Difficulty: Introductory to Intermediate | Prerequisites: Central dogma, DNA structure, base pairing, codon basics (see Part 1 notes).
Transcription is the first half of gene expression: the step where DNA's instructions are copied into a portable RNA message. Without it, the information locked inside the nucleus (in eukaryotes) could never reach the ribosomes that build proteins. This topic covers how RNA polymerase finds the right gene, reads it, and produces an RNA transcript. You should already be comfortable with the central dogma, the structure of nucleotides, and base-pairing rules before diving in.
RNA polymerase reads a gene's template strand (3' to 5') and builds a complementary mRNA strand (5' to 3'). The process has three stages: initiation (finding the promoter and assembling the machinery), elongation (building the RNA chain), and termination (releasing the finished transcript). In eukaryotes, transcription factors and the TATA box help RNA polymerase II find the right starting point.
RNA polymerase (RNAP)
The enzyme that catalyses the synthesis of RNA from a DNA template. It pries the DNA strands apart and adds complementary RNA nucleotides one by one. Think of it as the molecular machine that "reads" the DNA and "writes" the RNA copy.
RNA polymerase II (RNA Pol II)
The specific RNA polymerase in eukaryotes responsible for transcribing protein-coding genes into mRNA. It reads the template strand in the 3' to 5' direction and unwinds about 13 base pairs of DNA at a time.
Promoter
A specific DNA sequence upstream of a gene that signals where transcription should begin. Every gene has a promoter. It also includes regulatory sequences where activator or repressor proteins can bind. Think of it as the "start here" sign for RNA polymerase.
TATA box
A short DNA sequence (consensus: TATAAAA) within the promoter of many eukaryotic genes. It is the binding site for the transcription factor TFIID and is crucial for assembling the transcription initiation complex.
Transcription factors (TFs)
Proteins that help RNA polymerase bind to the promoter and initiate transcription. They act as recognisers and recruiters. Without them, RNA polymerase cannot begin transcribing in eukaryotes.
Transcription Factor II D (TFIID)
A multi-protein complex that binds to the TATA box and kicks off the assembly of the full transcription initiation complex. It is required for the transcription of all protein-coding genes.
Transcription initiation complex
The complete assembly of transcription factors and RNA polymerase II bound to the promoter, ready to begin transcription.
Template strand
The strand of DNA that RNA polymerase reads during transcription (in the 3' to 5' direction). The resulting RNA is complementary to this strand. Also called the antisense strand, non-coding strand, or minus strand.
Coding strand (non-template strand)
The strand of DNA that has the same sequence as the mRNA product (except with thymine instead of uracil). Also called the sense strand or plus strand. It is not directly read during transcription.
Polyadenylation signal
A specific sequence in the pre-mRNA (AAUAAA in eukaryotes) that triggers cleavage of the transcript and addition of the poly-A tail. In simple terms, it is the signal that tells the cell where to cut and finish the mRNA.
Transcription is the DNA-directed synthesis of RNA, and it is the first stage of gene expression.
RNA polymerase catalyses the entire process.
The resulting RNA strand is complementary to the DNA template strand.
The template strand (antisense / minus strand) runs 3' to 5' and is the strand RNA polymerase physically reads.
The coding strand (sense / plus / non-template strand) runs 5' to 3' and has the same base sequence as the mRNA, except with T where mRNA has U.
Exam tip: if given the coding strand sequence, swap every T for U and you have the mRNA sequence.
Initiation
Transcription factors recognise the promoter region and bind to it.
In eukaryotes, TFIID binds the TATA box first, then recruits additional transcription factors.
RNA polymerase II joins the complex, forming the transcription initiation complex.
RNA polymerase begins unwinding the DNA and synthesising the RNA transcript from the start point.
Elongation
RNA polymerase moves along the DNA in the 3' to 5' direction (on the template strand), unwinding the double helix as it goes.
New RNA nucleotides are added to the 3' end of the growing RNA molecule (the transcript grows 5' to 3').
RNA polymerase unwinds roughly 13 base pairs at a time; behind it, the DNA re-winds.
Multiple RNA polymerases can transcribe the same gene simultaneously, producing many RNA copies at once.
Termination
In bacteria, the polymerase reaches a terminator sequence and stops.
In eukaryotes, RNA polymerase II transcribes past the polyadenylation signal sequence (AAUAAA). The pre-mRNA is then cleaved at this signal, and a poly-A tail is added to the 3' end. RNA polymerase II continues briefly and then dissociates from the DNA.
A promoter is the DNA sequence that tells RNA polymerase where to start and which strand to read.
In eukaryotes, the promoter includes the TATA box (transcription factor binding site), the RNA polymerase binding site, and regulatory sequences for activator and repressor proteins.
The start point of transcription sits downstream of the TATA box.
TFIID is required for all transcription of protein-coding genes in eukaryotes. It is a conglomerate of many proteins.
TFIID binds the TATA box, which then triggers the sequential binding of other transcription factors.
Transcription factors help direct and regulate gene expression in response to environmental signals.
Regulatory proteins (activators and repressors) bind to regulatory sequences within the promoter to fine-tune when and how much a gene is transcribed.
Students often mix up which strand is "read." RNA polymerase reads the template strand (3' to 5'), not the coding strand. The mRNA sequence matches the coding strand.
Students sometimes think RNA polymerase needs a primer. Unlike DNA polymerase, RNA polymerase can start a new strand from scratch without a primer.
Students confuse the promoter with the start codon. The promoter is a DNA region that tells RNA polymerase where to begin transcription. The start codon (AUG) is an mRNA signal that tells the ribosome where to begin translation. They are different signals in different processes.
Students often forget that in eukaryotes, RNA polymerase does not bind the promoter on its own. It requires transcription factors to assemble the initiation complex first.
⚠️ Know the three stages of transcription (initiation, elongation, termination) and what happens at each.
⚠️ Be able to distinguish the template strand from the coding strand and state which direction each runs.
⚠️ Understand the role of the TATA box and TFIID in eukaryotic transcription initiation. Exams frequently ask you to order the events: TFIID binds TATA box, then other TFs bind, then RNA Pol II joins to form the initiation complex.
⚠️ Know that RNA polymerase reads the template in the 3' to 5' direction and synthesises RNA in the 5' to 3' direction.
⚠️ Be ready to explain how termination differs between prokaryotes (terminator sequence) and eukaryotes (polyadenylation signal, cleavage, poly-A tail).
True or false: RNA polymerase reads the coding strand during transcription. (False. It reads the template strand.)
Fill in the blank: RNA polymerase reads the template strand in the ______ to ______ direction and builds RNA in the ______ to ______ direction. (3' to 5'; 5' to 3')
True or false: In eukaryotes, RNA polymerase II can bind directly to the promoter without help. (False. It requires transcription factors to form the initiation complex.)
Fill in the blank: The ______ is a promoter element in eukaryotic genes where TFIID binds. (TATA box)
True or false: Multiple RNA polymerases can transcribe the same gene at the same time. (True.)
Q: Compare the roles of the template strand and the coding strand during transcription.
A: The template strand is the one RNA polymerase physically reads (3' to 5'). The coding strand is not read directly; its sequence matches the mRNA (with T instead of U). The coding strand's sequence tells you the amino acid sequence the mRNA will eventually specify.
Q: Outline the steps of transcription initiation in eukaryotes, beginning with the TATA box.
A: TFIID binds to the TATA box in the promoter. Additional transcription factors then bind to the DNA around the promoter. RNA polymerase II is recruited and joins the complex, forming the transcription initiation complex. RNA polymerase II then begins unwinding the DNA and synthesising RNA from the start point.
Q: How does transcription termination differ between prokaryotes and eukaryotes?
A: In prokaryotes, RNA polymerase stops when it reaches a terminator sequence in the DNA. In eukaryotes, RNA polymerase II transcribes past the polyadenylation signal (AAUAAA). The pre-mRNA is cleaved at this signal and receives a poly-A tail. RNA polymerase II then dissociates from the DNA.
Q: A gene can be transcribed by several RNA polymerases at once. What is the advantage of this?
A: It allows the cell to produce many copies of the same mRNA rapidly, which is essential when large quantities of a particular protein are needed in a short time.
Q: If you are given the coding strand sequence 5'-ATGCCTAAG-3', what is the mRNA sequence?
A: 5'-AUGCCUAAG-3'. Simply replace each T with U. The mRNA matches the coding strand sequence with uracil in place of thymine.
Transcription feeds directly into RNA processing (5' capping, polyadenylation, splicing), which is covered in the next set of notes. Understanding what the promoter does here prepares you for gene regulation topics later, where activators and repressors control how much of a gene is transcribed. The distinction between prokaryotic and eukaryotic transcription also sets up the comparison of gene expression regulation across domains of life.
transcription, RNA polymerase, RNA Pol II, RNAP, promoter, TATA box, TATAAAA, transcription factors, TFIID, transcription initiation complex, template strand, antisense strand, minus strand, coding strand, sense strand, plus strand, non-template strand, initiation, elongation, termination, polyadenylation signal, AAUAAA, poly-A tail, 5' to 3', 3' to 5', mRNA synthesis, gene expression stage 1, BIO 311C, molecular biology