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chapter 25
RNA and Protein Synthesis
reactions necessary for protein synthesis. It was not until
crystallization of the 50S subunit provided an atomic-level
view of its structure that it was finally proved that the op-
posite is actually correct. The ribosomal proteins provide
the structural framework for the 23 S which actually car-
ries out the peptidyltransferase reaction. Thus, the 23S
rRNA is an enzyme and the ribosome is a
ribozyme.
Al-
though the activity of the 23S rRNA is dependent on the
ribosomal proteins, the 50S subunit that is substantially
deproteinized still can perform the peptidyltransferase
reaction.
A crucial feature of the peptidyltransferase reaction is
a particular adenine that is conserved in rRNAs extracted
from the large ribosomal subunits of thousands of differ-
ent organisms from all three kingdoms. Sequence analysis
shows that this adenine base
(2451
A) always is present in
the active site of the ribosome and acts as a general acid-
base catalyst by deprotonating the nucleophilic amine as
shown below.
25.10 Protein Synthesis
Protein synthesis has three stages:
1. Polypeptide chain initiation,
2. Chain elongation, and
3. Chain termination.
The main features of the initiation step are binding of
mRNA to the ribosome, selection of the initiation codon,
and binding of the charged tRNA bearing the first amino
acid. In the elongation stage, there are two steps: joining
of adjacent amino acids by peptide bond formation, and
moving the mRNA and the ribosome with respect to one
another so that codons are translated successively
(trans-
location).
In the termination stage, the completed polypep-
tide dissociate from the ribosomes, which are released to
begin another cycle of synthesis.
H
aa-tRNA— N-
-O 0 .
hJ P
tRNA
2451A
tetrahedral intermediate
aa-tRNA— N
H
) = C
HO
2451A
tRNA
The positive charge on
2 4 5 1
A in the tetrahedral intermedi-
ate is probably transferred to adjacent tRNA nucleotides
that undergo tautomeric shifts. The evidence that riboso-
mal RNAs perform enzymatic functions critical to protein
synthesis lends weight to the evolutionary significance of
RNA in primordial chemical reactions that eventually led
to the development of cells.
Every polypeptide has an amino terminus and a car-
boxyl terminus. In both prokaryotes and eukaryotes, syn-
thesis begins at the amino terminus. For a protein having
the sequence H^N-Met-Trp-Asp.
.. Pro-Val-COOH, the
f Met (or Met) is the initiating amino acid and Val is the
last amino acid added to the chain. Translation of mRNA
molecules occurs in the 5' —>
• 3' direction.
Chemical Composition of Eukaryotic Ribosomes
The basic features of eukaryotic ribosomes are similar to
those of bacterial ribosomes, except for their larger size.
They contain a greater number of proteins (about 80) and
an additional RNA molecule.
A typical eukaryotic ribosome has a sedimentation co-
efficient of about 80 and consists of two subunits: 40S
and 60S. These sizes may vary by as much as 10% from
one organism to another in contrast with the homogeneity
of bacteria ribosomes. The components of the subunits of
eukaryotic ribosomes are as follows:
40S subunit : one 18S rRNA molecule + 30-35 proteins
60S subunit : one 5S, one 5.8S, and one 28S rRNA molecule
+ 45-50 proteins
Stages of Protein Synthesis
The mechanismsof protein synthesis in prokaryotes and
eukaryotes differ slightly in detail, but the prokaryotic
mechanism is used as a general model:
1.
Initiation.
Protein synthesis in bacteria begins by
the association of one 30S subunit (not the 70S
ribosome), an mRNA, a charged tRNA™61, three
protein initiation factors, and guanosine
5'-triphosphate (GTP). These molecules make up the
30S preinitiation complex. Association occurs at an
initiator AUG codon, whose selection was described
above. A 50S subunit joins to the 30S subunit to form
a 70S initiation complex (Figure 25-11). This joining
process requires hydrolysis of the GTP contained in
the 30S preinitiation complex. There are two tRNA
