352 Chapter 10. Enzymes and molecular machines[[Student version, January 17, 2003]]
ingredient (thermal motion), and obtain a rough picture of how molecular machines work. Thus,
many important biochemical details will be omitted; just as in Chapter 9, mechanical images will
serve as metaphors for subtle chemical details.
This chapter has a different character from earlier ones because some of the stories are still
unfolding. After outlining some general principles in Sections 10.2–10.3, Section 10.4 will look
specifically at a remarkable family of real machines, the kinesins. A kinesin molecule’s head region
is just 4× 4 × 8 nmin size (smaller than the smallest transistor in your computer), and is built from
just 345 amino acid residues. Indeed kinesin’s head region is one of the smallest known natural
molecular motors, and possibly the simplest. We will illustrate the interplay between models and
experiments by examining two key experiments in some detail. Although the final picture of force
generation in kinesin is still not known, still we will see how structural, biochemical, and physical
measurements have interlocked to fill in many of the details.
The Focus Question for this chapter is:
Biological question: How does a molecular motor convert chemical energy, ascalarquantity, into
directed motion, avector?
Physical idea:Mechanochemical coupling arises from a free energy landscape with a direction set
bythe geometry of the motor and its track. The motor executes a biased random walk on this
landscape.
10.1 Survey of molecular devices found in cells
10.1.1 Terminology
This chapter will use the termmolecular deviceto include single molecules (or few-molecule as-
semblies) falling into two broad classes:
1.Catalystsenhance the rate of a chemical reaction. Catalysts created by cells are called
enzymes(see Section 10.3.3).
2.Machinesactively reverse the natural flow of some chemical or mechanical process by coupling
it to another one. Machines can in turn be roughly divided:(a)One-shotmachines exhaust some internal source of free energy. The osmotic machine
in Section 1.2.2 on page 10 is a representative of this class.
(b) Cyclicmachines process some external source of free energy such as food molecules,
absorbed sunlight, a difference in the concentration of some molecule across a membrane,
or an electrostatic potential difference. The heat engine in Section 6.5.3 on page 189 is
arepresentative of this class; it runs on a temperature difference between two external
reservoirs. Because cyclic machines are of greatest interest to us, let us subdivide them
still further:
i.Motorstransduce some form of free energy into motion, either linear or rotary. This
chapter will discuss motors abstractly, then focus on a case study, kinesin.
ii.Pumpstransduce free energy to create concentration gradients.
iii.Synthasestransduce free energy to drive a chemical reaction, typically the synthesis
of some product. An example is ATP synthase, to be discussed in Chapter 11.