Biology · Gene Expression: RNA & Proteins
Transcription and the production of RNA
A short DNA fragment contains two complementary strands. Which strand should you copy into RNA? Without a template label and a direction, the task is underspecified. A useful transcription diagram must show both.
You need the ideas of DNA strands, complementary base pairing and cellular compartments. The DNA replication and repair chapter supplies that background. Here, direction labels and RNA base pairing are explained again before the worked examples; complete biochemical mechanisms need not be memorised.
Back to the Biology mapBy the end, you can
Read the strand directions and predict an RNA sequence from a stated DNA template.
An RNA chain has a direction
The labels 5′ and 3′, pronounced five-prime and three-prime, refer to chemically different ends of a nucleic-acid strand. RNA polymerase extends a new RNA at its 3′ end, so synthesis proceeds 5′ to 3′. It reads the DNA template in the opposite direction, 3′ to 5′. The directions are not the top and bottom of the page: they describe the molecular strand.
New RNA bases pair with template DNA: template A pairs with RNA U, template T with RNA A, and C with G. The coding, or nontemplate, DNA strand has the corresponding RNA sequence when both are written 5′ to 3′, with T in DNA where RNA has U. This equality describes the initially transcribed region; later processing can change the mature RNA.
Label the template and both molecular directions
Read the diagram in words
The constructed coding DNA runs 5′-ATG CCT GAA TGA-3′ above its complementary template, 3′-TAC GGA CTT ACT-5′. RNA runs 5′-AUG CCU GAA UGA-3′ and pairs with the template while being made. In this left-to-right display, polymerase reads the template 3′ to 5′ and extends RNA at its right-hand 3′ end.
| Molecule or orientation | Left end | Bases from left to right | Right end |
|---|---|---|---|
| Coding DNA | 5′ | ATG CCT GAA TGA | 3′ |
| Template DNA | 3′ | TAC GGA CTT ACT | 5′ |
| New RNA | 5′ | AUG CCU GAA UGA | 3′ |
| Aligned position | Coding DNA | Template DNA | New RNA |
|---|---|---|---|
| 1 | A | T | A |
| 2 | T | A | U |
| 3 | G | C | G |
| 4 | C | G | C |
| 5 | C | G | C |
| 6 | T | A | U |
| 7 | G | C | G |
| 8 | A | T | A |
| 9 | A | T | A |
| 10 | T | A | U |
| 11 | G | C | G |
| 12 | A | T | A |
| From | To | Relationship | Connection meaning |
|---|---|---|---|
| Coding DNA | Template DNA | Complementary DNA strands | Complementary base pairing |
| Template DNA | New RNA | RNA is complementary to the template | Template base pairing |
- RNA polymerase
- Template read: 3′ → 5′
- RNA growth: 5′ → 3′
- Addition at the RNA 3′ end
- Only a sequence fragment is displayed
Starting and stopping require a molecular context
A promoter is a DNA region involved in recruiting and positioning transcription machinery. Polymerase and associated factors locally open the DNA to access a template; they do not unzip an entire chromosome for each transcript. As polymerase advances, the RNA grows and DNA behind the transcription region can re-form its paired structure.
Initiation, elongation and termination describe stages of transcription. The signals and participating factors differ among systems. A translation stop codon is not, by itself, a signal telling RNA polymerase to stop. An mRNA can include regions before and after its translated coding region, so the transcription endpoint and translation endpoint answer different questions.
Keep the organism and compartment in view
In bacteria, transcription and translation can be coupled: a ribosome may begin translating a suitable mRNA while that RNA is still being transcribed. There is no nuclear envelope separating the processes. This does not mean every bacterial RNA is an mRNA, or that every transcript is translated immediately.
For a typical nuclear protein-coding gene in a eukaryotic cell, transcription occurs in the nucleus, RNA maturation is associated with that compartment, and exported mRNA is translated by cytoplasmic ribosomes. Mitochondria and chloroplasts have their own expression systems. Archaea lack a nucleus but their transcription machinery differs from the bacterial example in important ways; bacterial details should not be silently applied to all cells.
Worked example
Make the complement in the correct direction
Take the constructed template fragment 3′-TAC GGA CTT ACT-5′. Reading it left to right moves 3′ to 5′. Complementary RNA made in that direction is 5′-AUG CCU GAA UGA-3′. The corresponding coding DNA is 5′-ATG CCT GAA TGA-3′. Each strand label matters: the RNA is complementary to the template and resembles the coding strand with U replacing T.
This twelve-nucleotide fragment is a sequence exercise, not a complete natural gene or expression experiment. It omits promoters, untranslated regions and processing. If a template were instead supplied 5′ to 3′, you would need its reverse complement to write the RNA 5′ to 3′; replacing T with U in the template would give the wrong strand.
Check your understanding
An RNA polymerase extends an RNA chain. At which end are new nucleotides added?
Show reasoning
At the RNA's 3′ end, producing a chain in the 5′-to-3′ direction.
For template DNA 3′-TAC-5′, what RNA triplet is produced?
Show reasoning
5′-AUG-3′. A pairs with U, T with A and C with G, with template and product antiparallel.
Does a UGA translation stop codon automatically terminate transcription?
Show reasoning
No. It concerns ribosome-mediated translation under the stated code. Transcription termination uses its own signals and machinery.
What to carry forward
Specify template, strand direction and cell context before predicting what RNA is produced.
References
Resources supporting this lesson’s explanations and examples.
Mary Ann Clark, Matthew Douglas and Jung Choi · OpenStax2 sources
- Transcription in archaea: similarity to that in eucarya (Proceedings of the National Academy of Sciences, 1995; 92:5768–5772)D. Langer, J. Hain, P. Thuriaux and W. ZilligResearch abstract