Chain elongation prokaryotic

This antibiotic specifically inhibits the initiation ofRNA synthesis. Rifampicin does not block the binding of RNA polymerase to the DNA template rather, it interferes with the formation of the first few phosphodiester bonds in the RNA chain. The structure of a complex between a prokaryotic RNA polymerase and rifampicin reveals that the antibiotic blocks the channel into which the RNA-DNA hybrid generated by the enzyme must pass (Figure 28.14). The binding site is 12 A from the active site itself Rifampicin does not hinder chain elongation once initiated, because the RNA-DNA hybrid present in the enzyme prevents the antibiotic from binding. 

Erythromycin Inhibits prokaryotic peptide chain elongation... 

The details of the chain of events in translation differ somewhat in prokaryotes and eukaryotes. Like DNA and RNA synthesis, this process has been more thoroughly studied in prokaryotes. We shall use Escherichia coli as our principal example, because aU aspects of protein synthesis have been most extensively studied in this bacterium. As was the case with replication and transcription, translation can be divided into stages—chain initiation, chain elongation, and chain termination. 

Peptide chain elongation in eukaryotes is very similar to that of prokaryotes. The same mechanism of peptidyl transferase and ribosome translocation is seen. The structure of the eukaryotic ribosome is different in that there is no E site, only the A and P sites. There are two eukaryotic elongation factors, eEFl and eEF2. The eEFl consists of two subunits, eEFlA and eEFlB. The 1A subunit is the counterpart of EF-Tu in prokaryotes. The IB subunit is the equivalent of the EF-Ts in prokaryotes. The eEF2 protein is the counterpart of the prokaryotic EF-G, which causes translocation. 

Eukaryotic chain elongation is similar to the prokaryotic counterpart. With chain termination, there is only one release factor that binds to all three stop codons. 

RKamycins a group of antibiotics produced by Streptomyces medilerranei. They contain a naphthalene ring system bridged between positions 2 and 5 by an aliphatic chain. Rifamycin SV and rifampicin inhibit DNA-dependent RNA synthesis in prokaryotes, chloroplasts and mitochondna, but not in the nuclei of eukaryotes Inhibition is due to the formation of a stable complex between RNA polymerase and R. binding of the enzyme to DNA still occurs, but incorporation of the first purine nucleotide into RNA is prevented. Thus R. specifically inhibit initiation of RNA synthesis, but not chain elongation. Some R. also inhibit eukaryotic and viral RNA-poly-... 

There have been two recent reviews of protein synthesis that cover the area of peptide chain elongation in great detail. > I will attempt instead, to look at this process, specifically in the prokaryote system from an historical and personal view point in an attempt to provide the reader with a better understanding of those observations that I feel most influenced the development of this area. ... 

As in the replication process, initiation is the first stage in transcription and denotes the formation of first phospho-diester bond. Unlike in the case of DNA synthesis, RNA chains are initiated de novo without the need of a primer. However, when a primer oligonucleotide is present, RNA polymerases can also extend the primer as dictated by the template strand. A purine nucleotide invariably starts the RNA chains in both prokaryotes and eukaryotes, and the overall rate of chain growth is about 40 nucleotides per second at 37°C in E. coli. This rate is much slower than that for DNA chain elongation ( 800 base pairs per second at 37° for the coli genome). 

RNA polymerases of both prokaryotes and eukaryotes function as complexes consisting of a number of subunits. The E. coli RNA polymerase enzyme with a total molecular mass of about 465 kD contains two a-subunits, one fi-and one y3 -subunit each, and a promoter specificity. During chain elongation, a ternary complex of macromolecules among DNA template, RNA polymerase, and nascent RNA is maintained in which most of the nascent RNA molecule is present in a single-stranded unpaired form. The stability of the complex is maintained by about nine base pairs between RNA and the transcribed (noncoding) DNA strand at the growing point. 

Abbreviations aa-tRNA Amino-acyl tRNA eLF Eukaryotic translation initiation factor IF Prokaryotic translation initiation factor eEF Eukaryotic translation elongation factor EF Prokaryotic translation elongation factor eRF Eukaryotic translation termination factor (release factor) RF Prokaryotic translation release factor RRF Ribosome recycling factor Rps Protein of the prokaryotic small ribosomal subunit Rpl Protein of the eukaryotic large ribosomal subunit S Protein of the prokaryotic small ribosomal subunit L Protein of the prokaryotic large ribosomal subunit PTC Peptidyl transferase center RNC Ribosome-nascent chain-mRNA complex ram Ribosomal ambiguity mutation RAC Ribosome-associated complex NMD Nonsense-mediated mRNA decay... 

Prokaryotic and eukaryotic DNA polymerases elongate a new ChA strand by adding deoxyribonucleotides, one at a time, to the 3-end of the growing chain (see Figure 29.16). The sequence of nucleotides that are added is dictated by the base sequence of fie Figure 29.15 template strand with which the incoming nucleotides are paired. 

The pathway of protein synthesis translates the three-letter alphabet of nucleotide sequences on mRNA into the twenty-letter alphabet of amino acids that constitute proteins. The mRNA is translated from its 5 -end to its 3 -end, producing a protein synthesized from its amino-terminal end to its carboxyl-terminal end. Prokaryotic mRNAs often have several coding regions, that is, they are polycistronic (see p. 420). Each coding region has its own initiation codon and produces a separate species of polypeptide. In contrast, each eukaryotic mRNA codes for only one polypeptide chain, that is, it is monocistronic. The process of translation is divided into three separate steps initiation, elongation, and termination. The polypeptide chains produced may be modified by posttranslational modification. Eukaryotic protein synthesis resembles that of prokaryotes in most details. [Note Individual differences are mentioned in the text.]... 

In prokaryotes, each of the reactions of fatty acid synthesis is catalyzed by a separate enzyme. However, in eukaryotes, the enzymes of the fatty acid synthesis elongation cycle are present in a single polypeptide chain, multifunctional enzyme complex, called fatty acid synthase. The fatty acid synthase complex exists as a dimer, with the ACP moiety shuttling the fatty acyl chain between successive catalytic sites, and from one subunit of the dimer to the other. It is, in effect, a highly efficient production line for fatty acid biosynthesis. 

Be able to describe the mechanism for peptide chain initiation, elongation, and termination in prokaryotes and eukaryotes on the ribosome. 

Studies using intact ricin and its individual A and B chains with intact 80 S ribosomes and their 60 S and 40 S subunits have firmly established that the A chain is the toxic moiety and that it inhibits protein synthesis by inactivating a function of the 60S ribosomal subunit [113,114]. Prokaryotic 70S ribosomes, on the other hand, are insensitive to the toxin [115]. The A chain inactivates 60 S subunits catalytically [13, 15] and as a result elongation factor 2 (EF-2) is unable to bind to the subunit and protein synthesis does not occur. 

Elongation and termination - Eukaryotic chain termination, in contrast to prokaryotic termination, requires only one protein factor- eRF (Table 28.7), which can recognize all three stop codons (UAA, UAG, and UGA). Otherwise the mechanisms are very similar. 

Fig. 15.10. Elongation of a pol5 peptide chain. 1. Binding of valyl-tRNA to the A site. 2. Formation of a peptide bond. 3. Translocation. After step 3, step 1 is repeated using the aminoacyl-tRNA for the new codon in the A site. Steps 2 and 3 follow. These three steps keep repeating until termination occurs. (In prokaryotes, an exit site called the E site binds the t-RNA after it is displaced from the P site). EE = elongation factor.

Diagrammatic representation of translation on prokaryotic ribosomes. The elongation cycle starts by interaction of the 70S initiation complex with fMet- tRNA EFTu GTP. In all subsequent rounds of the cycle, fMet-tRNArEFT tGTP interacts with the mRNA ribosome complex carrying the growing polypeptide chain. Termination occurs when n amino acids have been incorporated, where n represents the number of codons between the initiation codon AUG and the termination codon (in this example UAA). 

---