An mRNA contains a series of codons that interact with the
anticodons of aminoacyl-tRNAs so that a corresponding series of amino acids is
incorporated into a polypeptide chain. The ribosome provides the environment for
controlling the interaction between mRNA and aminoacyl-tRNA. The ribosome
behaves like a small migrating factory that travels along the template engaging
in rapid cycles of peptide bond synthesis. Aminoacyl-tRNAs shoot in and out of
the particle at a fearsome rate, depositing amino acids; and elongation factors
cyclically associate with and dissociate from the ribosome. Together with its
accessory factors, the ribosome provides the full range of activities required
for all the steps of protein synthesis.
Figure 6.1 shows the relative
dimensions of the components of the protein synthetic apparatus. The ribosome
consists of two subunits that have specific roles in protein synthesis.
Messenger RNA is associated with the small subunit; ~30 bases of the mRNA are
bound at any time. The mRNA threads its way along the surface close to the
junction of the subunits. Two tRNA molecules are active in protein synthesis at
any moment; so polypeptide elongation involves reactions taking place at just
two of the (roughly) 10 codons covered by the ribosome. The two tRNAs are
inserted into internal sites that stretch across the subunits. A third tRNA may
remain present on the ribosome after it has been used in protein synthesis,
before being recycled.
The basic form of the ribosome has been conserved in
evolution, but there are appreciable variations in the overall size and
proportions of RNA and protein in the ribosomes of bacteria, eukaryotic
cytoplasm, and organelles. Figure 6.2 compares the
components of bacterial and mammalian ribosomes. Both are ribonucleoprotein
particles that contain more RNA than protein. The ribosomal proteins are known
as r-proteins.
Each of the ribosome subunits contains a major rRNA and a
number of small proteins. The large subunit may also contain smaller RNA(s). In
E. coli, the small (30S) subunit consists of the 16S rRNA and 21
r-proteins. The large (50S) subunit contains 23S rRNA, the small 5S RNA, and 31
proteins. With the exception of one protein present at four copies per ribosome,
there is one copy of each protein. The major RNAs constitute the major part of
the mass of the bacterial ribosome. Their presence is pervasive, and probably
most or all of the ribosomal proteins actually contact rRNA. So the major rRNAs
form what is sometimes thought of as the backbone of each subunit, a continuous
thread whose presence dominates the structure, and which determines the
positions of the ribosomal proteins.
The ribosomes of higher eukaryotic cytoplasm are larger than
those of bacteria. The total content of both RNA and protein is greater; the
major RNA molecules are longer (called 18S and 28S rRNAs), and there are more
proteins. Probably most or all of the proteins are present in stoichiometric
amounts. RNA is still the predominant component by mass.
Organelle ribosomes are distinct from the ribosomes of the
cytosol, and take varied forms. In some cases, they are almost the size of
bacterial ribosomes and have 70% RNA; in other cases, they are only 60S and have
<30% RNA.
The ribosome possesses several active centers, each of which
is constructed from a group of proteins associated with a region of ribosomal
RNA. The active centers require the direct participation of rRNA in a structural
or even catalytic role. Some catalytic functions require individual proteins,
but none of the activities can be reproduced by isolated proteins or groups of
proteins; they function only in the context of the ribosome.
Two types of information are important in analyzing the
ribosome. Mutations implicate particular ribosomal proteins or bases in rRNA in
participating in particular reactions. Structural analysis, including direct
modification of components of the ribosome and comparisons to identify conserved
features in rRNA, identifies the physical locations of components involved in
particular functions.