AP Syllabus focus:
‘During transcription, RNA polymerase binds a DNA template strand and assembles a complementary RNA molecule by incorporating ribonucleotides.’
Transcription is the first step of gene expression, converting genetic information in DNA into an RNA copy. Initiation selects the correct start site, and elongation extends RNA accurately by matching ribonucleotides to the DNA template.
Core idea: RNA polymerase builds RNA from a DNA template
RNA polymerase uses one DNA strand (the template strand) to direct assembly of an RNA strand with complementary base pairing (A–U, C–G).
RNA polymerase reads the DNA template strand while locally unwinding the helix to form a transcription bubble. Incoming ribonucleotides base-pair with the template and are joined to the growing RNA so synthesis proceeds 5′→3′. The diagram also highlights why the RNA sequence matches the coding strand except that U replaces T. Source
The RNA product is synthesized as a linear polymer of ribonucleotides.
Transcription: Synthesis of an RNA molecule from a DNA template by RNA polymerase.
The key syllabus emphasis is that RNA polymerase binds DNA and assembles complementary RNA by incorporating ribonucleotides during initiation and elongation.
Initiation: selecting and opening the start site
Initiation positions RNA polymerase at the correct gene and creates local DNA unwinding so RNA synthesis can begin.
Promoter recognition and binding
A promoter is a DNA sequence that recruits RNA polymerase and sets the start point and direction of transcription.
Promoter: A DNA sequence where RNA polymerase (with accessory proteins) binds to initiate transcription.
How binding occurs depends on the cell type, but the functional outcome is the same: stable polymerase positioning at a gene’s start region.
Prokaryotes: RNA polymerase commonly uses a sigma factor to recognise promoter sequences and form a stable initiation complex.
Eukaryotes: RNA polymerase typically requires multiple general transcription factors to bind promoter DNA and recruit the polymerase.
The diagram shows stepwise assembly of the eukaryotic transcription initiation complex at a promoter, with general transcription factors binding first and RNA polymerase II joining after the promoter has been “prepared.” This supports the idea that eukaryotic initiation depends on accessory proteins for promoter recognition and stable polymerase positioning. It also helps distinguish eukaryotic promoter recruitment from the sigma-factor strategy used in many prokaryotes. Source
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DNA unwinding and the transcription bubble
Once bound, RNA polymerase locally separates DNA strands, forming a transcription bubble (a short region of unwound DNA).
This figure visualizes the transcription bubble as a short, unwound region of DNA in which the template (antisense) strand pairs with the nascent RNA. It contrasts the bubble alone with the same structure positioned within RNA polymerase II, emphasizing how the enzyme encloses the DNA–RNA hybrid during elongation. The color coding makes strand identity and RNA growth direction easier to track while studying initiation and elongation. Source
The template strand is exposed and read by RNA polymerase.
The non-template (coding) strand is displaced but not copied.
The first ribonucleotides are aligned by base pairing to the template, enabling the first phosphodiester bonds of the RNA chain.
Initiation to promoter escape
Early RNA synthesis is often unstable until RNA polymerase undergoes conformational changes that allow it to move away from the promoter.
RNA polymerase begins incorporating ribonucleoside triphosphates (ATP, UTP, CTP, GTP).
Energy for polymerisation comes from cleavage of the high-energy phosphate bonds in incoming ribonucleotides.
As the RNA chain lengthens, RNA polymerase transitions into the elongation phase.
Elongation: building a complementary RNA strand
During elongation, RNA polymerase moves along DNA and extends the RNA by adding ribonucleotides that are complementary to the template strand.
Mechanism of nucleotide addition
At each position on the template strand:
A matching ribonucleotide enters the active site based on base-pair rules.
RNA polymerase catalyses formation of a phosphodiester bond between the 3' end of the growing RNA and the incoming nucleotide.
The polymerase advances by one DNA base, maintaining a moving transcription bubble.
What “complementary RNA” means in practice
Because the RNA is complementary to the template strand, it closely matches the coding strand except that RNA uses U instead of T.
Template DNA: used directly for pairing (e.g., DNA A pairs with RNA U).
RNA sequence: reflects the template complement, preserving the encoded information in RNA form.
Fidelity and continuity
RNA polymerase must maintain sufficient accuracy to preserve meaning in the RNA transcript.
Correct base pairing at the active site promotes accurate ribonucleotide incorporation.
Misincorporations can disrupt RNA function or downstream protein production, so polymerase accuracy is biologically important even without perfect error rates.
Key outputs of elongation
Elongation produces an RNA transcript that:
Is a single-stranded nucleic acid polymer.
Contains information copied from DNA via complementary base pairing.
Can serve as a functional RNA directly or as a precursor that later undergoes additional processing (details addressed elsewhere).
FAQ
It relies on DNA sequence motifs plus accessory proteins (e.g., sigma factors or general transcription factors) that increase binding specificity.
Spacing between promoter elements, local DNA shape, and the positioning of initiation proteins biases where the first successful RNA bond forms.
Before promoter escape, the complex can be unstable; polymerase may release short RNAs until it clears promoter contacts and becomes processive.
Temporary slowing can help coordinate RNA folding, synchronise with RNA-binding proteins, and regulate how much transcript is produced.
Some polymerases can backtrack, remove the mismatched ribonucleotide, and then resume synthesis, improving fidelity beyond simple base selection.
Practice Questions
Describe what RNA polymerase does during transcription initiation and elongation. (2 marks)
Binds to a DNA template region to begin transcription (1)
Assembles a complementary RNA strand by incorporating ribonucleotides (1)
Explain how RNA polymerase produces an RNA transcript from DNA during initiation and elongation, including promoter binding, DNA strand use, and nucleotide incorporation. (5 marks)
RNA polymerase binds at a promoter/start region to initiate transcription (1)
DNA locally unwinds to expose the template strand (1)
Only the template strand is copied; RNA is complementary to it (1)
Free ribonucleotides base-pair to the template and are joined into RNA (1)
Phosphodiester bonds form as ribonucleotides are incorporated, extending the transcript (1)
