HydrogenBond Posted May 18, 2006 Report Share Posted May 18, 2006 It is common knowledge that the DNA is a double helix that forms hydrogen bonds between specific base pairs. One thing that is not often discussed is that every based pair will have one or two extra hydrogen bonding hydrogen. Quote Link to comment Share on other sites More sharing options...
Mercedes Benzene Posted May 18, 2006 Report Share Posted May 18, 2006 I'm confused... hahaha. Quote Link to comment Share on other sites More sharing options...
hallenrm Posted May 19, 2006 Report Share Posted May 19, 2006 So! to what effect? Quote Link to comment Share on other sites More sharing options...
UncleAl Posted May 19, 2006 Report Share Posted May 19, 2006 Do you have neutron diffraction structure data to back up your apparently fact-free assertion? hallenrm 1 Quote Link to comment Share on other sites More sharing options...
ronthepon Posted May 19, 2006 Report Share Posted May 19, 2006 What exactly are you asserting or hinting at? As I understand, you are saying that there are extra hydrogen atoms present for hydrogen bonding? Quote Link to comment Share on other sites More sharing options...
Mercedes Benzene Posted May 19, 2006 Report Share Posted May 19, 2006 What exactly are you asserting or hinting at? As I understand, you are saying that there are extra hydrogen atoms present for hydrogen bonding? Yea. That's why I was confused. ronthepon 1 Quote Link to comment Share on other sites More sharing options...
HydrogenBond Posted May 21, 2006 Author Report Share Posted May 21, 2006 The extra hydrogen bonding hydrogen along the base pairs would love to form hydrogen bonds but can not do so within the base pairs due to limited electrons to share. One way to lower the potential is vertically instead of horizontally. This allows axial conduction of hydrogen bonding potential along the DNA double helix. The extra potential in those hydrogen bonds also means the very stable DNA double helix has a potential to get even more stable, if these hydrogen bonding hydrogen could form hydrogen bonds. This sets a potential for the DNA double helix to separate for other hydrogen bonding situations. The third reason is connected to configurational potential. All these extra hydrogen bonding hydrogen make the DNA slightly electrophilic. Quote Link to comment Share on other sites More sharing options...
Mercedes Benzene Posted May 21, 2006 Report Share Posted May 21, 2006 All these extra hydrogen bonding hydrogen make the DNA slightly electrophilic. I read that in an article put out by the NIH a while back. Interesting. Quote Link to comment Share on other sites More sharing options...
hallenrm Posted May 22, 2006 Report Share Posted May 22, 2006 I have a hunch about what you are hinting at! Are you suggesting that even when two individuals have the same genes, they may be different because of the DNA configuration that is susceptible to changes? Something akin to what I have been thinking, "extrachromosomal sources of info"!! :cup: Quote Link to comment Share on other sites More sharing options...
ronthepon Posted May 22, 2006 Report Share Posted May 22, 2006 The extra hydrogen bonding hydrogen along the base pairs would love to form hydrogen bonds but can not do so within the base pairs due to limited electrons to share. One way to lower the potential is vertically instead of horizontally. This allows axial conduction of hydrogen bonding potential along the DNA double helix. The extra potential in those hydrogen bonds also means the very stable DNA double helix has a potential to get even more stable, if these hydrogen bonding hydrogen could form hydrogen bonds. This sets a potential for the DNA double helix to separate for other hydrogen bonding situations. The third reason is connected to configurational potential. All these extra hydrogen bonding hydrogen make the DNA slightly electrophilic.What are the implications of your statements? Quote Link to comment Share on other sites More sharing options...
HydrogenBond Posted May 22, 2006 Author Report Share Posted May 22, 2006 Here is the basic theory, by using water as an example. If we look at a molecule, H2O, the molecule is slightly polarized. This is due to the higher electronegativity of oxygen compared to hydrogen. The induced dipole reflects the extra stability in oxygen, i.e., closer to completing its octet. The dipole also reflects an induced potential in the hydrogen. In the case of an isolated water molecule, the hydrogen carrries the entire burden of potential, since oxygen increased its stability by gaining the extra negative charge. When two water molecules are together, the hydrogen will lower potential by sharing electrons with the unbonded electron pairs on oxygen. This does not help the stability of oxygen. Oxygen took the extra electron density from its own hydrogen for stability. So when another hydrogen takes away some of its electron density, this will increase the potential of the oxygen, destabilizing it slightly. A good visual image is picture the oxygen and two hydrogen sitting at a poker table. Oxygen is the best player and wins all the chips from the two hydrogen. The oxygen stuffs its back pockets with all its winning chips. The game is called, with the hydrogen left in chip deficit and oxygen taking home the winnings. Next day, the game moves into a new area with many poker tables in the same room. The hydrogen at all the tables quickly lose their chips to oxygen and are desparate to stay in the game. So, they stealthly reach into a neigboring oxygen's back pocket and steal some of the chips that the oxygen won off the hydrogen at the table. This puts the hydrogen back into the game. But oxygen will always win again, overstuffing its pockets. Hydrogen picks its pocket to get back into the game, etc.. The bottom line is that the highly electronegative atom will always win in the end and hydrogen will always carry the burden of potential. Each individual molecule starts out that way. Within continuums, some of the hydrogen potential is lowered but will never go to zero, since that would mean that hydrogen is as electronegative as oxygen or nitrogen. What is significant is that all those extra hydrogen bonding hydrogen along the DNA double helix carry the burden of an electrophilic potential. This not only adds to the DNA's activity, but it gives the entire DNA molecule a configuration potential signiture. This signiture gives us a way of comparing different materials and structures within the cell. The cell is set up as gradients, with the DNA and cell membrane defining the highest average hydrogen potential gradient. Quote Link to comment Share on other sites More sharing options...
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