Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

CATALYSIS AND THE USE OF ENERGY BY CELLS
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Figure 2–24 Directing substrate molecules through a specific reaction
pathway by enzyme catalysis. A substrate molecule in a cell (green ball)
is converted into a different molecule (blue ball) by means of a series of
enzyme-catalyzed reactions. As indicated (yellow box), several reactions
are energetically favorable at each step, but only one is catalyzed by each
enzyme. Sets of enzymes thereby determine the exact reaction pathway that
is followed by each molecule inside the cell.
has a unique shape containing an active site, a pocket or groove in the enzyme
into which only particular substrates will fit (Figure 2–25). Like all other catalysts,
enzyme molecules themselves remain unchanged after participating in a reaction
and therefore can function over and over again. In Chapter 3, we discuss further
how enzymes work.
energy
How Enzymes Find Their Substrates: The Enormous Rapidity of
Molecular Motions
An enzyme will often catalyze the reaction of thousands of substrate molecules
every second. This means that it must be able to bind a new substrate molecule
in a fraction of a millisecond. But both enzymes and their substrates are present
in relatively small numbers in a cell. How do they find each other so fast? Rapid
binding is possible because the motions caused by heat energy are enormously
fast at the molecular level. These molecular motions can be classified broadly into
three kinds: (1) the movement of a molecule from one place to another (translational
motion), (2) the rapid back-and-forth movement of covalently linked atoms
with respect to one another (vibrations), and (3) rotations. All of these motions
help to bring the surfaces of interacting molecules together.
The rates of molecular motions can be measured by a variety of spectroscopic
techniques. A large globular protein is constantly tumbling, rotating about its axis
about a million times per second. Molecules are also in constant translational
motion, which causes them to explore the space inside the cell very efficiently by
wandering through it—a process called diffusion. In this way, every molecule in
a cell collides with a huge number of other molecules each second. As the molecules
in a liquid collide and bounce off one another, an individual molecule
moves first one way and then another, its path constituting a random walk (Figure
2–26). In such a walk, the average net distance that each molecule travels (as the
“crow flies”) from its starting point is proportional to the square root of the time
involved: that is, if it takes a molecule 1 second on average to travel 1 μm, it takes
4 seconds to travel 2 μm, 100 seconds to travel 10 μm, and so on.
The inside of a cell is very crowded (Figure 2–27). Nevertheless, experiments
in which fluorescent dyes and other labeled molecules are injected into cells show
that small organic molecules diffuse through the watery gel of the cytosol nearly
MBoC6 m2.46c/2.18
enzyme
enzyme
active site
CATALYSIS
molecule A
(substrate)
enzyme–
substrate
complex
enzyme–
product
complex
molecule B
(product)
Figure 2–25 How enzymes work. Each enzyme has an active site to which one or more substrate
molecules bind, forming an enzyme–substrate complex. A reaction occurs at the active site,
producing an enzyme–product complex. The product is then released, allowing the enzyme to bind
further substrate molecules.