Process of Transcription

Transcription unfolds through the same three stages in essentially every organism: initiation, elongation and termination, though the details differ meaningfully between prokaryotes and eukaryotes. In prokaryotes, a single kind of DNA-dependent RNA polymerase is responsible for transcribing all three major classes of cellular RNA -- messenger RNA (mRNA), which provides the template read during translation; transfer RNA (tRNA), which brings amino acids to the ribosome and reads the genetic code; and ribosomal RNA (rRNA), which plays structural and catalytic roles inside the ribosome during translation -- and all three RNA types together are required to make a protein. The polymerase, aided by its sigma factor, first binds the promoter and initiates transcription; the sigma factor is then released once transcription is under way, and the remaining core enzyme moves along the DNA, opening a small local 'transcription bubble' and progressively adding one ribonucleotide after another to the growing RNA chain, using nucleoside triphosphates as its raw material and reading the template strand according to the ordinary rule of base complementarity. Only a short stretch of the newly made RNA stays physically bound to the enzyme at any one moment; when the moving polymerase reaches a terminator sequence at the far end of the gene, often with the help of a recognition protein called rho, the finished RNA and the polymerase itself both detach and are released. Because bacterial cells have no nuclear membrane separating their DNA from the cytoplasm, and because bacterial mRNA requires no further processing before it becomes functional, translation of a bacterial mRNA can actually begin at its free end well before transcription of the far end of the same molecule has even finished -- transcription and translation are physically coupled in bacteria in a way that is impossible in eukaryotes. Eukaryotic cells instead maintain at least three distinct nuclear RNA polymerases (plus additional RNA polymerases dedicated to the organelles), each with its own division of labour: RNA polymerase I transcribes the large ribosomal RNAs (28S, 18S and 5.8S rRNA); RNA polymerase III transcribes tRNA, 5S rRNA and small nuclear RNA (snRNA); and RNA polymerase II transcribes the precursor of messenger RNA, called heterogeneous nuclear RNA (hnRNA). Because eukaryotic monocistronic genes contain interrupted coding sequences, called exons (the segments that are ultimately expressed), interspersed with non-coding intervening sequences called introns, the primary hnRNA transcript must first be processed before it can serve as functional mRNA: the introns are cut out and the flanking exons joined together in a step called splicing, and the transcript additionally receives capping, the addition of an unusual nucleotide, 7-methylguanosine triphosphate, at its 5' end, and tailing, the addition of a run of roughly 200 to 300 adenylate residues (the poly-A tail) at its 3' end. Only after this processing is complete is the molecule properly called mRNA and exported from the nucleus for translation. The split-gene arrangement of eukaryotic genes is almost completely absent in prokaryotic genomes. Because intron removal and exon rearrangement are chemically flexible, individual exons, each of which may originally have encoded a distinct functional protein domain, can be spliced together in different combinations, a process called alternative s …