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chapter 25
RNA and Protein Synthesis
in the cytoplasm where groups of three bases in the mRNA
(codons)
are recognized by
anticodons
in specific tRNAs
that carry a particular amino acid.
The
genetic code
consists of 64 different codons that
specify all
2 0
amino acids as well as codons that func-
tion to initiate and terminate translation. More than one
codon may specify the same amino acid, which is called
degeneracy of the genetic code. Finally, every organism
from bacteria to human uses the same codons to specify
the same amino acids; this is why the genetic code is said
to be universal.
Amino acids are joined together in a specific order deter-
mined by tRNAs, ribosomes, and associated enzymes that
translate the mRNA. Each amino acid is joined to its neigh-
bor by a peptide bond. The specific amino acid sequence of
a protein specifies its three-dimensional structure. Some
proteins require the help of
chaperonins
to fold into a
functional configuration. When synthesis of a polypep-
tide chain is completed on a ribosome, it is released from
the ribosome and may join with one or more similar or
different polypeptides to constitute a functional protein.
25.1 Structure of RNA
RNA is a single-stranded polynucleotide containing the
nucleosides adenosine, guanosine, cytosine, and uridine.
Roughly one-third to one-half of the nucleotides are en-
gaged in intrastrand hydrogen bonds, with single-stranded
segments interspersed between double-stranded regions
that may contain up to about 30 base pairs. The base pairing
produces conformations that are important to the function
of the particular RNA molecules.
Ribosomal RNA (rRNA)
Ribosomes contain several different RNA molecules, three
in prokaryotic ribosomes and four in eukaryotic ribo-
somes. For historical reasons, each class is characterized
by its sedimentation coefficient, which represents a typi-
cal size. For prokaryotes, the three
Escherichia coli
rRNA
molecules are used as size standards; they have sedi-
mentation coefficients of 5S, 16S, and 23S. The
E. coli
rRNA molecules have been sequenced and contain 120,
1541, and 2904 nucleotides, respectively. The sizes of
the prokaryotic rRNA molecules vary very little from one
species of bacterium to another.
Eukaryotic rRNA molecules are generally larger and
there are four eukaryotic rRNA molecules. Rat liver rRNA
molecules are used as standards; the S values and the av-
erage number of nucleotides are 5S (120), 5.8S (150),
18S (2100), and 28S (5050), respectively. The eukaryotic
5.8S species corresponds functionally to the prokaryotic
5S species; no prokaryotic rRNA molecule corresponds to
the eukaryotic 5S rRNA.
Transfer RNA (tRNA)
Transfer RNA molecules range in size from 73 to 93
nucleotides. Since they function as amino acid carriers,
they are named by adding a superscript that designates
the amino acid carried, e.g., tRNAAla for alanine tRNA.
All tRNA molecules studied contain extensive double-
stranded regions and form a cloverleaf structure in which
open loops are connected by double-stranded stems. By
careful comparison of the sequences of more than
2 0 0
different tRNA molecules, common features have been
found and a “consensus” tRNA molecule consisting of
76 nucleotides arranged in a cloverleaf form has been
defined (Figure 25-1). By convention, the nucleotides are
numbered 1 through 76 starting from the 5'-P terminus.
The standard tRNA molecule has the following features:
1. The 5'-P terminus always is base-paired, which
probably contributes to the stability of tRNA.
2. The 3'-OH terminus always is a four-base
single-stranded region having the base sequence
XCCA-3'-OH, in which X can be any base. This is
called the CCA or acceptor stem. The adenine in the
CCA sequence is the site of attachment of the amino
acid by the cognate synthetase.
3. tRNA has many “modified” bases. A few of these,
dihydrouridine (DHU), ribosylthymine (rT),
pseudouridine
(i
jr),
and inosine (I), occur in
particular regions.
4. tRNA has three large single-stranded loops. The
anticodon loop contains seven bases. The loop
containing bases 14-21 is called the DHU loop; it is
not constant in size in different tRNA molecules. The
loop containing bases 54-60 almost always contains
the sequence
TxfrC
and is called the
TtjrC
loop.
5. Four double-stranded regions called stems (or arms)
often contain GU base pairs. The names of the stems
match the corresponding loop.
6
. Another loop, containing bases 44-48, is also present.
In the smallest tRNAs it contains four bases, whereas
in the largest tRNA molecule it contains 21 bases.
This highly variable loop is called the
extra arm.
25.2 Messenger RNA
Messenger RNA
molecules in prokaryotic and eukaryotic
cells are similar in some structural aspects but also differ
significantly. All messenger RNAs contain the same four
nucleotides, A, C, G, and U, and utilize the codon AUG to
