Chapter 2: Water- Nucleophiles and Electrophiles.

Electron-rich atoms or groups are called nucleophiles (nucleus lovers) because they seek positively charged or electron-deficient species called electrophiles (electron lovers).

Nucleophiles are either negatively charged or have unshared pairs of electrons. They attack electrophiles during substitution or addition reactions.

The most common nucleophilic atoms in biology are oxygen, nitrogen, sulfur and carbon.

Because the oxygen atom of water has two unshared pairs of electrons, it is nucleophilic.

Water is relatively weak nucleophile, but its cellular concentration is so high that one might expect that many biological compounds such as polymers, would be easily degraded by nucleophilic attack by water. For example, proteins can be hydrolyzed, or degraded by water, to release their monomeric units, amino acids.

Another question immediately pops to mind here; if there is so much water in cells, why aren’t all biopolymers rapidly degraded to their components?

The linkages between the monomeric units of biopolymers, such as the amide bonds in proteins and the ester linkages in DNA, are relatively stable in solution at cellular pH and temperature (i.e., they are kinetically stable, although they are thermodynamically unstable).

Actually, there is some effect against these bonds, however, the rate of reaction is so slow under the physiological conditions (of temperature and pH) of the body that special enzymes, called hydrolases, are required to catalyze hydrolysis. Of course, these enzymes are stored in inactive forms or enclosed in special membrane-bounded compartments to avoid spontaneous hydrolysis.

Furthermore, cells can synthesize polymers in an aqueous environment by using the chemical potential energy of ATP to overcome an unfavorable thermodynamic barrier.

And, more importantly, the enzymes exclude water from the active site where synthetic reactions occur.