Ribosomes and protein synthesis

Porterfield, Brain and liver ribosomal protein synthesis and profiles in hypothyroid mothers and their progenies, American Thyroid Assoc., Abstract 106 (1987). 

Ribosomal Protein Synthesis Inhibitors. Figure 3 The chemical structure of tetracycline and possible interactions with 16S rRNA in the primary binding site. Arrows with numbers indicate distances (in A) between functional groups. There are no interactions obseived between the upper portion of the molecule and 16S rRNA consistent with data that these positions can be modified without affecting inhibitory action (from Brodersen et al. [4] with copynght permission). 

Ribosomal Protein Synthesis Inhibitors. Figure 4 The binding site of pactamycin on the 30S subunit. The positions of mRNA, the RNA elements H28, H23b, H24a, and the C-terminus of protein S7 are depicted in the E-site of the native 30S structure (left) and in the 30S-pactamycin complex (right). In the complex with pactamycin, the position of mRNA is altered (from Brodersen etal. [4] with copyright permission). 

Ribosomal Protein Synthesis Inhibitors. Figure 5 Nucleotides at the binding sites of chloramphenicol, erythromycin and clindamycin at the peptidyl transferase center. The nucleotides that are within 4.4 A of the antibiotics chloramphenicol, erythromycin and clindamycin in 50S-antibiotic complexes are indicated with the letters C, E, and L, respectively, on the secondary structure of the peptidyl transferase loop region of 23S rRNA (the sequence shown is that of E. coll). The sites of drug resistance in one or more peptidyl transferase antibiotics due to base changes (solid circles) and lack of modification (solid square) are indicated. Nucleotides that display altered chemical reactivity in the presence of one or more peptidyl transferase antibiotics are boxed. 

What could be the signal for the induction of the cold shock proteins It has been observed that shifting E. coli cells from 37 to 5 °C results in an accumulation of 70S monosomes with a concomitant decrease in the number of polysomes [129]. Further, it has been shown that a cold shock response is induced when ribosomal function is inhibited, e.g. by cold-sensitive ribosomal mutations [121] or by certain antibiotics such as chloramphenicol [94]. These data indicate that the physiological signal for the induction of the cold shock response is inhibition of translation caused by the abrupt shift to lower temperature. Then, the cold shock proteins RbfA, CsdA and IF2 associate with the 70S ribosomes to convert the cold-sensitive nontranslatable ribosomes into cold-resistant translatable ribosomes. This in turn results in an increase in cellular protein synthesis and growth of the cells. 

Like other cells, a neuron has a nucleus with genetic DNA, although nerve cells cannot divide (replicate) after maturity, and a prominent nucleolus for ribosome synthesis. There are also mitochondria for energy supply as well as a smooth and a rough endoplasmic reticulum for lipid and protein synthesis, and a Golgi apparatus. These are all in a fluid cytosol (cytoplasm), containing enzymes for cell metabolism and NT synthesis and which is surrounded by a phospholipid plasma membrane, impermeable to ions and water-soluble substances. In order to cross the membrane, substances either have to be very lipid soluble or transported by special carrier proteins. It is also the site for NT receptors and the various ion channels important in the control of neuronal excitability. 

The macrolide erythromycin inhibits protein synthesis and resistance is induced by N -dimethyl-ation of adenine within the 23S rRNA, which results in reduced affinity of ribosomes for antibiotics related to erythromcin (Skinner et al. 1983). Sulfonamides function by binding tightly to chromosomal dihydropteroate synthetase and resistance to sulfonamides is developed in the resistance plasmid through a form of the enzyme that is resistant to the effect of sulfonamides. 

Ribonucleic acid (RNA) Molecules including messenger RNA, transfer RNA, ribosomal RNA, or small RNA. RNA serves as a template for protein synthesis and other biochemical processes of the cell. The structure of RNA is similar to that of DNA except for the base thymidine being replaced by uracil. 

The RNA molecules, ribosomal RNA (rRNA) and messenger RNA (mRNA) play key roles in the protein synthesis. The amount of RNA in individual cells or in a community may, therefore, be taken as an indicator of protein synthesis and, thus, microbial activity. The number of active cells can be detected by fluorescent in situ hybridization (FISH) (Amann et al. 1995). By this method, individual cells carrying high concentrations of rRNA, situated on ribosomes, are quantified by fluorescence microscopy. The amount of rRNA in a community can also be detected by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), where rRNA extracted from soil is detected by creating a DNA copy and separating by gel electrophoresis (Duineveld et al. 2001). 

Based on our current understanding of ribosomal protein synthesis, several strategies have been developed to incorporate amino acids other than the 20 standard proteinogenic amino acids into a peptide using the ribosomal machinery . This allows for the design of peptides with novel properties. On the one hand, such a system can be used to synthesize nonstandard peptides that are important pharmaceuticals. In nature, such peptides are produced by nonribosomal peptide synthetases, which operate in complex pathways. On the other hand, non-natural residues are a useful tool in biochemistry and biophysics to study proteins. For example, incorporation of non-natural residues by the ribosome allows for site-specific labeling of proteins with spin labels for electron paramagnetic resonance spectroscopy, with... 

Ute Kothe studied biochemistry in Regensburg, Bochum, and Witten in Germany and completed her studies with a diploma in 2002. For her Ph.D. Ute Kothe worked under the supervision of Marina Rodnina at the Institute of Physical Biochemistry, University of Witten/Herdecke, Germany, where she studied the accuracy of ribosomal protein synthesis. Since 2006, Ute Kothe is an assistant professor of biochemistry at the University of Lethbridge, Alberta, Canada. 

At this stage, it is clear that ribosomal protein synthesis will not allow the incorporation of D-amino acids or those that are too bulky, and that only a-ami-no and a-hydroxy acids can be introduced those with extended backbones such as y-amino acids cannot be introduced in this manner. Also, in spite of the development of improved suppressor tRNAs, the incorporation of small, highly polar amino acids remains difficult. 

The ribosome is both the site of protein synthesis and an active participant in the process. The eukaryotic ribosome is constructed from two subunits the smaller 40S subunit and the larger 60S subunit. Basically, the 40S subunit binds the mRNA and monitors the recognihon between the mRNA codon and tRNA anticodon. The 60S subunit has the binding sites for aminoacyl-tRNAs and catalyzes the formation of peptide bonds. Remarkably, the catalytic entity for peptide bond formahon in the 60S subunit is the RNA component, not the protein component. Therefore, the 60S subunit acts as a ribozyme. 

Ricin is a potent cellular protein toxin contained in the beans of the castor been plant (Ricinus communis), which is extensively cultivated for oil production and is also a common ornamental garden plant. Ricin is able to inhibit ribosomal protein synthesis eventually causing cell death, and owing to these properties it has been allegedly used in terrorist and criminal activities. After trypsin digestion of castor bean crude extracts, Ostin et al. [105] were able to unambiguously... 

Macrolides and lincosamides have the same receptor site. They bind to the bacterial 50s ribosomal subunit, inhibiting protein synthesis and hence cell growth. Macrolides are usually bacteriostatic at low concentrations, but can become bactericidal for sensitive strains at high concentrations. 

Dresios J, Derkatch IL, Liebman SW, Synetos D (2000) Yeast ribosomal protein L24 affects the kinetics of protein synthesis and ribosomal protein L39 improves translational accuracy, while mutants lacking both remain viable. Biochemistry 39 7236-7244... 

Following Zamecnik s discovery that ribosomes are the complexes responsible for protein synthesis, and following elucidation of the genetic code, the study of ribosomes accelerated. In the late 1960s Masayasu Nomura and colleagues demonstrated that both ribosomal subunits can be broken down into their RNA and protein components, then reconstituted in vitro. Under appropriate experimental conditions, the RNA and protein spontaneously reassemble to form 30S or SOS subunits nearly identical in structure and activity to native subunits. This breakthrough fueled decades of research into... 

Requirements include all the amino acids that eventually appear in the finished protein, at least one specific type of tRNA for each amino acid, one aminoacyl-tRNA synthetase for each amino acid, the mRNA coding for the protein to be synthesized, fully competent ribosomes, protein factors needed for initiation, elongation, and termination of protein synthesis, and ATP and GTP as energy sources. 

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