Essential Cell Biology 5th edition

How Proteins Are Controlled
149
Another example of a protein that contains a nonprotein portion essential
for its function is hemoglobin (see Figure 4−24). A molecule of
hemoglobin carries four noncovalently bound heme groups, ring-shaped
molecules each with a single central iron atom (Figure 4−41B). Heme
gives hemoglobin—and blood—its red color. By binding reversibly to dissolved
oxygen gas through its iron atom, heme enables hemoglobin to
pick up oxygen in the lungs and release it in tissues that need it.
Enzymes, too, make use of nonprotein molecules: they frequently have a
small molecule or metal atom associated with their active site that assists
with their catalytic function. Carboxypeptidase, an enzyme that cuts polypeptide
chains, carries a tightly bound zinc ion in its active site. During
the cleavage of a peptide bond by carboxypeptidase, the zinc ion forms
a transient bond with one of the substrate atoms, thereby assisting the
hydrolysis reaction. In other enzymes, a small organic molecule—often
referred to as a coenzyme—serves a similar purpose. Biotin, for example,
is found in enzymes that transfer a carboxyl group (–COO – ) from one
molecule to another (see Figure 3−38). Biotin participates in these reactions
by forming a covalent bond to the –COO – group to be transferred,
thereby producing an activated carrier (see Table 3–2, p. 109). This small
molecule is better suited for this function than any of the amino acids
used to make proteins.
Because biotin cannot be synthesized by humans, it must be provided in
the diet; thus biotin is classified as a vitamin. Other vitamins are similarly
needed to make small molecules that are essential components of our
proteins; vitamin A, for example, is needed in the diet to make retinal, the
light-sensitive part of rhodopsin.
HOW PROTEINS ARE CONTROLLED
Thus far, we have examined how binding to other molecules allows proteins
to perform their specific functions. But inside the cell, most proteins
and enzymes do not work continuously, or at full speed. Instead, their
activities are regulated in a coordinated fashion so the cell can maintain
itself in an optimal state, producing only those molecules it requires
to thrive under current conditions. By coordinating not only when—and
how vigorously—proteins perform, but also where in the cell they act, the
cell ensures that it does not deplete its energy reserves by accumulating
molecules it does not need or waste its stockpiles of critical substrates.
We now consider how cells control the activity of their enzymes and
other proteins.
The regulation of protein activity occurs at many levels. At the most fundamental
level, the cell controls the amount of each protein it contains.
It can do so by controlling the expression of the gene that encodes that
protein (discussed in Chapter 8). It can also regulate the rate at which
the protein is degraded (discussed in Chapter 7). The cell also controls
protein activities by confining the participating proteins to particular subcellular
compartments. Some of these compartments are enclosed by
membranes (as discussed in Chapters 11, 12, 14, and 15); others are created
by the proteins that are drawn there, as we discuss shortly. Finally,
the activity of an individual protein can be rapidly adjusted at the level of
the protein itself.
All of these mechanisms rely on the ability of proteins to interact with
other molecules—including other proteins. These interactions can cause
proteins to adopt different conformations, and thereby alter their function,
as we see next.