Bases in RNA

The specific ribonucleotide sequence in mRNA forms a message that determines the order in which amino acid residues are to be joined. Each "word," or codon, along the mRNA chain consists of a sequence of three ribonucleotides that is specific for a given amino add. For example, the series UUC on mRNA is a codon directing incorporation of the amino acid phenylalanine into the growing protein. Of the 43 = 64 possible triplets of the four bases in RNA, 61 code for specific amino acids and 3 code for chain termination, fable 28.1 shows the meaning of each codon. 

RNA uses uracil instead of thymine. The component bases in RNA are adenine, uracil, guanine, and cytosine. 

The effect of platinum in a bacterial cell is to act in a very selective way — on cell division or causing lysis of lysogenic bacteria. It is likely that these changes are due to site specific attack on particular proteins or on particular bases in RNA or in DNA. It is necessary now to describe this attack in detail and to develop new probes for following the site in vivo. This exercise can be followed by a parallel examination of how cis- [Pt (NH3) 2CI2] acts as an anti-tumour agent. Here we only point to some interesting observations. 

Fig. 4.6. A short string of single-strand DNA giving the formulae of four bases. In RNA, thymine (T) is replaced by uracil (U) and deoxyribose is replaced by ribose.

Like RNAs (see p.82), deoxyribonucleic acids (DNAs) are polymeric molecules consisting of nucleotide building blocks. Instead of ribose, however, DNA contains 2 -deoxyribose, and the uracil base in RNA is replaced by thymine. The spatial structure of the two molecules also differs (see p.86). 

As with proteins, the nucleic acid polymers can denature, and they have secondary structure. In DNA, two nucleic acid polymer chains are twisted together with their bases facing inward to form a double helix. In doing so, the bases shield their hydrophobic components from the solvent, and they form hydrogen bonds in one of only two specific patterns, called base pairs. Adenine hydrogen bonds only with thymine (or uracil in RNA), and guanine pairs only with cytosine. Essentially every base is part of a base pair in DNA, but only some of the bases in RNA are paired. The double-helix structure... 

RNA is synthesized in the 5 - 3 direction by the formation of 3 -5 -phosphodiester linkages between four ribonucleoside triphosphate substrates, analogous to the process of DNA synthesis. The sequence of bases in RNA transcripts catalyzed by DNA-depen-dent RNA polymerases is specified by the complementary sequences of the DNA template strand. 

Ribonucleic acid, or RNA, also gets its name from the sugar group it contains, in this case, ribose. In many ways, RNA is like DNA. It has a sugar-phosphate backbone with nitrogen bases attached to it, and it also contains the bases adenine (A), cytosine (C), and guanine (G). However, RNA does not contain thymine (T). Instead, the fourth base in RNA is uracil (U). Unlike DNA, RNA is a single-stranded molecule. 

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.)...

The VCD of helical, single and double stranded ribonucleic add (RNA) polymers was first reported by Keiderling s group in vibrations associated with double bond stretching vibrations of the bases in RNA [53]. The optical activity was found to be due to the coupling of the virtually achiral stretching vibrations which are arranged in a... 

Besides having a much lower molar mass than DNA, RNA generally forms only single-strand helices. RNA is often found associated with proteins inside cells. The most prevalent bases in RNA are the same as those in DNA, except that uracil is present instead of thymine. Three common types of RNA are ribosomal (rRNA), transfer (tRNA), and messenger RNA (mRNA). They are all involved in protein synthesis, controlling the sequence of amino acids that make up the primary structure. Thus the base sequence in RNA is related to the amino acid sequence in the protein that is made from it. 

Polypeptides would have played only a limited role early in the evolution of life because their structures are not suited to self-replication in the way that nucleic acid structures are. However, polypeptides could have been included in evolutionary processes indirectly. For example, if the properties of a particular polypeptide favored the survival and replication of a class of RNA molecules, then these RNA molecules could have evolved ribozyme activities that promoted the synthesis of that polypeptide. This method of producing polypeptides with specific amino acid sequences has several limitations. First, it seems likely that only relatively short specific polypeptides could have been produced in this manner. Second, it would have been difficult to accurately link the particular amino acids in the polypeptide in a reproducible manner. Finally, a different ribozyme would have been required for each polypeptide. A critical point in evolution was reached when an apparatus for polypeptide synthesis developed that allowed the sequence of bases in an RNA molecule to directly dictate the sequence of amino acids in a polypeptide. A code evolved that established a relation between a specific sequence of three bases in RNA and an amino acid. We now call this set of three-base combinations, each encoding an amino acid, the genetic code. A decoding, or translation, system exists today as the ribosome and associated factors that are responsible for essentially all polypeptide synthesis from RNA templates in modem organisms. The essence of this mode of polypeptide synthesis is illustrated in Figure 2.8. 

There are 20 different amino acids but only four RNA bases. Thus, a single base cannot specify a single amino acid. In fact, a group of three, or a triplet of bases in RNA indicates a particular amino acid. For example, the sequence of bases GUC causes valine to be added to a growing polypeptide. The complete genetic code lists the RNA triplets and their corresponding amino acids. You can use Skills Toolkit 1 to decode RNA sequences to their corresponding amino acid sequences, as shown below. 

The genetic code is a triplet code, that is, a sequence of three bases in RNA codes for each amino acid in a peptide chain or protein. How many RNA bases are required to code for a protein that contains 577 amino acids ... 

The sequence of bases in RNA determines the sequence of amino acids in a protein. Three bases code for a single amino acid for example, CAG is the code for glutamine. Therefore, a strand of RNA 2.73 X 10 bases long codes for a protein that has... 

A nitrogenous heterocyclic base (either a purine or a pyrimidine) attached to the 1 -carbon atom of the sugar by an N-glycosidic bond. In DNA the purine bases are adenine (A) and guanine (G) and the pyrimidine bases are cytosine (C) and thymine (T). The bases in RNA are the same except that uracil (U), a pyrimidine, replaces thymine. 

Ribonucleic acid (RNA), like DNA, is a long unbranched polymer consisting of nucleotides joined by 3 -to-5 phosphodiester bonds (see Figure 4,3). The covalent structure of RNA differs from that of DNA in two respects. First, the sugar units in RNA are riboses rather than deoxyriboses. Ribose contains a 2 -hydroxyl group not present in deoxyribose. Second, one of the four major bases in RNA is uracil (U) instead of thymine (T). 

Ribonucleic acid is a class of polynucleotides, nearly all of which are involved in some aspect of protein synthesis. RNA molecules are synthesized in a process referred to as transcription. During transcription, new RNA molecules are produced by a mechanism similar to DNA synthesis, that is, through complementary base pair formation. The sequence of bases in RNA is therefore specified by the base sequence in one of the two strands in DNA. For example, the DNA sequence 5 -CC(1ATT ACG-3 is transcribed into the RNA sequence 3 -GGCUAAUGC-5. (Complementary DNA and RNA sequences are antiparallel.)... 

The nitrogenous bases in RNA differ somewhat from those observed in DNA. Instead of thymine, RNA molecules use uracil. In addition, the bases in some RNA molecules are modified by a variety of enzymes (e.g., methylases, thi-olases, and deaminases). 

RNA molecules differ from DNA in the following ways (1) RNA contains ribose instead of deoxyribose, (2) the nitrogenous bases in RNA differ from those of DNA (e.g., uracil replaces thymine and several RNA bases are chemically modified), and (3) in contrast to the double helix of DNA, RNA is single-stranded. 

Simple arithmetic indicates that the genetic code cannot be binary since there are only four bases in RNA (A, G, C, and U), yet 20 different amino acids (19 amino acids and 1 imino acid) are known to exist in cells. Therefore, the number of possible combinations using just two bases in the codon is not enough. For example, four bases in the first position and four bases in the second position would only be sufficient to encode 16 possible amino acids (4 4 = 16). However, a ternary- (or triplet-) based code would be more than enough by specifying 64 possible amino... 

The bases in RNA are adenine (A), guanine (G), cytosine (C), and uracil (U). These are the same bases as DNA except that the base uracil is used in place of thymine (T). Unlike DNA, RNA is rarely composed of two strands base paired with each other. Instead, RNA exists as a single-stranded entity, though extensive regions of many RNAs may form double helices within themselves by the base pairing rules. 

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