are different.
    My hypothesis is that his use of the word random is close to the definition of ergodic. He may be assuming that the motion of the large molecule in a cell eventually reaches every possible position with equal frequency given sufficient time. If that is what he means, then I would say no. The motion of a large molecule in a cell is not completely ergodic.
     
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