Protein synthesis amino acid activation

As we have noted, the outcome of a virus infection is the synthesis of viral nucleic acid and viral protein coats. In effect, the virus takes over the biosynthetic machinery of the host and uses it for its own synthesis. A few enzymes needed for virus replication may be present in the virus particle and may be introduced into the cell during the infection process, but the host supplies everything else energy-generating system, ribosomes, amino-acid activating enzymes, transfer RNA (with a few exceptions), and all soluble factors. The virus genome codes for all new proteins. Such proteins would include the coat protein subunits (of which there are generally more than one kind) plus any new virus-specific enzymes. 

A further important group of derivatives is that of amino acids activated by phosphoric acid or its esters. In nature, phosphorylation processes play an important activating role in peptide and protein synthesis. 

New insights into the analysis of hydrophobically post-translational modified proteins could be achieved by the construction of lipidated proteins in a combination of bioorganic synthesis of activated lipopeptides and bacterial expression of the protein backbone (Fig. 19). The physico-chemical properties of such artificial lipoproteins differ substantially from those of the corresponding lipopeptides. The pronounced dominance of the hydrophilic protein moiety (e.g., for the Ras protein 181 amino acids) over a short lipopeptide with one or two hydrophobic modifications provides solubility up to 10 4 mol/1, while the biotinylated or fluorescence labeled lipopeptides exhibit low solubility in aqueous solutions and can be applied in the biophysical experiments only in vesicle integrated form or dissolved in organic solvent. 

Energy requirements in protein synthesis are high. Four energy-rich phosphoric acid anhydride bonds are hydrolyzed for each amino acid residue. Amino acid activation uses up two energy-rich bonds per amino acid (ATP AMP + PP see p. 248), and two GTPs are consumed per elongation cycle. In addition, initiation and termination each require one GTP per chain. 

Why does mtDNA contain any protein genes, or why does mtDNA even exist It seems remarkable that the cells of our bodies make the 100 or so extra proteins (encoded in the nucleus) needed for replication, transcription, amino acid activation, and mitochondrial ribosome formation and bring these into the mitochondria for the sole purpose of permitting the synthesis there of 13 proteins. The explanation is not evident. What are the 13 proteins ... 

Synthesis of aminoacyl-tRNAs is crucially important for two reasons. First each amino acid must be covalently linked to a tRNA molecule in order to take part in protein synthesis, which depends upon the adaptor function of tRNA to ensure that the correct amino acids are incorporated. Second, the covalent bond that is formed between the amino acid and the tRNA is a high energy bond that enables the amino acid to react with the end of the growing polypeptide chain to form a new peptide bond. For this reason, the synthesis of aminoacyl-tRNA is also referred to as amino acid activation. Amino acids that are not linked to tRNAs cannot be added to the growing polypeptide. 

Jhe synthesis of proteins, as characterized by the in vitro incorporation of amino acids into the protein component of cytoplasmic ribonu-cleoprotein, is known to require the nonparticulate portion of the cytoplasm, ATP (adenosine triphosphate) and GTP (guanosine triphosphate) (15, 23). The initial reactions involve the carboxyl activation of amino acids in the presence of amino acid-activating enzymes (aminoacyl sRNA synthetases) and ATP, to form enzyme-bound aminoacyl adenylates and the enzymatic transfer of the aminoacyl moiety from aminoacyl adenylates to soluble ribonucleic acid (sRNA) which results in the formation of specific RNA-amino acid complexes—see, for example, reviews by Hoagland (12) and Berg (1). The subsequent steps in pro-... 

Anhydrides between adenosine 5-phosphate and amino acids are believed to be intermediates in protein synthesis. They have also been shown to be present in bacteria. - The amino acid activation proceeds as follows. 

The CCA terminus containing the amino acid attachment site extends from one end of the L. This single-stranded region can change conformation during amino acid activation and protein synthesis. 

Normal growth requires potassium involvement in enzyme activities. It plays a part in making muscle protein from amino acids, assists in the storage of glucose in the hver, and cooperates with sodium in maintaining blood pressure. It helps in the synthesis of nucleic acids and signals the kidneys to eliminate wastes in the urine. Potassium works with sodium to regulate the heartbeat. 

PPi is made in three ways (1) in the nucleus as a by-product of RNA synthesis (nNTP —> NMPn + nPPi) (2) in the cytosol as a by-product of amino acid activation for protein synthesis (aa + ATP —> aaAMP + PPi) and (3) by acetyl CoA synthetase on the outer mitochondrial membrane prior to its degradation for ATP production (R-COOH + ATP + HS-CoA —> R-Co-SCoA + AMP + PPi). Amino acid activation is the major source of cytosolic PPi, which is transported by the ANK protein to the osteoid matrix to inhibit premature mineralization (see Sect. 9.3.5). 

The nucleotide sequences of the four species (5S, 5.8S, 18S, and 28S) of rRNA have been determined, and these show remarkable homology among the three kingdoms (archaebacteria, eubacteria, and eukaryotes). In the case of ribosomal proteins, the amino acid sequences of about 35 proteins out of a total of about 80 have been determined. However, the exact roles of various rRNAs and proteins and their interactions in determining the activity, efficiency, and accuracy of the ribosomes is not very well understood at present. The coordinated synthesis of rRNAs and proteins, and the assembly of ribosomes is a process whose complexity is only beginning to be unravelled (Wool, 1991). 

Erythromycins bind reversibly with a single high-affinity site on the 50S subunit of susceptible bacterial ribosomes. The site appears to be proteins L-15 and L-16, two of the 34 proteins constituting the ribosomal protein mass of the 50S unit. Removal of several L-16 proteins (by LiCl extraction) from a 50S subunit eliminates its affinity for EM peptidyl transfer ability is also eliminated. Restoring the L-16 protein alone reestablishes both functions. By itself L-16 has no EM binding capacity L-15 possesses both the capacity to bind EM and to effect peptidyl transfer, participated in some way by L-16. Both events occur on the P-site. Whether the bacteriostatic antimicrobial action of EM is due to the drugs inhibition of peptide bond formation or by the prevention of its translocation following peptide formation has not been established. To clarify the picture somewhat, perhaps it should be pointed out which aspects of protein synthesis are not affected by EM. They are amino acid activation, synthesis of the amino acid /RNA derivative, ribosomal association with raRNA, and reassociation of the 30S and 50S subunits to the complete ribosome. 

Protein translation is the process of synthesizing proteins from amino acids. This series of reactions translates the code provided to messenger ribonucleic acid or RNA (mRNA) by deoxyribonucleic acid or DNA into a sequence of amino acids that makes up the active protein molecule. Protein synthesis begins with a strand of mRNA synthesized in response to the genetic code located in a gene on a strand of DNA. The process of translation is slightly different in eukaryotic cells from that in prokaryotic cells for the sake of simplicity, translation in prokaryotes will be discussed here. 

T. Pederson, 50 years ago protein synthesis met molecular biology the discoveries of amino-acid activation and transfer RNA, FASEB J. 2005, 19, 1583. 

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