Page 182 - Academic Press Encyclopedia of Physical Science and Technology 3rd BioChemistry

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Encyclopedia of Physical Science and Technology EN013D-617 July 27, 2001 11:42

222 Protein Synthesis

A. Conserved Features of tRNAs separation between anticodon and amino acid on the tRNA
is paralleled in the mRNA decoding and peptide bond
Transfer RNAs typically contain approximately 76 nu-
formation events that occur on two different subunits of
cleotides and have a molecular mass of about 25 kD. The
the ribosome. Furthermore, the domains of tRNA can be
characteristic “cloverleaf ” secondary structure represen-
physically separated such that an isolated acceptor stem
tation of tRNA was predicted based on regions of base
(“minihelix”) can in many cases accept its specified amino
complementarity, and the determination of hundreds of
acid, while an anticodon stem-loop helix can bind to the
tRNA sequences demonstrated that such a folding pattern
ribosome-bound mRNA.
is conserved. Several sequence and structural features are
alsoconsistentlypresentintRNAsfromallorganisms.The
sequence at the 3 -end of tRNAs is always –CCA, with a C. Codon–Anticodon Interactions

free hydroxyl group on the terminal adenosine that is the
Translation of a genetic message into its protein prod-
siteofaminoacidattachment.Nucleotidesnearthetermini
uct depends on base pairing interactions between mRNA
hybridize to make the 7-base-pair (bp) acceptor stem.
codon and tRNA anticodon. The 64 trinucleotide codons
The other arms of the tRNA cloverleaf also have distinc-
are more than sufficient to fully determine all 20 amino
tive conserved features. The modified base dihydrouridine
acids as well as one start and three stop codons. Thus,
(D) is typically present in the loop that closes off a short
the code is degenerate, with many amino acids having
3- or 4-bp stem following the acceptor stem. This stem
more than one codon. This codon degeneracy is primarily
and loop are therefore called the D-arm. The anticodon
due to variation in the third position of the trinucleotide,
arm consists of a 5-bp helix closed by a loop that contains
as shown in Table I. Although many organisms have more
the trinucleotide anticodon. Following the anticodon arm
than one tRNA molecule per amino acid (these are “isoac-
is the variable loop, which can contain 3–21 nucleotides,
ceptors”), in many cases a specific tRNA recognizes more
with a stem as long as 7 bp, depending on the particular
than one codon. Non-Watson–Crick base pairs are permit-
tRNA. The modified bases pseudouridine ( ) and ribo-
ted at the third position, because of room for some struc-
thymidine (T) are usually present in the loop of the T C
tural flexibility or “wobble” in the pairing geometry. For
arm, so named because of the presence of this highly con-
example, a U in the third position (5 nucleotide) of the an-

served sequence.
ticodon can base pair with an A (Watson–Crick pair) or a G
(wobble pair) in the codon. Several tRNAs contain an ino-
sine (I) nucleotide at the third anticodon position; inosine
B. The L-Shaped Structure of tRNAs
forms a standard base pair with C and wobble pairs with U
In three dimensions, tRNAs fold into an L-shaped struc- and A.
ture in which the acceptor stem and T C arm coaxially
stack to form one part of the L known as the minihelix,
and the D and anticodon arms likewise stack to form the III. AMINOACYL–tRNA SYNTHETASES
other part of the molecule. This structure is facilitated and
stabilized by tertiary interactions at the corner of the L that Decoding of the protein message occurs at the ribo-
bring together the D and variable loops. The nucleotides some, after prior attachment of amino acids to the tRNA
involved in these interactions are typically invariant or molecules. Aminoacyl–tRNA synthetases (AARSs) are
semi-invariant, indicating that the tRNA L shape is univer- the family of enzymes responsible for covalent attach-
sal. While most base pairs in tRNA helices are canonical ment of each amino acid to its correct, or cognate, tRNA
Watson–Crick pairs, the tertiary interactions at the cor- molecule. This first step in protein synthesis is responsi-
ner of the L make use of some unusual hydrogen-bonding ble for establishing the rules of the genetic code (which
conformations. For example, nearly all tRNAs contain a codon corresponds to which amino acid), as the aminoa-
U8:A14 reverse Hoogsteen base pair, and several base cylated tRNA has both the nucleic acid component of the
triples (where three bases are paired together) are also genetic message (the anticodon) and the amino acid. In
typically present at the core of the structure. most organisms, there are 20 AARSs, one for each amino
The two portions of the L can be considered distinct acid. Because of codon degeneracy, there is at least one
domains with separate contributions to protein synthesis. tRNA per amino acid; serine, for example, can be attached
The minihelix containing the acceptor arm includes the to one of five different isoaccepting tRNA molecules. Al-
site of amino acid attachment (the 3 -OH). It is considered though each enzyme catalyzes the same aminoacylation

by many investigators to be related to the historical or early reaction, the substrates are unique and must be effectively
form of tRNA. The anticodon trinucleotide is located at selectedfromamongthecellularpool.Forexample,valyl–
˚
the other end of the L, approximately 75 A away. This tRNA synthetase (ValRS) binds the amino acid valine