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Author Topic: How are water and organic materials partners in life?  (Read 5514 times)

Offline puppypower

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The idea of water being a co-partners in life, with the organics of life, is connected to experiments that were run in which the water in living systems was removed and then replaced with other solvents. The common result was, not only did none of the other solvents allow the affect called life to appear, but very little, if anything functioned properly, down to enzymes, without water. 

My conclusion was water can't be replaced, because water is directly involved in all aspects of life, at the chemical level, and is needed to integrate all the parts to create the condition called life.

Since life evolved in water, from simple molecules; abiogenesis, water, as the dominate phase, has set the chemical environment for natural bio-material selection. This is simply evolution at the nano-scale. Things may come and go, but only certain things were found to combine with water in ways that will maximize the functionality needed for life.

The purpose of this topic is I will try to develop this selection chemistry from scratch using the properties of water.
« Last Edit: 08/11/2015 14:04:51 by chris »


 

Offline chiralSPO

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Re: Water and Organics; Co-partners of life
« Reply #1 on: 07/11/2015 16:38:07 »
Well, all life as we know it depends on water and has evolved in the presence of water.

Water is definitely a special solvent: It's the smallest molecule that liquid at reasonable temperatures and pressures, it is very polar, has one of the highest dielectric constants of any liquid (http://depts.washington.edu/eooptic/linkfiles/dielectric_chart%5B1%5D.pdf), produces an extended hydrogen-bonded network that allows for very quick conduction of protons (https://en.wikipedia.org/wiki/Grotthuss_mechanism). And all of our proteins depend on hydrophobic/hydrophilic interactions for folding properly.

That said, I wouldn't be so quick to rule liquid water absolutely necessary! Liquid ammonia is also a very capable solvent, and can do interesting things like solvate and conduct electrons (https://en.wikipedia.org/wiki/Solvated_electron). One could also imagine liquid or supercritical CO2 as a very exotic sea! (who knows, we might be too liquid-centric--thick atmospheres could be ripe for unicellular organisms!) Given the feats accomplished by mere humans using anhydrous reaction media, I think it is entirely plausible that there could be a self-replicating, evolving (and possibly even sentient) set of chemicals that does not involve water. There are so many exotic worlds that do not have liquid water, how sure are we that nothing could arise under those conditions?

Of course, we know water/organic life forms best, and are most likely to recognize and have a chance at understanding water-based life, so I think it makes sense to take a water-centric approach to our exploration, but we must keep our minds open to these improbable possibilities as well. After all, so far we only have one datapoint to work with (all life on our planet shares the same basic biochemistry), who knows what is normal, common, rare or downright bizarre in a cosmic census of life forms...
« Last Edit: 07/11/2015 16:39:59 by chiralSPO »
 
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Offline puppypower

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Re: Water and Organics; Co-partners of life
« Reply #2 on: 07/11/2015 21:03:28 »
There is one main practical problem with others solvents, that is not a problem with water. The problem that comes to mind is water is not just a solvent. Water is also a reactant, as well as a product of many reactions in life. Water is a terminal product of combustion and metabolism.

If we did a parallel metabolic process,using an ammonia based solvent, how would that life form be able to stop the metabolism at an ammonia product, and not keep extracting energy, until it eats its own solvent and busts into flames? In we stop at ammonia, there is so much energy left over in the solvent, that life will learn to use it.

The bandwidth between ammonia and various organic compounds in life as we know it, is fairly narrow. You can't lower the energy of  food to below the solvent and not cause the solvent to become part of the food. That life will have to eat a lot of high energy things to get a little energy will eventually learn to over do it.

Water is so chemically stable, as a product of metabolism, it forms a terminal energy barrier that  life cannot pass. Being to low in energy, there is more food variety. One might speculate that if life did form in other solvents, it will eventually evolve a way to gain  energy from its solvent, until they eat their solvent all the way to water; the wall. Life that evolves in parallel, that can use water as its solvent, will have a long term energy stability advantage, allowing it to eat anything and not burst into flames if it evolves to fast.
« Last Edit: 07/11/2015 21:07:30 by puppypower »
 

Offline chiralSPO

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Re: Water and Organics; Co-partners of life
« Reply #3 on: 07/11/2015 22:12:10 »
Now you're being oxygen-centric!  :)

Here we do have some real examples to discuss! There are many chemical reactions that can be used to store and release energy, and many could be compatible with ammonia. Life living at hydrothermal vents in our ocean subsist on nitrates, NOx, sulfur, sulfides, sulfates, hydrogen, methane etc. (http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6976.2001.tb00576.x/abstract) Similar redox chemistry could be sufficient to sustain metabolism in non-aqueous environments as well. Your arguments about the energy limit imposed by water could also be used by some life form that is used to hydrofluoric acid seas and fluorine in its atmosphere (how do Earthlings keep from burning up if they're not already fluorinated? oh yeah, no fluorine around...)

In addition to redox-based metabolisms there could also be reactions analogous to hydration/hydrolysis (like ATP to ADP). For instance an organism could get about 55 kJ/mol by converting magnesium carbonate and ammonia to magnesium hydoxide and urea. Also ion gradients or pH gradients are perfectly compatible with ammonia solvents.

I'm mostly playing devils advocate here, but I think it's important to examine possibilities for non-aqueous life as well as our familiar wet life.
 

Offline puppypower

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Re: Water and Organics; Co-partners of life
« Reply #4 on: 07/11/2015 23:36:29 »
You make a valid point about other possible energy sources for life. However many more things also need to coordinate to make the entire package work. In terms of oxygen for life on earth, this oxygen came from life itself, with water being used as one of the reactants, in photosynthesis. Maybe other solvents can be used as a reactant for a reversible oxidant to make thing more compact.

When I look at a cell, I see a phase diagram composed of various organic phases; organelles, suspended in water, which is the continuous phase. This is from my engineering background. The shape of the lipid bi-layer membrane phase, is an artifact of hydrophobic, hydrophilic, aqueous and organic interactions. This way of looking at the cell is unique to me. It does have practical use for water.

This is where water sets the industry standard. Water creates a high phase potential with organics (water and oil do not mix) and therefore water has the unique ability to make organic things phase out into separate packets in an extremely precise way.

Protein packing, for example, is driven by hydrophobic interactions. The protein folds less due to its own internal attraction, as it does to avoid the water. This hydrophobic potential, induced by the water, allows protein to fold into unique folds, with a probability of 1.0. Water eliminated the odds from protein folding. This observation has been around for years and still defies a statistical explanation.

If you add another solvent to the same organics of earth life, the analogous hydrophobic push is much smaller. This is why if you substitute another solvent for water in earth life, the push of the hydrophobic action is reduced, and the folding is not perfect for anything. But even if the protein is pre-folded it does not work due to other lost interactions.

Ammonia is a good household cleaner for oil and grease. Therefore, the impact of ammonia and the same organics used by earth life, means you won't get the same phase diagrams; fewer precise organelles. An ammonia system for life would need a different type of counter material matrix, that can phase change in the proper places and proportions.
« Last Edit: 07/11/2015 23:41:58 by puppypower »
 

Offline alancalverd

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Re: Water and Organics; Co-partners of life
« Reply #5 on: 07/11/2015 23:59:00 »
The importance of water is actually secondary. The key to life, i.e. a selfreplicating molecule, is the hydrogen bond, which is what holds the strands of DNA together and determines how a single strand can precisely replicate its complement. It happens that the hydrogen bond is also responsible for all the remarkable and anomalous properties of water, and if you want to create daughter molecules from the mitosis of a DNA strand, that can only happen in an environment that does not distort hydrogen bonds - i.e. water.
 

Offline puppypower

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Re: Water and Organics; Co-partners of life
« Reply #6 on: 08/11/2015 12:54:49 »
A good summary of water science, that I will being using, almost exclusively, for data and for figures will be from Martin Chaplin's web site, Water Structure and Science. This site has hundreds of external links if more data is needed. If I forget to link or reference, assume this the case. This site can found at: 

http://www1.lsbu.ac.uk/water/water_structure_science.html

What is often overlooked and not often taught about self replicating molecules, such as, DNA, is the DNA double helix is intertwined with a double helix of water. Active DNA is actually a quadruple helix as shown below.

I remember years ago wondering why adenine had an extra hydrogen for hydrogen bonding beyond what it used with thymine. I thought it might shift back and forth to generate a signal inside the double helix. I found out later this hydrogen was designed with water in mind, with water playing a major role in the properties of the DNA. For example, the degree of hydration determines the phase of the DNA, with B-DNA being the most hydrated.

Quote
Nucleic acid hydration is crucially important for their conformation and utility [1093], as noted by Watson and Crick [828]. The strength of these aqueous interactions is far greater than those for proteins due to their highly ionic character [542b]. The DNA double helix can take up a number of conformations (for example, right handed A-DNA pitch 28.2 Å 11 bp, B-DNA pitch 34 Å 10 bp, C-DNA pitch 31Å 9.33 bp, D-DNA pitch 24.2 Å 8 bp and the left handed Z-DNA pitch 43Å 12 bp) with differing hydration. The predominant natural DNA, B-DNA, has a wide and deep major groove and a narrow and deep minor groove and requires the greatest hydration.

When proteins bind to the DNA, the water not only contributes to base recognition, but water also contributes to binding energetics via a significant entropy increase as water is displaced from its ordered binding to the DNA. The peak hydration level within B-DNA, gives B-DNA the most aqueous energetics. Theoretically, by varying the hydration level along the DNA, one can activate or deactivate genes.



 
 

Offline puppypower

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Re: Water and Organics; Co-partners of life
« Reply #7 on: 08/11/2015 13:55:47 »
The importance of water is actually secondary. The key to life, i.e. a selfreplicating molecule, is the hydrogen bond, which is what holds the strands of DNA together and determines how a single strand can precisely replicate its complement. It happens that the hydrogen bond is also responsible for all the remarkable and anomalous properties of water, and if you want to create daughter molecules from the mitosis of a DNA strand, that can only happen in an environment that does not distort hydrogen bonds - i.e. water.

Hydrogen bonding is unique among bonds because these have both polar and covalent character. The average water molecule, in liquid water, only lasts about 1 millisecond before it exchanges hydrogen to become a new molecule. A polar hydrogen bond will become covalent, and a covalent hydrogen will become a polar hydrogen bond, changing the position of the hydrogen bond, making a new water molecule. The pH effect is works this way, also.

The polar and covalent character of hydrogen bonds brings something else to the table, critical for life. The hydrogen bond can act as a binary switch, able to shift between these two bonding states without ever breaking the hydrogen bond. As shown below, these two hydrogen bonding states are close in energy and are separated by a small activation energy barrier.

The polar state (a) has more enthalpy, more entropy and define less volume, while the covalent state (b) has less enthalpy, less entropy and defines higher volume. (see note below). Not only can the hydrogen bond be used as a binary switch for information, without ever breaking the bond, but since the binary also contains differences in enthalpy, entropy and volume/pressure, the binary switch can generate and/or be impacted by chemical leverage.

Water will hydrogen bond to itself to form water clusters, with these cluster able to shift between various high (a) and low (b) density states. When ice forms we get mostly (b) with a 10% increase in volume that can be used to generate pressure.

Liquid water is a tight and sticky place for molecular movement and changes in molecular conformation. The binary cluster switch can be used to open and close the water matrix; pressure/volume change. For example, when you have a protein train, where the production of a product by one enzymes needs to coordinate with availability of reactant for the next enzyme, local water clusters will contract and expand in waves to assist and coordinate the water with changes in protein conformation. This is also a type of binary information that allows the cells to coordinate physical changes with information.




Note; The polar state of the hydrogen bond is based on charge attraction and therefore benefits by being close to lower change potential. There is more flexibility in terms of position; higher entropy. The covalent state has to align covalent bonding orbitals in specific ways so the wave functions overlap properly. This expands the bond, lowers enthalpy due to extra stability and lower entropy due to the need of an optimized position.
 

Offline chiralSPO

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Re: How are water and organic materials partners in life?
« Reply #8 on: 08/11/2015 14:28:25 »
Water also does some really cool stuff at interfaces. Water-mineral, water-air, and water-organic interfaces are all known to behave differently from bulk water, and can facilitate many reactions "on water" (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.428.1667&rep=rep1&type=pdf ; http://pubs.acs.org/doi/abs/10.1021/ja068120f?journalCode=jacsat ; http://onlinelibrary.wiley.com/doi/10.1002/anie.200705347/abstract ; http://pubs.acs.org/doi/abs/10.1021/bk-1998-0715.ch001)

Many proteins appear to be designed largely to arrange the water molecules around and within them, and it is the water that does a lot of the chemistry (though metalloproteins like hydrogenase, nitrogenase, photosystem II, hemoglobin etc. also work a lot of magic with metals that have partially filled d-orbitals).
 

Offline puppypower

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Re: How are water and organic materials partners in life?
« Reply #9 on: 09/11/2015 11:59:43 »
An interesting water affect is water flowing through carbon nanotubes. The water will move intermittently, like stop and go traffic, with flow rates higher than predicted by standard models.  One explanation is connected to the binary nature of hydrogen bonding.

The carbon nano-tubes have all the carbon atoms with four covalent bonds. The result is water cannot from the covalent state of the hydrogen bonding with the carbon, since the carbon can't share electrons that way. Rather water can only form the polar state of hydrogen bonding by interacting with the carbon via van der Waals forces. This one-sidedness causes the water to become potentiated; higher average enthalpy, since both bonding states would like to happen with the covalent state slightly more stable. The pure polar state of the hydrogen bonding also defines higher entropy than found in normal water.

The intermittent nature of the movement seems to show that the water is attempting to lower potential through covalent hydrogen bonding, causing the water to self gel for an instant; stops due to viscosity. But since the energy difference between this and the pure polar state is small and carbon is not cooperating, the water changes state back to polar, full of energy and entropy; traffic goes again. This affect is useful for water moving through membranes.
 

Offline chiralSPO

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Re: How are water and organic materials partners in life?
« Reply #10 on: 09/11/2015 17:16:11 »
An interesting water affect is water flowing through carbon nanotubes. The water will move intermittently, like stop and go traffic, with flow rates higher than predicted by standard models.  One explanation is connected to the binary nature of hydrogen bonding.

The carbon nano-tubes have all the carbon atoms with four covalent bonds. The result is water cannot from the covalent state of the hydrogen bonding with the carbon, since the carbon can't share electrons that way. Rather water can only form the polar state of hydrogen bonding by interacting with the carbon via van der Waals forces. This one-sidedness causes the water to become potentiated; higher average enthalpy, since both bonding states would like to happen with the covalent state slightly more stable. The pure polar state of the hydrogen bonding also defines higher entropy than found in normal water.

The intermittent nature of the movement seems to show that the water is attempting to lower potential through covalent hydrogen bonding, causing the water to self gel for an instant; stops due to viscosity. But since the energy difference between this and the pure polar state is small and carbon is not cooperating, the water changes state back to polar, full of energy and entropy; traffic goes again. This affect is useful for water moving through membranes.

I am unfamiliar with these studies, can you provide a link?

I am surprised that water in a carbon nanotube would have increased entropy. Typically water at interfaces is more ordered (as counterintuitive as it is, the separation of oil and water is actually driven by entropic terms, by reducing the surface area of the oil and water, more of the water is free to relax into the bulk state, rather than the highly ordered, almost ice-like, state that it adopts at the interface.) I would have expected water in a CNT to display the same behavior, thereby decreasing entropy.

Also, hydrogen bonding is not a covalent interaction. It is almost purely electrostatic (one can see this because the orientation is determined by the dipole moments of the H-bonded molecules, not by orbital symmetry)
 

Offline puppypower

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Re: How are water and organic materials partners in life?
« Reply #11 on: 10/11/2015 12:52:12 »
An interesting water affect is water flowing through carbon nanotubes. The water will move intermittently, like stop and go traffic, with flow rates higher than predicted by standard models.  One explanation is connected to the binary nature of hydrogen bonding.

The carbon nano-tubes have all the carbon atoms with four covalent bonds. The result is water cannot from the covalent state of the hydrogen bonding with the carbon, since the carbon can't share electrons that way. Rather water can only form the polar state of hydrogen bonding by interacting with the carbon via van der Waals forces. This one-sidedness causes the water to become potentiated; higher average enthalpy, since both bonding states would like to happen with the covalent state slightly more stable. The pure polar state of the hydrogen bonding also defines higher entropy than found in normal water.

The intermittent nature of the movement seems to show that the water is attempting to lower potential through covalent hydrogen bonding, causing the water to self gel for an instant; stops due to viscosity. But since the energy difference between this and the pure polar state is small and carbon is not cooperating, the water changes state back to polar, full of energy and entropy; traffic goes again. This affect is useful for water moving through membranes.

I am unfamiliar with these studies, can you provide a link?

I am surprised that water in a carbon nanotube would have increased entropy. Typically water at interfaces is more ordered (as counterintuitive as it is, the separation of oil and water is actually driven by entropic terms, by reducing the surface area of the oil and water, more of the water is free to relax into the bulk state, rather than the highly ordered, almost ice-like, state that it adopts at the interface.) I would have expected water in a CNT to display the same behavior, thereby decreasing entropy.

Also, hydrogen bonding is not a covalent interaction. It is almost purely electrostatic (one can see this because the orientation is determined by the dipole moments of the H-bonded molecules, not by orbital symmetry)

I could not find the original articles I read, but here is another article that says the same thing. This article may have been written before the other article. The article I read reported that the  observed the motion of the water was start and stop. Sorry but the link does not appear to be active.

http://www.rdmag.com/news/2013/05/are-carbon-nanotubes-capable-superfast-water-transport

Hydrogen bonds are not just polar but also have covalent character;

Quote
Hydrogen bonds tend to form with a geometry in which the hydrogen bond donor, the hydrogen and the hydrogen-bond acceptor are arranged in a straight line. In electrostatic terms this arrangement is clearly less favorable than an arrangement in which the two dipoles are “folded over” on top of one another to bring both positive charge centers directly into contact with the two negative charge centers. This is clearly not what is happening in the case of hydrogen bonds, so there has to be another component to hydrogen bonding beyond pure electrostatics.

Quantum mechanical calculations show that the free electron pairs found on nitrogen and oxygen are delocalized around the hydrogen nucleus similar to the way electrons are shared by bonded atoms in a normal covalent bond. This “covalent” component of the interaction is strongly orientation dependent, i.e. in order to get this covalent interaction the orbital with the free electron pairs of the hydrogen bond acceptor have to be aligned quite well just like the geometry of covalent bonding is rather restrictive.
http://www.bio.brandeis.edu/classes/biochem104/hydrogen_bonds.pdf

Hydrogen bonds can be polar, not requiring precise alignment yet still form a hydrogen bond, or they can align more precisely, so shared electrons become somewhat delocalized. The latter is restricted to highly electronegative atoms like O and N that have free electron pairs. Carbon does not have any free electron pairs, so any hydrogen bonding is limited to van der Waals type interactions, which allows for higher disorder or entropy.

Hydrogen bonding does not have the same bonding energy of your typical covalent bond, which may be why many people don't categorize the hydrogen bond as covalent. However, hydrogen bonds have directionality and electron delocalization in common.

 

Offline puppypower

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Re: How are water and organic materials partners in life?
« Reply #12 on: 10/11/2015 13:39:51 »
This discussion of the covalent character of hydrogen bonding brings up an important feature of hydrogen bonding called, cooperative hydrogen bonding. Water, for example, is a self assembling molecule, due to being able to form four hydrogen bonds. This allows water to create networks and even form repeatable units called clusters.

Cooperative hydrogen bonding occurs when each hydrogen bond added to the network will cause the strength of all the hydrogen bonds to increase. Even the original hydrogen bond will get stronger and stronger as more and more hydrogen bonds are added to the cooperative. What is interesting about a hydrogen bonding cooperative, is the first bond broken, no matter where it is in the network, will be the strongest bond. Once you break the first bond, the strength of all the bonds in the cooperative will decrease. It is like the cooperative reinforces any point of breech, but once broken, the cooperative gets weaker, everywhere. 

The easiest way to explain this behavior, is this is due to a type of resonance structure that is connected to covalent hydrogen bonding in the network, delocalizing electrons. This affect is very useful to life and can be used to explain a secondary function of ATP.

An enzyme does not work in a vacuum. Rather the enzyme is surrounded by hundreds of water molecules that are hydrogen bonded to each other and to the surface of the enzyme. The enzyme is sort of stuck in a tight network of water, which may also be acting as a cooperative cage. To be able to change conformation, so the enzyme can react, hundreds of water hydrogen bonds need to break, with ATP only having enough energy to maybe break one or two hydrogen bonds. If you do a full energy balance around an enzyme, that include hydrogen bonded water, ATP is under sized, yet it still works.

The way ATP is able to overcome the cooperative water cage is because, ATP not only binds to the active site on the enzyme; electron withdrawing, but the production of ADP, will extract a water molecule out of the cooperative. The formation ADP acts like a cooperative bolt cutter.

Picture a nylon stocking under tension; surface tension. If I cut one string, this will cause a fast propagating run in the stocking. The ADP formation bites out a focal point in the cooperative. The  run in the water cooperative propagates, freeing the enzyme, while adding significant surface entropy to the enzyme. Water will then quickly reassemble the cooperative, ready for another round. The nylon stocking run was done for visualization. In reality, the run is a conversion from covalent to polar, which is not as cooperative.
 
 

Offline puppypower

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Re: How are water and organic materials partners in life?
« Reply #13 on: 11/11/2015 15:49:40 »
One of the most important partnerships between water and organics is the folding of protein. Protein folding is driven by hydrophobic interactions, between the protein and water. The folding of protein is less about the protein wanting to bind to itself. Rather the protein is encouraged to  bind to itself, because it is afraid of the water.

The analogy is like the difference between you running down the street, because you like to run, compared to you running down the street because I am chasing you with a stick; stick-phobia. Because I have a stick, I can make you zig zag and jump, which you may not normally do when run for enjoyment. The protein does not blob together, but has to do so the way the stick man is leading it.

Hydrophobic is somewhat of a misnomer, in that organics of protein is not overly afraid water since water can form weak polar hydrogen bonds to almost all organic moieties. Rather, in terms of energetics, the water is more afraid of being trapped by the organic in a potentiated state, since the water can lower potential much better with water-water interactions. Protein folding is not just driven by hydrophobic actions, but it is also driven by water attempting to lower potential by increasing entropy; not be trapped. Water in carbon nanotubes wants out. This is due to polar hydrogen bonding needed for organic contact, with these having higher entropy. The water is loose and ready to move.

If you look at an energy landscape of protein folding, it begins by looking like a number of high energy peaks all spread out. In the final folded protein, all the high energy peaks, have collapsed into a sink hole type energy diagram. 



Say we begin with an unfolded protein surrounded by water; hot off the press. The mountain peaks in the beginning energy diagram, are based on water-organic interactions; hydrophobic. To lower this energy, the organic groups combine to lower potential. The water increases entropy and will cascade down the collapsing energy hills.  Like a running river, the entropy of the water is  keeping the base of the collapsing energy hills and valleys at higher energy. This allows for an orderly collapse; dry upper surfaces combining, until everything is perfectly folded with minimal water trapped. Some water is trapped and is part of residual below grade peaks.

What is interesting is the final folded protein is held together by the equivalent energy of 1-3 hydrogen bonds, making it easy to denature, yet the folding is very stable and always results in exact folding, with no statistical variation. It is weakly held together and should show variation but it does not.

Statistics predicts some randomness in protein folding due to the thermal energy of the water  yet this is not observed. Water makes the folding perfect each time and removes all the random and chaos. Life is about order, with water the traffic cop. If you consider how every protein in the cell perfectly folded like the linen at the Waldorf, one may even conclude that protein selection in water is based on water being able to fold it perfectly. 
« Last Edit: 11/11/2015 15:59:03 by puppypower »
 

Offline evan_au

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Re: How are water and organic materials partners in life?
« Reply #14 on: 11/11/2015 20:30:38 »
Quote from: puppypower
the folding is very stable and always results in exact folding, with no statistical variation. It is weakly held together and should show variation but it does not.

There are several diseases caused by misfolding of proteins, for example "Mad Cow Disease" is caused by misfolding of PrP, and hints that other important neurological diseases like Alzheimer's could be caused by misfolding and polymerization of several other proteins like amyloid and tau.

Water cannot protect these proteins, and it cannot refold the protein correctly once it is misfolded.

One must conclude that the genetic sequence of the protein and its sequence of construction are just as important in folding proteins as the temperature, salinity and polar characteristics of the water in which they are formed.

Water itself does not create life.

See: https://en.wikipedia.org/wiki/Prion
« Last Edit: 11/11/2015 20:33:20 by evan_au »
 

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Re: How are water and organic materials partners in life?
« Reply #15 on: 13/11/2015 20:42:49 »
Quote from: puppypower
the folding is very stable and always results in exact folding, with no statistical variation. It is weakly held together and should show variation but it does not.

There are several diseases caused by misfolding of proteins, for example "Mad Cow Disease" is caused by misfolding of PrP, and hints that other important neurological diseases like Alzheimer's could be caused by misfolding and polymerization of several other proteins like amyloid and tau.

Water cannot protect these proteins, and it cannot refold the protein correctly once it is misfolded.

One must conclude that the genetic sequence of the protein and its sequence of construction are just as important in folding proteins as the temperature, salinity and polar characteristics of the water in which they are formed.

Water itself does not create life.

See: https://en.wikipedia.org/wiki/Prion

Thanks for the continuing feedback. Your observation is consistent with my theory that proper folding in water, may be part of the natural selection process. These poorly folded protein will not be selected in the long term.

My contention is you need organics and water for life to work. The packing of protein is due to hydrophobic interactions, requiring water as the shaper. Other solvents don't set the same level of phobia in the organics. The organics of the protein, by being covalently bonded will provide bulk material stability for the stress and strains of conformational changes that will occur during reactions. Without organic covalent bonding, the protein would become more plastic and would not last very long.

Water also cages the surface of the protein with cooperative hydrogen bonding due to hydrophilic interactions lowering the surface energy. Poor protein folding can cause the water cage not to contain the proper amount of cooperation. A mis-packed protein will have residual peaks in its energy landscape graph. This adds energy to the protein, with too much energy meaning more need for the higher energy polar hydrogen bonding. This then means less hydrogen bonding cooperation; needs covalent hydrogen bonding.
 

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Re: How are water and organic materials partners in life?
« Reply #16 on: 14/11/2015 12:04:46 »
Say we start with a gene on the DNA, which is being transcribed into mRNA, which is then translated into protein, which is then folded via hydrophobic interaction with water. If the protein does not fold properly, the  pathway, from the DNA to the final protein, ends in higher energy, compare to protein with proper folding.

As these protein accumulate, they begin to form a protein dead zone, where the poor packing leads to inhibitions in further reactions, which bottleneck what should be further steps. The potential at the end to the reaction train will rise, causing the potential of the local water to rise.

If we conduct this higher aqueous potential, counter current back to the DNA, the water potential around the initiator gene will rise. Now we have potential for change such as post transriptual modification; higher entropy hydrogen bonding. Or if the cell is replicating, equilibrium might end in base pair defects.

The current assumption about evolving life is it is based on randomness and selection. But water is not about random organic materials, as witnessed by protein folding having probability equal to 1.0. The protein grid, which is the bulk of the cell, makes the bulk of the cell's material non-statistical. Poor packing is the exception.

There is a ground state of zero random based on extensive molecular capacitance. Random deviates from this ground state, adding a potential in the water, from which corrections will appear; lower the odd by stacking the deck. This is how the cell can interact and adapt, since all such interactions will set a potential with perfection, which then needs to be addressed.
 

Offline puppypower

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Re: How are water and organic materials partners in life?
« Reply #17 on: 18/11/2015 14:06:35 »
I would like to go back to the basics, and look at the basic system of water and oil. When water and oil come into contact, surface tension is created at the interface. Normally pure water will form an extended network of hydrogen bonding composed of both polar and covalent hydrogen bonding. With a drop of oil present, water at the interface can't form the covalent hydrogen bonding , since the carbon and hydrogen of the oil cannot form any further covalent bonds.

The water is limited to polar hydrogen bonding at the surface. Since polar "only" hydrogen bonding will increases water's energy and water can form four hydrogen bonds, water will attempt to lower this extra energy by forming covalent hydrogen bonding with other water. This creates a network of ordered water near the oil interface.

Although the covalent cage is lowering the surface energy, somewhat, it does not totally compensate for the weaker water-oil polar hydrogen bonding. The result is the surface contact potential is conducted deeper into the water, beyond the net. There is sort of a triple layer that defines the surface tension.

In terms of entropy, there is high entropy zone where the water and oil touch, then there is low entropy zone at the covalent cage, then the entropy becomes higher again beyond the net to reflect the excess potential that lingers.

Let us take the oil and water, and agitate these into an emulsion. What we have done is increase the entropy of the water-oil system; less order. We have increased the surface contact between water and oil, which defines higher entropy, we have formed more surface tension caging, which lowers entropy, and we have increased the potential of the water beyond the net, thereby increasing that entropy. Essentially we have shifted the average polar-covalent equilibrium of the water toward the higher polar entropy; emulsion.

If we let the emulsion settle, it will spontaneously lower system entropy back into two phases. The bulk water will try to move the aqueous polar-covalent hydrogen bonding equilibrium back to more average covalent, since this will lower the enthalpy/internal energy of the water. This will requires that the oil drops combine until two layers appear.

This spontaneous lowering of the water-organic entropy; oil and water separate, is useful for the evolution of life. Since the entropy of the universe has to increase, but water and oil want to separate and lower entropy and enthalpy, there is a lingering second law potential for change in the oil and water to increase their entropy.

The water is simple and sturdy and can't change too much. Therefore the oil will need to change in ways that allows more system entropy, while still being under the constraint of water's free energy needs; hydrogen bonding binary. For example, we can add polar groups to the oil. Or we can add protein to the oil. These two things are expected to happen, since both can increase the entropy of the water and oil while not violating the needs of water. Water becomes the shaper of life, in its own image.

Most of the active materials of life, like DNA, RNA and protein all form hydrogen bonds, to reflect more cooperation with water. DNA and RNA are the most hydrated materials in the cell and reflect later stage tweaks needed to satisfy water. Water's need are strong, but since water is Plane Jane, water never changes.
 

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Re: How are water and organic materials partners in life?
« Reply #18 on: 20/11/2015 12:52:22 »
Sodium Na+ and potassium K+ ions are important to life because these two ions impact pure water in different ways. Although both cations will carry a single positive charge, the smaller sodium ions will bind to the oxygen of water stronger than water binds to itself. Potassium ions will bind to the oxygen of water weaker than water binds to itself. The net affect is sodium helps to create some order in water (kosmotropic), while potassium helps to create some disorder in water (chaotropic). The Na+ will slightly shift the polar-covalent hydrogen equilibrium of the water slightly toward covalent, while K+ will shift this slightly to the polar.

Cells accumulate K+ inside and Na+ outside. The impact of these cations is the water outside the cell gains a greater sense of order. This makes the water able to accept more reduced materials, which will shift water toward polar. The kosmotropic Na+ allows the cell to attract more food without being rejected by the water-oil affect. Inside the K+, by creating more polar disorder compensates for the cooperative covalent bonding that will form on the surface of proteins. It helps the ATP bite through by softening the cooperatives with a pinch or disorder. If ATP carries K+ with it, this pinch can be targeted. 

An interesting observation that tells us something about evolution of life in water, is if we remove the outer membrane of cells, so there are no ion pumps, naked cell bodies will still accumulate K+. The cation pumping is not even necessary for the accumulation of K+ and is often assumed to be a failsafe. The reason for this attraction of K+ is the inside of the naked cell has shifted the aqueous hydrogen bonding equilibrium toward covalent hydrogen bonding, due to protein surface cooperatives. The water does not like this so the K+ is welcome to restore the balance slight back toward polar.

What this suggests is, when life or pre-life learned to pump and exchange K+ and Na+, that one change connected to the forced accumulation of K+, by shifting the internal water equilibrium, made the cell too polar, thereby making its much more favorable to form perfectly packed protein as a balance.

The K+ would also exaggerate the impact of poorly packed protein since these would also shift the water equilibrium toward too much polar, adding higher aqueous entropy at the DNA/RNA for needed changes. The impact would be the cells making a lot of new protein until perfection is able to shift the water to its sweet spot. Once the protein grid is set up, the ion pumping is not needed to accumulate K+, but is needed to force the addition of new protein as the cells evolve more complexity.

Neurons have the highest concentration of internal K+. Neurons will also fire and cause Na+ to flood the inside of the neuron. The impact inside the neuron is aqueous equilibrium is shifting causing materials to dance to the beat of the neural aqueous equilibrium. This allows ionic signals to become translated into pliable material capacitance.
 

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Re: How are water and organic materials partners in life?
« Reply #19 on: 22/11/2015 13:48:56 »
If you look at life and cells, in general, life/cells builds up energy value. The growing tree provides  more and more fuel for the wood stove. Or the larger cow produces more meat. What this means, relative to the water, is the increasing organic energy build up of life creates an oil-water affect, and therefore this will induce a shift in the water, toward the polar hydrogen bonding side.

If you look at the cellular material grid (still snap shot of a cell) water by packing protein into unique folds with probability equal one, causes the entropy of the cell's material grid to decrease relative to its starting monomers. Small monomers, like amino acids, become polymers; less freedom, which then pack to perfection, for even less freedom. This shifts the water toward the covalent side due to the cooperative cages around the protein.

The accumulation of energy value, and the lowering of the material grid's entropy due to water,  creates a balancing offset, within the water. As the cell grows the water near the protein grid it can handle more high energy food and maintain balance. Although the water is balanced, the cell has created a situation of increased energy and lowered entropy in the organics. This is unique to life.

If we factor out this unique property of life; build energy and lower entropy, all other inanimate systems, like leaves and rocks, will try to lower energy and/or increase entropy. Life has created a situation, in the organics, due to the needs of the water, that places the organics in opposition to the natural flow of energy and entropy within the universe.  If life dies, it will lower energy and increase entropy. But when alive, the water balance keeps it contrary.

So the question becomes, how does nature alter the organics, so the needs of water and the needs of universal energy and entropy are all met? This is called cell cycles. The goal is to lower energy; high metabolism, and increase entropy; high synthesis and disruption of the mother cell, until the mother cell, balances the needs of the water while having less universal potential; two skinny daughter cells. They are full of protein and cooperative hydrogen bonding and will welcome food for the polar offset.

If you look at multicellular differentiation, the same DNA differentiates into a wide variety of states to generate various protein grids. This is an entropy increase, with each differentiated cell forming its own water based equilibrium into protein perfection.

Life is designed to have an internal balance between water and organics, while also being designed to interact with the environment in ways that lower energy and increase system entropy. Water and universal potentials compete via the organics, with the organics of life becoming molded to the best possible compromise; life perpetuates and evolves to the changing environment.
 

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Re: How are water and organic materials partners in life?
« Reply #20 on: 25/11/2015 12:28:11 »
I would like to look at the DNA/water partnership. The DNA contains a double helix of water bonded to the DNA within the major and minor grooves of the double helix. The result is the DNA, due to its large size, is the most hydrated material in the cell. One can throw the DNA into a centrifuge and it will retain significant chemically bound water; part of its active structure.

Relative to the water-oil affect, the high level of hydration of the DNA, implies that the DNA is an evolutionary driven equilibrium material that is positioned closer to the water side (compared to the oil side). Water is simple and conservative and can't change much, while the organics are pliable into infinite variation. The closeness of the DNA to the water (compared to oil side), was driven by the second law; increase in total system entropy. This is the inanimate affect asserting itself on the water-oil analogy.

If we start with fully packed DNA; condensed chromosomes, this configuration will minimize water contact beyond the internal water of the double helix. The DNA, in general, shifts the local aqueous equilibrium toward the covalent side, exposure.

As we unpack the DNA and expose more of the DNA to water, we add more covalent hydrogen bonding to the water. This is enzyme driven in response to an induced equilibrium as environmental input adds polar impact to water (oil side). The water need more covalent hydrogen bonding to balance this out. This means more exposure of the DNA; unpacking.

The RNA, by being more polar than DNA, helps to add additional covalent hydrogen bonding to the water.  While going from DNA to RNA to protein (perfect folds) amplifies the covalent hydrogen bonding of water. This makes food input more inviting.
 
 

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Re: How are water and organic materials partners in life?
« Reply #21 on: 28/11/2015 13:17:14 »
Water and Osmosis:

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Osmosis is the spontaneous net movement of solvent molecules through a semi-permeable membrane into a region of higher solute concentration, in the direction that tends to equalize the solute concentrations on the two sides.



Osmosis is a colligative property. A colligative property is only dependent on the concentration of solute (in water), but is not dependent on the specific solute particles. For example, although sodium and potassium cations are kosmotropic and chaotropic, respectively, equal concentrations of each will generate the same osmotic pressure. We can substitute these with Calcium and Chloride ions of the same concentration, and will get the same pressure.

Osmosis is driven by  entropy with the water spontaneously moving, through the membrane, in the direction of increasing entropy to mingle with the solute particles. Since potassium ions create more hydrogen bonding disorder in water than sodium ions, yet the same concentration of both cations have the same entropy potential, osmosis is a water-solute system property. This is different from the hydrogen bonding binary within water. If we apply a pressure to the A side of the diagram; reverse osmosis, we can cause the water to move in the reverse direction through the membrane and lower its entropy back to pure water. Osmosis and reverse osmosis allows for reversible entropy in the water. 

Osmosis is a classic example of the uniqueness of liquid state physics. If you look at the diagram above, at steady state, water is freely moving back and forth across the semi-permeable membrane, even though there is a hydrostatic force vector going from A to B, connected to the osmotic pressure. In liquid state physics the macro; pressure, and micro; water diffusion, can appear to work independent of each other.

Since the osmotic pressure is created by entropy, and since pressure is force/area, osmotic pressure is technically generated by an entropic force; entropy based force. I like to think of the entropic force as the fifth force of nature. The entropic force is not formally recognized as a fifth force of nature, but entropic force is how the micro and macro, at osmotic steady state, are connected. If we only assume four forces, these appear disconnected.

This fifth force of nature has been traditionally called the life force, since osmosis is widely used by life. It allows reversible liquid state entropy to be generated with any force including mechanical. When water expands and contracts via hydrogen bonding transitions, the volume changes can generate mechanical forces that can be translated into entropic force, which can then be used to reverse and regulate system entropy.

 
 

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Re: How are water and organic materials partners in life?
« Reply #22 on: 29/11/2015 13:40:36 »
If we look at any cell, since the organics structures of the cell are immersed and surrounded by water, the hydrogen bonding water at the surface of the organics, will reflect the surface of the organic. This creates a situation like me (organic) and my water shadow. The value of this is since different materials and organelles will have different aqueous shadows, the organics can induce local, regional and global potentials in the water that can create gradients in the water.

The water will attempt to create a local, regional and global equilibrium, but since the organics are sturdy, different and often anchored in place, these gradients will linger. One work around by the water is to make use of smaller diffusing ions, products and reactants to balance out the potential. If we have too much covalent hydrogen bonding on one surface, the water will draw in moieties that induce more polar hydrogen bonding to balance this zone. But since enzymes will catalyze a reaction, the shadow changes. The need may be a continuous flux of reactants to that zone. 

On the other hand, say water shadow gradients are established, and the organics use ATP energy to actively transport a protein into a hot zone to make that zone even hotter. This is useful in that it can make a protein work harder because ti will be assisted by a much hotter water shadow.

In general, the main shadow gradient is from the DNA to the cell membrane. The DNA is the most hydrated molecule in the cell, while also being the largest. The DNA favors covalent hydrogen bonding in the water shadow. The lipid membrane is more like oil, with water able to freely diffuse due to extensive higher entropy polar hydrogen bonding.

The bulk directions of cellular material movement reflects this main gradient. The DNA will make and then expel RNA, since RNA will cause the covalent hydrogen bonding to enhance. This has to leave the nucleus. While the membrane will attract  but have to shed reduced food materials inward to avoid too much polar hydrogen bonding in the membrane, while also attempting to lower the covalent potential deeper in the cell. There are other materials in the middle that connected the gradient and alter the starting materials, which then will detour to help other aspects of the gradients, etc.
 

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Re: How are water and organic materials partners in life?
« Reply #23 on: 17/03/2016 11:15:09 »
Water is also essential for the relative permittivity of consciousness. The vibrational spectrum of liquid water inside microtubules is the causal agency of synaptic activity. Thus, I believe the coherent delocalization of atomic water channels in biological systems is necessary for synaptic quantum tunnelling during neuronal exocytosis.

http://www.thenakedscientists.com/forum/index.php?topic=66137.0
 

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Re: How are water and organic materials partners in life?
« Reply #24 on: 17/03/2016 13:17:40 »
The partnership of water and organics in life is connected to hydrogen bonding, especially in water. Anything dissolved in water or in surface contact with water, will impact the hydrogen bonding of bulk water. The degree of residual hydrating power in the water, after things are added, is called activity which is defines as 1.0 for pure water. As we add things to the water, the activity of the water will decrease. This change in activity of the water, both locally (local material) and globally (summation), allows the water to control and coordinate enzyme shapes and kinetics. 

Quote
Protein hydration is very important for their three-dimensional structure, dynamic ensemble of conformations [2249] and activity [472, 1093, 1345, 2005]. Indeed, proteins lack biological activity in the absence of sufficient hydrating water (usually at least a monolayer covering; > 1.5 mols H2O mol-1 aminoacid residue). The aqueous structuring around proteins is affected out to at least 1 - 1.5 nm from its surface or 2 - 3 nm between neighboring proteins, as shown by terahertz spectroscopy [1368, 2102], e with even small proteins (e.g. bovine serum albumin, 66,463 Da) affecting the whole of its unstirred (Nernst) layer of about 20,000 neighboring water molecules [2102].

In solution, proteins possess a conformational flexibility, which encompasses a wide range of hydration states, not seen in the crystal a or in non-aqueous environments. Equilibrium between these states will depend on the activity of the water within its microenvironment; that is, the freedom that the water has to hydrate the protein [434]. Thus, protein conformations demanding greater hydration are favored by more (re-)active water (for example, high density water containing many weak bent and/or broken hydrogen bonds) and 'drier' conformations are relatively favored by lower activity water (for example, low-density water containing many strong intra-molecular aqueous hydrogen bonds).

A differentiated cell has unique materials of given amounts, and therefore will define a certain global activity in the water, which can be tweaked though input from the environment. This sets the active global activity, which will then define the protein conformations, so they all coordinate. This also applies to genes, since these are also hydrated and can assume different conformations based on the degree of hydration. Water is sort of the CEO that sets the activity policies of the cell, so the entire organization of the cell is able to coordinate its effort.

One of the tricks of the cell, is the organics of the cell, by being of different materials, have levels of local hydration. For example, the DNA is the most hydrated molecule of life. The local activity of the water is not only defined by the bulk water; summation of everything in the water, but also by the impact of the local organic materials. The result is the water activity of the cell has a bulk value, that then impacts localized activity.

As an analogy, say we had a pool of warm water at constant temperature; 35C. To this I will add twelves floating sealed bottles of water at at different temperatures; 0C-100C. The bulk water is the same for all, but near each bottle, there is a local temperature connected to the average of the bulk and temperature of each bottle. If we could fix this so all the bottles and bulk water stays constant, a thermal convection gradient set up.

It is not coincidence that mRNA moves from the DNA to the ribosomes. It follows the activity gradient. In early evolution, this was based on activity convection. This was later speeded up via active transport. Active transport is more efficient in dealing with the activity gradients. What has been added are more materials to reflect and deal with the activity gradient.

The reason why most cells of in human body have nerve tissue nearby, is to help control the surface water activity of all the cells through ionic fluxes. The activity of water can be altered with anything that is dissolved in the water.This means even ionic changes at one surface, can means changes in how the organic behave deeper in the cell.

Relative to our tank of warm water with 12 bottles floating; I can surround this tank with a bath of warm oil being heated through radiational heating, from a fire that is 10 meters away. On the other side I can have solid CO2 ice. It does not matter where the heat is coming from. It does not have to be water or plastic since heat by any source defines the activity. This will alter the bottle gradient. Now there is new convection being set up.

Movement of signals in water is super fast, since it can be transmitted as energy signals through the binary switches of the hydrogen bonds. No hydrogen bonds ever has to break. This is really slick since the activity; hydration, gradients can stay very tight, while information is being moved around the cell. Water can also use quantum tunneling, if need be, to transmit information and activity changes, across barriers. Membranes pose little problem, but can be used for some time delay features.




 
 
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Re: How are water and organic materials partners in life?
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