How transcription works · Chapter 12

Transcription makes a working RNA copy of a gene. The DNA itself isn’t changed, so the same gene can be copied again whenever the cell needs more.

What a gene is, at the molecular level

At the level of molecules, a gene is a stretch of DNA organized so that it can be transcribed into RNA, and that RNA ultimately leads to a working product. For most genes, the protein-coding genes, the RNA is an mRNA. The mRNA is only a go-between: the gene’s functional product is the polypeptide made from it.

For other genes, the RNA itself is the final product and is never translated. These are non-coding RNAs (ncRNAs). Two of them do jobs in translation, so you’ll meet them again and again in this chapter: transfer RNA (tRNA) and ribosomal RNA (rRNA).

RNA	Job	Translated?
mRNA	Carries a gene’s coding message to the ribosome	Yes
tRNA	Reads the mRNA and brings the matching amino acid	No
rRNA	Forms much of the ribosome, where translation happens	No

Two DNA sequences mark where transcription starts and stops. The promoter controls when and where transcription begins. The terminator marks where it ends. Everything between them is copied into RNA, including the stretch that codes the polypeptide.

Nearby regulatory sequences act as landing spots for regulatory proteins. When one of these proteins binds, it speeds up or slows down transcription of the gene.

The enzyme that builds RNA is RNA polymerase. Like DNA polymerase, it links nucleotides into a strand that pairs with a DNA template. In bacteria, RNA polymerase finds genes with the help of a protein called sigma factor. Transcription then runs in three stages.

Initiation: sigma factor binds RNA polymerase, recognizes the promoter’s sequence, and holds the polymerase there. RNA polymerase then separates the two DNA strands over a short stretch. The polymerase with this small bubble of unwound DNA is the open complex.
Elongation: sigma factor leaves, and RNA polymerase slides along the gene, carrying the open bubble with it. RNA nucleotides pair with one DNA strand and are linked into a growing RNA. Behind the bubble, the DNA winds back into a double helix.
Termination: RNA polymerase reaches the terminator. The polymerase and the finished RNA transcript both let go of the DNA.

Figure 12.2 Notice that sigma factor is needed only to start. Once RNA polymerase is copying, sigma factor leaves, and the DNA rewinds behind the moving bubble.

Check yourselfA mutation changes a gene’s promoter so that sigma factor can no longer recognize it. What happens to the gene?

It isn’t transcribed. Without sigma factor binding the promoter, RNA polymerase never settles at the start of the gene, so no open complex forms and no RNA is made.

RNA polymerase reads only one of the two DNA strands. As in DNA replication, the strand being read is the template strand, and the new RNA is complementary to it. The pairing follows the AT/GC rule with one change: RNA has uracil (U) where DNA has thymine (T), so an A in the template calls for a U in the RNA.

The other DNA strand of a protein-coding gene is the coding strand. Both the coding strand and the RNA are complementary to the template, so they carry the same sequence, except that the RNA has U wherever the coding strand has T. The coding strand gets its name because, like the mRNA, it spells out the code for the polypeptide.

Neighboring genes on a chromosome don’t all use the same strand. One gene may use the bottom strand as its template and be transcribed left to right, while the next uses the top strand and runs right to left. Each gene’s promoter sets which strand is read and in which direction.

Two rules never change. RNA is always built in the 5′ → 3′ direction, so the template strand is always read 3′ → 5′.

Check yourselfA template strand reads 3′–GCAATG–5′. What RNA is made from it?

5′–CGUUAC–3′. Each base pairs with its partner (G→C, C→G, A→U, T→A), and the RNA runs antiparallel to the template.