Chain initiation prokaryotic

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

Synthesis of all polypeptide chains In prokaryotic and eukaryotic cells begins with the amino acid methionine. In most mRNAs, the start (initiator) codon specifying this amino-terminal methionine is AUG. In a few bacterial mRNAs, GUG is used as the initiator codon, and CUG occasionally is used as an initiator codon for methionine in eukaryotes. The three codons UAA, UGA, and UAG do not specify amino acids but constitute stop (termination) codons that mark the carboxyl terminus of polypeptide chains in almost all cells. The sequence of codons that runs from a specific... 

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. 

The general mechanisms by which proteins are synthesized appear to be similar in both prokaryotes and eukaryotes. There are some minor differences, particularly in chain initiation and termination and in designation and chemical characteristics of the various soluble factors. 

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... 

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 addition, several ribosomes can independently and simultaneously translate a mRNA molecule and, hence, synthesize several identical polypeptide chains concurrently (Figure 12.3). Such clusters or groups of ribosomes are called polyribosomes or polysomes. The number of attached ribosomes depends on the size of the mRNA and how frequently ribosomes can initiate at the start of a gene sequence. Because RNA transcription and translation are neither temporally nor spatially separated in prokaryotes, it is possible for translation to begin before transcription is completed. However, we have already noted that prokaryotic mRNAs have short half-lives this is probably a result of their continuous degra-... 

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. 

Dolichols are a family of long-chain polyisoprenols that occur only in eukaryotes. They are related in structure and function to undecaprenyl phosphate, a prokaryotic polyisoprenol used in the synthesis of peptido-glycan (see below). Dolichols contain 65-110 carbons arranged as 13-22 isoprene units, two in the trans configuration, the remainder in the cis configuration. The initial isoprene unit is saturated and carries a hydroxyl group, which is esterified with orthophosphoric (monophosphoric) or pyrophosphoric (diphosphoric) acid in dolichol phosphate and pyrophosphate, respectively (Figure 16-6). 

The codon AUG has two functions. It corresponds to the amino acid methionine when AUG occurs within a coding sequence in the mRNA, i.e., within a polypeptide chain. It also serves as a signal to initiate polypeptide synthesis—with methionine for eukaryotic cells but with N-formylmethionine for prokaryotic cells. How the protein-synthesizing system distinguishes an initiating AUG from an internal AUG is discussed below. The codon GUG also has both functions, but it is only rarely used in initiation. Once initiation has occurred at an AUG codon, the reading frame is established and the subsequent codons are translated in order. 

Eukaryotic initiator tRNA molecules differ from the prokaryotic initiator molecule in several ways. The most striking difference is that whereas eukaryotic organisms produce both a normal tRNA and an initiator tRNA, which is also charged with methionine, the methionine does not undergo formylation. In eukaryotes, the first amino acid in a growing polypeptide chain is Met and not fMet. The codon for both kinds of tRNA molecules in eukaryotes is AUG, just as for prokaryotes. 

Every polypeptide has an amino terminus and a carboxyl terminus. In both prokaryotes and eukaryotes, synthesis begins at the amino terminus. For a protein having the sequence HaN-Met-Trp-Asp... Pro-Val-COOH, the f Met (or Met) is the initiating amino acid and Val is the last amino acid added to the chain. Translation of mRNA molecules occurs in the 5 3 direction. 

---