Why we can't live without water?

Discussion in 'Chemistry' started by Plazma Inferno!, Jun 23, 2016.

  1. Plazma Inferno! Ding Ding Ding Ding Administrator

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    Scientists are getting closer to directly observing how and why water is essential to life as we know it.
    A study in this week’s Proceedings of the National Academy of Sciences provides the strongest evidence yet that proteins—the large and complex molecules that fold into particular shapes to enable biological reactions—can’t fold themselves.
    Rather, the work of folding is done by much smaller water molecules, which surround proteins and push and pull at them to make them fold a certain way in fractions of a second, like scores of tiny origami artists folding a giant sheet of paper at blazingly fast speeds.
    Dongping Zhong, leader of the research group at The Ohio State University that made the discovery, called the study a “major step forward” in the understanding of water-protein interactions and said it answers a question that’s been dogging research into protein dynamics for decades.

    https://news.osu.edu/news/2016/06/20/waterfold/
     
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  3. exchemist Valued Senior Member

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    Yes I saw this on another forum and I thought it was a late April Fool.

    The headline is idiotic. Organisms on Earth need water as a solvent. The folding of proteins is a mere detail by comparison with this obvious fact. No solvent, no medium for biochemical reactions in an easily confined zone (e.g. a cell), ergo no life.

    Secondly, the article is annoyingly misleading in that it pretends to suggest water in some way actively connives in pushing proteins into the correct shape. What rubbish. If we're not careful this will bring Wellwisher out of the woodwork, for one of his sermons on the mystical role of water.

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    What in fact the authors seem to have done is observed the role of Brownian Motion in helping proteins take up the configuration in which they are active. Well, no shit? I cannot see what is so terribly remarkable about this.
     
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  5. origin Trump is the best argument against a democracy. Valued Senior Member

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    I was thinking the exact same thing as I read the OP...
     
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  7. Edont Knoff Registered Senior Member

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    I believe that there is a number of molecules that are similar enough to water, which could do a similar job for proteins (maybe not quite the proteins that "our" life uses, but similar ones).

    - SO2, liquid from -10°C to -75°C, a polar molekule, much like H2O
    - NH3, liquid from -33°C to -77°C, also a polar molecule, but more different in geometry than SO2 is to H20

    There is also CO2, which is liquid in the right pressure and temperature range, even that on earth normal pressure it will not become a liquid. CO2 is a powerful solvent, but not a polar molecule, so it might not be a good replacement for water, but still is a good solvent, which might be useful to extraterrestrial life.

    I think our research on "habitable" planets and "life" focuses too much on water. Earth has plenty of water, so it's no surprise that water became the favorite solvent and transport agent for life, but I think that on planets where e.g. NH3 is similarly abundant as water is here, NH3 can take that role.

    SO2 seems to be generally more scarse in the universe though, but CO2 is more frequent again, a good solvent, but not polar. There are also liquid silicones, which have very interesting properties, but they don't seem to occur naturally on the planets we know ...

    tl;dr

    Even that water is very important to life on earth, I'd like to see more reports about substances that can take the role of water on other planets and which are able to support life in different shapes as we know it from earth.
     
  8. exchemist Valued Senior Member

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    I agree. Like you, I suspect there are advantages in a polar solvent. I've always been rather captivated by liquid ammonia as a solvent, due its ability to solvate electrons (Birch reduction etc). Solutions of alkali metals in ammonia have some very interesting properties and chemistry. Whether any of them could be the basis of an alien life biochemistry I have no idea, though.
     
  9. timojin Valued Senior Member

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    The solvents you mention have good physical property, now let see are the mentioned solvents reactive with the biological chemicals . I remember in my early life treat gelatine with SO2 what we obtained was a sulfonated protein . If you use ammonia would it anhydrous , I would expect also there will be some reaction with the cellular material.
     
  10. exchemist Valued Senior Member

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    What cellular material? If life develops with a different solvent, then one would obviously expect an entirely different biochemistry to develop.
     
  11. wellwisher Banned Banned

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    Proteins fold with exact folds, which means the classical statistical assumption, still being used, are not even real for most of a cell's structures. I am not sure why that pseudo science is still taught. Water allows protein to fold with exact folds, that are not subject to statistics. The affect is similar to why water and oil will separate into two layers.

    Water can form hydrogen bonds to any organic, including oil. However, these hydrogen bonds are not as low in potential as water-water hydrogen bonding. The term hydrophobic is misleading, since water can hydrogen bond to organics with strength similar to van der Waals that form between organic, so organics do not fear water. The real push is water, is exclusionary since it can lower potential better by hydrogen bonding to other water.

    To minimize the enthalpy, of the two component system of water-protein, means maximizing the number of water-water hydrogen bonds and minimizing the water-organic hydrogen bonds. Since the water-organic hydrogen bonds can't become zeroed due to a residual interface between water and protein, minimization of potential means the organic surface needs to be a small as possible and/or covered with groups that form the best hydrogen bonding of minimized energy; polar side groups.

    As shown below, the pic on the left is an unfolded protein in water. The peaks represent the energy potential that exists between the organic side groups of the unfolded protein and water. The highest potential peaks will fold first, water is excluded, to minimize the highest potential. This is consistent each time, so protein nucleate and fold the same way each time.

    Say you used ammonia instead of water, to fold natural protein, since ammonia can dissolve in water and is also a good solvent for organics, the curve on the left will not start out with its energy peaks quite as high. The hierarchal potential for folding is weaker, causing a higher level of folding variation. This is one of the reasons proteins experimentally folded in ammonia are not bioactive. These tend to be more under the laws of statistics. Water allows random to be transcended, which is needed for life.

    If we wanted to use ammonia for life, we would need to figure out a polymer, similar to protein, where we can get high peaks. This would need to be made of side groups insoluble ammonia. This may not be common organics.


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  12. wellwisher Banned Banned

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    The statistical assumptions used for the living state are a useful tool in terms of applied science. However, in terms of pure science and observed reality, this assumption is not appropriate to water and life. The statistical assumption may be better for other potential solvents for life. Water allows the elimination of statistical variation, as reflected in protein folding. This makes water a unique solvent for life.

    If we took any organic, found at any level of life, and burned it in oxygen, one of the common terminal products of combustion will be H2O. Water is unique in that it is part of the energy floor, for all the organics of life. Water, as an energy floor, is very stable and can't be transformed into a different product using the dynamics of life, with even lower energy. This is good for evolution, since all the change has to occur via the organics. Water stays the same and offers a reliable platform.

    If we use ammonia for a solvent, then ammonia would need to become the energy floor. The problem this creates is ammonia is energy rich. Therefore, what prevents a cell from evolving to where it can use its ammonia solvent for energy, causing its energy floor to open up like a trap down. If this happened, in a nondestructive way, life would continue to evolve it the solvent until it finally reaches a stable energy floor, which will be water. Once it reaches water, it can no longer get any extra energy from its solvent, and now can change only via the organics, and not via the solvent and the organics at the same time.

    Although water or H2O, is the stable energy floor of the cell, water is unique, because it is not an inert energy floor, due to hydrogen bonding. Water has a second level of potential connected to hydrogen bonding. Ammonia can also do the hydrogen bond thing, but ammonia is not a stable energy floor. While sulfur oxide is a stable energy floor, but does not have the second stage potential, connected to hydrogen bonding. Water is the only one that does both equally well, allowing it to eliminate statistical variations; two levels of energy. The ability to form four hydrogen bonds makes its hydrogen bonding a different type of energy floor, connected to the secondary, tertiary and quaternary structures.
     
  13. timojin Valued Senior Member

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    I have heard in my early life living structure made of silicon . The cellular material , such as nucleotide , which are composed of phosphates , ribose . I picture myself How ribose will react with SO2 and phosphates in ammonia
     
  14. wellwisher Banned Banned

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    There is plenty of speculation about life using other solvents, and with other atoms, like silicon, being used for the biomaterial besides carbon. These theories are all dependent on statistical assumptions; odds. The value of water is water eliminates the need for statistics and odds, which is necessary for life. Life is not about odds. The idea of odds is an applied science assumption, which allows scientists to make progress even when they don't fully understand; black box approach. Life does not use black boxes, this is what statistics does. There is no parallel in life based on this procedure. It is a man made, but useful, modeling procedure.

    For example, if you attempted to let proteins fold in any other solvent besides water, folding will show statistical variations, none of which will be bioactive. If you use water, there will only be one specific fold, with this fold, bioactive. To make life work, since there are so many parts that need to coordinate, each part can't be varying in a random way. This creates an impossible process control problem.

    It may be possible to make all the polymers and chemical analogies using other solvents. However, the parts alone do not make life. Life does not suddenly appear from parts anymore than an automobile will self assemble and then start to drive itself. This is where water comes in. Water is an energy floor, that can eliminate statistics, and then also allow all the parts to coordinate.
     
  15. wellwisher Banned Banned

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    The way water allows all the parts of the cell to coordinate is connected to hydrogen bonding. Water can form four hydrogen bonds with other water molecules. This is the gold standard in terms of lowest energy in water. While organics in water create molecular surfaces that will prevent the ideal hydrogen bonding within the water from occurring. The result is residual energy is often left in the water when organic are in the water. The water will push and shape the organics in the attempt to maximize aqueous hydrogen bonding.

    Since different organic materials will impact the local water differently, these difference in materials can be used to create different local potentials in the water. This, in turn, can be used to set up potential gradients in the water.

    As an analogy, say I have a pool of water and add ice on one side and a heater on the other side. The energy difference, between the two sides, will cause a convection to become established. The ice will cause cold water to sink, while the heater will make warm water rise, with the two zones coordinating with each other as way to equilibrate the potential in the water.

    The DNA is the most hydrated molecule in the cell in terms of total hydrogen bonded water. The energy in the water, around the DNA is relatively low, with much of this water able to use DNA for strong hydrogen bonding. The membrane is essentially lipid oil, which creates the higher oil-water potential in the water. The water will attempt to equilibrate the gradient potential, but it can't eliminate this, because these are two fixed structures. The alternative is for a convection to occur, with other materials; organics and ions, expressing the potential, as a surrogate for the water. The goal is to make this all this add up, so the energy in the water stays at a minimum.

    When water causes protein to fold with perfect folds, this keeps zones at uniform potential in the water. It makes it easier to establish very s specific gradients which need very specific material flow.
     
  16. timojin Valued Senior Member

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    I imagine in the process of folding and unfolding water plays an important role . Probable to fold there have to be a withdrawal of water and the surface becomes less hydrated, in order to achieve that an additional chemical molecules have to be brought into the place to remove the water which helped to unfold.
     
  17. wellwisher Banned Banned

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    The way water folds and unfolds as you put it, is inherent in hydrogen bonding.

    Hydrogen bonding shows both polar and covalent character. Hydrogen bonds can form via polar attraction, as well as though the overlap of covalent bonding orbitals. Although both are hydrogen bonds, the polar and covalent aspects of hydrogen bonding have different properties. The polar has higher entropy, higher enthalpy and occupies less volume. While the covalent has lower entropy, lower enthalpy and occupies more volume.

    Without any hydrogen bonds breaking, water can shift between these two states, altering the parameters in the local water. It can put on the squeeze via covalent hydrogen bond expansion, and then release the pressure by collapsing into the polar state.

    This is call low density water (LDW) and high density water (HDW).

    The polar/covalent binary switch of hydrogen bonding, allows hydrogen bonding to express information. Each base and gene on the DNA has its own unique water fingerprint. As things enter the cell, the water will form hydrogen bonds. The sum of the hydrogen bonding switches, around and extending from the molecule will fingerprint the molecule. This information can then be transmitted through the water via the hydrogen bonding matrix of water. This can tell the DNA to get ready. The cell can also use energy to flip the switches on the input information layer, helping to get the molecule prepped.
     
  18. timojin Valued Senior Member

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    Would this not be the other way ?
    Higher entropy, higher disorder
    Lower enthalpy, less lover energy
    Lover energy, at constant pressure , lover volume .
    In ice, lover energy higher volume
    As for me I would question the geometry of the angle of separation between the two hydrogen ?
     
  19. exchemist Valued Senior Member

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    S=k lnW, so a greater number,W, of available states means more entropy, S. More available states can often be loosely equated with more disorder.

    I'm not sure about "lover energy". I'm getting a bit old for that sort of thing - not enough lover energy, I suppose.

    What do you mean by saying you "question" the angle of separation between two hydrogen (atoms?)? The bond angle of an undistorted water molecule is 104.5 deg: http://www.sciencedirect.com/science/article/pii/0022285279900195 . In ice, this angle changes slightly and becomes close to the theoretical angle for a regular tetrahedral structure, which is 109.5 deg. Did you mean that, or some other angle?
     
  20. timojin Valued Senior Member

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    Thanks for the jocke . Yes that is what I meant from 103 to 109 degree in ice
     
  21. exchemist Valued Senior Member

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    OK.

    That change will be the result of optimising the H-bonding in the ice structure to keep the H-bond lengths as short a possible, thereby reducing the energy of the structure to a minimum. There is a slight energy penalty in squeezing the lone pairs on the oxygen atom a bit more than in the free molecule, but evidently this is the optimum (minimum energy) configuration.

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  22. wellwisher Banned Banned

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    One of the main uses of water, as connected to life, is the transmission of information. The hydrogen bond is unique in that it has partial covalent character; directional bond. The hydrogen bond can also be polar using charge attraction. The net affect is the hydrogen bond can act like a binary switch, change between these two states without ever having to break the hydrogen bond.

    This is more than just a binary switch used in computer memory. The two states have different properties with respect to entropy, enthalpy and volume. This makes the hydrogen bond is a binary switch with both different muscle and energy in each setting. This switch is not just for moving information, but it can be used to move matter. The line between matter and information become blurred; firmware. Information being transmitted through water, via its hydrogen bonding, is more than an abstraction, it also has tangible impact.

    Water, via hydrogen bonding, builds upon binary using cooperative hydrogen bonding. Hydrogen bonded chains (that is, O-H····O-H····O) are cooperative; the breakage of the first bond is the hardest, then the next one is weakened, and so on. Such cooperatively is a fundamental property of liquid water where hydrogen bonds are up to 250% stronger than the single hydrogen bond in the dimer.

    Using quantum chemical calculation of different clusters of water molecules has shown that the hydrogen bonding strength can vary for as much as 90% between extreme cases of cooperatively and anti-cooperativity with cooperatively increasing (~3 kJ mol-1) the bond strength and reducing (~0.03 Å) the hydrogen bond length per added molecule and anti-cooperativity reversing these effects by the same amounts.

    Hydrogen bonds facilitate correlated electron movement between molecules. Clusters linked by extensive hydrogen bonding can be considered as being connected by extensive, but complementary, electron delocalization. Long range organization (> 100 nm) has been detected by hyper-Rayleigh light scattering (HRS). As electrons are not held by individual molecules but are easily distributed amongst water clusters, with correlated many-body quantum-mechanical tunneling, with local electromagnetic radiation. The water protons are also not held by individual molecules but may switch partners in an ordered manner within distinct networks. Also, phonons (vibrational energy) can propagate through the hydrogen-bond network over several nanometers in spite of the hydrogen-bonded chains constantly being broken.
     
  23. exchemist Valued Senior Member

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    Wellwisher, this is a rather remarkable figure. I have never come across this before. Can you provide a reference, please?
     
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