Organization of Genes Differs in Prokaryotic and Eukaryotic DNA

Having outlined the process of transcription, we now briefly consider the large-scale arrangement of information in DNA and how this arrangement dictates the requirements for RNA synthesis so that information transfer goes smoothly. In recent years, sequencing of the entire genomes from several organisms has revealed not only large variations in the number of protein-coding genes but also differences in their organization in prokaryotes and eukaryotes.

The most common arrangement of protein-coding genes in all prokaryotes has a powerful and appealing logic: genes devoted to a single metabolic goal, say, the synthesis of the amino acid tryptophan, are most often found in a contiguous array in the DNA. Such an arrangement of genes in a functional group is called an operon, because it operates as a unit from a single promoter. Transcription of an operon produces a continuous strand of mRNA that carries the message for a related series of proteins (Figure 4-12a). Each section of the mRNA represents the unit (or gene) that encodes one of the proteins in the series. In prokaryotic DNA the genes are closely packed with very few noncoding gaps, and the DNA is transcribed directly into colinear mRNA, which then is translated into protein.

This economic clustering of genes devoted to a single metabolic function does not occur in eukaryotes, even simple ones like yeasts, which can be metabolically similar to bacteria. Rather, eukaryotic genes devoted to a single pathway are most often physically separated in the DNA; indeed such genes usually are located on different chromosomes. Each gene is transcribed from its own promoter, producing one mRNA, which generally is translated to yield a single poly-peptide (Figure 4-12b).

When researchers first compared the nucleotide sequences of eukaryotic mRNAs from multicellular organisms with the DNA sequences encoding them, they were surprised to find that the uninterrupted protein-coding sequence of a given mRNA was broken up (discontinuous) in its corresponding section of DNA. They concluded that the eukary-otic gene existed in pieces of coding sequence, the exons, separated by non-protein-coding segments, the introns. This astonishing finding implied that the long initial primary tran-script—the RNA copy of the entire transcribed DNA sequence—had to be clipped apart to remove the introns and then carefully stitched back together to produce many eukaryotic mRNAs.

Although introns are common in multicellular eukary-otes, they are extremely rare in bacteria and archaea and

(a) Prokaryotes E. coli genome

trp operon

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