Proteins on ribosomes

There are many different applications of intermolecular cross-linkages of proteins. A currently active area is the mapping of the positions of proteins on ribosomes (36). 

The nucleus is separated from the rest of the cell (the cytoplasm) by the nuclear envelope, which consists of two membranes joined at nuclear pores. The outer nuclear membrane is continuous with the rough endoplasmic reticulum. To convert the genetic code of the DNA into the primary sequence of a protein, DNA is transcribed into RNA, which is modified and edited into mRNA. The mRNA travels through the nuclear pores into the cytoplasm, where it is translated into the primary sequence of a protein on ribosomes (Fig. 10.21). Ribosomes, which are generated in the nucleolus, also must travel through nuclear pores to the cytoplasm. Conversely, proteins required for replication, transcription, and other processes pass into the nucleus through these pores. Thus, transport through the pore is specific for the molecule and the direction of transport. 

The synthesis of proteins on ribosomes is shown diagrammatically in Fig. 5.7. The messenger RNA becomes bound to the smaller subunit, most likely in the cleft between the two subunits. The transfer RNA makes contact with the mRNA and, as a result, a polypeptide chain is biosynthesized on the larger subunit. 

Nathans, D. and Lipmann, F. (1961) Amino acid transfer from aminoacyl ribonucleic acids to protein on ribosomes of Escherichia coli. Proc. Nat. Acad. Sci. U.S.A. 47, 497-504. 

RNA is a special macromolecule in biology because it is able to store and transmit information as well as catalyze some processes. One of these processes is protein synthesis where mRNA molecules direct the assembly of proteins on ribosomes. In contrast to DNA, it has a single strand structure. There are several types of RNA, which are differentiated by their functions. The three most common types are messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA). 

The synthesis of proteins on ribosomes is shown diagrammatically in Fig. 5.7. The messenger RNA becomes bound to the smaller subunit. 

Transfer or soluble RNAs are specific carrier molecules for amino-acids during protein synthesis on ribosomes with ribosomal RNA as the template. There is at least one t-RNA molecule for each amino-acid. 

Although the interior of a prokaryotic cell is not subdivided into compartments by internal membranes, the cell still shows some segregation of metabolism. For example, certain metabolic pathways, such as phospholipid synthesis and oxidative phosphorylation, are localized in the plasma membrane. Also, protein biosynthesis is carried out on ribosomes. 

The primary cellular function of mRNA is to direct biosynthesis of the thousands of diverse peptides and proteins required by an organism—perhaps 100,000 in a human. The mechanics of protein biosynthesis take place on ribosomes, small granular particles in the cytoplasm of a cell that consist of about 60% ribosomal RNA and 40% protein. 

The synthesis of virtually all proteins in a cell begins on ribosomes in the cytosol (except a few mitochondrial, and in the case of plants, a few chloroplast proteins that are synthesized on ribosomes inside these organelles). The fate of a protein molecule depends on its amino acid sequence, which can contain sorting signals that direct it to its corresponding organelle. Whereas proteins of mitochondria, peroxisomes, chloroplasts and of the interior of the nucleus are delivered directly from the cytosol, all other organelles receive their set of proteins indirectly via the ER. These proteins enter the so-called secretory pathway (Fig. 1). 

McMullin, T.W. Hallberg, R.L. (1986). Effect of heat shock on ribosome structure Appearance of a new ribosome associated protein. Mol. Cell. Biol. 6,2527-2535. 

Important products derived from amino acids include heme, purines, pyrimidines, hormones, neurotransmitters, and biologically active peptides. In addition, many proteins contain amino acids that have been modified for a specific function such as binding calcium or as intermediates that serve to stabilize proteins—generally structural proteins—by subsequent covalent cross-hnk-ing. The amino acid residues in those proteins serve as precursors for these modified residues. Small peptides or peptide-like molecules not synthesized on ribosomes fulfill specific functions in cells. Histamine plays a central role in many allergic reactions. Neurotransmitters derived from amino acids include y-aminobutyrate, 5-hydroxytryptamine (serotonin), dopamine, norepinephrine, and epinephrine. Many drugs used to treat neurologic and psychiatric conditions affect the metabolism of these neurotransmitters. 

With some RNA vimses, e.g. poliovims, the RNA strand fi cm the particle can act directly as mRNA and is translated into viral proteins on the host-cell ribosomes. In many other RNA vimses, however (e.g. the influenza vimses), the RNA strands are negative-sense RNAs (anhmessages) that have first to be transcribed to the complementary sequence by RNA-dependent RNA polymerases before they can function in protein synthesis. Sinee eukaryotie eells do not have these enzymes, the negative-sense RNA vimses must earry them in the virion. 

Nemoto, N., Miyamoto-Sato, E., Husimi, Y. and Yanagawa, H. (1997) In vitro virus bonding of mRNA bearing puromycin at the 3 -terminal end to the C-terminal end of its encoded protein on the ribosome in vitro. FEBS Letters, 414, 405 408. 

Peptide bond synthesis Protein synthesis (on ribosomes) ATP, GTP... 

Ehrlich, W., M Mangir, and E.R. Lochmann. 1987. The effect of pentachlorophenol and its metabolite tetrachlorohydroquinone on RNA, protein, and ribosome synthesis in Saccharomyces cells. Ecotoxicol. Environ. Safety 13 7-12. 

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). 

It is the purpose of this article to review die characteristics of the ribosomal proteins which have been studied to date. By necessity, the conformation of the ribosomal RNA and the architecture of the ribosomal subunits themselves must be discussed since the placement of the proteins on the subunits is essential in elucidating the function of the ribosome. 

Since this technique was first used by Wabl (1973) for studies of ribosomes, it has been used extensively by Stbffler et al (1980) and Lake (1980) as a powerful tool by which to delineate the external topography of ribosomal subunits. Initially both groups made comprehensive preliminary studies to define the loci of many ribosomal proteins on Iwth subunits (Tischendorf et al, 1974, 1975 Lake 1976, 1978). However, difficulties with antibody purity and specificity as well as differences in the models proposed for the ribosomal subunits caused a considerable discrepancy between the two groups. The results were reexamined, and... 

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