RNA chain

The information needed to reproduce and support an animate species is given by the order in which the nitrogen bases occur along the DNA or RNA chains (-C-T-T-A-G-, for example). A sequence of three such bases (a codon) provides the fundamental unit of information. 

Codon (Section 28.5) A three-base sequence on a messenger RNA chain that encodes the genetic information necessary to cause a specific amino acid to be incorporated into a protein. Codons on mRNA are read by complementary anticodons on tRNA. 

Template binding RNA polymerase (RNAP) binds to DNA and locates a promoter (P) melts the two DNA strands to form a preinitiation complex (PIQ. (2) Chain initiation RNAP holoenzyme (core + one of multiple sigma factors) catalyzes the coupling of the first base (usually ATP or GTP) to a second ribonucleoside triphosphate to form a dinucleotide. (3) Chain elongation Successive residues are added to the 3 -OH terminus of the nascent RNA molecule. (4) Chain termination and release The completed RNA chain and RNAP are released from the template. The RNAP holoenzyme re-forms, finds a promoter, and the cycle is repeated. 

The information crisis , i.e., the fact that, because of the error frequency, longer RNA chains have so many errors after only a few reproduction steps that they can no longer be replicated, cries out for catalysts which can guarantee more exact replication. While only protein catalysts (enzymes) had been discussed until recently, ri-bozymes are now possible candidates. More complex catalysts would have required more complex matrices but where did the matrix molecules come from This serious problem, referred to by Eigen himself as an information crisis, is sometimes referred to as Eigen s dilemma (Blomberg, 1997). 

DIRECTIONALITIES in the flow of information from DNA to RNA to protein. All new DNA or RNA chains grow by adding new nucleotides to a free 3 end so that the chain lengthens in the 5 to 3 direction. Protein is made by reading the RNA template starting at the 5 end and making the protein from the N to the C terminus. 

F ig U re 1 3.1 A schematic view of RNA chain elongation catalyzed by an RNApolymerase. In the region being transcribed, the DNA double helix is unwound by about a turn to permit the DNAs sense strand to form a short segment of DNA-RNA hybrid double helix. That forms the transcription bubble. Note that the DNA bases in the bubble on the antisense strand are now exposed to the enzyme and are useable as a template for chain elongation. The RNApolymerase works its way down the DNA molecule until it encounters a stop signal. (Reproduced from D. Voet and J. G. Voet, Biochemistry, 3rd, edn, 2004 Donald and Judith G Voet. Reprinted with permission of John Wiley and Sons, Inc.)... 

The large subunit of a typical eubacterial ribosome (MW ca. 1,600,000) is composed of 2 RNA chains and about 35 different proteins, the small subunit (MW ca. 700,000) comprises 1 RNA chain and about 21 proteins. 

Only one of the two DNA strands is transcribed into RNA and is called the sense strand. The DNA is unwound in order to make the sense strand available for base pairing. As the transcriptional complex moves along the DNA template extending the RNA chain, a region of local unwinding moves with it. Termination of transcription involves the ability of RNA polymerase II to recognize the sequences that indicate that the end of the gene has arrived and no further bases should be added to the RNA chain. 

II A radically different type of nucleoprotein is that provided by the smaller RNA viruses of the elongated spiral type like tobacco mosaic, or of the polyhedral type such as tomato bushy stunt, tipula virus or poliomyelitis virus. The only one of these adequately studied has been tobacco mosaic virus, Franklin [19, 20], and here it appears that the protein and not the nucleic acid determines the structure. There is only one RNA chain and this is wound helically so that one protein is in contact with three successive nucleotides. 

A theoretical model to determine the probability of loop formation, based on an elaborated form of the Jacobson-Stockmayer theory of cyclization equilibria, is developed and used on RNA chains of homogeneous puckering and lengths up to 2 residues. 

Mooney, R.A., Artsimovitch, I., Landick, R. (1998) Informational processing by RNA polymerase recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180, 3265-3275. 

Termination The process of elongation of the RNA chain contrv ues until a termination signal is reached. An additional protein, p (rho) factor, may be required for the release of the RNA product (p-dependent termination). Alternatively, the tetrameric RNA polymerase can, in some instances, recognize termination regions on the DNA template (p-independent termination). 

Figure 5-29 Formation of a pseudoknot in an RNA chain. After Puglisi et al.325...

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