Making a Cell from scratch

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The extra hydrogen bonding hydrogen, within the base pairing of DNA, and the extra hydrogen bonding hydrogen of the DNA packing proteins, induce DNA packing structures to define the highest hydrogen potential, with more DNA packing meaning more hydrogen potential. The observed methylation of packed DNA is a simple reflection of packing equilibrium since the extra methyl groups add more surface tension to the DNA to reflected the higher hydrogen potential implicit of packing. What the relationship between packing and hydrogen potential implies is that the doubled condensed chromosomes are the highest hydrogen potential structures of the cell.

 

After the doubled chromosomes condense, the nuclear membrane will disappear. This is a well documented observation. This observation is due, in part, to a surface tension affect that is created by the condensed chromosomes. The nuclear membrane is induced into nonequilibrium and needs to define a new equilibrium shape and position because of the aqueous hydrogen potential induction cause by this highly packed DNA.

 

I not going to get into a detailed discussion of how all the observations of mitosis reflects a systematic lowering of the packing potential within the double packed DNA. Essentially, the ATP that runs the spindle focuses a lot of countering negative charge and low aqueous potential near the DNA. The result is a lower hydrogen potential DNA configuration implicit of two sets of separated condensed chromosomes.

 

As each set of chromosomes continue to lower their hydrogen potential by unpacking further, the nuclear membrane will eventually reform around the DNA, due to a much more favorable aqueous equilibrium. The aspects of the DNA that remain packed, such as the centromere, will define the highest hydrogen potential structures within the nucleus of a nondividing cell and will create a hydrogen potential gradient with the lower hydrogen potential nuclear membrane. The rest of the structures within the nucleus will assume equilibrium positions within this dynamic nucleus gradient.

 

It is not cooincidental that the active (unpacked genes) are often found near the nuclear membrane. These define a relatively low potential, due to lack of packing proteins. This state of the DNA is induced, in part, by the aqueous channels within the nuclear membrane. The lower hydrogen potential cytoplasm (due to the negatively charged inside of the cell membrane) sends global and specific aqueous hydrogen potential signals into the nuclear membrane. This lowers the potential of the DNA causing aspects to unpack and migrate toward the nuclear membrane. The unpacking of the DNA is resisted by the higher potential of the packed aspects of the DNA. These two countering hydrogen potentials help the nucleus maintain a specfic DNA packing/unpacking differentiation.

 

If we look at DNA unpacking, this can not happen by itself due to steric hindrance within the DNA packing structures. What is typically required are unpacking enzymes. The low potential signal coming into the nucleus, from the cytoplasm, will create nonequilibrium for certain packed genes. It is nonequilibrium because these genes should be unpacked at that aqueous hydrogen potential but can not unpack spontaneously due to the steric hindrance. The unpacking enzymes find the most potentiated points on the packed DNA and combine to form the needed equilibrium. In the process, they unpack the DNA, altering the local equilbrium. This will cause the next batch of enzymes and biochemicals to flow to these newly created potential zones, etc., leading to the transription of RNA.

 

One of the prominent features within the nucleus is the nucleolus. This is where the ribosomes are assembled. If we consider the long length of the ribosomal RNA, this area of the DNA define the longest continuous lengths of unpacked DNA. The mRNA of active genes are smaller by comparision, although many adjacent genes may add up to very similar lengths. The net affect of the long lengths of DNA unpacking is that the nucleolus is the lowest potential pole of the DNA. As the lower potential rRNA accumulates within this zone (RNA defines a lower hydrogen potential than DNA) the hydrogen potential of the DNA will drop further until the lower potential ribosomes begin to form to reflect equilibrium. These are lower potential, as inferred by the observation that they leave the nucleus to assume positions within the top of the cytoplasm gradient.

 

The nucleolus's ribosomal production rate sort of coordinates with all the RNA production within the nucleus. All the formed RNA and unpacked DNA lowers the nucleus aqueous hydrogen potential, while being resisted by the packed DNA. The equilbrium seen by the nucleolus will coordinate the ribosomal production rate to maintain the needed proportions to the entire RNA production.

 

One important consideration within respect to other subgradients within the nucleus is how hydrogen potential is conducted withing the nucleus. The most obvious means is via the water within the nucleus. This would explain why altering the transcription parameters of one gene can sometimes cause a distant gene to react. The gene grouping is part of a local aqueous cluster with its own little subgradients set up locally. It is not quite as simple as centromere to nucleolus to nuclear membrane to cytoplasm, although the subgradients are within these gradients.

 

It also seems theoretically possible for hydrogen potential to conduct axially along the DNA double helix, via the hydrogen bonding of the base pairing. The extra hydrogen bonding hydrogen, within each base pair, might lower potential via an axial connection between adjacent base pairs on the DNA double helix. The DNA double helix might actually be a type of hydrogen potential wire.

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I keep writing with the hopes that others can benefit by what will become the newest frontier in the life sciences. It should really speed up progress in medicine, since we should be able to target using equilibrium designs. The virus already does this. Its protein shell says one equilibrium state to help sneak into and out of the cell. When it sheds its skins, it is able to define another equilibrium zone close to the DNA.

 

The cell gradient, as a whole, has its maximum potential between the inside of the cell membrane (negative) and the packed aspects of the DNA. The nuclear membrane acts as a buffer that breaks this primary internal gradient into two compartments. We already discuss the basics within the nucleus. From the nuclear membrane to the cell membrane, there are actually two overlapping gradients of parallel potential within the primary gradient. One aspect begins at the DNA and extends to the cell membrane. The second aspect starts at the cell membrane and extends to the nuclear membrane.

 

The observed cell hierarchy of RNA/protein biosynthesis activity, starting at the DNA lines up with a decreasing hydrogen potential. From the DNA, to the rough ER, to the smooth ER, to the Golgi apparatus and then to the cell membrane reflects an ever lowering of structural hydrogen potential. There are also lateral branchings as proteins assume their equilibrium positions within the gradient.

 

One interesting tidbit is the base uracil on RNA. It has a lower surface tension induction than the thymine of DNA. This lower aqueous hydrogen potential induction allows larger proteins to form on the ribosomes than if the RNA contained thymine. The thymine would increase the local water potential near the mRNA and ribosomes, and would decrease how much hydrogen potential the proteins could define before the entire translation complex reaches nonequilbrium. Smaller proteins would be one result.

 

The other aspect of the gradient begins at the cell membrane with the protein flux from the DNA down gradient helping to populate it. The gradient from the cell membrane is actually two-fold. One aspect goes from inside to outside the cell membrane The second go from inside the cell membrane to the nuclear membrane.

 

There is a high hydrogen potential difference between the inside and outside of the cell membrane, with the outside being at the higher hydrogen potential due to its positive charge. The parallel between high surface tension and high aqueous hydrogen potential allows external organics to form an equilibirun on the outer membrane surface. The aqueous signal from the external membrane surface is sort of a tracker beam for the organics to follow so they can reach this better equilibrium zone. The bulk exterior water, is also trying to lower its global potential, pushing organics toward the cell.

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This will be my last post on this topic. It is hard to stay motivated not knowing if I am reaching anyone or whether I am making my ideas clear enough to understand. Like I said last time, hydrogen potential is the future of the life sciences, those who get a jump will gather the spoils.

 

What I would like to do is discuss some of the main hydrogen potential considerations of cell cycles. One of the observations that begins the cell cycle is the increasing unsaturation of the cell membrane. This will make the membrane more fluid and will increase the cationic leakiness lowering the cellular membrane potential. The lowering of the membrane potential makes the inside less negative and the outside less positive. The outside lowers its food attraction/equilibirum potential, while the inside of the cell increases its aqueous hydrogen potential.

 

The equilibrium trigger that causes the unsaturation is connected to the accumulation of food reserves needed for the cell cycle. This will cause a local change in aqueous equilibrium that will alter lipid production toward unsaturation. What unsaturation implies less surface tension due to less reduced hydrogen on the lipids. This suggests the food reserves will lower the local aqueous hydrogen potential shifting the strucutural equilbrium of the lipid production machinery.

 

The lowering of the membrane potential will increase aqueous hydrogen bonding potential within the cytoplasm. This will increase the top end of the mitochondria's proton pumps as well as the electrophilic potential of all the metabolic enzymes. The result is an increasing metabolism and ATP production rate.

 

There is sort of a paradox at work at the DNA. With the cytoplasm hydrogen potential increasing, due to the lower membrane potential, one would expect the DNA to pack. Instead more and more genes unpack to form the materials for the two daughter cell. The reason this occurs is due to the increase production rate of ATP and other RNA triphosphate monomers, which flow into the nucleus. These will have alow aqeous hydrogen potential affect, that will lower the nucleus hydrogen potential.

 

The increased production rate of RNA and proteins needs to form two daughter cells implies the accumuation of moderately high hydrogen potential materials within the cytoplasm. The result is the aqueous hydrogen potential of the cytoplasm steadily increasing. This steadily increases the metaboliic rate and ATP production rate.

 

The eventual shift from RNA production to DNA duplicaiton occurs due to the increase aqueous potential within the cytoplasm. The DNA monomers define a higher surface tension affect than RNA monomers. The shift from RNA into DNA monomers is due the higher aqueous hydrogen potential equilibrium due the affect of the accumulating daughter cell materials.

 

After the DNA is duplicated there is still a lot of monomer triphosphate and ATP in the nucleus. It begins to realize that there is no more reaction here and a better chemical potential can now be found within the cytoplasm (recycle). During the period of indecision these accumulative materials help maintain the moderately low nucleus water potential. The enzymes that correct defective base pairing will see the higher potential nonequilibrium zones on the DNA where base pairing is not optimized. They combine there to help the DNA define equilibrium, fixing the DNA in the process. Fixing the defect creates nonequilibrium for them causing them to drift to another nonequilibrium zone on the DNA.

 

As the DNA monomers and ATP exits the nucleus the nucleus potential begins to increase. The equilibrium state of the DNA is maintain by the flux of packing proteins that pack the DNA to condensed chromosomes. These are the highest hydrogen potential structures of life. When the condensed chromosome form, the nuclear membrane will define nonequilibrium causing it to disperse. The high hydrogen potential signal from the doubled condensed chromosomes is so strong that even the structural proteins and the Golgi apparatus will disperse due to the high surface tension created within the cytoplasm. These maximized potential structures equilibrium break up cellular structures for easier distribution between the two daughter cells.

 

The centriole, as inferred by their normal position within the cell, are at a lower potential than even unpacked DNA. Their positioning at the poles of the cell sets up a dual gradient within the cell. The spindle is a structural way to connect the gradient between these structures, almost like wires. The flux of ATP, which works the spindle, is a way for the cell to lower the nonequilibrium potential defined by the double condensed chromosomes. The result is the separation of the chromosomes. This lowers the structural potential defined by the DNA.

 

The poles of the cell, which align the centriole, are structures of lower hydrogen potential value than the centriole. The position between the separated DNA, where they formly were, defines a zone of high hydrogen potential. This potential is lowered with membrane flowing into this zone.

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I guess I should never say never. It dawned on me that the original post was making a cell from scratch, more or less. Now that I have build background, let me add some equilibrium detail to show the logic of cell building. The implications are provocative to say the least.

 

As a teaching example and logical experiment of integrated hydrogen potential, I would like to begin with two complementary strands of DNA. If we place the DNA double helix into a beaker of neutral water, the DNA double helix might coil and uncoil somewhat, but for the most part, it will remain a double helix that stretches out within the beaker. The negative charges along the phosphate backbone will repel and cause the DNA to assume a minimum potential expanded double helix configuration.

 

Next, let us take the DNA and transcribe two long strands of RNA from the DNA, which reflect all the exact template relationships and ordering on the genes. If we place these two long strands of RNA into a second similar beaker, the complexity of RNA folding would be higher than the DNA. Some sections of the RNA would remain a double helix. Other areas would exist as two separated single helixes. Still other areas would have each single helix folding onto itself or onto new areas of the RNA to define new sections of double helix, etc. The net affect is that the hydrogen bonding equilibrium of the RNA, with the same hydrogen potential water will result in a much greater packing variety, in spite of roughly the same number of negatively charge phosphate groups.

 

Next, let us make two long strands of protein translated from the two RNA helixes such that the two long protein strands reflect all the ordering of the template relationships. If we place the two long protein strands into a third similar beaker, the two protein strands will form an even greater variety of hydrogen bonding induced packing relationships than the RNA, in its attempt to form an equilibrium with the same water. This greater packing variety is due to the greater variety of amino acid side groups along the two long protein chains, compared to the simpler four bases of the RNA or DNA.

 

Let us return to the first beaker that contains the DNA and carefully separate part of the double helix in the middle somewhere. The exposed reduced pentose sugar moieties on a single strand of DNA will increase the surface tension within the local water and therefore increase the hydrogen potential within the local water. The increased local aqueous hydrogen potential, in turn, will increase the hydrogen bonding potential of the bases along the DNA. The overall potential is minimized via the DNA double helix reforming. The double helix lowers the hydrogen bonding potential of the base pairs along DNA. It also lowers the surface area and surface tension of the sugar moieties that are in contact with the water and places the negatively charged phosphate groups near the packed sugar moieties thereby minimizing any residual aqueous hydrogen bonding potential. Any separation from the double helix will increase the local aqueous bonding potential.

 

The RNA differs from the DNA, in part, in that its pentose sugar moieties has an –OH group exchanged for one of DNA’s pentose sugar’s hydrogen atoms. This adds extra available electron density to the sugar moiety thereby lowering the surface tension with water relative to the DNA. The lower surface tension lowers the local aqueous hydrogen bonding potential, and therefore the hydrogen bonding potential induction onto the bases of the RNA. This will weaken the hydrogen potential of the base pairs along the RNA double helix making more packing variety possible with the same aqueous hydrogen bonding potential.

 

The substitution of the base uracil of RNA for the base thymine of DNA has a parallel effect. The loss of the methyl group on thymine in exchange for the hydrogen on uracil implies a lower surface tension effect stemming from uracil relative to thymine. This will allow the RNA single helix to define an even lower hydrogen bonding potential compared to the DNA, resulting in more packing variety.

 

The third beaker with the two long proteins strands will have the greatest variety of packing because of the wide variety of amino acid side groups available. In cells, many of these protein segments containing hydrophobic side groups would bind with lipids. Without the lipids, these organic side groups will increase the surface tension in the water and will thereby need to assume positions that will help minimize the hydrogen bonding potential within the water. This will result in the hydrophobic moieties clustering and/or becoming the interior regions of proteins. In many places surface tension will remain. While the crude protein packing will result in steric hindrance that prevents every hydrogen bonding hydrogen from minimizing potential. The net result is the aqueous hydrogen potential will increase with the two protein strands defining residual hydrogen potential equilibrium packing states.

 

At this time, I would like to add some lipid membrane material to the third beaker, which contains the two long strands of protein. The initial addition of lipids will further increase the surface tension within the water. Some of the hydrophobic protein segments along the two long protein strands will associated with the lipids to help lower van der Waals potential and surface tension. Other protein aspects will be repelled by the lipids and will try to move away. The lipids themselves will cluster as a bi-layer to help minimize potential, i.e., lower surface area with water for lower surface tension. The minimum hydrogen bonding potential shape will be a spherical bi-layer shell surrounding the protein strands with hydrophobic protein segments embedded within the lipid bi-layer.

 

After the membrane material surrounds and integrates the two long strands of protein, I would like to insert some mitochondria. Because many of the proteins along the two long protein strands have innate ATP active areas, the increasing concentration of ATP, due to the mitochondria, will eventually begin to hydrolyze on these roughly packed protein segments. The ATP site firing will add a snap to these proteins that will shake them into lower hydrogen bonding potential states, i.e., ATP and phosphate will induce decreasing hydrogen potential inductions onto the active proteins due to the negative charges on the ATP and/or phosphate.

 

Under optimum conditions the ATP will quickly find the sodium pumps and begin to differentiate them from the protein blend. Their cation firing/exchange will cause them to repel each other and break away from the mother strands, until they all end up in the membrane. The firing sodium pumps within the membrane will lower the hydrogen potential within the water volume contained by the membrane due to the three to two exchange of sodium ions out and potassium ions in. The lower internal aqueous hydrogen potential induction will loosen things up by lowering the equilibrium structural hydrogen bonding potential of the remaining proteins. This will form a new blend of active ATP sites, due to the ATP active sites now being able to more easily share electron density with ATP. This will increase the differentiation of other enzymatic proteins.

 

The membrane potential will also help establish a simple protein gradient within the water volume, where the higher hydrogen bonding potential proteins will move toward the negative charge stemming from the inside of the membrane to help lower their hydrogen bonding potential. The lower hydrogen bonding potential proteins, by being crowded out, will move away from the membrane to form an equilibrium aqueous volume. This protein gradient will help minimize the internal aqueous hydrogen potential.

 

When steady state is reached, we next add the two strands of RNA. Because the RNA defines a different hydrogen potential equilibrium than the proteins, it will assume its place in the gradient while also altering the gradient by its massive presence. The negative charge phosphate groups will make the RNA repulsive to the inside of the membrane, due to the sodium pump potential, causing it to go to the center. The dual negative zones within the volume, due to the membrane and the RNA, will alter the protein gradient causing the higher hydrogen bonding potential proteins to divide with some grouping both near the RNA and the membrane. The lower hydrogen bonding potential proteins will group in the middle thereby minimizing the aqueous hydrogen bonding potential.

 

This new dual gradient will eventually allow the RNA to associate with the proteins that it normally integrates with. Other proteins in combination with ATP will help to break the RNA down into smaller sections. The optimum results are crude ribosomes and the rough machinery needed for protein production. These will extend down the structural gradient toward the central protein zone between the RNA and the membrane.

 

When a new steady state is reached, we then add the DNA double helix. The DNA will also find its place in the gradient and will alter the gradient by its massive presence. All its negatively charged phosphate groups will make it avoid the membrane. The association of the RNA with protein by neutralizing some of the negative charge along the RNA will skew the DNA toward this central region near the RNA. The addition of the extra negative charge of DNA within the center of the volume will once again alter the bulk protein/RNA gradient bringing more high hydrogen potential proteins toward the center near the DNA and RNA.

 

When the histone packing proteins find the DNA, the DNA packing will simplify the number of available genes open for possible transcription. This packing will also result in less repulsion between the RNA and DNA causing them to increasingly associate. The packing of the DNA will also increase the hydrogen bonding potential of the DNA and alter the gradient potential between the DNA and the membrane, with the DNA moving toward increasing hydrogen potential.

 

The net effect is that the DNA packing will increase the gradient potential between the lower hydrogen potential membrane and the increasing hydrogen potential bare bones nonpacked genetic configuration that will slowly emerge. The RNA will help lower the increasing hydrogen bonding potential of the DNA by associating with the barebone genes.

 

When a new steady state is reached, the final step of our experiment will be to induce our pseudo-cell into a preliminary cell cycle using the mitochondria. Because the pseudo-cell has only bare bones genes exposed and no reliable machinery for the cell cycle, the first replication cycle will primarily cause the mitochondria to divide and accumulate. The latter will have an evolving impact on the protein gradients that will reform and be better integrated via the mitochondria. One of these teaching experiments should create a simple viable life form, which is centered on the mitochondria, which will gradually integrate itself with the bare bones genetic differentiation.