56 Chapter 2. What’s inside cells[[Student version, December 8, 2002]]
2.3.3 Enzymes and regulatory proteins
Enzymes are molecular devices whose job is to bind particular molecules, under particular condi-
tions, and promote particular chemical changes. The enzyme molecule itself is not modified or used
up in this process—it is acatalyst,orassistant, for a process that could in principle happen on its
own. Enzymes may break down large molecules, as in digestion, or build small molecules into big
ones. One feature of enzymes immediately apparent from their structures is their complicated and
well-definedshape(Figure 2.28). Chapter 7 will begin a discussion of the role of shape in conferring
specificity to enzymes; Chapter 9 will look more deeply into how the shapes actually arise, and how
an enzyme maintains them despite random thermal motion.
Another context where binding specificity is crucial concerns control and feedback. Nearly every
cell in your body contains the same collection of chromosomes,^6 and yet only pancreas cells secrete
insulin; only hair cells grow hairs, and so on. Each cell type has a characteristic arrangement of
genes that are active (“switched on”) and inactive (“switched off”). Moreover, individual cells
can modulate their gene activities based on external circumstances: If we deny a bacterium its
favorite food molecule, but supply an alternative food, the cell will suddenly start synthesizing
the chemicals needed to metabolize what’s available. The secret to gene switching is a class of
“regulatory proteins,” which recognize and bind specifically to the beginning of the genes they
control (Figure 2.29). One class, the “repressors,” can physically block the start of their gene,
preventing transcription. Others help with the assembly of the transcriptional apparatus and have
the opposite effect. Eukaryotic cells have a more elaborate implementation of the same general
idea.
Finally, the pumps and channels embedded in cell membranes are also quite specific. For
example, a remarkable pump to be studied in Chapter 11 has an operating cycle in which it binds
only sodium ions, ferries them to the other side of the membrane, then binds only potassium ions
and ferries them in the other direction! As shown in Figure 2.30c, this pump also consumes ATP,
in part because the sodium ions are being pulled from a region of negative electrical potential (the
cell’s interior) to a positive region, increasing their potential energy. According to the First Law
(Section 1.1.2 on page 4), such a transaction requires a source of energy. (The Example on page 419
will explore the energy budget of this pump in greater detail.)
2.3.4 The overall flow of information in cells
Section 2.3.3 hinted that the cell’s genome should not be regarded as ablueprint,orliteral repre-
sentation, of the cell, but rather as specifying analgorithm,orset of instructions, for creating and
maintaining the entire organism containing the cell. Gene regulatory proteins supply some of the
switches turning parts of the algorithm on and off.
Wecan now describe a simplified version of the flow of information in cells (Figure 2.31).^7
1.The DNA in the cell nucleus contains the master copy of the software, in duplicate. Under
ordinary circumstances this copy is not modified, but only duplicated during cell division. A
molecular machine calledDNA polymeraseaccomplishes the duplication. Like the machines
mentioned in Section 2.3.2, DNA polymerase is made from proteins. The DNA contains
genes, consisting of regulatory regions along with code specifying the amino acid sequences(^6) Exceptions include germ cells (genome not present in duplicate) and human red blood cells (no nucleus at all).
(^7) Some authors refer to this scheme as the “central dogma” of molecular biology, an unfortunate phrase due to
F. Crick, who proposed it in 1958. Several amendments to this scheme are discussed in Section 2.3.4′on page 61.