Making a Cell from scratch

[sunspot]

I would like to propose a way to make a viable cell sort of from scratch. This is predicted by my hydrogen bonding equilibrium theory. It has never been done and we may not yet have the needed capability, but here goes.

 

Here is what you do. First we start with a DNA double helix. Human will work just fine, since it has the most sophisticated genetic repetoire. We put this in beaker one. Step two, we make two long RNA strands from the DNA double helix to reflect the exact template relationships on both DNA helix strands. If the RNA breaks that is OK, because it will help the cause. We put this in beaker two. Next, we make two long stands of protein from the two strands of RNA to reflect all the template relationships. We put this in beaker three.

 

To beaker three we add some lipids to make a cell membrane. Equilibrium hydrogen bonding should result in a protein gradient forming. Hydrophilic proteins will group anjd hydrophobic will find the membrane. We may have to help by adding some cleavage enzymes and by encouraging the ions pumps to reach the outer membrane. At steady state, we add some mitochrondia and all its needed resources so they can make ATP. The ATP will cause many of the ATP active sites along the long strands of proteins to sort of fire, helping to break the proteins apart and maybe even helping to assemble some of the enzymes around their ATP active sites.

 

When steady state is reached we add the RNA. The negative charges on the RNA will alter the hydrogen bonding gradient. It will also cause the RNA and protein to combine. Remember we have all the RNA and protein needed for a human cell and it will find each other due to equilibrium hydrogen bonding. When a new steady state is reached we add the DNA. The DNA and RNA will also find each other. While the packing proteins will find the DNA. With a little prodding a simple viable cell will form.

[Cap'n Refsmmat]

That's not exactly a cell from scratch. That's a cell made out of already-created complex ingredients. Like an Instant Cell--Just Add Lipids.

[sunspot]

I agree with you. This was intended as a thought experiement to show how cellular placement of materials reflects equilibrium positioning. Also, if one had some dinosaur DNA, this technique would provide a way to could grow a real dinosaur instead of mutants.

 

The original analysis is actually more complex and was used to introduce all the equilibrium layerings within cells, starting with proteins and then building from there.

 

What I would like to do is start very simple, without using any hydrogen bonding considerations, to give one a feeling for the foundation layer of cells. I will start with a cell membrane with ion pumps, and some DNA. The sodium pumps, in particular, will set up a membrane potential with the inside becoming negative due to the three to two pumping of sodium ions out and potassium ions into the cell.

 

The DNA double helix is full of negative charges along its length due to the phosphate residues. The result will be that the DNA will need to repel the cell membrane and will find a posititon, sort of in the middle, so it can minimize the affects of negative charge repulsion. These are the two structural poles of all cells. All the rest of the large materials will assume equilibrium positions, between the membrane and the DNA.

 

Next, if we add some histone packing proteins, which have positive charges, these will pack part of the DNA, neutralizing some of the negative charge along the DNA's length. If the sodium pumps are tuned to repel the entire unpacked DNA, packing part of the DNA, allows other sources of negative charge to collect near the DNA to get the same charge balance. This allows RNA to collect closer to the DNA, since the negative phosphates residues on the RNA will also repel the cell membrane.

 

If we look at nervous tissue, part of its activity is based on the movement of sodium cations along its surface and out of axons. In the human body, nervous tissue is near nearly all the cells of the body. Essentially, nervous tissue helps maintain and can pertubate the celll membrane potential and tereby change or maintain the gradient to the DNA using sodium cations.

 

It is more complicated than this, but this is the base layer of potentials.

[Bluenoise]

I would like to propose a way to make a viable cell sort of from scratch. This is predicted by my hydrogen bonding equilibrium theory. It has never been done and we may not yet have the needed capability' date=' but here goes.

 

Here is what you do. First we start with a DNA double helix. Human will work just fine, since it has the most sophisticated genetic repetoire. We put this in beaker one. Step two, we make two long RNA strands from the DNA double helix to reflect the exact template relationships on both DNA helix strands. If the RNA breaks that is OK, because it will help the cause. We put this in beaker two. Next, we make two long stands of protein from the two strands of RNA to reflect all the template relationships. We put this in beaker three.

 

To beaker three we add some lipids to make a cell membrane. Equilibrium hydrogen bonding should result in a protein gradient forming. Hydrophilic proteins will group anjd hydrophobic will find the membrane. We may have to help by adding some cleavage enzymes and by encouraging the ions pumps to reach the outer membrane. At steady state, we add some mitochrondia and all its needed resources so they can make ATP. The ATP will cause many of the ATP active sites along the long strands of proteins to sort of fire, helping to break the proteins apart and maybe even helping to assemble some of the enzymes around their ATP active sites.

 

When steady state is reached we add the RNA. The negative charges on the RNA will alter the hydrogen bonding gradient. It will also cause the RNA and protein to combine. Remember we have all the RNA and protein needed for a human cell and it will find each other due to equilibrium hydrogen bonding. When a new steady state is reached we add the DNA. The DNA and RNA will also find each other. While the packing proteins will find the DNA. With a little prodding a simple viable cell will form.[/quote']

 

Mixxing random proteins dna and rna with mitochondria doesn't cause them to magically assemble into a living organism ha ha ha ha ha ha ha ha

[ecoli]

Mixxing random proteins dna and rna with mitochondria doesn't cause them to magically assemble into a living organism ha ha ha ha ha ha ha ha

 

well, if you put phospholipids into a solution of water, they naturally form double layered membranes. So perhaps it isn't entirely out there.

[Bluenoise]

well, if you put phospholipids into a solution of water, they naturally form double layered membranes. So perhaps it isn't entirely out there.

 

Oh no it is entirley out there.

[prion]

equilibrium hydrogen bonding

[Klaynos]

equilibrium hydrogen bonding

 

Just smile and nod, you may cry later...

 

I read an interesting article in new scientist, I think it was, about a prize to make "life" and how several groups are going about doing it, oil droplets seems to be an interesting area of attack...

[YT2095]

I hope it`s a completely Synthetic oil, otherwise I`de consider that Cheating.

 

didn`t some other guy attempt this many many years ago, in a chamber with air and salt water and methane etc... and intoduced massive electical charges into it (as if Lightening) as a simulation?

IIRC I think he did manage a few basic Amino Acids.

[mattbimbo]

stanley miller and harold urey in 1953 did the experiment YT is talking about, NASA are still repeating these expts, presumably trying to improve the flavour of 'prebiotic soups' by lowering its 90% tar content.

[Sisyphus]

The experiment was to try to recreate as accurately as possible the chemical composition of primordial Earth's atmosphere, then run electrical current through it and see what happens. After only an hour, the container was coated with a thick sludge of every basic organic molecule imaginable. That's not creating life, of course, but it does show that we're allowed to use some pretty complex ingredients and still call it "from scratch."

[YT2095]

but given near infinate stars and planets, and load and loads of time, that organic matter stood no chance of staying as it was, life must have been almost inevitable.

to my reconing anyway

[mattbimbo]

as far as i know, no one has explained in any prebiotic evolution theory the emergence of chirality. am i mistaken? there is also the problem of evolving a system which can replicate accurately, or distinguish between enantiomers, etc, without having a very advanced system to begin with.

 

as argued by AG Cairns-Smith, it is not the 'organicity' of the molecules which is important, rather the machinery which uses them. what is important is that the machinery is preserved over time, if it is not preserved there is no basis for evolution. does anyone dispute this?

 

but at the moment i am more curious about the source of ATP in SUNSPOTs thought experiment.

[Bluenoise]

as far as i know' date=' no one has explained in any prebiotic evolution theory the emergence of chirality. am i mistaken? there is also the problem of evolving a system which can replicate accurately, or distinguish between enantiomers, etc, without having a very advanced system to begin with.

 

as argued by AG Cairns-Smith, it is not the 'organicity' of the molecules which is important, rather the machinery which uses them. what is important is that the machinery is preserved over time, if it is not preserved there is no basis for evolution. does anyone dispute this?

 

but at the moment i am more curious about the source of ATP in SUNSPOTs thought experiment.[/quote']

 

It's best not to be concerned with anything he says, lest you stay concerned forever...

 

...plus I doubt it was ment as a thought experiment. Knowing sunspot he's on the verge of writing a patent application.

[bascule]

Perhaps sunspot's artificial cells can interact with the earth's fusion core to reverse the circulation patterns of tropical depressions

[mattbimbo]

i totally fukced up the 2nd year of my degree reading about 'prebiotic evolution'. my only excuse is that my lectures were boring. the more i read on the subject, the more i realised the limitations of theory of any kind. prebiotic evolution is a total mind melt, i have every sympathy for SUNSPOT and where his thoughts may now take him.

[sunspot]

The creation of life is important, not so much because it would be a hoot, but because it will tell us how cells are layered, starting from base layers. Currently the assumption is a random series of events. I worked under the assumption of an orderred sequence of events. Whether this is true or not, it makes the cell much more logical and less empirical.

 

Let me give everyone an analogy. If we never saw an automobile before, we would take it apart and analyze all its parts. Before long we would know how it works and realize that the motor is the center of the auto. Because of its important position one may assume that this was the first thing that was developed and the rest built up around this.

 

The reality, the first thing that evolved was the wheel. Then the axile. Then the chassis, carriage, seats, stirring, springs, etc. The motor didn't come in until very recently. These are boring things and are not as key as the motor so they must have come later.

 

If one insists the motor came first because of its central role, then the theory goes something like this. The cavemen spent millions and millions of years pounding out the first engine block with their stone tools.

 

I don't not mean this as a criticism. The life science are the least logical of all the sciences, because they are far too dependant on empiricism and statistics. Thats makes anything possible as long as the data correlates. One can find broken stone age tools. This is valid data to justify the cavemen building the original engine block, especially if one run tests to break stone tools and can demonstrate the fragments are similar within the range of statistical error.

 

I realized, when I was in college that this approach to science not that too far from modern alchemy and it came down to access to resource and not common sense.

 

I just proposed something logical like a simple negative charge repulsion between the membrane and the DNA. There is not enough logic associated with the life sciences to see even this simple connection. One actually needs to run experiments to see this? Pitiful.

[Cap'n Refsmmat]

I just proposed something logical like a simple negative charge repulsion between the membrane and the DNA. There is not enough logic associated with the life sciences to see even this simple connection. One actually needs to run experiments to see this? Pitiful.

Science likes evidence. In fact, obtaining evidence is part of the scientific method.

 

Many logical proposals have been made that have been proven wrong. The aether made perfect sense when it was introduced, but that didn't mean it actually existed.

[sunspot]

I am going to shift directions a little and talk about multicellular differentiation control within higher animals. I will come back to the inside of the cell a little later.

 

If we look at the most of the cells within our human bodies, there are three tissues almost everywhere near most cells; circulatory for the blood, lymphatic for the immune system and nervous tissue. Nobody has a problem with the blood being connected to cellular differentiation control. One can inject things into the blood to get the cells to change. The lymphatic tissue places the immune systen everywhere to help get rid of foreign invaders like bacteria, virus, etc., that could alter our cells. The circulatory system and the lymphatic team together to regulate cellular differentiation control when we inject medicines into the blood.

 

The nervous tissue has not yet been given a prominent role. Maybe it has no direct role. Its pupose may be purely decorative. Maybe the DNA likes to wraps its cell membrane in the rich luxurious feel of "nervous tinsel". It is not important that the nervous tinsel has the highest external positive charge per unit surface area of all the cells and the blood is alkiline (negative). Maybe it is purely cooincidental that the external cellular membrane surface charges of all the other cells remain differentiated within this nervous/blood charge range.

 

Part of the problem of using nervous tissue as the third aspects of the cellular differentiation control system is philisophical. Consider the implications. Cationic impulses, from local nervous memory and even directly from the brain, could theoretically alter the local cell membrane potential of cells via the local nervous branches. This would not only affect the engine associated with active membrane transport, but it will also impact the internal charge gradient between the membrane and the DNA. This could hypothetically cause the DNA to pack/unpack to balance the affect of the nervous potential. Where philosophy comes in, is that the DNA is no longer the king wrapped in decorative nervous tinsel.

[sunspot]

I was being a litle silly to lighten things up. I was also trying to discuss the possiblity of nervous tissue and cellular differentiation control. I have no direct data because it is new and not a big area of study. The choice is wait until then, or logically continue along this line of reason.

 

One of the practical problems of this hypothesis is that there are not enough chemicals given off by local nervous tissue to cells to explain such an important role. The blood supply is very obvious. Even the surface charge of sodium cations is sort of stuck to the nervous tissue and is not being trinkled in a steady stream to the cells. If it does flow it probally ends in the blood for recycle.

 

There is a way for the potential to conduct. This is connected the hydrogen bonding within the local water. If we look at the surface of nervous tissue, the external positive surface is in contact with water. The hydrogen of water needs to compete with all these sodium cations, creating a hydrogen bonding potential. The hydrogen proton is the fastest thing in water. This will conduct outward from the nervous tissue, through the water, as the protons bump the next guy. When the signal reaches a cell surface, the hydrogen bonding potential will be made higher on that surface than what is being created by the local surface charge. This will increase the effective outside potential of the cell or a side of the cell.

 

If we look at the nervous tissue, its outside positive charge is not static. The neurons needs to constantly use ATP energy to maintain the potential, up to 90% of metabolic ouptut. There is always leakage, much of it to drive the active membrane transport. There are also cationic current flows, including hydrogen proton flows, along the surface due to neuron firing. The sodium pumps are pumping, sending out signals at the level of the hydrogen bonding. The hydrogen bonding gradient from the nervous tissue to the control cell is being expressed by pulse patterns connected to what the local nervous surface is doing.

 

If we look at the outside positive surface of any cell, being positive means electron deficient. This is loosely analogous to the potential of metabolic oxidation, where molecular oxygen is electron deficit. This is the cellular trick or lure that draws reduced foods materials to the cell. It creates the scent of an oxidation potential which can lower the reduction potential of biomaterials. The food travels up the projected aqueous hydrogen bonding potential gradient stemming from the outer cell surface. The cells in the body lure food from the blood in this way.

[sunspot]

I was going to go into the cell and discuss the gradient between the membrane and the DNA, but before doing that I would like to stay outside the cell to discuss the nervous and lymphatic connection. The primary gradient for cellular differentation control lies between nervous tissue and the blood supply. This is inferred by the high positive surface of nervous tissue and the negative or slightly alkaline pH of the blood. Aqueous hydrogen bonding connects the potential.

 

The lymphatic tissue is within this range but much closer to the nervous potential. This is inferred from the observation that baby brain cells crawl with amaeboid motion. This implies the bottom end of nervous tissue is sort of close to the top end of blood cells. This leads to the theory of making new brain cells from the blood cells within brain. How that can be done, I haven't figure out yet, but it appears theoretically possible.

 

Sorry for the detour. Getting back on path, the potential between the lymphatic tissue and the nervous tissue is a way to charge up the blood cells for the immune response. When they reach a certain potential they become attracted to the lower blood potential. Once in the blood or around cells, they begin to lower potential. This changes their aqueous hydrogen bonding output, allowing a spectrum of attraction and surface potential.

 

Once they discharge their potential, they now become attracted to the higher nervous potential and begin to flow back up the gradient into the lymphatic tissue. Here they get powered up again. They increasing surface charge allows them to alter the internal protein gradients to digest a very wide range of complex food patterns. This is very over simplified and is intended to show what is happening at the hydrogen bonding potential level. The biochemistry makes use of the changing external and internal hydrogen bonding gradients for an integrated response.

 

If we look at cancer cells, many replicate out of control. When a cell is in the cell cycle, the membrane potential lowers. One theory for some types of cancer is due to defects in local nervous tissue control system. Certain cells can lose the high end of cellular differentiation control and are only seeing the lower blood potential. This one sided control system (bottom end) not only pulls them down into the cell cycle, but continues to feed food into in the constant cell division. I have no proof of this, just logic. But if it is true, the corrective measure is simple. Grow nervous tissue into cancers. This should not only slow the cell cycle turn-over, but it will keep the local immune system powered up for a better local response.

[sunspot]

I am going to change gears and look at the five atoms of life; C,N,O,H,P. There are others but this set is the vast bulk of biochemistry. I do not have time to patent or copyright any of my ideas. My mind stays in flux making it difficult to focus on one thing for too long. Everyone is free to make use of my seed ideas.

 

Here is the breakthrough stuff. If we look at H covalently bonded to O, N and C, this occurs via sp3 hybrid orbitals. What this means is the 2S and 2P orbitals of each of these three atoms, combine to make four similar orbitals with blended S and P character, instead of one S and three P's.

 

When hydrogen covalently bonds into an sp3 orbtial, it shares electrons but at P orbital distance. The hydrogen atom is actually optimized for 1S orbitals and can only be truly optimized as H2. Sharing within sp3 hybrid orbitals sort of gives hydrogen slightly ionized electrons to balance its positve charge, due to the P character of the shared electrons.

 

Within the living state, hydrogen essentially lives in the land of sp3 orbital giants (O,N,C) and is induced by these giants to wear baggy electron clothes. The result is that hydrogen is not only induced slightly positive, due to their higher electronegativity, but also carries the burden of the sp3 ionization. As such, going into a hydrogen bond it carries more burden of potential than any of the big three. Technically, only O and N will form hydrogen bonds in the traditional sense. However, newer and older studies indicate that C-H actually forms lower potential versions of hydrogen bonds due to the lower electronegativity of C compared to N or O. The charge within C-H is tiny but the baggy clothes is still there.

 

Although one little H is no match in the land of giants, H has numbers of its side and as a team is a formidable force. The team effort adds another layer to the biochemistry of the three giants. If we look at a cell, the biochemistry is manhandled by the vast numbers of little H, each with a potential chip on its shoulder. This is not standard chemisty lingo but is intended to draw a picture of the force that organizes everything in the cell. The biochemistry of the giants has the capactance of life, but the H is light weight choreographer that integrates everything.

 

Before gettiing into particulars I would like to look at P. Phosphorus is very important to the cell. It is part of DNA and RNA and is the basis for the ATP molecule. If we look P, it is a bigger giant among the smaller giants. It has electrons in the 3S and 3P orbitals. When its reacts to make phosphate PO4, it essentially loses all its 3 orbital electrons and is forced to share the level 2 orbital electrons of oxygen. Within phosphate, P is a giant wearing the tight electron clothes of the slightly smaller O giant. This is not exactly true. P will stretch out its electron clothes a little bit and O's electron clothes will get a little baggy. P sort of does to oxygen what oxygen does to H. When ATP forms from ADP, the extra P adds a slight potential to the O (baggy clothes), which is the stored energy value within ATP. Oxygen wants better fitting electron clothes and will team up with other oxygen atoms to get them.

 

The phospate in DNA and RNA is a little under stress. The O is slightly ionized with baggy P clothes. As such, although it has a negative charge for membrane repulsion, it is does not put out a full charge signal with respect to the hydrogen bonding hydrogen. In other words, the electrons of the oxygen of phosphate are even baggier for the H and is not their first choice. Someone like K+ is a different story, since these baggy clothes fit better for this series 3 atom.

[sunspot]

Pardon the elementary approach to the chemistry of life atoms. I thought it might get the point across easiler without requiring overbroard science. What I would like to look at is the left handed nature of bioactive proteins. The two terms, lefthanded and bioactive, implies that lefthanded proteins have a natural built-in potential, that right handed proteins lack. This built in potential, within lefthanded bio-active proteins, stems from the potential within the hydrogen bonding hydrogen of the cell, with the cell water, local and global, playing a very important role. Even the manufacture of the animo acids feels this local and global hydrogen bonding tension causing them to form the slightly potentiated left handedness. This tension is compounded further as proteins form.

 

In human culture, left handed people are stereo-typically considered more creative. If so, it may be due, in part, to the neural wiring into the right hemisphere. But it is also a function of simple needed adaptation. If one is left handed in a world which is primarily right handed, one, by necessity, needs to adapt themselves to the simple things of everyday cultural life that are easier for a righthanded person. In the past, a left handed child would soon realize that there are no left handed baseball gloves at the ball field. The choices were to learn to catch and throw the ball with only the left hand, or learn to throw the ball with the right hand. Nature is sort of similar in that lefthandedness required adaptation to the simple things of the inanimate world, which creates more of a balance between the left and righthanded amino acids and proteins.

 

If we take a long protein and stretch it out in water and then let the protein recompress into a 3-d strucuture, there are several potentials at work. The protein has its own secondary bonding forces built in that will attempt to minimize potential. One of the most important is the internal hydrogen bonding that will twist the protein into a helix. The protein is also dissolved in water. The hydrogen bonding potential within the water, due to the potential within the water's hydrogen, will also have an impact. For example, surface tension will force all the hydrophobic side groups of the linear protein to immediately avoid the water. At the same time, the protein is trying to minimize its own molecular potential. The result might be a compromise between the external and the internal potentials.

 

It we take the same protein and manufacture it fresh on a ribosome, it starts out as a little end piece, which is surrounded by water. Under these conditions, with the overall protein still in the works, the little protein fragment becomes the whole internal potential. This is being molded by the external water potential. If the needs of the water potential stores additional packing potential into the fragment, as new protein comes out hot off the press, its new internal potential is the sum of the internal potential of the new fragment, the hot internal molded potential of the old fragment, and the external potential. The final assembled 3-D protein can become something that is different than the 3-D isolated protein in water. It has built in potential that is quite useful for catalytic purposes.

 

What these packing stresses and strains essentially do is place internal hydrogen bonding hydrogen in nonoptimized orientations. If an internal hydrogen bond length is too long, or the bond angle is nonlinear, or if the hydrogen is place in a position where it is surround by a bunch of high surface tension hydrophobic moities, etc., each little hydrogen maintains residual potential for electron density. The overall sum makes the protein configuration electrophilic or needing electron density to lower the stress and strain. Unfortuneately, the structure is often very stable so the innternal potential remains.

 

In enzymes, this electrophilc strain helps the surface active site pull a substrate into an excited state. In other words, the excited state of the substrate is an attempt to share its electrons with the protein. The surface active side still needs the proper lock and key relationship to work right, but the calaysis potential is amplified by the structural stress and strain. If we took a nano-scissors and cut out the surface active site, the reaction rate would drop because the active would lose the extra electrophic affect stemming from the protein's structural electrophilic potential.

[sunspot]

I would like to discuss two potential paradoxes, associated with cellular hydrogen bonding. If we look at water, the hydrogen has a partial positive charge and slightly ionized shared electrons due to sharing 2sp3 orbitals with the highly electronegative oxygen. The oxygen has less potential in its slight negative dipole charge, since it induced this dipole charge for better octet stability. In fact, oxygen is able to accommodate even more negative charge as reflected by the formation of the OH- anion at neutral pH. Even that does not fully satisfy oxygen’s need for electrons under all conditions. Oxygen can reach O-2 or oxide in many cases. If one considers oxides, it is very difficult to take electrons back from oxide. Typically the best that occurs is ionic sharing with cations. The crystals that form spread out the negative charge of oxide to many cations, due to the stability of the oxide octet and oxygen’s resistance to giving up the electrons.

 

If we go back to water, the oxygen has little reason to share its puny excess electron density or negative dipole charge. In fact, it would like to have even more electron density all the way to the stable oxide. This is one of the potential paradoxes; a slightly negatively charged entity, oxygen of water, wanting more negative charge, i.e., wants even more electron density. The hydrogen is a horse of a different color. It is induced positive and has baggy electron clothes, i.e., slightly sp3 ionized. This double potential makes hydrogen look for electron density within the water. With oxygen being the only source of electrons, the hydrogen takes what it can, with the oxygen trying to twist away to retain it’s stabilized negative charge. The hydrogen bonding that does form within water lowers hydrogen’s potential, somewhat, but some potential still remains due to the constant evasiveness of the oxygen of water. This left over hydrogen potential is why metals will oxidize faster in water than in air. Hydrogen’s residual electrophilic potential acts as the catalyst.

 

The continued potential within the hydrogen of liquid water is loosely analogous to an oxidation potential in that it contains an electrophilic potential just like molecular oxygen. They both are looking for electron density. This is evident in the increased corrosion of metals in water. The hydrogen tries to share the easy metal electrons, pulling these electrons into a slight excited state, with molecular oxygen scooping them up because of its higher electrophilic potential.

 

If take a hydrocarbon and burn it with oxygen, this is highly exothermic because the reduced electrons within the hydrocarbon. Based on this reduced electron density within hydrocarbons, one might expect that this rich source of electrons should help lower the aqueous hydrogen bonding potential. The paradox is, the opposite will occur. The hydrocarbons will increase the potential of the aqueous hydrogen. The reason this occurs is that the hydrocarbon surface is not a good place for aqueous hydrogen to find electron density. It can actually do much better with the stubborn oxygen of water. The result is surface tension due to the hydrogen losing aqueous electron density by being in contact with the organic surface. This increases the local and global aqueous hydrogen potential. The hydrocarbons will lower their water contact surface area to help lower the increased aqueous hydrogen potential, while be pushed by the hydrogen to lower its local/global potential.

 

If we look in a cell, all the membrane lipid material, both inside and at the perimeter of the cell acts to increase the aqueous hydrogen bonding potential. While the increased aqueous hydrogen bonding potential acts as an electrophilic catalyst for the metabolic oxidation potential, sort of a second cousin of corrosion. The potentiated hydrogen of the cellular water energizes the top end of the mitochondria’s proton pumps, as well as the hydrogen/electrons of the Krebs cycle, which combine with molecular oxygen to form water.

 

This aqueous hydrogen bonding induction is directly reflected, during cell cycles. During cell cycles, the membrane potential will lower; implying the inside of the cell becomes less negative. This increases the impact of the high surface tension membrane materials. This results in the aqueous hydrogen potential increasing, thereby increasing the potential of all the hydrogen associated with the metabolic oxidation potential. The increased aqueous hydrogen bonding potential also changes the hydrogen bonding equilibrium of the metabolic enzymes (become more electrophilic), to increase reaction rates.

[sunspot]

To understand how the cell creates an aqueous hydrogen potential gradient from the inside of the cell membrane to the DNA, one needs to understand why the DNA defines a high hydrogen potential. There are at least three causes within the DNA double helix. The first is connected to the hydrogen bonding within the base pairing. In the base pair thymine and adenine there is an extra hydrogen bonding hydrogen that can not fully participate within the base pair hydrogen bonding. In the base pair cytosine and guanine, there are two such hydrogen. Actually, these hydrogen sort of share electrons with a lot of steric hindrance. As such, every base pair has considerable hydrogen potential built into them.

 

 

The second two reasons are easier to see by contrasting DNA and RNA. The DNA will form a double helix while the RNA typically has more variety often forming a single helix. The double helix of DNA is implicit of its higher hydrogen bonding potential. Both have the same extra hydrogen on all their bases. This makes them both sort of high with respect to their structural hydrogen potential. The extra hydrogen potential of the DNA is connected, in part, to the slight difference in the pentose sugars of DNA and RNA.

 

 

The pentose sugars ribose and deoxyribose differ only by the ribose of RNA having an C-OH group and the deoxyribose of DNA having an C-H group at the same spot on the sugar. The polar C-OH creates a lower surface tension affect within the local water, while the nonpolar C-H creates a higher surface tension affect. Although both pentose sugars create some surface tension within the local water, due to their slight imbalanced polar/nonpolar natures, the higher surface tension defined by deoxyribose will increase the local aqueous hydrogen potential impact of DNA more than ribose does for RNA.

 

The next difference has to do with DNA containing the base thymine and RNA containing the base uracil. The only difference between these two bases is a methyl -CH3 group for DNA's thymine, and a -H for RNA's uracil in the same position on the base. Everything else is the same. It comes down to the -CH3 of DNA's thymine creating more surface tension within the water, i.e., more aqueous hydrogen potential.

 

The real kicker that makes the DNA the high hydrogen potential pole of the cell (inside of the cell membrane is the low hydrogen potential pole due to its dynamic negative charge), are the histone packing proteins.

 

 

The lysine and arginine residues contain positive charges to neutralize the negative charges of phosphate groups along the DNA backbone. This amplifies others aspects of DNA. These packing proteins residues also both contain many extra hydrogen bonding hydrogen. These retain hydrogen potential within the packing structures. The result is that the packed DNA are the highest hydrogen potential structures within the cell. The more packed the DNA, the higher the hydrogen potential.

 

The next time I will rough out the cellular gradient