Getting work done

Previously I described how enzymes can catalyse a reaction. If this were all enzymes could do then cells would be very limited - they could only ever move subsets of reactions towards equilibrium. In fact enzymes are limited to moving reactions to equilibrium, however, they can expand the repertoire of reactions available by coupling two or more together, effectively, creating a new reaction. For example, real life cells couple the synthesis of DNA to the hydrolysis of GTP. The addition of a nucleotide to a strand of DNA would normally be energetically unfavourable (the equilibrium favours removing a nucleotide), but the hydrolysis of GTP is more favourable. The coupled reaction therefore favours DNA synthesis.

In order for the simulated cells to drive energetically unfavourable reactions, such as DNA synthesis, they therefore require enzymes that can couple reactions. For example, in a solution of 1% EH and 0.5% E and H, EH synthesis is unfavourable. Similarly, in a solution of 1% AD and 05% A and D, AD synthesis is unfavourable. Adding ADase and EHase to the pool causes both EH and AD to become hydrolysed.

(The concentrations of D and H are equal to the concentrations of A and E respectively, so are not shown.)

Pores and transporters

Because transporters and enzymes work in the same way in this simulation, transporters can also be coupled, which means several types of protein can now be defined:

• tra-f-A: a pore that allows the passive diffusion of A across the membrane.
• tra-f-A-tra-f-B: an A/B symporter
• tra-f-A-tra-r-B: an A/B antiporter
• tra-f-A-tra-f-CDase: an active transporter of A, powered by CD hydrolysis

In fact, if the balance of equilibria is right, the final protein can also act like ATP synthase, using the concentration gradient of A to synthesise CD.