A list of key differences between prokaryotes and eukaryotes with respect
to protein synthesis is shown in Table 9-1. These include the existence of
multiple eukaryotic initiation factors that facilitate the assembly of the riboso-
mal protein synthetic machinery, whereas there are only three for prokary-
otes. An initiation site on bacterial mRNA consists of the AUG initiation
codon preceded with a gap of approximately 10 bases by the Shine-Dalgarno
polypurine hexamer, whereas the 5' Cap (a 7-methylguanylate residue in a
5'^5' triphosphate linkage) acts as an initiation signal in eukaryotes. In
prokaryotes, the first or A-terminal amino acid is a formyl-methionine
(fMet), but in eukaryotes it is usually a simple methionine. Additionally, the size
and nature of the prokaryotic ribosomes are quite different from the eukaryotic
Ribosomal RNA (rRNA) is a component of the ribosomes, the protein
synthesis factories in the cell. rRNA molecules are extremely abundant,
making up at least 80 percent of the RNA molecules found in a typical
eukaryotic cell. Virtually all ribosomal proteins are in contact with rRNA.
Most of the contacts between ribosomal subunits are made between the 16S
and 23S rRNAs such that the interactions involving rRNA are a key part of
ribosome function. The environment of the tRNA-binding sites is largely
determined by rRNA. The rRNA molecules have several roles in protein syn-
thesis. 16S rRNA plays an active role in the functions of the 30S subunit. It
interacts directly with mRNA, with the 50S subunit, and with the anticodons
of tRNAs in the P- and A-sites. Peptidyl transferase activity resides exclusively
in the 23S rRNA. Finally, the rRNA molecules have a structural role. They fold
into three-dimensional shapes that form the scaffold on which the ribosomal
proteins assemble.
Many antibiotics act to inhibit protein synthesis in prokaryotes without
affecting eukaryotic cells much. Several important targets in protein synthesis
have been identified that are blocked by these agents to curb microorganism
Table 9-1
Recognition sequence
Shine-Dalgarno sequence
5' caps direct e-IFs
Initiation factors
IF-1, IF-2, IF-3
multiple e-Ifs (>10)
Elongation factors
EF-Tu, EF-G, EF-Ts
Multi-subunit eEF-1,
eEF-2, eEF-3
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