Ribosomal machinery

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... 

The simplification of the ribosomal machinery, and of the enzyme battery devoted to RNA and DNA synthesis, is probably a necessary step. (Luisi et al, 2006). 

Simplicity argues that the genetic blueprint specifying amino acid sequences in proteins should consist of consecutive, nonoverlapping triplets. This assumption turned out to be correct, as is illustrated by the DNA sequence for a gene shown in Fig. 5-5. In addition to the codons that determine the sequence of amino acids in the protein, there are stop codons that tell the ribosomal machinery when to terminate the polypeptide chain. One methionine codon serves as an initiation codon that marks the beginning of a polypeptide sequence. One of the valine codons sometimes functions in the same way. 

Variations in the code for cytoplasmic proteins have been found. In Tetrahymena and other ciliates the codon TAA represents glutamine rather than being a termination codon.375 A few proteins, including some in the human body, contain selenocysteine, the selenium-containing analog of cysteine. Selenocysteine is encoded by termination codon TGA. See Chapter 29 for details. However, even though TGA is occasionally used in this way, it serves as a termination codon for most proteins within the same cells.376 Thus, the context in which the codon TGA occurs determines how it is read by the ribosomal machinery. 

Bushuev et al.56 observed extensive flexibility in the dimeric L7/L12 protein from E. coli bacterial ribosomes (mass 25kDa). In this case, however, the protein has folded N- and C-terminal domains with an unstructured flexible linker in between, encompassing residues 37-50. The flexibility of this region of the protein is believed to be important for its function, to enable efficient interaction with other components of the ribosome machinery. 

Also called mRNA display, this method was derived from ribosome display technology. Puromycin-tagged mRNA and several additional steps must be used to achieve covalent coupling between the protein product and its mRNA, as shown in Figure 8.7(h). Puromycin, which mimics aminoacyl-tRNA (tRNA = transfer RNA), can be attached covalently to mRNA by the ribosomal machinery. 

Bashan, A., Agmon, I., Zarivach, R., Schluenzen, F., Harms, J., Berisio, R., Bartels, H., Franceschi, F., Auerbach, T., Hansen, H.A., Kossoy, E., Kessler, M., Yonath, A. Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression. Mol. Cell. 2003,11(1), 91. 

Peptide biosynthesis may occur through two different systems. Most of cellular peptides and proteins are produced by the ribosomal machinery connecting 20 proteino-genic amino acids to the desired products. However, most of the bioactive peptides are produced non-ribosomally by large peptide synthetases. These peptides are used as antibiotics, enzyme inhibitors, toxins, and other medically useful drugs. The biosynthesis of... 

Chrom-DNA-Protein.mpg Chromosomal DNA in the nucleus is transcribed in mRNA and at the ribosomal machinery eventually translated into protein. (Kindly provided by The National Human Genome Research Institute, National Institute of Health, www.nhgri.nih.gov)... 

The remaining key structural feature of a tRNA is the anticodon stem, a stem-loop structure that contains the anticodon triplet responsible for hydrogen bonding to the complementary sequence of mRNA and consequent delivery of the proper amino acid to the ribosomal machinery. 

Transfer RNA A specialised kind of RNA molecule about 80 bases long, which recognises a codon in mRNA and feeds the corresponding amino acid to the growing protein molecule via the ribosomal machinery. 

This scheme (Fig. 2.5) thus shows how oligonucleotides can direct the synthesis of polypeptides in the absence of protein or ribosomal machinery and, as such, is an appealing bioorganic model for the origin of prebiotic protein synthesis (see Section 3.7.2.1). Indeed, it seems most probable that primitive biosystems used a similar concept to carry out primitive protein synthesis where Watson-Crick base pairing provided the intrinsic mechanism for achieving fidelity of replication and direction of protein synthesis. In time, the carrier oligonucleotides could have evolved into more efficient species such as the present-day tRNA molecules. 

Final control element Transcription apparatus ribosomal machinery for protein translation... 

The mechanisms by which proteins are synthesized in cells are now quite well explained. Information encoded in DNA is transcribed in messenger RNA, and then mRNA is translated on the ribosome machinery to give a polypeptide chain with a well-defined primary structure. The genetic code (three bases determining one amino acid) is given in Fig. 1.3 the universality of this code is generally accepted. One can remark that when U is the second base of the codon, the amino acid residue is nonpolar and when A is the second base, it is polar (see Dickerson and Geis, 1969). 

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