Nucleic Acids in Chemistry and Biology

RNA Structure and Function 275

7.3.2 Transfer RNA and Aminoacylation

tRNAsare commonly referred to as adapter molecules, because the ribosome uses them to translate
mRNA triplet codons into protein sequence. tRNA architecture is remarkably conserved throughout all
kingdoms of life. It is typically organized into a common secondary structure (the cloverleaf) that contains
various stems and loops that are essential for tRNA function (Figure 7.6). For example, the seven base-pair
acceptor stemalways terminates with the sequence 5
–CCA-3
, which becomes directly attached to an
amino acid upon aminoacylation by synthetase enzymes. At the other end of the molecule, the anticodon
loopcontains the three nucleotides that pair with corresponding mRNA codons. All regions of the tRNA
molecule play important roles in recognition by proteins, decoding of mRNA, ribosome binding, and in
formation of the tertiary structure. For example, the tRNA molecule is not a cloverleaf in solution. Under
physiological conditions, it adopts an L-shaped tertiary foldthat has been visualized by X-ray crystallog-
raphy and biochemical methods (Figure 7.6). The D-loopand the TC-loop(also known simply as the
T-loop) serve as hinges that permit the L-shaped structure to form. The variable loopcan be expanded with
extra nucleotides, thus explaining why tRNA molecules can vary significantly in size (
74–95 nucleotides),
without substantial deviation in their secondary or tertiary structures.
In order for tRNA molecules to function as adapters, they not only form codon–anticodon interactions,
they must also carry amino acids into the ribosome so that they can be added to the growing peptide chain.
Indeed, tRNA molecules are not even admitted into the ribosome or allowed to pair with mRNA unless
they bear “cargo” in the form of an amino acid. This is because only charged, or aminoacylated, tRNAs
are bound to the ribosomal helper protein EF-Tu, which is required for tRNA placement within the ribo-
some. The 3
-terminus of tRNA is attached to an amino acid through an aminoacylation reactionthat is
catalyzed by a tRNA synthetaseenzyme (Figure 7.26)^55. Although synthetases help to stimulate the rate
of aminoacylation (which is already a facile chemical reaction), their primary role is in specificity. A given

O

HO OH

O N

N

N

N NH 2

P

O

O

O

tRNA

N

N

N

N NH 2

O

O OH

O

P

O

O O

tRNA

O

CHR

H 3 N

O

P

O

O

P

O

O

P

O

OAdo

O O O

H 3 NCH

R

O

O H 3 NCH

R

O

OP

O

O OAdo

CH

R

O

OP

O

O OAdo

+ PPi

+ AMP

a amino acid

b

H 3 N

Figure 7.26 Steps in aminoacylation of tRNAs catalyzed by aminoacyl-tRNA synthetases. (a) Activation of the amino
acid. (b) Transfer of the activated amino acid to the correct tRNA. Note that the reaction of aminoacyl
adenylate with tRNA can occur either on the 2
or 3
-hydroxyl group of the terminal adenosine depending
on the particular aminoacyl-tRNA synthetase