Start x-UCCUCCA^ site
mal RNA. Consequently, the mRNA and the 16S rRNA bind together by base pairing between these two sequences. The start codon is the next AUG codon after the ribo-some binding site. Typically there are about seven bases between the S-D sequence and the start codon. In some cases, the S-D sequence exactly matches the anti-S-D sequence and the mRNAs are translated efficiently. In other cases, the match is poorer and translation is less efficient. [Note that eukaryotes do not use an S-D sequence to locate the start of translation; instead they scan the mRNA starting form the 5'-cap— see below.]
Occasionally, coding sequences even start with GUG (normally encoding valine) instead of AUG. This leads to inefficient initiation and is mostly found for proteins required only in very low amounts, such as regulatory proteins, for example, LacI, the repressor of the lac operon (see Ch. 9). Note that when GUG acts as the start codon, the same initiator fMet-tRNA is used as when AUG is the start codon. Consequently, formyl-Met is the first amino acid, even for proteins that start with a GUG codon. This is apparently due to the involvement of the initiation factors, especially IF3—see below.
Proteins known as initiation factors help the ribosomal subunits, mRNA and tRNA assemble corre ctly.
Before protein synthesis starts, the two subunits of the ribosome are floating around separately. Because the 16S rRNA, with the anti-Shine-Dalgarno sequence, is in the small subunit of the ribosome, the messenger RNA binds to a free small subunit. Next the initiator tRNA, carrying fMet, recognizes the AUG start codon. Assembly of this 30S initiation complex needs three proteins (IF1, IF2 and IF3), known as initiation factors, which help arrange all the components correctly.
IF2 recognizes fMet-tRNA. IF3 is also involved in recognition of the start codon and the matching anticodon end of the initiator tRNA. IF3 prevents the 50S subunit from binding prematurely to the small subunit before the correct initiator tRNA is present. Once the 30S initiation complex has been assembled, IF3 departs and the 50S subunit binds. IF1 and IF2 are now released, resulting in the 70S initiation complex. This process consumes energy in the form of GTP, which is split by IF2 (Fig. 8.14).
The tRNA Occupies Three Sites During Elongation of the Polypeptide
After the large subunit of the ribosome has arrived, the polypeptide can be made. Amino acids are linked together by the peptidyl transferase reaction, which is catalyzed by the 23S rRNA of the large subunit. The amino acids are carried to the ribosome attached to transfer RNA. The ribosome has three sites for tRNA: the A (acceptor)
30S initiation complex Initiation complex for translation that contains only the small subunit of the bacterial ribosome 70S initiation complex Initiation complex for translation that contains both subunits of the bacterial ribosome A (acceptor) site Binding site on the ribosome for the tRNA that brings in the next amino acid initiation factors Proteins that are required for the initiation of a new polypeptide chain
B) 30S INITIATION COMPLEX
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