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Transcription and mRNA structure

Several aspects of the structure of genes can be illustrated by examining the general features of a bacterial gene as now understood.

A gene is a string of nucleotides in the duplex DNA that encodes a mRNA, which itself codes for protein. Only one strand of the duplex DNA is copied into mRNA (Fig. 1.22). Sometimes genes overlap, and in some of those cases each strand of DNA is copied, but each for a different mRNA. The strand of DNA that reads the same as the sequence of mRNA is the nontemplate strand. The strand that reads as the reverse complement of the mRNA is the template strand.




Figure 1.22.Only one strand of duplex DNA codes for a particular product.



NOTE: The term "sense strand" has two oppositeuses (unfortunately). Sidney Brenner first used it to designate the strand that served as the template to make RNA (bottom strand above), and this is still used in many genetics texts.  However, now many authors use the term to refer to the strand that reads the same as the mRNA (top strand above). The same confusion applies to the term "coding strand" which can refer to the strand encoding mRNA (bottom strand) or the strand "encoding" the protein (top strand).  Interestingly, "antisense" is used exclusively to refer to the strand that is the reverse complement of the mRNA (bottom strand).

Figure 1.22 helps illustrate the origin of terms used in gene expression.  Copying the information of DNA into RNA stays in the same "language" in that both of these polymers are nucleic acids, hence the process is called transcription.  An analogy would be writing exercises where you had to copy, e.g. a poem, from a book onto your paper - you transcribed the poem, but it is still in English.  Converting the information from RNA into DNA is equivalent to converting from one "language" to another, in this case from one type of polymer (the nucleic acid RNA) to a different one (a polypeptide or protein).  Hence the process is called translation.  This is analogous to translating a poem written in French into English.  

Fig. 1.23 illustrates the point that a gene may be longer than the region coding for the protein because of 5' and/or 3' untranslated regions.



Figure 1.23.Genes and mRNA have untranslated sequences at both the 5’ and 3’ ends.

Eukaryotic mRNAs have covalent attachment of nucleotides at the 5' and 3' ends, and in some cases nucleotides are added internally (a process called RNA editing).  Recent work shows that additional nucleotides are added post‑transcriptionally to some bacterial mRNAs as well.

Regulatory signals can be considered parts of genes

In order to express a gene at the correct time, the DNA also carries signals to start transcription (e.g. promoters), signals for regulating the efficiency of starting transcription (e.g. operators, enhancers or silencers), and signals to stop transcription (e.g. terminators).  Minimally, a gene includes the transcription unit, which is the segment of DNA that is copied into RNA in the primary transcript.  The signals directing RNA polymerase to start at the correct site, and other DNA segments that influence the efficiency of this process are regulatory elements for the gene. One can also consider them to be part of the gene, along with the transcription unit.