Wet Monomers shouldn't become polymers - but ...

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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on August 12th, 2017, 10:29 am 

scientificphilosophe » 04 Aug 2017 02:31 am wrote:Hi BioWizard

Apologies for the delay in replying.
This is for several reasons. Firstly I have been away for a few days, but more importantly I still, genuinely, do not understand several aspects of your replies, and I am becoming concerned that our conversation is mismatched because I am somehow not articulating myself in the right way.

I am therefore trying to consult with a colleague who is now away for a few weeks (on conference and then holiday) so it may take me a while to respond again on this subject.


This is fine.

scientificphilosophe wrote:While I do understand the basic nature of the reversible reactions you are focusing on I feel that we cannot say that a polymer has been formed until it has reached a stable condition. A momentary existence before it reverts back to its constituent monomers (or worse) is not, in my layman's opinion, truly forming the polymer because it has to be usable in a practical way.


>Exactly<

You got it. This is actually one of the very points that I was trying to convey to you. Things aren't so cut and dried at the molecular level, and tend to exist on a continuum. As such, a polymer's stability is a function of both its formation and reversion rates. When we colloquially say that a "polymer forms", what we're actually saying is that "the formation rate is sufficiently larger than the reversion rate for the polymer to last long enough for us to measure its presence (or utility of sorts)". Conversely, colloquially saying that a "polymer does not form" is not very different from saying that "the reversion rate is sufficiently higher than the formation rate that no polymer forms and lasts long enough for us to measure its presence (or utility)".

By extension of this, the stability of a polymer can be modulated by altering the formation and reversion rates with respect to each other. If you make the formation rate much higher, you make the polymer more stable. If you make the reversion rate much higher, you decrease the stability of the polymer - and if you keep going there will be a point where the polymer's existence is as good as none, and we say the polymer doesn't form.

scientificphilosophe wrote:You are implying that formation and reversal is constant - which it might well be in the lab, or possibly even in a primal ocean. If correct, the polymers must be harvested at the right moment to become usable. Without the human element, how is that to be done in a natural process?


This might come as a shock to you, but these processes are a lot more dynamic inside cells than we can ever hope to recreate in the lab at present.

Let's say you put a DNA polymer in a buffered solution in a test tube today. You measure its length tomorrow and you find out its still the same. You measure it the day after that and it is still the same. So you conclude that the polymer is stable. But when if you measure it in ten years? A hundred years? A thousand years? You will suddenly start to measure significant decomposition. Suddenly, the process isn't so static anymore. Why? Because you started to observe it at the time scale that matches its slow dynamics.

Alternatively, you can add an enzyme that degrades DNA. Now your DNA polymer will start decomposing in a matter of minutes. If you measure its length tomorrow, it will seem like it disappeared in an instant. But it didn't. It disappeared gradually over a matter of minutes. And if you want to measure that disappearance dynamically, you would have to do your measurements every few minute or seconds after you add the enzyme. Because the enzyme has changed the rates of the process (by speeding up the rate of reversion), and the timescale of your observation needs to match the new dynamics of the system.

Nothing is fixed, everything is contextual. To understand the stability of a polymer, you need to understand the formation and reversion rates, and the factors influencing them.

scientificphilosophe wrote:What we see in living cells is that the polymers are stable and do not reverse instantly. They are preserved ready for use elsewhere in the cell.


Correct. The reversion rates are slow enough that the polymers in cell can perform measurable functions and "do not reverse instantly". But when happens as cells grow and divide? These structures are turned over and recycled in a dynamic process.

Since we're on the subject, do you know that cells move themselves round specifically by modulating polymerization dynamics? Here's an (incredibly simplified example): To move to the right side, a cell causes polymerization of its cytoskeleton in the right direction and depolymerization of its cytoskeleton in the left direction. The net outcome is that the cell shimmies to the right. How can polymerization and depolymerization be locally controlled within the very same cell? Enzymes. How is the process done regulated directionally? You send enzymes that stabilize polymerization to the right, and enzymes that de-stabilize polymerization to the left side.

These processes are very dynamic and occurring all the time. If you measure them instantly, you won't catch the dynamics. If you measure them over time, you will find that all these polymers are constantly forming and breaking down as the cell responds to its environment, grows, divides, migrates, and so on.

scientificphilosophe wrote:Overall, even with a constantly reversing process, you are still implying that the right conditions have to be created in order to 'shift a balance' and produce more/many polymers. So we are still back to creating the right conditions for assembly not disassembly. Again I am puzzled why you do not focus on answering the point about assembly. This may be where my colleague can help me to re-phrase my point.


Because assembly is only 50% of the process. If these polymers were as stable as you seem to think, cells wouldn't be able to divide, grow, migrate, polarize, and so on. Cells would be frozen down. The stability of these polymers is constantly manipulated inside cells to allow all these processes to occur. In fact, some cancer drugs, such as taxol, capitalize on this - they increase the stability of intracellular polymers to the point that it becomes detrimental for the cell's survival. Others, such as Cytochalasin, do the opposite - they mess up with cells by destabilizing polymers.

Here, read this: https://en.wikipedia.org/wiki/Cytoskeletal_drugs

It's all in the balance between the two process. I would be stunned if you still don't see that by now.

scientificphilosophe wrote:When you say...

Consider these two statements:
1- A polymer doesn't form because the monomers never come together
2- A polymer doesn't form because the monomers fall apart as soon as (or faster than) they come together

While these two statements may sound different to you (and apparently they do), they are actually the same from a chemical/thermodynamic viewpoint. The outcome is the same in both: a polymer fails to form.


The two statements are not the same even from a thermodynamic viewpoint. We may not even get the same outcome.

If only one monomer is present it can only react with ions in the water (if at all) and not with another monomer.
If two monomers are present and react, before then disassembling, it is a very different reaction and depending on the background level of heat and other chemicals/ions present, might produce something else - possibly wit ha change of energy levels in an exothermic/endothermic reaction.

We are back again to determining the right conditions for assembly and stability.



Wait. Didn't you yourself earlier say:

scientificphilosophe wrote:While I do understand the basic nature of the reversible reactions you are focusing on I feel that we cannot say that a polymer has been formed until it has reached a stable condition. A momentary existence before it reverts back to its constituent monomers (or worse) is not, in my layman's opinion, truly forming the polymer because it has to be usable in a practical way.


You literally said "a momentary existence......is not truly forming". Are you saying that this makes sense to you when it suits you, and doesn't make sense when it does not suit you?
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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on August 12th, 2017, 10:57 am 

scientificphilosophe wrote:While you may wish to respond to this in the near future I won't be able to respond again until I have consulted my colleague,


No worries, take your time.

so can I ask you to revert again to the other topic of 'Origin and Evolution' where there are many unanswered points?


scientificphilosophe I prefer to do one thread at a time, due to time constrains. I look forward to getting back to the other thread - after we finish with this one.
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Re: Wet Monomers shouldn't become polymers - but ...

Postby neuro on August 21st, 2017, 1:33 pm 

Ehi, BioWiz,
just to be picky... :°)
BioWizard » August 12th, 2017, 2:28 pm wrote:ATP synthase, for instance, harnesses the flow of electrons across the membrane to shift the equilibrium from ADP + P towards ATP.

It actually harnesses the flow of protons across the membrane...
(the flow of electrons from donors to acceptors down to oxygen fuels the transmembrane transport of such protons, which then flow back through the ATP-synthase).

But I must admit that - although I took care of specifying "a single reaction" - you are right: an enzyme can drive a single reaction in one direction by harvesting energy from a physical process (such as a photon) instead of a coupled chemical process:
Other enzymes can harness light radiation. And so on.

And, BTW, sorry about diverting the topic... :°)
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Re: Wet Monomers shouldn't become polymers - but ...

Postby BioWizard on August 21st, 2017, 7:45 pm 

Neuro,

While one can argue that the flow of electrons is the source the proton gradient and therefore posit that the statement isn't in essence incorrect, that was admittedly not my intended meaning. I was indeed thinking of the H+ flow through complex V, but for some reason typed "electrons" instead =) I was going to talk about the ETC but decided to ommit that part, and the rest is histo... freudian? Thanks for the correction.
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