Ribosomal RNA structure

Gerbi, S.A. (1 996) Expansion segments regions of variable size that interrupt the universal core secondary structure of ribosomal RNA. In Dahlberg, A.E. and Zimmermann, R.A. (eds) Ribosomal RNA Structure, Evolution, Processing and Function in Protein Synthesis. CRC Press, Boca Raton, Florida, pp. 71-87. 

Gutell, R. R. (1993). Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucleic Acids Res. 21, 3051—3054. 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

In contrast, RNA occurs in multiple copies and various forms (Table 11.2). Cells contain up to eight times as much RNA as DNA. RNA has a number of important biological functions, and on this basis, RNA molecules are categorized into several major types messenger RNA, ribosomal RNA, and transfer RNA. Eukaryotic cells contain an additional type, small nuclear RNA (snRNA). With these basic definitions in mind, let s now briefly consider the chemical and structural nature of DNA and the various RNAs. Chapter 12 elaborates on methods to determine the primary structure of nucleic acids by sequencing methods and discusses the secondary and tertiary structures of DNA and RNA. Part rV, Information Transfer, includes a detailed treatment of the dynamic role of nucleic acids in the molecular biology of the cell. 

Ribosomes, the supramolecular assemblies where protein synthesis occurs, are about 65% RNA of the ribosomal RNA type. Ribosomal RNA (rRNA) molecules fold into characteristic secondary structures as a consequence of intramolecular hydrogen bond interactions (marginal figure). The different species of rRNA are generally referred to according to their sedimentation coefficients (see the Appendix to Chapter 5), which are a rough measure of their relative size (Table 11.2 and Figure 11.25). 

Ribosomal RNA has a complex secondary structure due to many intrastrand hydrogen bonds. 

Wunschel, D. K. Fox, K. Black, G. Fox, A. Discrimination among the Bacillus cereus group, in comparison to B. subtilis, by structural carbohydrate profiles and ribosomal RNA spacer region PCR System. Appl. Microbiol. 1994,17, 625-635. 

Fig. 1.1. The phylogenetic structure of the Nematoda revealed by small subunit ribosomal RNA analysis. (A) Neighbour-joining (NJ) analysis of aligned ssu rRNA genes from nematodes. The alignment is based on that of Blaxter etal. (1998), with the addition of sequences from Aleshin etal. (1998), Nadler (1998)...

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. 

After attachment of amino acids to tRNA, the amino acids are assembled beginning with the amino terminus and proceeding in the direction of the carboxy terminus. The ribosome is the machinery that translates the mRNA into protein. The ribosome is a very complex protein that contains ribosomal RNA as a functional and structural component. The ribosome assembles around the mRNA, and the cap and other signals allow alignment of the mRNA into the correct position. The initial assembly of the mRNA into the ribosome requires association of the small ribosomal subunit with an initiator tRNA (Met or fMet). Small is a misstatement, because the small ribosomal subunit is a large, complex assembly of numerous smaller proteins—it s just smaller than the... 

Microscopic examination of the mature neutrophils reveals two striking features a single multilobed nucleus and a dense, granular appearance of the cytoplasm (see Fig. 1.1a). The nucleus typically comprises two to four segments, and within this organelle the chromatin is coarsely clumped. Until recently, this abnormal chromatin structure was taken as evidence that the nucleus was transcriptionally inactive however, it is now appreciated that the mature neutrophil does perform active transcription ( 7.3), although rates of biosynthesis are somewhat lower than those observed in cells such as monocytes. There is no detectable nucleolus, so there can be only limited synthesis of ribosomal RNA in these cells. 

Ginisty H, Serin G, Ghisolfi-Nieto L, Roger B, Libante V, Amalric F, Bouvet P (2000) Interaction of Nucleolin with an Evolutionarily Conserved Pre-ribosomal RNA Sequence Is Required for the Assembly of the Primary Processing Complex. J Biol Chem 275 18845-18850 Ginisty H, Sicard H, Roger B, Bouvet P (1999) Structure and functions of nucleolin. J Cell Sci 112 761-772... 

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