Chapter 10
Enzymes and molecular machines
If ever to a theory I should say:
‘You are so beautiful!’ and ‘Stay! Oh, stay!’
Then you may chain me up and say goodbye—
Then I’ll be glad to crawl away and die.- Delbr ̈uck and von Weizacker’s update toFaust, 1932
Aconstantly recurring theme of this book has been the idea that living organisms transduce
free energy. For example, Chapter 1 discussed how animals eat high-energy molecules and excrete
lower-energy molecules, generating not only thermal energy but also mechanical work. We have
constructed a framework of ideas allegedly useful for understanding free energy transduction, and
even presented some primitive examples of how it can work:
- Chapter 1 introduced the osmotic machine (Section 1.2.2); Chapter 7 worked through the
details (Section 7.2). - Section 6.5.3 introduced a motor driven by temperature differences.
Neither of the devices mentioned above is a very good analog of the sort of motors we find in living
organisms, however, since neither is driven by chemical forces. Chapter 8 set the stage for the
analysis of more biologically relevant machines, developing the notion that chemical bond energy is
just another form of free energy. For example, the change ∆Gof chemical potential in a chemical
reaction was interpreted as a force driving that reaction: The sign of ∆Gdetermines in which
direction a reaction will proceed. But we stopped short of explaining how a molecular machine can
harnessachemical force to drive an otherwise unfavorable transaction, such as doing mechanical
work on a load. Understanding how molecules can act as free energy brokers, sitting at the interface
between the mechanical and chemical worlds, will be a major goal of this chapter.
Interest in molecular machines blossomed with the realization that much of cellular behavior
and architecture depends on the active, directed transport of macromolecules, membranes, or chro-
mosomes within the cell’s cytoplasm. Just as disruption of traffic hurts the functioning of a city, so
defective molecular transport can result in a variety of diseases.
The subject of molecular machines is vast. Rather than survey the field, this chapter will focus
on showing how we can take some familiar mechanical ideas from the macroworld, add just one new
©c2000 Philip C. Nelson351