Transcription is the synthesis of RNA using DNA as template. Transcription of DNA produces three types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
The initial RNA transcripts (called primary transcripts) contain many more bases than the final functional ribonucleic acid molecules; the extra nucleotides are removed by a mechanism called RNA processing.
The net effect of RNA processing is that certain nucleotides are removed, others are added, and a number are chemically modified. Unlike replication, transcription does not progress along the entire length of a chromosome. Instead, certain parts of the chromosome are transcribed. Moreover, only one of the two strands of a DNA duplex is transcribed; this strand is called the sense strand (Fig. 21-18).
The ribo-nucleotides are added to the growing 3′-OH end of the RNA transcript by DNA- dependent RNA polymerase. In prokaryotes, RNA polymerases are multimeric proteins. For example, E. coli RNA polymerase consists of six polypeptides and one of these (called the sigma factor) is responsible for initiation of transcription.
The sigma factor ensures that the enzyme binds to the initiation site by recognizing the promoter of the DNA. Like DNA, RNA is synthesized in the 5’→3′ direction but proceeds without the need for primers. A transient hetero-duplex consisting of the sense strand and a portion of the newly synthesized RNA is formed (Fig. 21- 18b). The transcript soon separates from the sense strand, the hetero-duplex structure being maintained only in the region of RNA elongation (Fig. 21-18c). As a result, a number of RNA polymerases can simultaneously transcribe the same region of the DNA (Figs. 21-18d and 21-18e).
Five different RNA polymerases have been identified in eukaryotic cells. Of these, three are localized in the nucleus, one is present in mitochondria, and one is present in chloroplasts. Mitochondrial and chloroplast RNA polymerases are presumed to function during the expression of the limited amount of DNA present in these organelles.
The nuclear RNA polymerases are called RNA polymerase I, RNA polymerase II, and RNA polymerase III. RNA polymerase I is concentrated in the nucleolus where it synthesizes the various ribosomal RNAs (except 5 S rRNA). RNA polymerase II is responsible for the synthesis of transcripts destined to become messenger RNA, and RNA polymerase III transcribes DNA into a variety of low molecular weight RNAs, including transfer RNA and 5 S ribosomal RNA.
To initiate transcription, the RNA polymerases bind to specific regions of the DNA called promoters, each promoter consisting of about 40 nucleotide pairs. Synthesis of the primary transcript continues until a terminating signal is encountered in the sense strand. In a number of prokaryotes, the termination signal is a nucleotide sequence that gives rise to a hairpin loop in the elongating RNA; that is, the base sequence of the growing RNA molecule in this region is self- complementary and results in spontaneous folding into the double-helix conformation. Typically, the hairpin loop is followed by a poly U tail. Completion of the hairpin loop and poly U tail is followed by dissociation of the RNA polymerase from the template and release of the primary transcript.