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A similar situation has been observed in other viruses and bacteria. The employment of overlapping reading frames optimizes the limited amount of genetic material present. However, such an approach to storing information has a distinct disadvantage in that a single mutation may affect more than one protein and thus increase the chances that the change will be deleterious or lethal. In the example we just discussed [Figure 13.8(b)], a single mutation in the middle of the B gene could potentially affect three other proteins (the A, A′, and K proteins). It may be for this reason that, while present, overlapping genes are not common in other organisms.

13.8 Transcription Synthesizes RNA on a DNA Template 

Even while the genetic code was being studied, it was quite clear that proteins were the end products of many genes. Hence, while some geneticists were attempting to elucidate the code, other research efforts were directed toward the nature of genetic expression. The central question was how DNA, a nucleic acid, can specify a protein composed of amino acids. 

The complex, multistep process begins with the transfer of genetic information stored in DNA to RNA. The process by which RNA molecules are synthesized on a DNA template is called transcription. It results in an mRNA molecule complementary to the gene sequence of one of the two strands of the double helix. Each triplet codon in the mRNA is, in turn, complementary to the anticodon region of its corresponding tRNA, which inserts the correct amino acid into the polypeptide chain during translation. 

By 1976, two other genes of MS2 and their protein products were sequenced. The analysis clearly showed that the genetic code in this virus was identical to that which had been established in bacterial systems. Other evidence suggests that the code is also identical in eukaryotes, thus providing confirmation of what seemed to be a universal code.

Bacteria such as E. coli usually complete a replication–division cycle in from 20 to 40 minutes but, in eukaryotes, the cycle can vary from 1.4 hours in yeast to 24 hours in cultured animal cells and may last from 100 to 200 hours in some cells. Eukaryotes have to solve the problem of coordinating the replication of more than one chromosome, as well as the problem of replicating the complex structure of the chromosome itself. The origins of the simple eukaryote, yeast, are very much like Oric in E. coli. They have AT-rich regions that melt when an initiator protein binds to adjacent binding sites. Origins of replication are not well characterized in higher organisms, but they are known to be much longer, possibly as long as thousands or tens of thousands of nucleotides. Unlike prokaryotic chromosomes, each chromosome has many replication origins in order to replicate the much larger eukaryotic genomes quickly. Approximately 400 replication origins are dispersed throughout the 16 chromosomes of yeast, and there are estimated to be thousands of growing forks in the 23

The significance of transcription is enormous, for it is the initial step in the process of information flow within the cell. The idea that RNA is involved as an intermediate molecule in the process of information flow between DNA and protein was suggested by the following findings:

1. DNA is, for the most part, associated with chromosomes in the nucleus of the eukaryotic cell. However, protein synthesis occurs in association with ribosomes located outside the nucleus, in the cytoplasm. Therefore, DNA did not appear to participate directly in protein synthesis. 

2. RNA is synthesized in the nucleus of eukaryotic cells, in which DNA is found, and is chemically similar to DNA. 

3. Following its synthesis, most messenger RNA migrates to the cytoplasm, in which protein synthesis (translation) occurs. 

Collectively, these observations suggested that genetic information, stored in DNA, is transferred to an RNA intermediate, which directs the synthesis of the proteins. As with most new ideas in molecular genetics, the initial supporting experimental evidence for an RNA intermediate was based on studies of bacteria and bacteriophages. The results of these experiments agreed with the concept of a messenger RNA (mRNA) being made on a DNA template and then directing the synthesis of specific proteins in association with ribosomes. This concept was formally proposed by François Jacob and Jacques Monod in 1961 as part of a model for gene regulation in bacteria. Since then, mRNA has been isolated and studied thoroughly. There is no longer any question about its role in genetic processes.

FIGURE 13.8 Illustration of the concept of overlapping reading frames. (a) Translation initiated at two different AUG positions out of frame with one another will give rise to two distinct amino acid sequences. (b) The relative positions of the sequences encoding seven polypeptides of the phage fX174.