Monday, 10 February 2014

Molecule of the Month for February

This month we celebrate water; I like this quote from one of Hungary's (and in fact the world's) greatest Biochemists (Albert Szent-Gyorgi): "Life is water dancing to the tune of solids". Superficially, water is one of the simplest of molecules found in all living organisms, yet at the same time one of the most versatile; and a molecule that lies at the heart of Biology. As you can see from the diagram left, water in solution makes full use of its Hydrogen Bonding (1) potential, and this is an important aspect of its role in Biology. But first, where does it come from? We ingest water with our food and we produce water as a bye-product of the oxidation of nutrients. The final step in the catabolism of glucose, after glycolysis, the Krebs Cycle and Oxidative Phosphorylation (which generates energy in the form of ATP) is the reduction of oxygen to water.

"Water, water, everywhere, nor any drop to drink". We believe that life first emerged in the oceans (which are mostly water), which is where we inherited this dependency on water for the Chemistry of Life. The evolution of mechanisms to preserve and capture water in desert regions and to maintain liquid water under the ice, are remarkable adaptations that Sir David Attenborough discusses regularly in his books and documentaries on Life on Earth. I am sure you are well aware of these issues. If not, make sure you watch everything he has made! I particularly like his 10 minute radio podcasts on evolutionary anecdotes (look on the Radio 4 website).

Back to chemistry! Water molecules form a structured network owing to the non-linear arrangement of the OH bonds. This leaves water molecules
polarised and therefore able to form a Hydrogen bonded networks (left). However, these are weak interactions that can exchange: so we say that water molecules form a dynamic network of hydrogen bonded interactions: this is partly responsible for its unusual physical properties. The importance of this network is found in protein interactions with ligands: for example enzyme and substrates or antibodies and antigens. In order to appreciate this we have to consider the phenomenon of Entropy. 

Clausius. Gibbs, Boltzman and Maxwell (as well as others) are amongst the early pioneers of our understanding and formalisation of Entropy and the second law of thermodynamics. Entropy is often described a a measure of the disorder of matter or a system. The Universe tends to disorder (a little like an adolescent's bedroom or my research bench) and this is known to be energetically favourable. So, when a small substrate molecule interacts with and enzyme, it has been shown that this is often entropically favoured. Like a dog shaking off the water when it emerges from a pond, as a molecule binds to a protein, water is dispersed, giving a net, favourable Entropic change and thus promoting the interaction with the substrate.

Water not only provides the aqueous environment that solubilises cellular molecules, it also provides the foil to oily compounds that provides the cell with its plasma membrane. The favourable interactions between hydrophobic molecules and their "rejection" of water molecules, are central to the folding of proteins: where a soluble protein is polar on the surface and oily in the core. However, a cell membrane comprise polar phospholipids, that are oily in the core and polar on the outside and inside surfaces. Think about the proteins that straddle these membranes, they tend to be the inverse of the soluble proteins: they are oily on the outside and polar in the middle! They often provide a polar channel for communication between the inside and outside of cells. We call these channels, they include channels for ions and hormones, and sometimes even water: such as Aquaporin, which is found in the kidney for obvious reasons? This is a taste of the role of water in Biology, I haven't touched on water in a more global context, or indeed as a key molecule sitting in between metal ions in the active sites of enzymes, it is a truly exceptional molecule and one that underpins most aspects of the Life Sciences.

1 comment:

  1. Does ice float or sink? Normally when liquids turn to solids, they become more closely packed (organized structure packs more molecules per unit volume) and therefore become more dense. Denser materials will sink. But not water; it is less dense and therefore floats on liquid water. How fortunate for us because it is doubtful that life would exist on this planet (or anywhere?) if this did not happen. Sinking ice would freeze the oceans solid, but floating ice allows life to go on beneath the ice. Another interesting tidbit is water is the only molecule on earth that exists naturally in the three states of matter: gas, liquid and solid.