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Life Sciences => Cells, Microbes & Viruses => Topic started by: tkadm30 on 10/11/2017 09:51:38

Title: Where does the geometry of a cell come from?
Post by: tkadm30 on 10/11/2017 09:51:38
How do cells naturally form complex geometric patterns?

What do you think?
Title: Re: Where does the geometry of a cell come from?
Post by: puppypower on 10/11/2017 12:04:45
The geometry of the cell comes from the continuous phase and the majority component of the cell, which is water. To minimize potential, water will self hydrogen bond with other water molecules, while also being in contact with all the organics and ions within the cell.  The minimal potential global configuration results in the geometry seen in the cell.

A good example of this in action is the impact of water in terms of the folding of protein. Water helps to create and maintain perfect folding for any given protein. Below is an energy landscape diagram of an unfolded (left) and folded protein (right). These potentials are relative to the water.

The highest peaks on the left are hydrophobic moieties which set the highest potential, These will need to fold and tuck first. The diagram on the right is fully packed, has lost all its large peaks, and has collapsed into a low potential energy funnel, that minimizes the energy with the water; final geometry.

 If we removed the water; dehydrate, or used any other solvents in place of water, the energy landscape diagrams would change and the cell would exhibit different geometries, most of which will not longer be active or useful to life. Water is the Swiss army knife of the cell and has a finger in all pies. Water accounts for about 20 times as many molecules, as the rest of all the cell organic molecules combined. 

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Title: Re: Where does the geometry of a cell come from?
Post by: evan_au on 11/11/2017 00:03:51
Quote from: tkadm30
How do cells naturally form complex geometric patterns?
These patterns are encoded in their DNA.
Title: Re: Where does the geometry of a cell come from?
Post by: RD on 11/11/2017 05:39:20
How do cells naturally form complex geometric patterns?
Title: Re: Where does the geometry of a cell come from?
Post by: puppypower on 11/11/2017 12:06:38
The cell is a partnership between the organics and water of the cell. The patterns may be traced back to genes on the DNA.  However, without the presence of water, the DNA and the cell will become inanimate, and the patterns will not appear.

Water is everywhere in the cell and has a finger in every pie. Even the DNA double helix contains a double helix of water. The DNA has evolved hydration sites, along the bases, where water will hydrogen bond to the bases, and then to other water molecules, to form helixes of water in the major and minor grooves. For example, as shown below, Adenine is equipped with an extra hydrogen bonding hydrogen, that is not needed for base pairing. This is earmarked for water.


The degree of hydration of the DNA, will then define the conformation of the DNA. Water will define the geometry of the bulk DNA, based on how much water is chemically attached.

The DNA double helix can take up a number of conformations (for example, right-handed A-DNA pitch 28.2 11 bp, B-DNA pitch 34 10 bp, C-DNA pitch 31 9.33 bp, D-DNA pitch 24.2 8 bp and the left-handed Z-DNA pitch 43 12 bp) with differing hydration. The predominant natural DNA, B-DNA, has a wide and deep major groove and a narrow and deep minor groove and requires the greatest hydration.

One important aspect of cellar patterns is connected to the water potential gradient between the DNA and the cell membrane. The DNA is the most hydrated organic material in the cell. It has the most water attached of all the molecules in the cell, partially due to its huge size. It is at the lowest energy with the water. The DNA is the main partner of water, where organics become designed to merge with water. The DNA was always the goal.

At the other end of the spectrum is the outside membrane and the accumulation of potassium ions on the inside of the membrane. This potassium accumulation is in reaction to ion pumping and the concentration gradient to the outside; very low potassium outside. This has the opposite impact on water; high potential pole.

When protein are translated, water helps to fold them; energy landscapes with water, as they diffuse to their equilibrium spots in the gradient. There further stacking may become necessary, to lower the potential in the water, leasing to more complex patterns.

The cell also has a trick up its sleeve, where proteins can also be actively transported, and then fixed into non equilibrium positions in the gradient, by scaffold proteins. This is energy intensive. However this is a good way to turbo charge the protein by fixing in a higher energy environment. This can alter the gradient profile and lead to some alternate geometries, due to the lingering potentials.

Virus can always find the DNA, simply by flowing with the gradient to the low potential side, near the DNA. This is connected to the way the water is hydrogen bonding at different places in the gradient. Near the DNA is the sweet spot for viral DNA or RNA. If we add protein to virus, we can make it float outward, driven by the cell's water gradient on the protein surface.

Theoretically, we can alter the pattern of the virus life cycle by tweaking the gradient. Cancer has a different type of gradient. It is more connected to cell cycles where the ion pumps reverse, such that the gradient between the membrane and the DNA is lessoned. Patterns become different.
Title: Re: Where does the geometry of a cell come from?
Post by: puppypower on 12/11/2017 14:44:34
I am going to change direction somewhat with an idea that came to me years ago, but reappeared last night. This is connected to unique aspects of DNA geometry. There appears to be an extrapolation of the genetic code that is not discussed. If you notice, in the figure below, there are two hydrogen bonding pairings between the fours bases; GC have three hydrogen bonds and AT has two hydrogen bonds. This is well known.

This is not the whole story, If we include water. G has 4 hydrogen bonded water and C has 2.  While Adenine has 3 hydrogen bonded water and T has 2.

This can be broken down further, with G having two hydrogen proton donor waters and two receiver hydrogen protons.   C has one donor and one receiver. Adenine has two donors and one receiver, while T has only two donors.

All the four bases are different in terms of the number plus donor/receiver orientation of the attached water. This means blended with the binary coding of the base pairings, is a quaternary type of water coding. This extra coding makes practical sense for several key applications. The first application is connected to improper based pairing. This may not necessarily change the water coding in a bad way. Or the water coding can be induced resulting in the needed improper base pairing used for further genetic change.

This water coding also makes sense, in areas of the DNA, where there are no coding genes, but only noncoding genes along with plenty of coding water. This offers a command platform for shape shifting on the DNA; active and deactivate coding genes, and allows the DNA stay in to touch with the cellular water.

Title: Re: Where does the geometry of a cell come from?
Post by: tkadm30 on 27/11/2017 23:19:38
Thank you @puppypower for theses highly informative comments!

Title: Re: Where does the geometry of a cell come from?
Post by: adianadiadi on 29/01/2018 00:25:56
Interesting question. It might be encoded in DNA.
It is different for different organisms like plants and animals
It also depends on the tissues and organs. Function, position etc. will decide the geometry.
Title: Re: Where does the geometry of a cell come from?
Post by: puppypower on 29/01/2018 12:00:25
Interesting question. It might be encoded in DNA.
It is different for different organisms like plants and animals
It also depends on the tissues and organs. Function, position etc. will decide the geometry.

If you look at the cells of the human body, there are many cellular differentiations, with all these cells having the exact same DNA. Kidney cells has a certain differentiation, which is different from liver cells, or brain cells. The kidneys, liver and brain all have their own unique geometry and size. This observation suggests that the DNA is secondary in terms of final geometry. This is not say the DNA is not a critical secondary aspect, because it is moldable into the differentiations needed to define the final composite shape(s) of a complex organism.

After thinking about this, a more logical and simple source for geometry induction, is connected to the local and global potential between the blood supply and the nervous system. The brain moves positive ions; Na+ and K+, while the blood has a slight negative pH. This sets up an electromagnetic gradient, at the level of water, with water the majority component within life; 80-90%. Water is responsible for the shapes of individual proteins, due to final packing being a shape that minimizes the potential in the water.

Circulatory and nervous tissue extends throughout the body. If you look at the various organs, each has various amounts and various ratios of blood to nerve tissue. These establish specific gradients within the external water of the cells, which then translates to the potential seen by the DNA, helping to maintain bulk differentiation.

If you look at a fertilized human ovum, after being fertilized, it replicates a number of times to form essentially a cluster of uniform cells. It is not until it attaches to the uterine wall, when it sees a gradient created by the mother's blood supply, do the uniform cells begin to differentiate; differentiation reflects the gradient between the cells and the blood supply. Early in this differentiation process, the stem cells for the future brain and nervous system form, establishing the based gradient that amplifies with time. The brain is the ultimate computer able to maintain differentiation control over billions of cells, through feedback loops. 

Many but not all forms of cancer are states of DNA differentiation that result from defects in the control gradient  This is most typically caused by loss of the nervous aspect of the gradient. A growing cancer will have a blood supply but typically does not have a nervous system connection. It is out of the control loop. This suggests many forms of cancer could be treated by growing nerves back into the cancer so it regains differentiation control. We may need to tweak nerves further up stream to fine tune the sculpturing, This is the future of cancer prevention and treatment. If we could send a pulse through the nervous system and have a computer determine dead zones, we could target treatment even beyond the cancer forms.
Title: Re: Where does the geometry of a cell come from?
Post by: puppypower on 02/02/2018 12:32:09
In terms of nerves and cellular differentiation control, this is done via cations and water. All cells pump and exchange sodium and potassium ions. The sodium cations will accumulate on the outside of the cell membrane, while potassium ions will accumulate on the inside the cell membrane.

Although both sodium and potassium ions both have a single positive charge, each has a different impact on the water. Sodium cations are kosmotropic, meaning they create order in the water. Potassium cations are chaotropic; chaos, and create disorder in the water. The sodium cations are smaller; denser positive charge, and will bind to water stronger than water binds to itself. The potassium ions stem from larger atoms and will bind to water weaker that water binds to itself. Essentially sodium and potassium cations, are on either side of water's hydrogen bonding, in terms of binding strength to water. It is very subtle, yet an important design element, critical to life. A 10% change in natural hydrogen bonding strength, either way,  would mess this up.

The kosmotropic nature; induces order, of sodium ions, causes water to cluster around the sodium ions, essentially making the sodium cation and its attached water, too large to freely diffuse through the membrane. The chaotropic nature of potassium ions, on the other hand, is more disruptive to water clustering, allowing potassium cations-water to be smaller allowing diffusion though the membrane.

The result is although the cation pumping and ion exchange will result in a charge balance across the membrane, only the potassium cations can act under the potential of the concentration gradient, very low outside, and will be driven by entropy to diffuse out of the cell, to balance the potassium ion concentration. The sodium ion sees the concentration gradient, but is stuck due to being kosmotropic and too large. The entropy potential cannot overcome the small pores and large hydration cluster. The result is extra positive charge; due to the potassium ion diffusion, will accumulate outside the cell. This means that less positive charge will remain inside the cell, than generated by the cation pumps. When potassium entropy potential is balance by the increasing charge potential, the final result is called the membrane potential.

The potassium ions inside the cell are important because the chaotropic nature of potassium ions impacts the water near all the bio-structures. The potassium ions inside the cell helps to disrupt the ordering in water that forms on the surfaces of proteins, RNA and DNA. This is important to enzyme activity. Enzymes need to change shapes to be active, with structured water like a cage. Potassium ions have the keys the cages.

In terms of the nerves near cells, these are mostly sensory nerves that response to changes in the local environment. These local sensory systems respond to stimulus, will fire, and then send signals to the brain. The firing of the sensor, is similar to a neuron firing, in the sense that potassium ions leaks out and sodium ions leak into the sensor for transmission to the brain. The added concentration of potassium ions, from the firing sensor, onto the outside of the control cell, has a chaotropic impact on the outside of the control cell.

This added chaos onto the outside cell water, has an impact on the sodium ion clusters and also a further positive charge imbalance impact, across the membrane. The net affect the sensory nerves are connected to the membrane potential. From this connection, the nerves can impact the cell's input and output, and the strength of the internal chaotropic environment, all while keeping the brain informed.

Let me give one example of the impact. When you dissolve organics in water, surface tension will form between water and the organics. The word "tension" means stretching of the hydrogen bonds. This stretching  is connected to the covalent nature of hydrogen bonding, which is also the condition for order in water. The kosmotropic nature of sodium ions, by generating order in water, has a similar impact as the surface tension based order, due to organics in water. The net affect is sodium ions makes it inviting for organics to approach the cell. It is not a large jump for water to go from sodium induced water clustering to surface tension clustering, due to organics. The energy hill is not too bad.

When we add potassium ions, due to sensory nerve firing, we add some chaos, and make it a little harder for the food materials to approach the membrane. There is a slightly higher energy hill to climb. This helps to control the mother cell's appetite; diet. A mother cell on a diet will not reproduce as often. It will need to depend more on the potential within there transport proteins characteristic of its differentiation. Cancer cells are not on diet.