How to picture the cell?

Diderot

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-a...ed-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.

Simon Bridge

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.

Pythagorean

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



from:
http://learn.genetics.utah.edu/conte...lls/membranes/

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

mishrashubham

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.

Ryan_m_b

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.





Older students then use more detailed diagrams that show organelles





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





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).

Diderot

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?

Ryan_m_b

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.

Andy Resnick

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.

Diderot

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?

Ryan_m_b

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).

Simon Bridge

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.

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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.

Diderot

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.

atyy

"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.

Darwin123

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).

Andy Resnick

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.

Darwin123

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.

Darwin123

[QUOTE=Diderot;4046425]Which mechanism is dominant in the cell 'diffusion' or 'transport'?

Physicists and biologists think of diffusion as one specific type of diffusion. Transport is any process that gets a scalar from one location to the other. Two types of transport studied by physicists and biologists are diffusion and advection.
Diffusion is the transport that is characterized by "random" motions of the molecules. Advection is the transport that is characterized by "coherent" motion of the molecules.
On large distance scales, advection is usually greater than diffusion. On distance scales comparable to the diameter of a prokaryote cell, diffusion is usually greater than advection.
Eukaryote cells are broken up into compartments called organelles. Each organelle has a size on the order of a prokaryote cell. Therefore, diffusion dominates within an organelle. However, the cytoskeleton provides a type of advection between organelles. Advection is at least as important as diffusion between organelles.
I think the OP was asking about chemical reactions that occur inside prokaryotes or inside organelles. On this distance scale, collisions are truly random. However, the probability per collision of a useful chemical reaction is relatively high. There are millions of collisions per second, so a useful reaction are quite probably in one second.
The correct answer to the OP's question may be this. The description of "random collisions" at a "rapid rate" is probably valid inside a prokaryote cell. However, eukaryote cells have a higher level of complexity. The description of "random collisions" at a "rapid rate" is probably valid inside individual organelles of the eukaryote cell, but not in the cytoplasm between organelles. Between organelles, one has to take into account the cytoskeleton.
One way to visualize this is to think of some of the organelles as being prokaryotes. Some prokaryotes evolved to live together as a eukaryote cell. The cytoskeleton is a "telephone network" to aid communication between prokaryote cells. A eukaryote cell is basically a colony of prokaryote cells.