Chain elongation eukaryotic

Figure 7 The direct and indirect pathways of tRNA asparaginylation. The direct pathway consists of charging by AsnRS on tRNA " of free Asn formed with asparagine synthetase A or B. The Asn-tRNA " binds the EF-Tu factor in bacteria (or EF-1A in eukaryotes and archaea) to be carried to the ribosome, in the indirect pathway, a nondiscriminating AspRS (ND-AspRS) charges Asp on tRNA " Asp-tRNA " does not bind the eiongation factor but is converted by the tRNA-dependent trimeric amidotransferase GatCAB into Asn-tRNA ", which binds the EF-Tu factor and is carried to the ribosome where it is used for polypeptide chain elongation.

Once the initiating fMet-tRNA of bacteria or the eukaryotic Met-tRNA is in place in the P site of a ribosome and is paired with the initiation codon in the mRNA, peptide chain growth can commence. Amino acid residues are added in turn by insertion at the C-terminal end of the growing peptide chain. Elongation requires three processes repeated over and over until the entire peptide is formed. 

Eukaryotic peptide chain elongation factor-2 Triosephosphate isomerase Myo-inositol-phosphate synthase Mannose-1-phosphate guanylj transferase Alcohol dehydrogenase Aldehyde reductase Ade5... 

Cook HW, McMaster CR. Fatty acid desaturation and chain elongation in eukaryotes. In Biochemistry of Lipids, Lipoproteins and Membranes, 4th edition. Vance DE, Vance JE, eds. 2002. Elsevier, Amsterdam, The Netherlands. 

In eubacteria and eukaryotes, several types of DNA polymerases have been characterized three in eubacteria (DNA polymerases I, II and III), and five in eukaryotes (DNA polymerases a, 3, 6, e and )). Some of these enzymes, named DNA replicases , are specifically involved in DNA-chain elongation at the replication fork. They have a multi-subunit structure and can prime and perform DNA replication in a processive way when they are associated with the other replicative proteins. In eubacteria, only one DNA replicase has been isolated (DNA polymerase III), whereas several DNA replicases co-exist in eukaryotes DNA polymerases a, 6 and e, which are essential for the replication of nuclear DNA, and DNA polymerase y, which is responsible for the replication of the mitochondrial genome. The other eubacterial and eukaryotic DNA polymerases are monomeric and are preferentially involved in mechanisms which require replication of short DNA fragments, in the course of either DNA repair (DNA polymerases I and II from E. coli, eukaryotic DNA polymerase 3), or DNA replication (maturation of Okasaki fragments by E. coli DNA polymerase I). 

Another possible explanation for the lack of observed export block is the difference in rate of translation in vivo and in vitro. The rate of chain elongation in vivo in eukaryotes is about 180 residues/minute, while in vitro translation proceeds at about 30 residues/minute. If an SRP-nascent chain-ribosome complex has a half-life of, e.g., 1 second, it would cause a significant pause in synthesis in vitro, but would probably not be noticed in vivo. Such a short-lived complex may be sufficient to couple translation to translocation in vivo, but not in vitro, as the time required for the ribosome to diffuse to the membrane will depend on how far it has to go. Inside the cell, the ribosome will have a much smaller distance to travel than in an in vitro translocation mixture. 

Figure 29.13). The binding site is 12 A from the active site itself. Rifampicin does not hinder chain elongation once initiated, because the RNA-1 )NA hybrid present in the enzyme prevents the antibiotic from binding. The pocket in which rifampicin binds is conserved among bacterial RNA polymerases, but not eukaryotic polymerases, and so rifampicin can be used as an antibiotic in antituberculosis therapy. 

The correctly positioned eukaryotic SOS ribosome-Met-tRNAj complex is now ready to begin the task of stepwise addition of amino acids by the in-frame translation of the mRNA. As is the case with initiation, a set of special proteins, termed elongation factors (EFs), are required to carry out this process of chain elongation. The key steps in elongation are entry of each succeeding aminoacyl-tRNA, formation of a peptide bond, and the movement, or translocation, of the ribosome one codon at a time along the mRNA. 

Following peptide bond synthesis, the ribosome Is translocated along the mRNA a distance equal to one codon. This translocation step is promoted by hydrolysis of the GTP in eukaryotic EF2-GTP. As a result of translocation, tRNAj , now without its activated methionine, is moved to the E (exit) site on the ribosome concurrently, the second tRNA, now covalently bound to a dIpeptIde (a peptIdyl-tRNA), Is moved to the P site (Figure 4-26, step U). Translocation thus returns the ribosome conformation to a state in which the A site Is open and able to accept another amlnoacylated tRNA complexed with EFlct-GTP, beginning another cycle of 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-... 

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. 

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