Homework # 5

Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation The basic plan of protein synthesis in eukaryotes and archaea is similar to that in bacteria. The major structural and mechanistic themes recur in all domains of life. However, eukaryotic protein synthesis entails more protein components than does prokaryotic protein synthesis, and some steps are more intricate. Some noteworthy similarities and differences are as follows: 1. Ribosomes. Eukaryotic ribosomes are larger. They consist of a 60S large subunit and a 40S small subunit, which come together to form an 80S particle having a mass of 4200 kd, compared with 2700 kd Prokaryotic has 70S ribosome. The 40S subunit contains an 18S RNA that is homologous to the prokaryotic 16S RNA. The 60S subunit contains three RNAs: the 5S and 28S RNAs are the counterparts of the prokaryotic 5S and 23S molecules; its 5.8S RNA is unique to eukaryotes. 2. Initiator tRNA. In eukaryotes, the initiating amino acid is methionine rather than N-formylmethionine. However, as in prokaryotes, a special tRNA participates in initiation. This aminoacyltRNA is called Met-tRNAi or Met-tRNAf (the subscript i stands for initiation, and f indicates that it can be formylated in vitro). 3. Initiation. The initiating codon in eukaryotes is always AUG. Eukaryotes, in contrast with prokaryotes, do not use a specific purine-rich sequence on the 5 side to distinguish initiator AUGs from internal ones. The AUG nearest the 5 end of mRNA is usually selected as the start site. A 40S ribosome attaches to the cap at the 5 end of eukaryotic mRNA (Section 28.3.1) and searches for an AUG codon by moving step-by-step in the 3 direction (Figure 29.33). This scanning process in eukaryotic protein synthesis is powered by helicases that hydrolyze ATP. Pairing of the anticodon of Met-tRNAi with the AUG codon of mRNA signals that the target has been found. In almost all cases, eukaryotic mRNA has only one start site and hence is the template for a single protein. In contrast, a prokaryotic mRNA can have multiple Shine-Dalgarno sequences and, hence, start sites, and it can serve as a

template for the synthesis of several proteins. Eukaryotes utilize many more initiation factors than do prokaryotes, and their interplay is much more intricate. The prefix eIF denotes a eukaryotic initiation factor. For example, eIF-4E is a protein that binds directly to the 7-methylguanosine cap (Section 28.3.1), whereas eIF-4A is a helicase. The difference in initiation mechanism between prokaryotes and eukaryotes is, in part, a consequence of the difference in RNA processing. The 5 end of mRNA is readily available to ribosomes immediately after transcription in prokaryotes. In contrast, premRNA must be processed and transported to the cytoplasm in eukaryotes before translation is initiated. Thus, there is ample opportunity for the formation of complex secondary structures that must be removed to expose signals in the mature mRNA. The 5 cap provides an easily recognizable starting point. In addition, the complexity of eukaryotic translation initiation provides another mechanism for gene expression. 4. Elongation and termination. Eukaryotic elongation factors EF1 and EF1 are the counterparts of prokaryotic EF-Tu and EF-Ts. The GTP form of EF1 delivers aminoacyl-tRNA to the A site of the ribosome, and EF1 catalyzes the exchange of GTP for bound GDP. Eukaryotic EF2 mediates GTP-driven translocation in much the same way as does prokaryotic EF-G. Termination in eukaryotes is carried out by a single release factor, eRF1, compared with two in prokaryotes. Finally, eIF3, like its prokaryotic counterpart IF3, prevents the reassociation of ribosomal subunits in the absence of an initiation complex.

Figure 29.33Eukaryotic Translation Initiation In eukaryotes, translation initiation starts with the assembly of a complex on the 5 cap that includes the 40S subunit and Met-tRNAi. Driven by ATP hydrolysis, this complex scans the mRNA until the first AUG is reached. The 60S subunit is then added to form the 80S initiation complex.

Source: Biochemistry. 5th edition. Berg JM, Tymoczko JL, Stryer L.New York: W H Freeman; 2002.