Monday, 22 January 2007


I have been kind of busy these days. But there is always some time to play with graphics. Today's molecule is ATP. It's the body's immediate energy source. It works as a cofactor in many enzymes of different kinds. It is also a building block of RNA.

The active part is a double phosphoric acid anhydride. This is an instable "high energy" bond. The hydrolisation to ADP and phosphate has a biological standard free energy of -35 kJ/mol. It is used coupled with endergonic reactions. You can compare the reaction to the hydrolisation of P4O10[1].

Besides the two energetic bonds you have ribose and adenine forming a "handle".

In physiological conditions ATP can form a complex with Mg2+. This stabilises the negative charges on the oxygen atoms.

The structures were calculated in ArgusLab using the Universal Force Field method. The images were drawn in PyMOL with the ray function.

[1] Don't call it P2O5 unless glucose is H2CO for you.


GCT said...

I remember having to draw the exact structure of this molecule for my biochemistry exam, in addition to ATP I had to memorize NADP as well as most of the coenzymes and other selected molecules. Multicomponent molecules (Ribose, glycerol sungar, etc....) where the function depends on the charge and oxidation levels weren't too fun to memorize with all of their nooks and crannies of functional groups and anomalies that are characteristic to the structure.

Felix said...

I have to say that I kind of like these molecules though. and we don't have to memorize too many of them. I think people who don't know the DNA bases are missing out on a lot :-)