Course 23.2Lesson 3 of 3

Transcription and the processing of RNA

Genetic information flows from DNA to RNA to protein. Transcription copies one strand of a gene, the template strand, into RNA, from a promoter to a terminator, with RNA polymerase. In eukaryotes the first transcript, the hnRNA, has its introns spliced out, a cap added at the 5 prime end and a tail of adenylate residues at the 3 prime end.

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From the gene to the protein

Francis Crick put the flow of information into a rule, the central dogma.

\displaystyle \text{DNA} \longrightarrow \text{RNA} \longrightarrow \text{protein}

The copying of DNA into RNA is transcription. The making of a protein from the RNA is translation. In some viruses, such as HIV, the flow goes backwards, from RNA to DNA. This is reverse transcription.

Transcription is the copying of one strand of DNA into RNA. The rules of base pairing are the same, but the RNA has uracil in the place of thymine. So A of the DNA pairs with U of the RNA.

The transcription unit

The part of the DNA that is copied into one RNA is the transcription unit. It has three regions.

The promoter is the place where RNA polymerase binds. It lies at the 5′ side of the gene, which is called upstream.
The structural gene is the part that is copied.
The terminator is the place where the copying stops. It lies at the 3′ side, which is called downstream.

Upstream and downstream are named from the coding strand. The two strands have two names.

The template strand is read by the polymerase. It runs 3′ to 5′.
The coding strand has the same sequence as the RNA, except that it has T where the RNA has U. It runs 5′ to 3′.

Why is only one strand copied? If both were, the two RNAs would have different sequences and would give two different proteins. They would also be complementary, so they would pair into a double-stranded RNA that cannot be translated.

How the RNA is made

An RNA polymerase, a large pale oval, sits on the DNA. The DNA comes in as a double helix from the right, opens into two separate strands inside the enzyme, and closes again on the left. An arrow above shows that the polymerase moves to the right. The lower strand, the template, is green and the upper strand is blue. A red RNA strand runs out of the enzyme to the lower left. Its 3 prime end, where nucleotides are added, is inside the enzyme, and its 5 prime end is free at the lower left.

RNA polymerase opens a short stretch of the DNA and reads the template strand from 3′ to 5′. It adds ribonucleoside triphosphates to the 3′ end of the growing RNA, so the RNA grows 5′ to 3′. The DNA closes again behind the enzyme.

In bacteria, one DNA-dependent RNA polymerase makes all three kinds of RNA. An initiation factor, sigma ( $\sigma$ ), helps it to start at the promoter. A termination factor, rho ( $\rho$ ), helps it to stop at the terminator. The RNA made by a bacterium does not need any processing. So in a bacterium, the RNA can be translated while it is still being made.

Three kinds of RNA

RNA	What it does
mRNA (messenger)	Carries the message of a gene to the ribosome
tRNA (transfer)	Brings the amino acids, and reads the code
rRNA (ribosomal)	Is part of the ribosome, and helps to make the peptide bond

Eukaryotes: genes in pieces

The genes of eukaryotes are split. The coding parts are the exons. They appear in the mature RNA. The parts between them are the introns. They do not appear in the mature RNA. A bacterium has no introns.

In the nucleus of a eukaryote, there are three RNA polymerases.

Polymerase	Product
RNA polymerase I	rRNAs (28S, 18S and 5.8S)
RNA polymerase II	the precursor of mRNA, the heterogeneous nuclear RNA (hnRNA)
RNA polymerase III	tRNA, 5S rRNA and snRNAs (small nuclear RNAs)

The hnRNA is the first transcript, and it has both exons and introns. It is processed in three ways before it leaves the nucleus.

Three horizontal bars drawn to scale. The top bar is the hnRNA, the first transcript, with four orange exons of 150, 210, 180 and 240 nucleotides separated by three grey introns of 900, 1500 and 600 nucleotides. An arrow marks splicing, in which the introns are removed. The middle bar is the four exons joined, 780 nucleotides in all. A second arrow marks capping at the 5 prime end and tailing at the 3 prime end. The bottom bar is the mature mRNA, the four exons with a purple cap at the left and a tail of A residues at the right.

Splicing. The introns are cut out and the exons are joined in a fixed order.
Capping. An unusual nucleotide, methyl guanosine triphosphate, is added to the 5′ end.
Tailing. About 200 to 300 adenylate residues are added to the 3′ end. This does not need a template.

The finished RNA is the mRNA. It goes out into the cytoplasm for translation.

Genes also differ in how many proteins they code for. A gene with one protein is monocistronic, as in most eukaryotes. A transcription unit that codes for several proteins, as in bacteria, is polycistronic.

You should find that most of the first transcript can be removed, and that the mature mRNA is far shorter.

Try it in Python

The program makes the mRNA and the coding strand from a template strand.

Practise with new numbers

Common mistakes

Saying that the RNA has thymine. It has uracil.
Saying that the RNA is the same as the template strand. It is the same as the coding strand, with U in the place of T.
Saying that introns are in the mature mRNA. They are removed. The exons stay.
Saying that the tail is made from the template. The tailing needs no template.
Saying that bacteria splice their RNA. The bacterial mRNA needs no processing.

Remember these

DNA to RNA to protein is the central dogma. Reverse transcription goes from RNA to DNA, as in HIV.
Transcription unit: promoter, structural gene, terminator. The template strand runs 3′ to 5′, and the RNA grows 5′ to 3′.
Bacteria: one RNA polymerase, with sigma to start and rho to stop. Eukaryotes: three polymerases, I, II and III.
hnRNA is spliced, capped (methyl guanosine triphosphate at the 5′ end) and tailed (200 to 300 adenylate residues at the 3′ end).

Check yourself

Try each one on your own first. If you are stuck, open a hint. Then check with Show the answer.

Which strand of the DNA is the template, and in which direction is it read?

How is the coding strand different from the mRNA?

Name the three regions of a transcription unit, and say where the polymerase binds.

Which RNA polymerase of a eukaryote makes the hnRNA?

List the three steps of the processing of the hnRNA.

References

NCERT (2023). Biology, Textbook for Class XII, chapter 5, Molecular Basis of Inheritance.
Clark M. A. et al. (2018). Biology 2e, OpenStax, chapter 15, sections 15.2 to 15.4, Prokaryotic Transcription, Eukaryotic Transcription and RNA Processing in Eukaryotes.
Crick F. (1970). Central dogma of molecular biology. Nature, 227, 561 to 563.