3. Describe the main events in the transcription of genetic
information from DNA into mRNA.
4. Explain the difference between an exon and an intron.
5. What is the function of a spliceosome?
6. Identify the site of ribosomal subunit assembly.
7. Describe the role of tRNA in protein assembly.
8. Describe the events of protein translation that occur on the
surface of a ribosome.
9. Describe the effects of transcription factors on gene
10. List the factors that regulate the concentration of a protein in a
11. What is the function of the signal sequence of a protein? How
is it formed, and where is it located?
12. Describe the pathway that leads to the secretion of proteins
13. List the three general types of effects a mutation can have on a
Binding Site Characteristics
In the previous sections, we learned how the cellular machin-
ery synthesizes and processes proteins. We now turn our atten-
tion to how proteins interact with each other and with other
The ability of various molecules and ions to bind to spe-
ciﬁ c sites on the surface of a protein forms the basis for the
wide variety of protein functions. A
is any molecule
that is bound to the surface of a protein by one of the follow-
ing forces: (1) electrical attractions between oppositely charged
ionic or polarized groups on the ligand and the protein, or (2)
weaker attractions due to hydrophobic forces between non-
polar regions on the two molecules. Note that this binding
does not involve covalent bonds; in other words, binding is
generally reversible. The region of a protein to which a ligand
binds is known as a
A protein may contain sev-
eral binding sites, each speciﬁ c for a particular ligand.
The force of electrical attraction between oppositely charged
regions on a protein and a ligand decreases markedly as the
distance between them increases. The even weaker hydropho-
bic forces act only between nonpolar groups that are very close
to each other. Therefore, for a ligand to bind to a protein, the
ligand must be close to the protein surface. This proximity
occurs when the shape of the ligand is complementary to the
shape of the protein-binding site, so that the two ﬁ t together
like pieces of a jigsaw puzzle (
The binding between a ligand and a protein may be so
speciﬁ c that a binding site can bind only one type of ligand
and no other. Such selectivity allows a protein to identify (by
binding) one particular molecule in a solution containing hun-
dreds of different molecules. This ability of a protein binding
site to bind speciﬁ c ligands is known as
because the binding site determines the type of chemical that
In Chapter 2 we described how the conformation of a
protein is determined by the location of the various amino
acids along the polypeptide chain. Accordingly, proteins with
different amino acid sequences have different shapes and,
therefore, differently shaped binding sites, each with its own
city. As illustrated in
, the amino
acids that interact with a ligand at a binding site need not be
adjacent to each other along the polypeptide chain, because
the three-dimensional folding of the protein may bring vari-
ous segments of the molecule into juxtaposition.
Although some binding sites have a chemical speciﬁ city
that allows them to bind only one type of ligand, others are
less speciﬁ c and thus can bind a number of related ligands.
For example, three different ligands can combine with the
binding site of protein X in
, because a portion
of each ligand is complementary to the shape of the binding
site. In contrast, protein Y has a greater chemical speciﬁ city
and can bind only one of the three ligands. It is the degree of
speciﬁ city of proteins that determines, in part, the side effects
The complementary shapes of ligand and protein-binding site
determine the chemical speciﬁ city of binding.