Hydrogen Bonding

[Michaelangelica]

Ho ray

I understood one of your post on hydrogen bonding!!

Want to try for two?

[HydrogenBond]

Analyzing biomaterials in terms of hydrogen bonding is not as difficult as it may seem. Only a few conceptual tools are needed. The first tool is too look at in vitro biomaterials as being dissolved in water and that the local water will have an impact on form and function. The easiest to analyze is also the most important, i.e, DNA and RNA. Below are some basic diagrams for DNA and RNA.

 

If we look at the pic on the left one should notice the extra hydrogen bonding hydrogen on the upper left of adenine. There are also two extra hydrogen bonding hydrogen on the bottom base pair, one on the upper right of cytosine and the other on the lower left of guanine. These extra hydrogen bonding hydrogen are equililent to the ones within the hydrogen bonding between the base pairs. These create stuctural hydrogen bonding and proton potential that retains high potential.

 

DNA and RNA are different with respect to their basic structures. The DNA will always exist as a double helix, while the RNA can form a single helix. This difference is connected to the differences within the hydrogen bonding potential of these two molecules within water. If we were to start out with two single strands of DNA in one beaker and two single strands of RNA in another beaker, the DNA will have a stronger nonequilibrium impact on the hydrogen bonding potential within the water. The DNA will need to form the double helix to lower the aqeuous potential, while the RNA, because it has a lower aqueous hydrogen bonding affect is able to lower the aqueous potential by forming only a single helix.

 

If we compare DNA and RNA, there are only two places they are different. The pentose sugar(near the phosphate) of RNA has an extra -OH group, while DNA has an -H in this same location The other difference is that RNA uses the base uracil and the DNA uses the base thymine. The only difference between these two bases is an extra methyl group -CH3, on the thymine of DNA compared to an -H group on the same position of the uracil base of RNA. These two differences have a significant impact on the surrounding water.

 

Relative to the pentose sugars the -OH group on the RNA will allow the sugar to define a lower surface tension affect in the water compared to the organic -H moiety on the pentose sugar of DNA. The extra surface tension on the DNA will increase the local aqueous hydrogen bonding potential. The extra -CH3 group on thymine of DNA relative to the -H on the uracil of RNA will have a similar affect with thymine creating more surface tension in the water and therefore inducing higher hydrogen bonding potential within the water. The DNA double helix is a better way to shield the water from the impact of the high surface tension.

 

The phosphate group has the impact of sharing electron density with the hydrogen bonding potential within the water. But if we look at it closely, the four highly electronegative oxygen atoms combined with the +5 oxidation state central phosphorous atom place a limit on the impact of its negative charge within the water, being a relatively weak base.

 

The DNA double helix is packed with packing proteins. The two most important animo acids within DNA packing proteins are shown below.

 

The positive charges interact with the negative charges on the phosphate. This increases the electron withdrawal from the phosphate groups relative to being dissolved in water. As such, the positive charge with DNA packing increases the potential of the hydrogen bonding hydrogen of the base pairs of DNA relative to their being dissolved in water.

 

One may also notice the large number of hydrogen bonding hydrogen on these two animo acids. Lysine has six and arginine has eight. When these pack the DNA, they also create a situation where all these hydrogen bonding hydrogen are not able to form hydrogen bonds. This adds even more stuctural hydrogen bonding potential to DNA/packing structures relative to DNA that is unpacked. This structural difference in potential is one of the ways the nucleus of a cell creates structural gradient potentials.

[IDMclean]

Sorry, I am going to have to take some time to soak in your theory my elemental friend.

 

However I immediately identified it as a Quantum branch of Chemsitry, and Organic at that.

 

I was wondering though if perhaps you had heard about the theory that pure water may actually be something more like:

[math]H_{1.5}O[/math] and not the traditional [math]H_2O[/math]. Something to look into, I am no chemist, though I would surely like to be, It rang true of my Physics/Quantum Physics understanding.

[Michaelangelica]

hydrogenbond

I keep reading your posts in the hope that a Bear of Little Chemistry and lots of Honey will understand

You are either a nut case or a geniuis.

I am backing the second.

but you need to explain it all to dumb-belles like myself

M

[HydrogenBond]

I am having a little problem finding the right mix. If I am too general more people can understand but the experts think it is speculation. If I get highly detailed the experts are happier but I lose most of the broad audience. I am trying to hook on somewhere, by varying the blend.

 

Hydrogen bonding is one varaible that is everywhere within the cell. Currently, hydrogen bonding is assumed to be just a secondary bonding force that helps define cellular stuctures. Beyond that it is not considered a dynamic part of the cell since organic chemistry and mainstream biochemisty appears sufficient to explain how things work within the cell.

 

My thesis is that hydrogen bonding is not just a secondary bonding variable but it is also a dynamic variable that integrates the cell. I have been attempting to show how this is possible by showing the nature of hydrogen bonding, and have applied the principles to a few examples. If I wanted, I could translate a biology textbook into the model. The reason this is so is because one defines the other. The advantage of the hydrogen bonding angle is that it only uses one universal variable.

 

Personally, I still beleive that others in the life sciences should be ecstatic over this major advancement. The reality reaction is luke warm to cold. Part of the problem I see is that, this is a new branch of science, which still needs to be developed in a more formal manner.

[Michaelangelica]

 

Personally, I still beleive that others in the life sciences should be ecstatic over this major advancement.

The reality reaction is luke warm to cold. Part of the problem I see is that, this is a new branch of science, which still needs to be developed in a more formal manner.

 

Scientific ideas survive or die according to the models they make.

Very complex ideas in all sciences are pared down to make a model that expresses the idea in a way that people can understand it.

You can even have two different models to explain aspects of the same thing

 

A simple model I can think of is the "Supply and Demand" model in economics.

If supply goes down, price goes up, demand goes down. . . and vice versa.

A very simplistic view of the economy but it helps us to understand some fundamentals.

 

John Gribben in his book "Almost Everyone's Guide to Science" spends his first chapter discussing models

"To a physicist, a model is a combination of a mental image of what some fundamental (or not so fundamental entity is like, and a set of mathematical equations that describes its behaviour. . .'

He goes on and on but I feel that if you need your ideas and enthusiasm to be communicated to the rest of the world you need a nice, elegant, simple model that any idiot can understand and/or visualise.

[HydrogenBond]

A simple model will reach the most people, which is why I like conceptual modelling. It reduces things down to simplicity and simplicity is closer to the truth than complexity. Science is different; sciences wants to see tangible proof. On the one hand, proof helps weed out clever illusions. On the other hand, proof is easier so see than a strong reasonable logic line. Logic can be tricky and scientists are not willing to gamble their credibility except on a sure thing. I wish I could have a competition to demonstrate the advantage of the hydrogen bonding model.

[HydrogenBond]

I would like to totally shift directions and talk about hydrogen bonding and weather. The engine of weather on earth is water. The fuel is the sun. For example, the ocean is water and contain thermal gradients that affect the movement of ocean currents, which have an impact on the movement of air currents. The polar caps are ice, which is another form of water. The clouds are also a form of water something between vapor and liquid, i.e., stuctured vapor due to hydrogen bonding. When clouds condense into rain, this lowers the volume within vapor space pulling a vacuum, i.e, low pressure, which can create a movement of air from high pressure to create wind.

 

When the sun evaporates liquid water, it breaks the hydrogen bonds and single water molecules form, with maximized proton potential. Clouds form to lower this potential but can only go so far against the potential of continued evaporation. In hot summer days, the sun is quickly evaporating water and the water is trying to lower potential. At times, so much proton potential is created that severe weather phenomena like thunderstorm and tornadoes can form, driven by proton engines. Even lightning, which results in positve charge going down and negative charge going up demonstrates hundreds of millions of volts of electropotential can be generated by the water in thunderclouds.

 

Hydrogen bonding and proton potential may look wimpy if we only look at one bond. It the case of a hurricane, a lot of wimpy hydrogen bonds working together create a formidable force of nature. In the cell, the energy amplification is smaller, but still uses the power of the proton.

[HydrogenBond]

If we go back to the cell the ion pumping at the cell membrane provides a capacitance for localized hydrogen bonding potential amplification with the cell. Although the ion pumping makes the inside negative and outside positive, this situation stores potential energy within the membrane. Much of it use to actively transport materials.

 

When a material is transported in, the cations reverse, reversing the local membrane polarity. This change of potential not only allows material to come into the cell but it also creates a local positive pulse, into the cell water, down the attached protein train that is designed to deal with the input material.

 

The neuron pumps cations everywhere on its surface, but is designed to allow a high proportion of the cationic impulse to come into the dendrites. The DNA knows where this impulse is coming from, which helps the DNA stay in line with the needs of the memory impulse.

 

When I began looking at the cell and hydrogen bonding, I began at the beginning, which is the evolution of the cell. The conclusion I came to was that ion pumping was one of the most important advances for life. It not only creates an internal potential that helps materials form some of the needed shapes, but it also creates impulse potentials, which helps get the rest of the good stuff to line up.

 

Here is an interesting tidbit of the importance of ion pumping. During cell cycles, the cell membrane unsaturates and the sodium pumps increasingly reverse. At the same time, the amount of ATP going into the membrane and ion pumps steadily increases. This is the only time this occurs and creates all kinds of new activity leading to two daughter cells.

[HydrogenBond]

Here is an advanced application of the hydrogen bonding model. Below is a picture of the fluid chambers within the brain called the ventricles.

 

 

These fluid chambers are filled with cerebral spinal fluid (CSF). The CSF is mostly water with small amounts of ions and neuro-chems. The brain is essentially a beaker of water, within the scull. Part of this volume contains brain matter and part contains just CPF. The water is continuous. With water able to form hydrogen bonding shapes around any biomaterial, the venticles appear to represent a set of chambers where hydrogen bonding water shapes can form without the needs of extensive biomaterials. The fluid nature of consciousness appears to indicate that the venticles participate in consciousness. It is not so much a projection theater as a fluid/changing capactance related to the activity of the brain matter. The CSF goes beyond the ventricles and also separates all the convolutions within the brain.

[HydrogenBond]

In these posts I have tried to show part of the range of applications for hydrogen bonding. It is a whole new/old layer of potential that integrates molecues via water. This integration includes weather, cells, multicellular phenoman and consciousness. It is a new frontier that could use a wider range of collective investigation.

[Michaelangelica]

This is for you HB

Speed plays crucial role in breaking protein's H-bonds

Medical Science News

Published: Wednesday, 31-Oct-2007[/i

 

 

Researchers at MIT studying the architecture of proteins have finally explained why computer models of proteins' behavior under mechanical duress differ dramatically from experimental observations.

 

This work could have vast implications in bioengineering and medical research by advancing our understanding of the relationship between structure and function in these basic building blocks of life.

 

In a paper published as the cover article of the Oct. 16 issue of the Proceedings of the National Academies of Science (PNAS),

http://www.news-medical.net/?id=31998

I still don't understand it.

[HydrogenBond]

One unique thing about hydrogen bonding, is that if there are a chain of hydrogen bonds, such as an extended water structure, each additional hydrogen bond gets stronger and stronger. The last can be 2-3 times stronger than the first, in large extended structures. Each hydrogen bond that forms, causes the hydrogen, which will form the next hydrogen bond to gain potential, such that when it forms, its bond will be ,stronger. In water, the electrophilic potential of the H tries to lower by bonding to the O. The O is more electronegative. I does not take the entire hit, but will passe some of the burden on to its own H. These H now have more potential so when they are able to bond it is stronger.

 

It is not so much that the last is stronger than the first in the chain. Once the chain forms, all the hydrogen bonds are stronger, because the more electonegative atom is keeping its fair share of electron density and passing some of the burden onto the H When the chain is formed, breaking any of the bonds, first, will be the hardest one to break. The second random breaking is easier, etc. This is due to the oxygen not being put under the gun as much by H, so it can relax some of the potential it will need to transfer to the remaining H.

 

When you place something under stress, the force will increase depending on the speed of the impulse. For example, if you stand on a scale, one will get their weight. If you bouncing in place, without leaving your feet, you can get the scale to pike, making you weigh another 50lbs. They have increased the force impulse so they can break more bonds. The number three sort of shows them jumping down the H-bond strength curve due to more H-bond in the chain. Instead of one at a time, they now jump in 3's, as they move down the curve to minimum strength.

[Michaelangelica]

Hydrogen Bond I thought you might be interested in this research.

Full article here:-

Strength of spider silk lies in geometric configuration of structural proteins

Strength of spider silk lies in geometric configuration of structural proteins

Medical Science News

Published: Monday, 18-Feb-2008

 

Researchers in Civil and Environmental Engineering at MIT reveal that the strength of a biological material like spider silk lies in the specific geometric configuration of structural proteins, which have small clusters of weak hydrogen bonds that work cooperatively to resist force and dissipate energy.

 

This structure makes the lightweight natural material as strong as steel, even though the "glue" of hydrogen bonds that hold spider silk together at the molecular level is 100 to 1,000 times weaker than the powerful glue of steel's metallic bonds or even Kevlar's covalent bonds.

 

. . .

 

. . .

 

. . used atomistic modeling to demonstrate that the clusters of three or four hydrogen bonds that bind together stacks of short beta strands in a structural protein rupture simultaneously rather than sequentially when placed under mechanical stress.

. . .

"Using only one or two hydrogen bonds in building a protein provides no or very little mechanical resistance, because the bonds are very weak and break almost without provocation," said Buehler, the Esther and Harold E. Edgerton Assistant Professor in the Department of Civil and Environmental Engineering. "But using three or four bonds leads to a resistance that actually exceeds that of many metals. Using more than four bonds leads to a much-reduced resistance. The strength is maximized at three or four bonds."

Strength of spider silk lies in geometric configuration of structural proteins

MIT Department of Civil and Environmental Engineering - CEE