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Formation of DNA Double Helix
In any given biochemical reaction, there are many factors to consider when determining what the reaction pathway is and what the structure of the final product molecule is. For instance, we can consider the types of intermolecular interactions that are involved (hydrogen bonds, London dispersion forces, hydrophobic interactions, etc), the properties of the solvent, the thermodynamics of the reaction and the pH of the solution. All of these factors play a crucial role in determining how the reaction proceeds. Lets consider a common reaction that takes place in every nucleated cell of our body - the formation of the double helix structure of DNA. At body temperature, DNA does not exist as a single-stranded molecule but rather as a double-stranded molecule? Why is this so? It turns out that the formation of the double stranded DNA molecule is thermodynamically favorable. That is, even though the entropy of the system (the stands of DNA) decreases, enough energy is released into the surrounding as to ensure that the entropy of the universe increases (second law of thermodynamics). The formation of the double helix forms hydrogen bonds between the bases. Since the bases are parallel and stacked on top of one another, London dispersion forces also play an important role in stabilizing the structure, as do hydrophobic interactions of the non-polar bases. Water, which is the solvent inside the cell, plays a role in stabilized the negatively charged phosphate groups found on the outside of the double helix DNA structure. All these factors help this biochemical process, as well as many others, move forward.
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