Chemistry separates from Physics

[sunspot]

What goes on with respect to the physics of the nuclei of atoms, is not 100% necessary to study chemistry. All the chemists needs to know is the number of protons within the nucleus, to know the atom, and the atomic orbitals being used by the atom. This is not to say that the physics of the nucleus and elementary particles is not important. But for the chemist, chemistry begins at the outer orbtial layers.

 

The reason I made this knit picking distinction is connected to the introduction of a new frontier in chemistry. This frontier is associated with modeling cells in terms of a single variable found within all cells, i..e, hydrogen bonding. As a first approximation, to get this new science up and running, I did something very analogous to the separation between physics and chemistry.

 

Using that analogy, the model is simplified, but still useful, by viewing molecules as the backbone, analogous to an atomic nucleus, with the molecular distinctions playing a role in hydrogen bond distinctions. In essense, molecular states create an interactive hydrogen bonding layer of dynamics within the cell, where molecular classes set the foundation for the hydrogen bonding distinctions.

 

For example, the DNA is a very unique foundation class for hydrogen bonding in that the entire molecule can define dynamic (breaking and reforming) and static (slight vibration) states of hydrogen bonding. During a nonreplicating cellular state, only part of the DNA becomes hydrogen bonding dynamic, while junk genes, etc. stay static. During the duplication of the DNA, the entire molecule becomes dynamic.

 

RNA is only a little different, chemically from DNA. This change in the chemical foundation alters the properties of the hydrogen bonding. When DNA is present, long RNA becomes mostly static as ribosomal RNA, while short RNA classes, like messenger RNA, exhibits dynamic hydrogen bonding. Proteins are different chemical foundations from both RNA and DNA, being mostly static hydrogen bonding with some proteins having a catalytic zone of dynamic hydrogen bonding. Proteins have animo acid diversity that can alter the potential defined by their static hydrogen bonds. This allows proteins to define a very wide range of hydrogen bonding foundation states.

 

The integrating medium of the cell is the water. Water can exist throughout the range of the static and dynamic hydrogen bonding states displayed by DNA, RNA and protein. It can also be in equilbrium with high surface tension molecules like lipids. This allows water to not only be in equilibrium with the exterior of the local foundation molecules, but the continuity of water within the cell, also allows the water to connect the hydrogen bonding gradients between the various foundations molecules.

 

I am not saying that the contemporary biochemistry of the cell is not important, just as the chemist does not say that the physics of the nucleus is not important. What I am saying is that just as the chemists can start outside the nucleus, the hydrogen bonding model can start outside the molecular diversity and still produce useful results. After the foundation theory is set in place, the hope is that others can help interface the model to existing biochemistry.

[patcalhoun]

Uh, where are you going with this?

[sunspot]

This model took many paths during its development. The hardest and key component only came to me last year about this time. This key has to do with using existing principles of chemistry to define hydrogen bonding potential within static hydrogen bonding states. Early models used physics speculation, which was impossible to prove with existing data and theory.

 

The heart of the analysis is connected to the high electronegativity of oxygen and nitrogen. If we look at water, the high electronegativity of oxygen causes the shared electrons within its covalent bonds with hydrogen to become skewed toward the oxygen. This reveals some of the positive charge on the hydrogen. The result is a molecular dipole. Pardon my crude analysis.

 

This is where it gets subtle. The high electronegativity of oxygen allows the oxygen to accommodate the extra electron density that is delocalized or else it would not have taken it in the first place. If we look at a single water molecule, the oxygen aspect is stable even though it has slightly more electron density than it has protons in its nucleus. Again, if this was not stable, it would have not taken the electrons in the first place. The hydrogen proton also wants electron density but loses out somewhat due to the higher stability or electonegativity of the oxygen.

 

The reason this is so, is connected to the full 2P orbitals of oxygen allowing magnetic addition of the six electrons in a 3-D arrangment. The magnetic addition overcomes the induced charge repulsion of having extra electrons, due to the EM force being the force integration of both the electrostatic and magnetic forces. The S, D and F orbitals do not magnetic add quite as well as P orbitals, resulting in atoms with these orbtials as their outer orbtials, all having lower electronegativity.

 

Getting back to our water molecule. The stability of the oxygen implies that the hydrogen carries the burden of potential. The oxygen doesn't need external positive charge for stability, or else it could just give back electrons to its covalent bond with hydrogen to get the same effect. As such, going into a hydrogen bond, the hydrogen carries the primary burden of potential. When the hydrogen forms a hydrogen bond with the oxygen of an external water molecule it lowers its induced potential. The oxygen will lower its charge potential, but it will lose some of its 2P orbital magnetic addition. These two opposite affects may or may not be a wash for oxygen, but the bottom line is that hydrogen lowers its potential in two ways (electrostatic and magnetic), while oxygen only lowers potential in one way (electrostatic).

 

What this subtle analysis implies is that if a hydrogen bond forms but is not optimized with respect to both distance and angle, more residual potential will remain within the hydrogen of that hydrogen bond than within the oxygen or nitrogen. The living state, especially the proteins, create odd angles and nonoptimized bond lengths due to their bulky amino acid side groups. This creates molecular configurations with a large number of hydrogen bonding hydrogen that contain lingering potential.

[insane_alien]

1. Its already defined that Chemistry doesn't study the interaction in the nuclei of atoms to any great detail because its not a chemical reaction.

 

2. Hydrogen bonding in cells is already very well reasearched and is in no way a "new frontier in chemistry" its been around for 100+ years already.

 

3. Are you copying this from somewhere?

[sunspot]

I did not copy this or anything I write. Years ago, I took, I think it was Walt Whitman's advice. He said something to the effect, " learn all that you can by reading the works of all the great thinkers, and then forget it all, and try to come up with your own ideas.

 

Although knowledge of the hydrogen bonding has been around for quite some time, everyone wrongfully assumed that both hydrogen and the highly electronegative atom participate equally in the hydrogen bond. Intuitively, I saw this to be false and worked to explain why. This little extra for the hydrogen makes all the difference in the world and allows the cell to integrate via the hydrogen bonding.

 

As an additional example, to make things clearer, if we look at Cl- ion, it is a very weak base. The question that came to my mind is why should this be, if it has an extra electron and therefore extra negative charge. The best answer was that the magnetic addition defined by the 2P orbitals not only allows Cl- to have more electrons than nuclear protons, but its also stabilizes the extra negative charge so well as to cancel out what should be strong electrostatic attraction to any positive charge.

 

Something similar is true for oxygen and nitrogen (also have high electronegativity due to 2P orbital magnetic addition). This cancels out some of the electrostatic affect on the negative side of a hydrogen nitrogen or oxygen dipole. Hydrogen is not so fortunate and therefore carries a higher burden of potential within O-H or N-H bonds. Hydrogen wants to form the hydrogen bond, nitrogen and oxygen care less due to their stability.

 

The next post will discuss how the DNA is the most important foundation molecule for the hydrogen bonding potential within the cell. I realize everyone also believes that the DNA is the king of the cell, but in reality the DNA actually plays a very important support role.

[Borek]

All the chemists needs to know is the number of protons within the nucleus, to know the atom, and the atomic orbitals being used by the atom.

 

No. There are high differences in kinetics of H and D, and they are not due to number of protons

 

Best,

Borek

--

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[sunspot]

I agree that there are significant differences in chemical properties due to the number of neutrons within the nucleus. For example, diffusion rates are faster for H than D. One could separate these isotopes based on their distinct diffusion rates. However, what I was originally speaking of was that the chemist does not need to know the physical configuration of the nucleus, for example, proton orbitals, to be able to approach chemistry. If a chemist was interested, say in super extreme pressure chemistry, where nuclear reactions and atomic disentegtations begin to occur, than the induced excitation of the proton orbtials would be very important.

 

The point of my bringing this up, had to do with creating perspective, so I could introduce how cells are integrated via the hydrogen bonding. I was using this analogy to show that molecular foundations, like DNA, are a nucleus of sorts for hydrogen bonding states. An intro to this will be my next post.

[sunspot]

The DNA foundations for hydrogen bonding

 

As was discussed earlier in this topic, hydrogen bonds have a disproportionate distribution of potential, with the hydrogen containing more potential than the highly electronegative atom.

 

If we look at the base pairing along the DNA double helix as show in the figure below something subtle is also evident. In particular, one will notice that the thymine/adenine base pairs have an extra nonbonded hydrogen bonding hydrogen, while the cytosine/guanine base pair have two unbonded hydrogen bonding hydrogen. What this implies is that each base pair has residual hydrogen bonding potential built into its foundation structure.

 

 

In a cell, where the DNA is not being duplicated, the DNA will exist in both packed and unpacked states. The transcribed genes are unpacked, while things like junk genes, etc., are packed with various layers of packing proteins. In the figure below, the most important amino acids that are used for packing the DNA are shown.

 

 

The significance of lysine and arginine are all the extra hydrogen bonding hydrogen along these amino acids side chains. The positive charge aspects bind with the negatively charge phosphates of the DNA. This neutralizes some of the electron density that have been helping to stabilize the extra hydrogen bonding hydrogen within the base pairing. But beyond that, packing causes extra lysine and arginine residues to become part of the packing structure. This places extra hydrogen bonding hydrogen in physical positions where they can not form hydrogen bonds effectively. This allows packed DNA to define even more hydrogen bonding potential.

 

The significance of this is that there is a potential between packed and unpacked DNA. The so-called junk genes, for example, are actually there as an anchor, so to speak, that resists unpacking and which can help induce repacking via the potential they create in the nucleus water. The aqueous hydrogen bonding potential within the nucleus of the cell, will help the packed/unpacked DNA foundation form an equilibrium structure that can be pertubated by pertubations of the hydrogen bonding potential within the cellular water that passes through the nuclear membrane.

 

One of the most obvious is connected to the lowering of the membrane potential during cell cycles, i.e., the average aqueous hydrogen bonding potential of the cell increases. This begins a series of events ultimately leading to the condensation or total packing of the doubled DNA into chromosomes. This creates a DNA foundation with a maximize hydrogen bonding potential. The lower of this maximized hydrogen bonding potential within the DNA (chromosomes separate and unpack) contains an energy capacitance that helps the separation into two daughter cells. The eariest cell cycles did not have to be so molecular fancy as today. They only had to push the DNA foundation up and over the hydrogen bonding energy hill.

[sunspot]

I would like to add one more layer to the model; cell membrane. The cellular membrane will create a potential across itself due to the pumping of cations. In very general terms, three sodium cations are pumped out and two potassium cations are let in. The cation inbalance makes the outside positive and the inside negative. This is sort of an interesting way to make the membrane potential, in that only the movement of cations creates both the negative and positive sides of the potential. This is not coincidental, since the movement of cations is tuned to the hydrogen bonding hydrogen within the water.

 

Relative to the membrane potential, the positively charged outside of the membrane competes with the hydrogen of the external water for the electrons of the oxygen of water. This implies a zone of very high hydrogen proton potential. This potential is transmitted into the external water, to help spread out the potential. It can be shown that this helps attract reduced food molecules toward the cell. In other words, reduce materials increase the surface tension within water (increase the hydrogen bonding potential). As such, the external membrane ,by defining high hydrogen bonding potential, also define an equilibrium position for high surface tension materials. This also helps lower the potential within the external water.

 

Relative to the inside of the cellular membrane, the negatively charge inside implies a relatively rich electron density area of the cell that defines very low aqueous hydrogen bonding potential. With the DNA so huge and at least partially packed and containing so much structural hydrogen bonding potential, a hydrogen bonding potential gradient is established within the cell between the cell membrane and the DNA. The rest of the foundation materials within the cell can be shown to define equilibrium positions within this primary gradient. What is slick about the DNA, is that he negative charges on the exposed phosphate repel the inside of the membrane helping to anchor the DNA pole of the gradient away from the membrane.

 

Getting back to the food materials equilibrium stuck on the outside of the cell, the cell will use the potential within the membrane to transport this food in. What this involves is the local reversal of the membrane potential where the local inside briefly becomes positive, and as such now becomes the new best equilibrium place for the food. Unfortuneately for the food, the cell quickly resets the local potential, via the sodium pumps, to create nonequilibrium for food, with no way to back out. This nonequilbrium state of the food is then addressed in a number of ways by cell in an attempt to restore the hydrogen bonding gradient within the cell.

[sunspot]

Comparing DNA and RNA

 

Both DNA and RNA will form hydrogen bonds in the same way, via base pairing, and will both have the extra nonhydrogen bonded hydrogen built into the bases The differences between DNA and RNA are quite simple and comes down to only two things. The first has to with the slight differences within the pentose sugars of RNA and DNA. The first pic is the ribose of RNA and the second is deoxyribose of DNA.

 

 

 

The two differ by only the -H on the deoxyribose and an -OH on ribose (botton right of the pentose). The -H of deoxyribose will create more surface tension in water than the polar -OH group, causing the DNA to define more surface tension in the water than RNA. This amount to the sugars of DNA inducing a higher aqueous hydrogen bonding potential.

 

The second aspect has to do with the base pair difference between RNA and DNA. The only difference is that DNA uses thymine and RNA uses uracil to hydrogen bond with adenine. Both have the other three bases in common.

 

 

 

The only difference between these two is that thymine in the first pic has a -CH3 group where uracil of the second pic only has a -H. This little distinction for DNA creates more surface tension in water. The higher surface tension of the DNA will increase the aquoeus hydrogen bonding potential and therefore the hydrogen bonding pootential of the DNA causing the DNA to form the double helix. The lower surface tension and hydrogen bonding potential of the RNA allows it to form both double and single helixes.

 

Relative to the histone packing proteins discussed earlier, the lysine and arginine residues of the histone packing proteins not only have all those extra hydrogen bonding hydrogen, but they also contain short sections of -CH2-CH2-CH2- before these hydrogen. These organic sections will ball up to lower the surface tension within the water, but they will nevertheless add some extra hydrogen bonding potential value or surface tension to the local water. The net effect is that the histones will prefer the DNA over the RNA because of DNA's higher hydrogen bonding potential value.

[sunspot]

Metabolic Oxidation Potential

 

I would like to add another layer to the onion. I am not going to go into great detail with respect to cellular metabolism, only a single, but very important consideration.

 

The terminal electron acceptor of cellular metabolism, for the most energetic metabolic reactions is O2. Oxygen is highly electronegative and the two O's of O2 can easily accept extra electrons. Consider the effects of the aqueous hydrogen bonding potential. When it is high, the hydrogen of water also needs electron density. This will increase the potential for O2 to accept electrons from metabolism, due to the hydrogen trying to share its unbonded electrons.

 

If we look at a cell getting ready to enter the cell cycle, the membrane will desaturate and the cation pumps will increasely reverse. This lowers the membrane potential, such that the inside of the membrane increases its effective aqueous hydrogen bonding potential. The result is the observed increase in the cellular metabolic potential and an increased production of ATP (energy unit of the cell). This gets the ball rolling.

 

The ball beginning to roll will cause the cellular synthesis to increase. The result is the increased production and steady accumulation of the protein materials needed to form the two daughter cells. This accumulation of proteins, implies the accumulation of relatively high hydrogen bonding potential materials within the cell. The result is a steady increase in the aqueous hydrogen bonding potential, and the observed steady increase in the metabolic oxidation potential and ATP production.

 

If we look at enzymes they are highly specific with respect to reactants, almost like a key and lock. Along with this enzyme specificity, enzymes have one important thing in common. They pull the attached reactant into an excited state. This excited state of the reactant helps to temporarily lower the hydrogen bonding potential that is built into the enzyme's structure. After the reaction, the product key no longer fits the enzyme lock, releasing the product, resetting the enzyme specificity and the hydrogen bonding potential of the enzyme, for another cycle. As the aqueous hydrogen bonding potential climbs ,during the cell cycle, so does the average hydrogen bonding potential defined by all the enzymes due to their immersion in water, increasing the rate of synthesis within the cell. The increase production of ATP also plays an important role.

[sunspot]

Duplication of the DNA

 

I am going to add one last layer to this introduction of the Hydrogen Bonding Model of the cell. In the past, I took a freshman college biology textbook and paralleled the hydrogen bonding analysis to the standard biochemical analysis. The practical value of the model was that only basic observational data, basic principles of chemistry, and logic were required.

 

This last layer of this introduction will explain some basic hydrogen bonding considerations that can explain why the cell shifts from RNA to DNA synthesis late in the cell cycle. The explanation is rather simple. As was shown before, the DNA defines a higher hydrogen bonding potential than the RNA due to its two higher surface tension distinctions in its pentose sugar and thymine base. As such, DNA monomers will also define higher hydrogen bonding potential than RNA monomers. As the cellular water potential increases, due to the accumulation of all the proteins needed for the two daughter cells, the increasing aqueous hydrogen bonding potential within the cytoplasm favors the production of DNA monomers.

 

During cell cycles a potential paradox occurs within the nucleus. In particular, if the aqueous hydrogen bonding potential of the cytoplasm is increasing during the cell cycle, why does the DNA want to unpack into a lower hydrogen bonding potential state (for widescale RNA synthesis and DNA duplication) instead of packing tighter into a higher hydrogen bonding potential configuration? The answer is also quite simple. The increase production rate of RNA and then DNA monomers flowing into the nucleus will lower the aqueous hydrogen bonding potential within the nucleus causing the DNA to increasingly unpack. In other words, the aqueous hydrogen bonding potential within the cell becomes segregated by the nuclear membrane. All these monomers (plus ATP) flood the nucleus because of the increasing nucleus reaction kinetics.

 

Once the DNA is duplicated, the doubled DNA is no longer active for synthesis. To my knowledge a third strand of DNA does not form. With the monomers concentration still high, the doubled DNA seeks a further lowering of hydrogen bonding potential. This provides the protential for enzymes to fix any improper base pairing (optimum base pairing implies the lowest equilibrium potential). Eventually, the monomers realize, there is no longer any chemical potential in the nucleus, so they return to the cytoplasm for recycle, where a secondary chemical potential exists. The DNA begins to feel the nucleus water potential increasing. This induces the DNA to begin packing toward condensed chromosomes.

 

The packing toward condensed or totoally packed chromosomes appear to get a momentum going that causes them to exceed the nucleus water potential. This causes them to increase the nucleus water potential beyond the influence of the cyctoplasm. One important result is the nucleur membrane being induced to increase its hydrogen bonding potential until it disperses due to its higher equilibrium surface tension.

[rakuenso]

sorry but wtf??

[sunspot]

The f is, there is another layer of potential within the cell called hydrogen bonding potential. Did you ever stop to think why the life sciences are more dependant on empirical models than any other branch of science. The reason is, this large branch of science is missing something very important and are trying to ignor it with statistics. If one adds what is left out, i.e., hydrogen bonding potential, the life sciences become more logical, allowing things to progress faster.

[sunspot]

I am going to end this analysis here, for the time being. I am going back to the fundamental premise; the potential imbalance within hydrogen bonds. Once that is proven scientifically, everything else follows logically. I worked under the assumption is was and extrapolated from there.

 

The point I would like to present today is to contrast the empirical nature of the life sciences with the more rational sciences. For example, in exams within physics, chemistry, math, engineering, one can solve unknown problems using only basic principles and a little ingenuity. For example, the chemistry student can be given an alcohol molecule, they have never seen before and be asked to predict its reaction based on the reagents supplied. The logical principles of chemistry make this possible. Within the life sciences, apart from the biochemistry, this is not possible.

 

When I was younger in both high school and university, I was strongly attracted to biology, but never bothered to take it. There was too much memory work for my tastes and very few fundamental principles, like in math, physics, chemistry, engineeering, where one could predict and invent things using a little ingenuity and a small set of principles. The genetic theory is the cure all but has a lot of practical limitations.

 

It was during second semester organic chemistry class that the author of the textbook (Morrison and Boyd) pointed out the importance of hydrogen bonding for biomaterials, and suggested that it needed to be explored, yet nobody seemed to bother with that path or could figure how to exploit it. Years later that became my goal. After many many years, I found that by using hydrogen bonding to explain life phenomena, the life sciences can finally be brought to par with the rational sciences.

 

Let me give multicellular examples; the human body. The primary hydrogen bonding potential gradient is between the brain (nervous tissue) and the blood supply. Cellular differentiation is based on hydrogen bonding gradients. The chemistry is important but it represents the material capactiance behind the hydrogen bonding potential. The model is holographic with a similar analysis used at any level of the living state. The basic ideas are gradients and potentials.