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

PROTEIN FUNCTION
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rate of reaction
V max
Figure 3–46 Enzyme kinetics. The rate
of an enzyme reaction (V) increases as
0.5V max
catalyzing only a single type of reaction. Thus, hexokinase adds a phosphate group
to D-glucose but ignores its optical isomer L-glucose; the blood-clotting enzyme
thrombin cuts one type of blood protein between a particular arginine and its
adjacent glycine and nowhere else, and so on. As discussed in detail in Chapter 2,
enzymes work in teams, with the product of one enzyme becoming the substrate
for the next. The result is an elaborate network of metabolic MBoC6 m3.45/3.42 pathways that provides
the cell with energy and generates the many large and small molecules that
the cell needs (see Figure 2–63).
Substrate Binding Is the First Step in Enzyme Catalysis
For a protein that catalyzes a chemical reaction (an enzyme), the binding of each
substrate molecule to the protein is an essential prelude. In the simplest case, if
we denote the enzyme by E, the substrate by S, and the product by P, the basic
reaction path is E + S → ES → EP → E + P. There is a limit to the amount of substrate
that a single enzyme molecule can process in a given time. Although an
increase in the concentration of substrate increases the rate at which product is
formed, this rate eventually reaches a maximum value (Figure 3–46). At that point
the enzyme molecule is saturated with substrate, and the rate of reaction (V max )
depends only on how rapidly the enzyme can process the substrate molecule. This
maximum rate divided by the enzyme concentration is called the turnover number.
Turnover numbers are often about 1000 substrate molecules processed per
second per enzyme molecule, although turnover numbers between 1 and 10,000
are known.
The other kinetic parameter frequently used to characterize an enzyme is its
K m , the concentration of substrate that allows the reaction to proceed at one-half
its maximum rate (0.5 V max ) (see Figure 3–46). A low K m value means that the
enzyme reaches its maximum catalytic rate at a low concentration of substrate and
generally indicates that the enzyme binds to its substrate very tightly, whereas a
high K m value corresponds to weak binding. The methods used to characterize
enzymes in this way are explained in Panel 3–2 (pp. 142–143).
Enzymes Speed Reactions by Selectively Stabilizing Transition
States
Enzymes achieve extremely high rates of chemical reaction—rates that are far
higher than for any synthetic catalysts. There are several reasons for this efficiency.
First, when two molecules need to react, the enzyme greatly increases the
local concentration of both of these substrate molecules at the catalytic site, holding
them in the correct orientation for the reaction that is to follow. More importantly,
however, some of the binding energy contributes directly to the catalysis.
Substrate molecules must pass through a series of intermediate states of altered
geometry and electron distribution before they form the ultimate products of the
reaction. The free energy required to attain the most unstable intermediate state,
called the transition state, is known as the activation energy for the reaction, and
it is the major determinant of the reaction rate. Enzymes have a much higher
affinity for the transition state of the substrate than they have for the stable form.
K m
substrate concentration
the substrate concentration increases
until a maximum value (V max ) is reached.
At this point all substrate-binding sites on
the enzyme molecules are fully occupied,
and the rate of reaction is limited by
the rate of the catalytic process on the
enzyme surface. For most enzymes,
the concentration of substrate at which
the reaction rate is half-maximal (K m ) is
a measure of how tightly the substrate
is bound, with a large value of K m
corresponding to weak binding.