This genetic code is used universally in all present-day organisms. Although a few slight differences in the code have been found, these are chiefly in the DNA of mitochondria. Mitochondria have their own transcription and protein-synthesis systems that operate quite independently from those of the rest of the cell, and it is understandable that their tiny genomes have been able to accommodate minor changes to the code (discussed in Chapter 14).
In principle, an RNA sequence can be translated in any one of three different reading frames, depending on where the decoding process begins (Figure 6–49). However, only one of the three possible reading frames in an mRNA encodes the required protein. We see later how a special punctuation signal at the beginning of each RNA message sets the correct reading frame at the start of protein synthesis.
tRNA Molecules Match Amino Acids to Codons in mRNA
The codons in an mRNA molecule do not directly recognize the amino acids they specify: the group of three nucleotides does not, for example, bind directly to the amino acid. Rather, the translation of mRNA into protein depends on adaptor molecules that can recognize and bind both to the codon and, at another site on their surface, to the amino acid. These adaptors consist of a set of small RNA molecules known as transfer RNAs (tRNAs), each about 80 nucleotides in length.
Figure 6–48 The genetic code. The standard one-letter abbreviation for each amino acid is presented below its three-letter abbreviation (see Panel 3–1, pp. 112– 113, for the full name of each amino acid and its structure). By convention, codons are always written with the 5ʹ-terminal nucleotide to the left. Note that most amino acids are represented by more than one codon, and that there are some regularities in the set of codons that specifies each amino acid: codons for the same amino acid tend to contain the same nucleotides at the first and second positions, and vary at the third position. Three codons do not specify any amino acid but act as termination sites (stop codons), signaling the end of the protein-coding sequence. One codon—AUG—acts both as an initiation codon, signaling the start of a protein-coding message, and also as the codon that specifies methionine.
Figure 6–49 The three possible reading frames in protein synthesis.
In the process of translating a nucleotide sequence (blue) into an amino acid sequence (red), the sequence of nucleotides in an mRNA molecule is read from the 5ʹ end to the 3ʹ end in consecutive sets of three nucleotides. In principle, therefore, the same RNA sequence can specify three completely different amino acid sequences, depending on the reading frame. In reality, however, only one of these reading frames contains the actual message.
Figure 6–50 A tRNA molecule. A tRNA specific for the amino acid phenylalanine (Phe) is depicted in various ways. (A) The cloverleaf structure showing the complementary base-pairing (red lines) that creates the double-helical regions of the molecule. The anticodon is the sequence of three nucleotides that base-pairs with a codon in mRNA. The amino acid matching the codon/anticodon pair is attached at the 3ʹ end of the tRNA. tRNAs contain some unusual bases, which are produced by chemical modification after the tRNA has been synthesized. For example, the bases denoted ψ (pseudouridine—see Figure 6–41) and D (dihydrouridine—see Figure 6–53) are derived from uracil. (B and C) Views of the L-shaped molecule, based on x-ray diffraction analysis. Although this diagram shows the tRNA for the amino acid phenylalanine, all other tRNAs have similar structures. (D) The tRNA icon we use in this book. (E) The linear nucleotide sequence of the molecule, color-coded to match (A), (B), and (C).