Saturday, September 21, 2013

Noncovalent interactions (part 2)

As mentioned in my first post about the non-covalent bonds , they are something essential in biochemistry!

At one side, since they are weak forces, they allow dynamic communications between molecules or within the same molecule. In other words, since they are weak they may allow, for example, that two molecules interact temporarily with one another, or that certain macromolecules acquire specific conformations temporarily . But in either case, if you need to change this situation, it is not complicated as these are weak forces... Examples of the first situation are an interaction between a substrate and the active site of an enzyme (please note that in some cases the substrate can interact with the enzyme covalently!), an interaction between a receptor and its ligand, an interaction between two proteins , etc. . Examples of the latter are an enzymatic conformational changes induced by binding of a substrate or by binding of an allosteric modulator, a protein conformational changes in response to a pH change (which happens, for example, with phosphofructokinase -1 during lactic fermentation, and this is one of the factors associated with muscle fatigue...), etc.
But do not be fooled by the individual weakness of each non-covalent interaction. In fact, as in biochemistry we often deal with large molecules (polysaccharides, proteins, nucleic acids , for example) , there are numerous locations within those molecules that can interact with each other. Thus, they form a network of non-covalent interactions that is responsible for maintaining the 3D structure of these molecules. The sum of all forces becomes huge, giving a greater stability to biomolecules. This is why, for example, a protein acquires one or a few possible conformations, despite virtually there is an enormous number of protein conformations that could be present...
Finally, there is a very important aspect that is related to non-covalent forces that molecules may be involved with: its solubility! In fact, often when someone dissolves something in water (salt or sugar, for example), does not think on why the dissolution occured. The idea is quite simple... for a substance to dissolve in a particular solvent, the molecules that compose it must be able to interact with the molecules of the solvent, in an energetically way more favorable than their initial arrangement . For example, the sum of the network of interactions between the atoms of Na+ and Cl- in the salt is less than the sum of the interactions of such ions with water molecules. Thus, in the presence of water the salt dissolves. And the reasoning is valid for any solute and/or solvent. Therefore it is said that "Like dissolves like" , which in reality tells us that the dissolution occurs when there is chemical affinity between the molecules of solute and solvent .

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