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10 formy' tetrahydrofolate tetrahydrofolate

N-formyl-Met-tRNAf

10 formy' tetrahydrofolate tetrahydrofolate

FIGURE 8.12 Initiator tRNA Carries N-Formyl-Methionine

A) The structure of the initiator tRNA, fMet-tRNA, is unique. A CA base pair at the top of the acceptor stem is needed to allow formylation (violet). The initiator tRNA must enter the P-site directly (see below), which requires the three GC base pairs in the anticodon stem (blue). B) The initiator tRNA is first charged with unmodified methionine. Then a formyl group carried by the tetrahydrofolate cofactor is added to the methionine.

To choose the correct start codon, the messenger RNA binds to 16S ribosomal RNA at a specific sequence.

The Start Codon Is Chosen

A special tRNA, the initiator tRNA, is charged with methionine and binds to the AUG start codon (Fig. 8.12). In prokaryotes, chemically tagged methionine, N-formyl-methionine (fMet) is attached to the initiator tRNA whereas in eukaryotes unmodified methionine is used. Consequently all polypeptide chains begin with methionine, at least when first synthesized. Sometimes the initial methionine (in eukaryotes), or N-formyl-methionine (in prokaryotes), is snipped off later, so mature proteins do not always begin with methionine. In bacteria, even when the fMet is not removed as a whole, the N-terminal formyl group is often removed leaving unmodified methionine at the N-terminus of the polypeptide chain.

AUG codons also occur in the middle of messages and result in the incorporation of methionines in the middle of proteins. So how does the ribosome know which AUG codon to start with? Near the front (the 5'-end) of the mRNA of prokaryotes is a special sequence, the ribosome binding site (RBS), often called the Shine-Dalgarno or S-D sequence, after its two discoverers (Fig. 8.13). The sequence complementary to this, the anti-Shine-Dalgarno sequence, is found close to the 3'-end of the 16S riboso-

anti-Shine-Dalgarno sequence Sequence on 16S rRNA that is complementary to the Shine-Dalgarno sequence of mRNA initiator tRNA The tRNA that brings the first amino acid to the ribosome when starting a new polypeptide chain N-formyl-methionine or fMet Modified methionine used as the first amino acid during protein synthesis in bacteria ribosome binding site (RBS) Same as Shine-Dalgarno sequence;sequence close to the front of mRNA that is recognized by the ribosome;only found in prokaryotic cells

Shine-Dalgarno (S-D) sequence Same as RBS;sequence close to the front of mRNA that is recognized by the ribosome;only found in prokary-otic cells

The tRNA Occupies Three Sites During Elongation of the Polypeptide 211

FIGURE 8.13 Shine-Dalgarno Sequence of mRNA Binds to 16S rRNA

The Shine-Dalgarno sequence on the mRNA is recognized by base pairing with the anti-Shine-Dalgarno sequence on the16S rRNA. The first AUG downstream of the S-D/anti-S-D site serves as the start codon.

Shine-Dalgarno Sequence fMet Val Ala Lys Ser

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