RNA, molecular structure

Rich, A., and RajBhandary, U. L., 1976, Transfer RNA Molecular structure, sequence, and properties, Annu. Rev. Biochem. 45 805. 

In terms of their molecular structures, the nucleotide and protein realms are usually considered to be rather independent of each other. However, these two families of molecules are covalently linked in the translational aminoacyl- RNAs and ribonucleoproteins as well as in the nucleoproteins involved in cellular and viral replication. In these hybrid biomolecules, a (deoxy)ribose phosphate moiety serves as the structural connection between the nucleoside and peptide moieties. 

Hunt T DNA Makes RNA Makes Protein. Elsevier, 1983-Watson JD, Crick FHC Molecular structure of nucleic acids. Nature 1953 171 737. 

Figure 37-9. The eukaryotic basal transcription complex. Formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site (+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and ofTBP bound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 A resolution. The structure of TFIID complexes have been determined by electron microscopy at 30 A resolution. Thus, the molecular structures of the transcription machinery are beginning to be elucidated. Much of this structural information is consistent with the models presented here.

All this is basic chemical research that has wide importance, determining the molecular structure of a component of living cells. Simply, it tells us the details of how proteins are now made, but more generally it strengthens the picture of how life may have started in a world where RNA was both information molecule and catalyst. It is a major advance in scientific understanding. 

Nitrogenous base plus sugar moiety are called nucleosides. Ribonucleic acids (RNA) resemble DNA in that nucleoside monophosphates are joined through phosphodiester bonds. RNAs differ in that the sugars are p-D-ribose units and the pyrimidine uracil is found in place of thymine. Molecular structures and nomenclature for nitrogenous bases, nucleosides, and nucleotides are delineated in Table 2.2. 

The use of alkali and alkaline earth group metal ions, especially those of sodium, potassium, magnesium, and calcium, for maintenance of electrolyte balance and for signaling and promotion of enzyme activity and protein function are not discussed in this text. Many of these ions, used for signaling purposes in the exciting area of neuroscience, are of great interest. In ribozymes, RNAs with catalytic activity, solvated magnesium ions stabilize complex secondary and tertiary molecular structure. Telomeres, sequences of DNA at the ends of chromosomes that are implicated in cell death or immortalization, require potassium ions for structural stabilization. 

The determination of the molecular weight of animal cell RNA, using electrophoresis on exponential polyacrylamide gels under fully denaturing conditions, has been described. Effects due to RNA secondary structure are fully suppressed if dry formamide and high temperatures are used.177... 

Fluorescent labeling of cDNA can be a potential source of technical variability. In a typical two-color experiment, fluorescently labeled cDNA probes are transcribed from separate mRNA populations (e.g., cerebral ischemia versus sham). One set of cDNA probes is labeled with one fluorescent dye (typically Cy5) and the second set with a different fluorescent dye (Cy3). A number of methods for making labeled cDNA from the RNA samples have been tested and reviewed (Stears et al., 2000 Vernon et al., 2000 Li et al., 2002) and a number of potential sources for variation must be appreciated. First, the molecular structure of the fluorescent dyes used in making labeled cDNA can affect efficiency of dye incorporation. Second the mode of dye incorporation (direct verses indirect labeling) can affect subsequent hybridization kinetics (Stears... 

A rod-shaped plant virus. The tobacco mosaic virus (Figs. 5-41, 7-8) is a 300-nm-long rod constructed from 2140 identical wedge-shaped subunits whose detailed molecular structure is known.40 Each 158-residue subunit contains five helices and a small (3 sheet. A single strand of RNA containing 6395 nude-... 

Figure 7.1. Molecular structure of RNA. The single-stranded RNA molecule consists of ribo-nucleoside residues linked to each other via phosphodiester bonds. The four nitrogenous bases in RNA are shown with their linkage at the Q position of ribose. The RNA chain elongates from the 5 to the 3 direction as the new nucleotide residues are added at the 3 -OH end of the chain during RNA synthesis in a cell. (Adapted from Textbook of Biochemistry with Clinical Correlations, T. M. Devlin, ed., Wiley, New York, 1982.)...

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