Complementary base pairs, representation

A generalized representation of a possible template-based self-replicating system is shown in Scheme 1. Here and EZ3 could represent complementary base-pairs... 

A tRNA molecule is specific for a particular amino acid, though there may be several different forms for each amino acid. Although relatively small, the polynucleotide chain may show several loops or arms because of base pairing along the chain. One arm always ends in the sequence cytosine-cytosine-adenosine. The 3 -hydroxyl of this terminal adenosine unit is used to attach the amino acid via an ester linkage. However, it is now a section of the nucleotide sequence that identifies the tRNA-amino acid combination, and not the amino acid itself. A loop in the RNA molecule contains a specific sequence of bases, termed an anticodon, and this sequence allows the tRNA to bind to a complementary sequence of bases, a codon, on mRNA. The synthesis of a protein from the message carried in mRNA is called translation, and a simplified representation of the process as characterized in the bacterium Escherichia coli is shown below. 

Figure 16.15 A schematic representation of a duplex formed from the self-complementary monomer, d(GAATTC), that illustrates base-pairing and nearest-neighbor stacking interactions.

Figure 17-7 is a diagrammatic representation of tRNA folded into the typical cloverleaf structure, containing a number of stems (base-paired) and loops. While the sequences of the different tRNAs are different, there are regions that remain invariant. Most of these are in the loops, within which the unusual bases are concentrated, and at the 3 end of the molecule contained within the acceptor stem. The sequence at this end is always CCA, and it is to the 3 OH that the appropriate amino acid is attached through its carboxyl group. The three nucleotides complementary to the codon for the amino acid make up what is known as the anticodon (shaded part of Fig. 17-7). The three-dimensional structure of tRNA is known. In this structure, there are additional H bonds, which stabilize the cloverleaf in a more elongated L-shaped structure, with the acceptor sequence at one end and the anticodon loop at the other.

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