Page 124 - Genetics_From_Genes_to_Genomes_6th_FULL_Part2

8.2 Transcription: From DNA to RNA 283

FEATURE FIGURE 8.10 (Continued)

(a) The Initiation of Transcription
1. RNA polymerase binds to double-stranded DNA at the beginning of the gene to be copied. RNA polymerase recog-
nizes and binds to promoters, specialized DNA sequences near the transcription start site. Although specific promoters vary
substantially, all promoters in E. coli contain two characteristic short sequences of 6–10 base pairs (Fig. 8.11a). In bacteria, the
complete RNA polymerase (the holoenzyme) consists of a core enzyme, plus a σ (Sigma) subunit involved only in initiation.
The σ subunit reduces RNA polymerase’s general affinity for DNA but simultaneously increases RNA polymerase’s affinity for
the promoter. As a result, the RNA polymerase holoenzyme can home in on a promoter and bind tightly to it, forming a closed
promoter complex.
2. After binding to the promoter, RNA polymerase unwinds part of the double helix, exposing unpaired bases on the
template strand. The complex formed between the RNA polymerase holoenzyme and an unwound promoter is called an
open promoter complex. The enzyme identifies the template strand and chooses the two nucleotides to be copied. Guided
by base pairing with these two nucleotides, RNA polymerase aligns the first two ribonucleotides at the 5′ end of the new RNA.
The DNA transcribed as the 5′ end of the mRNA is the 5′ end of the gene. RNA polymerase then forms a phosphodiester
bond between the first two ribonucleotides. Soon thereafter, the RNA polymerase releases the σ subunit, marking the end of
initiation.

(b) Elongation: Constructing an RNA Copy of the Gene
1. When the σ subunit is released, RNA polymerase loses its enhanced affinity for the promoter sequence and regains its
strong generalized affinity for any DNA. These changes enable the core enzyme to leave the promoter yet remain bound to the
gene. The core enzyme moves along the chromosome, unwinding the DNA to expose the next single-stranded region of the
template. The enzyme extends the RNA by adding the correct ribonucleotide to the 3′ end of the growing chain. As the enzyme
extends the mRNA in the 5′-to-3′ direction, it moves in the antiparallel 3′-to-5′ direction along the DNA template strand. RNA
polymerase synthesizes RNA at an average speed of about 50 nucleotides per second.
The region of DNA unwound by RNA polymerase is the transcription bubble. Within the bubble, the nascent RNA chain
remains base paired with the DNA template, forming a DNA–RNA hybrid. However, in those parts of the gene behind the bubble
that have already been transcribed, the DNA double helix re-forms, displacing the RNA, which hangs out of the transcription
complex as a single strand with a free 5′ end.
2. Once an RNA polymerase has moved off the promoter, other RNA polymerase molecules can move in to initiate
transcription. If the promoter is very strong, that is, if it can attract RNA polymerase rapidly, many enzyme molecules can
transcribe it simultaneously. Here we show an electron micrograph and an artist’s interpretation of simultaneous transcrip-
tion by several RNA polymerases. The promoter for this gene lies very close to where the shortest RNA is emerging from
the DNA.
Geneticists often use the direction traveled by RNA polymerase as a reference when discussing gene structure. If, for ex-
ample, you started at the 5′ end of a gene at point A and moved along the gene in the same direction as RNA polymerase to point
B, you would be moving downstream. If, by contrast, you started at point B and moved in the opposite direction to point A, you
would be traveling upstream.

(c) Termination: The End of Transcription
RNA sequences that signal the end of transcription are known as terminators. Two types of terminators exist: intrinsic ter-
minators, which cause the RNA polymerase core enzyme to terminate transcription on its own, and extrinsic terminators, which
require additional proteins—particularly a polypeptide known as Rho—to bring about termination. All terminators, whether intrin-
sic or extrinsic, are specific sequences in the mRNA that are transcribed from the gene. Terminators often form hairpin loops (also
called stem loops) in which nucleotides within the mRNA pair with complementary nucleotides in the same molecule. Upon
termination, RNA polymerase and a completed RNA chain are both released from the DNA.

related, but not identical, to the complete set of DNA nu­ connected through a triphosphate linkage to the first nu­
cleotide pairs in the original gene. cleotide in the primary transcript. This “backward G” is not
transcribed from the DNA. Instead, a special capping en-
zyme adds it to the primary transcript after polymeriza­
Adding a 5′ methylated cap and a 3′ poly-A tail tion of the transcript’s first few nucleotides. Enzymes
The nucleotide at the 5′ end of a eukaryotic mRNA is a G known as methyl transferases then add methyl (–CH 3 )
in reverse orientation from the rest of the molecule; it is groups to the backward G and to one or more of the