10.1. Survey of molecular devices found in cells[[Student version, January 17, 2003]] 353
Athird class of molecular devices will be discussed in Chapters 11–12: the “gated ion channels”
sense external conditions and respond by changing their permeability to specific ions.
Before embarking on the mathematics, Sections 10.1.2 through 10.1.4 describe a few represen-
tative classes of the molecular machines found in cells, in order to have some concrete examples in
mind as we begin to develop a picture of how such machines work. (Section 10.5 briefly describes
still other kinds of motors.)
10.1.2 Enzymes display saturation kinetics
Chapter 3 noted that a chemical reaction, despite having a favorable free energy change, may
proceed very slowly due to a large activation energy barrier (Idea 3.27 on page 80). Chapter 8
pointed out that this circumstance gives cells a convenient way to store energy, for example in
glucose or ATP, until it is needed. But what happens when itisneeded? Quite generally, cells need
to speed up the natural rates of many chemical reactions. The most efficient way to do this is with
some reusable device—a catalyst.
Enzymes are biological catalysts. Most enzymes are made of protein, sometimes in the form of a
complex with other small molecules (“coenzymes” or “prosthetic groups”). Other examples include
ribozymes, which consist of RNA. Complex catalytic organelles such as the ribosome (Figure 2.33)
are complexes of protein with RNA.
Toget a sense of the catalytic power of enzymes, consider the decomposition of hydrogen
peroxide at room temperature, H 2 O 2 →H 2 O+^12 O 2 .This reaction is highly favorable energetically,
with ∆G^0 =− 41 kBTr,yet it proceeds very slowly in pure solution: With an initial concentration
1 Mof hydrogen peroxide, the rate of spontaneous conversion at 25◦Cis just 10−^8 Ms−^1 .This rate
corresponds to a decomposition of just 1% of a sample after two weeks. Various substances can
catalyze the decomposition, however. For example, the addition of 1mMhydrogen bromide speeds
the reaction by a factor of 10. But the addition of the enzymecatalase,ataconcentration of
binding sites again equal to 1mM,results in a speedup factor of 1 000 000 000 000!
Your Turn 10a
Reexpress this fact by giving the number of molecules of hydrogen peroxide that asinglecatalase
molecule can split per second.In your body’s cells, catalase breaks down hydrogen peroxide generated by other enzymes (as a
byproduct of eliminating dangerous free radicals before they can damage the cell).
In the catalase reaction, hydrogen peroxide is called thesubstrateupon which the enzyme acts;
the resulting oxygen and water are theproducts.The rate of change of the substrate concentration
(here 10^4 Ms−^1 )iscalled thereaction velocity. The reaction velocity clearly depends on how
muchenzyme is present. To get a quantity intrinsic to the enzyme itself, we divide the velocity
bythe concentration of enzyme^1 (taken to be 1mMabove). Even this number is not completely
intrinsic to the enzyme, but also reflects the availability (concentration) of the substrate. But most
enzymes exhibitsaturation kinetics:The reaction velocity increases up to a point as we increase
substrate concentration, then levels off. Accordingly we define theturnover numberof an enzyme
as the maximum velocity divided by the concentration of enzyme. The turnover number really is
an intrinsic property: It reflects one enzyme molecule’s competence at processing substrate when
(^1) More precisely, we divide by the concentration of active sites, which is the concentration times the number of
such sites per enzyme molecule. Thus for example catalase has four active sites; the rates quoted above actually
correspond to a concentration of catalase of 0. 25 mM.