The cell in one variable, i.e., hydrogen bonding

[insane_alien]

okay, so hat happens if you increase the H-potential in the cell?

 

what happens when you decrease it?

 

if you can't answer these then the last speck of credibility you have will evapourate away.

[pioneer]

The relative basicity of can looked up in any chemistry book, with OH- being a stronger base than Cl-. Relative basicity is the measure of how easy that entity is able to share electrons. Because Cl- is a weak base, it can not share the electrons that easy, allowing the H to leave.

 

If you look at anything in the cell, everything is surrounded by water. Water is the dominant material within the cell in the order of 70-90%. When a protein forms in water, it places its hydrophobic groups on the inside and its hydrophilic groups on the surface. The operative word is "hydro or water". The potential in the water is at the level of hydrogen bonding. Or the hydrogen bonding potential in the water causes the enzyme to place its hydrophobic groups in the interior and its hydrophilic groups at the surface. If we used a different solvant, without H-bonding, one would get a different enzyme. For example, in hexane the opposite would occur, with hydrophobic groups preferring to be on the surface.

 

In biology and biochemistry, the enzyme is often modeled out of the context of the water that surrounds it, even though this water is what is creating a dual potential to give it its proper shape. This is a good first approximation. But how does one justify taking the enzyme out of the context of the extended water structure that will surround it? I don't wish to be mean, but this first approximation is not fully reflecting reality.

 

If we look at ATP, it is does not exist like it is drawn in bio-books. It will actually have extended water as part of its structure. There are plenty of O atoms on the triphosphate for the hydrogen water to bind too. If you explain ATP out of the context of the extended water you will get one explanation, which is a good first approximation. If you look at the reality of anything dissolved in water, the explanation will have to include the water since the water is part of ATP extedned structure. Look at it this way, all the hydrogen of water, have an electron withdrawing affect when they bind onto the the many O of the tri-phosphate. The net affect is that the final potential in the ATP is different with or without water. The water itself, is the continuous phase of the cell, with everything in the water having an impact on the local and global potential of the water. So the water around the ATP is not just its own water, but is also connected to the aqueous potentials which are created by the environment the ATP is in.

 

okay, so hat happens if you increase the H-potential in the cell?

what happens when you decrease it?If you can't answer this then the last speck of credibility you have will evapourate away.

Today 09:35 AM

 

Many things can happen, but the most important is called the cell cycle. At the onset, the membrane will unsaturate i.e., more fluid, and the cation pumps become more prone to reversal. The result is the cellular membrane potential gets lower than it was. Because of the change in the global water potential, the activities of the cell shift to the needs of the cellular replication. In a modern cell there are all types of extra biochemistry going on. But the general mechanism has not change in billions of years. The extra stuff helps to make the entire process far more perfect but the bulk affect can be explain with 100% correlation by taking into affect water potential at the level of hydrogen bonding.

 

Let me give one global example. When the ion pumps reverse the inside of the menbrane will become less negative. What this means is the water of the cell now as less bulk reduction potential, i.e., less negative influence because of the lower negative induction at the membrane. This means less bulk aqueous potential with the metabolic oxidation potential. Or the lower negative charge in the water implies less oppposing affect on the oxidation potential, allowing the metabolic oxidation to occur easier, resulting in higher metabolism. Again there are many things going on, but the direction is consistent.

 

Here is the problem and solution as I see it. The first approximation method is good. But it is not the final solution. I have mellowed. At one time, I would have held the first approximation's feet to the fire. But I don't want to fight anymore. I am ready to generate the step.

 

A Few More Comments

 

 

I realize that my explanation for carbon monoxide poisioning was not correct. But the question was nebulous. It did not say carbon monoxide poisoning in humans. That was easy. I had not been addressing multicellular applications, but was limiting myself to single cellular. The question I saw was, what would be the affect of CO on a single cell if it was exposed to CO? The CO will react with O2. If the CO gets deep enough inside the cell, it will impact the O2 of metabolism.

 

Also the ATP discussion was not as complete as possible. The ATP is active at the terminal phosphate group. The positive charge on the terminal P is the sweet spot on that molecule. If we add the affect of hydrogen bonded water onto the ATP, this will be electro-withdrawing making that P more positive so it can react even easier with the -OH group on an enzyme. Because the hydrogen bonded water is withdrawing electron density from the O's of phosphate, this means the O of those attached water will see slightly more electron density. This extra electron density allows one of these water to be the easiest/closest water to add to the second phosphate to make the (OH) end cap of ADP. The ATP will carry the water with it via h-bond that will help make the the ADP end cap. You won't read that in any book. I just used simple logic.

 

If we use an historical perspective, the discovery of the cell was the first major global understanding of the living state. Much cateloging had been down with the diversity of life, but the understanding of the cell allowed a global explanation that could be used to explain all aspects of life. Although this rasied the bar, it could not address the common link that could explain the cellular innards in a global way. So science went back to cateloging the microspopic structure to show similarities in cells.

 

The genetic theory was the next important global variable. Within the genetic templates of the DNA were all the ingredients needed to make any protein within the cell and therefore was able to correlate all the innards. If there was an affect, that meant a protein or protein train, which in turn, had a genetic basis. Genetic theory helped to narrow down research and change simple cateloging to better predictions.

 

What is still left to explain in the mysteryof life, is how does shuff know where to go? We have cateloged where it goes. We also know it comes from the DNA. Even the DNA will make more DNA. But once it leaves the DNA, how does everything know where to go. In cell cycles. the mother cell separates the contents and the daughter cells start out disorganized. Yet everything finds the correct spot so the cell can become active. To answer the hows of directed movement we need another global variable.

[insane_alien]

To answer the hows of directed movement we need another global variable.

 

so your saying your initial premise of a cell having only one variable is a load of BS then?

[pioneer]

I am trying to tone down my confidence so it doesn't come across like arrogance that is trying to compensate for lack of understanding. The one variable is hydrogen potential, which includes H-bonding but extends into other aspects of hydrogen such as reduced hydrogen.

 

If I asked you to explain all we know about life in one paragraph it would not be easy inspite of the thousands of good research papers, books and extended knowledge on the subject. It is easier to a favorable audience, that has plenty of background, like yourself. But in that short space, those who know a limited amount about life science, would have a bunch of questions.

 

The H potential model covers the same scope. It is not developed that far, but I tried to do a wide variety of application over the entire range. I don't think I could ever write a paragraph that will answer all the critics. Without some background, the discussion will get bogged down into comparing what is known with something that reaches different conclusion, due to adding the affect of the extended water.

 

The ATP example should allow one to see the importance of the water attached to ATP. This addtion of the water is entirely consistent with all the observation but adds a little extra to the analysis that changes things. I don't mean to offend anyone, but I simple follow the logic. Maybe what I need is a suggestion of what I could do to make it easier. I am not looking for a trick question but a thoughtful question to settle it.

 

Let give another example of how extended water is consistent. I will explain why the DNA forms a double helix and RNA has more variety. If we look at one helix of each, there are only two simple chemical differences between the two. The first is the pentose sugar of RNA has an -OH group in the position where the pentose sugar of DNA has a -H group. Relative to the extended water, the -OH on the sugar of RNA can form a hydrogen bond with water, and therefore pull in a little more electron density from the water than can the -H group of the DNA. This lowers the hydrogen bonding potential of RNA relative to the DNA. This gives the RNA more flexibility with respect to the types of helixes it has to form. The higher potential of the DNA causes the need to form double helix.

 

The other difference is connected to only one of the bases. Chemically the DNA has an -CH3 group on the same position, the base of RNA has an -H. When a single strand is open to the water, both of these groups create a surface tension affect like oil-water, with the -CH3 group creating more surface tension in the water than the -H. In other words, the -CH3 makes it hard for the water to hydrogen bond due to this organic group taking up more space in the water in an unfavorable way, than the tiny -H. This will increase the local aqueous hydrogen bonding potential, since more water will be put in a position where it can't form h-bonds. As such, the DNA has another built in feature that further increases its H-bonding potential. The result is DNA will form a double helix and RNA has more flexibility.

 

To extend this in another direction, if I see methylation on the DNA, I know that aspect of the DNA has been induced to even higher potential. This may make it a little more difficult to separate the helix there.

[foodchain]

In response to pioneer.

 

Right, but in biochem if memory serves the molecular wight for instance of some proteins in rather immense, so I think that’s why they use the Dalton. To get more to the point the chemistry of life is diverse, such as with the double helix or chromosomes where do you place the role of histones?

 

I mean I don’t doubt that your idea has some good potential, as in I don’t want to be scene as a naysayer simply to play devils advocate. I just don’t think its fully respective of the reality of say a living cell. What about the golgi apparatus, or the cis and trans of such? To the cell wall, to just about anything you can find details that are of importance. Down to even the structure of say a protein has an importance. Also the cell takes on many physical aspects, such as microtubules, as in its not all just a reaction per say...

 

Again I think your idea is a good idea, and I don’t think its totally bad, but I don’t think you can use it to explain the basic building block of life as we know it. I mean I think understanding how hydrogen behaves in a living system is a perfectly empirical idea, but I don’t however think that hydrogen alone can explain the cell.

[pioneer]

I agree that hydrogen alone can not fully explain cell. It adds another layer to what we already know. It complements existing understanding and adds the addtional understanding of how cells integrate. The easiest to see is connected to the cellular membrane potential. This is where a cell puts the majority of its energy. So it must be important to the cell.

 

The net affect is the inside of the cell membrane in induced negative. Since the water is everywhere, this constant negative induction is conducted into the water. It has the affect, of lowering the hydrogen-potential of the global water. As such, the water around everything in the cell is less demanding for electron density. This means the hydrogen bonding of everything is a little looser than if the water was not seeing this negative induction.

 

So if we take a protein out of the confines of the cell, to investigate, it will see a slightly different external water than occurs within the cell. That is part of the reason the results often come out empirical. It is not exactly the same situation as occurs within the cell. It is a good approximation. If we add the complementary aquoeus affect due to the cell membrane, we will be able to generate results closer to the reality.

 

Average water potential is only useful in a very limited way. We also need to know the more specific local water potentials. To do this one has to work with a reciprocity, i.e., bio-materials inducing the water. This is where the known structures of the cell become mirrored in the H-potential affect they will create within the water.

 

Let me give an example. If we look at the DNA double helix, this structure is the best way to bury the organic aspects, i.e., bases, sugar, to lower their surface tension affects, which can increase the potential of water. Or to minimize the potential in the continuous bulk water phase, i.e, 70-90%, these organic groups are buried to minimize the potential in the bulk water. In other words, if we started with two DNA strands and used hexane, instead of water, one would not get the same structure, since the continuous phase of hexane would bury all the charge/polar groups.

 

For the DNA to be useful for transcription we need to separate the helix. By doing this we are causing the organic groups to have more contact with water. This will have the affect of increasing local water potential near the separated the double helix. Or the water around the separated double helix will define more potential than the water near the double helix that is still together. It is more compicated than that, but these two states of DNA will have two different impacts on the local water.

[foodchain]

I agree that hydrogen alone can not fully explain cell. It adds another layer to what we already know. It complements existing understanding and adds the addtional understanding of how cells integrate. The easiest to see is connected to the cellular membrane potential. This is where a cell puts the majority of its energy. So it must be important to the cell.

 

The net affect is the inside of the cell membrane in induced negative. Since the water is everywhere, this constant negative induction is conducted into the water. It has the affect, of lowering the hydrogen-potential of the global water. As such, the water around everything in the cell is less demanding for electron density. This means the hydrogen bonding of everything is a little looser than if the water was not seeing this negative induction.

 

So if we take a protein out of the confines of the cell, to investigate, it will see a slightly different external water than occurs within the cell. That is part of the reason the results often come out empirical. It is not exactly the same situation as occurs within the cell. It is a good approximation. If we add the complementary aquoeus affect due to the cell membrane, we will be able to generate results closer to the reality.

 

Average water potential is only useful in a very limited way. We also need to know the more specific local water potentials. To do this one has to work with a reciprocity, i.e., bio-materials inducing the water. This is where the known structures of the cell become mirrored in the H-potential affect they will create within the water. This is the other universe.

 

Let me give an example. If we look at the DNA double helix, this structure is the best way to bury the organic aspects, i.e., bases, sugar, to lower their surface tension affects, which can increase the potential of water. Or to minimize the potential in the continuous bulk water phase, i.e, 70-90%, these organic groups are buried to minimize the potential in the bulk water. In other words, if we started with two DNA strands and used hexane, instead of water, one would not get the same structure, since the continuous phase of hexane would bury all the charge/polar groups.

 

For the DNA to be useful for transcription we need to separate the helix. By doing this we are causing the organic groups to have more contact with water. This will have the affect of increasing local water potential near the separated the double helix. Or the water around the separated double helix will define more potential than the water near the double helix that is still together. It is more compicated than that, but these two states of DNA will have two different impacts on the local water.

 

So basically you are treating the cell as an ion or electron gradient in which Hydrogen becomes the focal point of activity? I don’t know, I mean I always wondered about protein movement in a cell and densities of such proteins, but I think that’s outside of the topic at hand.

 

Most signaling activities in cells revolve around proteins and physical structures though. I see you go into that with the DNA example but I think the form of DNA when in its double helix is the product of a series of steps and of course histones. Structural biology is interesting though. I always wondered about how primitive a modern cell is compared to say bacteria and what the organization alone allows for.

[pioneer]

I need to go back to the beginning. If you look at a single H2O molecule, the O has higher electronegativity than H, and withdraws electron density away from the H. The result is a dipole with H slightly positive and O slightly negative. If we could equalize the electrons to remove the dipole, it would form again, since the dipole moves H2O in the direction of lowest potential. Thehigher electronegativity of O is stabilzed by the extra electron density (negative charge) or it would not have taken it in the first place. The net result is the primary burden of potential is on the H.

 

The H-bond in cells are mostly due to H being connected to O and N. With both of these being highly electronegative, and being stabilzed by taking electron density from H, these with alos pass the burden of potential to H. The H will try to lower this potential by forming H-bonds.

 

If we look at the DNA double helix, in every base pair, there are more possible H that can form hydrogen bonds than there are possible H-bonds. If you look at adenine the upper N has two H and only one H-bond. In the bottom pair, both cytosine and Guanine both have an extra H (5 possible and only 3 forming).

 

 

What that means is each of these extra H retain near max H-potential. They would like to lower this potential but they structurally prevented. What these extra H do is cause the DNA to retain H-potential, with every base pair having one or two of these max potential H built it. This is part of the configurational signature of the DNA at the level of H-potential.

 

Since RNA does not have to always form a double helix, these extra H can interact with the water a little better and alter their potential. This give sthe RNA a slightly different signiture, even though it has the same H. In RNA, any particular combination of loops, straight single helix or double helix, the sum of all these H will give it a specific H-potential signature.

[foodchain]

I need to go back to the beginning. If you look at a single H2O molecule, the O has higher electronegativity than H, and withdraws electron density away from the H. The result is a dipole with H slightly positive and O slightly negative. If we could equalize the electrons to remove the dipole, it would form again, since it move H2O in the direction of lowest potential. So the O is stabilzed by the extra electron density (negative charge) or it would not have taken it in the first place and lower its energy. The net result is the primary burden of potential is on the H.

 

All the h-bond in cells are do to H being connected mostly to O and N. With both being highly electronegative and being stabilzed by taking the electron density from the H, these all pass the burden of potential to H. The H will try to lower this potential by forming H-bonds.

 

If we look at the DNA double helix, in every base pair, there are more possible H that can form hydrogen bonds that there are possible H-bonds. If you look at adenine the upper N has two H and only one H-bond. In the bottom pair, both cytosine and Guanine both have an extra H.

 

 

What that means is each of these extra H retain near max H-potential. They would like to lower this potential but they structurally prevented. What these extra H do is cause the DNA to retain H-potential, with every base pair having one or two of these max potential H built it. This is part of the configurational signature of the DNA at the level of H-potential.

 

Since RNA does not have to always form a double helix, these extra H can interact with the water a little better and alter their potential. This give sthe RNA a slightly different signiture, even though it has the same H. In RNA, any particular combination of loops, straight single helix or double helix, the sum of all these H will give it a specific H-potential signature.

 

Give me some time to go over this as my words happen to be jumbled at this point in time.

[pioneer]

The water shroud or extended water around bio-chems, due to water being the continuous phase or dominant material in the cell, can be addressed easy enough with current understanding of H-bonding. But one needs to modernize this understanding to highly electronnegative atoms being stabilized by being negative with the result H carries the potential if we wish to address situations like the extra H within the double helix. This approach is more flexible and provides a way to mix oil and water.

 

Rather than extrapolate on the DNA I would like that sink in. Instead I would like to look at Na+ and K+ cations. In water these cations exist with hydration spheres or extended water structure. The cation is the pit of the cherry and the extended water is sort of like the flesh of the cherry. The Na+ hydration sphere is larger than that of K+. They both have a single positive charges but their EM effectiveness is different. In other words, K is more reactive in water than Na because K+ is a little more stable than Na+, causing K to release its electrons easier to the water. The less electropositive K+ (more stable than Na+) will therefore have a smaller hydration sphere.

 

Nature makes use of this size difference when pumping Na+. The Na+ cherry is bigger than the K+ cherry and therefore takes more energy to pull off its extended water, so it can skinny down and get through the cation pump. But once it is outside, the larger water flesh returns making it harder to skinny down and work its way back into the cell, spontaneously. The K+ cherry starts out smaller and therefore this makes it a little easier to go back and forth, i.e., takes less energy.

 

Picture Na+ about to be pumped. We need to burst its water shell so it can skinny through the narrow channel of the Na+-K+ pump. This snap of the water sends a potential disturbance into the nearby water. The Na+ competes with the H of its extended water. When its bubble burst, this sort of relaxes the local aqueous potential shifting the local water. When a K+ appears in the inside of the cell, its forms its water ball and creates a slightly different disturbance associated with higher H potential but not as high as had been with the Na+ cation and its hydration sphere.

 

When material is transported in the cell, its uses the potential stored within the membrane that the cation pumps creates. The reversal alters the types of cherry signals that are entering the cell, in an opposite way that is created by the forward cation pumping. It is a type of complex binary coding at the level of H. If we add to this the extended water signals coming from the input chemicals, the membrane sort of paints a picture in the cell's water of what is happening at the membrane.

 

Actively transported molecules continue to be transported along protein rails, using ATP energy to move them along. What this internal transport train is also seeing are the high H-potential waves due to the Na+ cherries reforming as the local membrane potential is used up. This has the affect of transmitting increasing H potential down the train. ATP, with all its O groups, helps lower this aqueous potential to reflect the needs of the bulk aqeous potential, i.e., average membrane potential is negative. If nothing is being transported into a cell, there is no local Na+ inpulse so ATP is not needed at that zone. If stuff is coming in at a fast rate, the local Na+ impulse conducts down the train requiring more ATP diffuse into the transport train to reduce the increased in the H-potential signal.

 

ATP and ADP have their own extended water shrouds, which differ. As ATP converts to ADP, the ADP creates its own disturbances within the water. The ATP is not just limited to the membrane but is found everywhere. The mitochondria, by being the primary output source of ATP, are the big guns in the cell which sort of propagate their own bulk disturbance in water, with in this case are more connected to a lower H-potential signal.

 

With the lion's share of the ATP energy of the cell going into the cation pumping, the affect of the ATP is to lower cell's H-potential. This is reflected by the inside of the cell becoming slightly negative. But the membrane potential, via the external high H-potential (positive), keeps attracting materials, causing reversal of potential in an organized way. The mitochondria, now has to use ATP to put out these brushfires. The ATP energy budget is distributed in a way that minimizes H-potential. But the mitochnodria are also within the water which has an impact on it. This water is a function of all the other things that glow or not.

 

Pardon my chemistry terms like cherry, glow and big guns Sometimes it is easier to paint a visual image of complex things using simple analogies.

 

More on the extra H within the DNA double helix

 

I don't like answering my own posts but I thought it would be useful to discuss some of the rational behind the extra H within the DNA double helix. The DNA double helix is a very stable bi-molecule making it useful for the templates called genes. The extra H that can't form H bonds, add some extra potential to an otherwise very stable situation. If nature didn't have a reason for this extra H potential, it could have added -OH groups instead of the -NH2 groups, so it could avoid having any extra H. But this would have been too stable for the needs of life.

 

What these extra H do, among other things, is give the DNA double helix some extra potential to do a little better than the double heliix, with respect to achieving minimum potential. In other words, these extra H help the DNA take the bait, separate the helix, with the hope the final state will lead to an even lower potential. If these -NH2 groups had been replaced with -OH, to get rid of the potential of the extra H, the DNA would have zero incentive to separate the double helix since it would already be as low in potential energy as is possible.

 

Once the DNA double helix separates and the organic innards of the single helixes see the affects of the water, these extra H will also help counter surface tension by helping to stabilze the water relative, to these H not being there. In summary, the extra H give the stable DNA bimolecule incentive to separate. They also give extra stability within the water if and when the DNA decides to separate and expose its organics innards. The extra H help narrows the potential bandwidth for helix separation in water relative to there not being any extra H.

 

As was shown in an earlier post, the two different features of RNA, relative to the DNA, i.e., the -OH on the pentose sugar and -H instead of -CH3 on one of the bases, causes RNA to have a lower H-bonding potential. This allows more variable helix structures including the single RNA helix. As such, when RNA forms on the DNA it partially forfills the hope of the DNA by lowering the potential of the DNA relative to the DNA double helix.

 

That is all well and good for the DNA. But with respect to the RNA, by combining with the DNA its potential will see an increase. Eventually, the loss by RNA will begin to outweight the partial gain the DNA. This will cause the RNA to strike out on its own, causing the DNA double helix to reform, since the DNA double helix becomes better than exposure to the water. In modern cells, this is all assisted with enzymes. But in ancient pre-cells with little or no enzyme support, these simple built in potentials, might have allowed this to occurred, spontaneously on a small scale.

 

If we add the affect of the cation pumping, which is to lower the H-potential in the interior cell water of the cell, the DNA now sees an even more favorable environment with respect to exposing innards to water. Some mechanism of cation pumping even proton pumps was one of the most important breakthroughs for life due to making everything easier. This is relatively simple in the sense of few components, it still uses the lions share of the cells energy and is still quite conservative in cells.