You already know that RNA polymerase copies a gene. But how does it know which gene, where to begin, which way to travel and when to stop? None of that is guesswork — it is written into the DNA around the gene, in stretches that are never transcribed at all.
📘 What you need to know
Transcription happens in three stages: initiation, elongation and termination.
The promoter is a non-coding sequence next to a gene. It is the binding site for RNA polymerase and is not itself transcribed.
Transcription factors are proteins that bind to specific DNA sequences and help RNA polymerase attach, so the gene can be switched on.
In elongation, RNA polymerase moves along the template strand and adds each new nucleotide to the 3′ end of the growing mRNA, so the mRNA is built 5′ to 3′.
Termination happens at a terminator sequence, which makes the enzyme and the mRNA detach.
mRNA is also read 5′ to 3′ at the ribosome.
Only about 1.5% of the human genome codes for polypeptides. The rest has other jobs: regulation, tRNA and rRNA genes, introns and telomeres.
Initiation: finding the right starting line
Before anything is copied, RNA polymerase has to land in exactly the right place. It cannot simply attach anywhere — if it did, the cell would transcribe random fragments of chromosome.
The landing site is the promoter, a short non-coding sequence sitting just before the gene. General transcription factors bind to the promoter first, and their presence lets RNA polymerase attach. Once it is bound, the DNA strands separate to form an open region, and copying can start.
The promoter is a signpost, not part of the message. It says “the gene starts here” but never appears in the mRNA. Students frequently transcribe it by mistake in diagrams.
Block the promoter and nothing gets transcribed, however healthy the gene beside it is. That is one of the main ways cells control gene expression.
Elongation: which way, and which end?
Once it is bound, RNA polymerase moves along the template strand, opening the double helix in front of it and letting it zip back up behind. Free RNA nucleotides pair with the exposed template bases as it goes.
The direction matters. Each new nucleotide is joined onto the 3′ end of the growing mRNA, which means the molecule is always built in the 5′ to 3′ direction. There is no way to add to the other end.
Directionality
mRNA is built 5′ → 3′ • mRNA is read at the ribosome 5′ → 3′
A neat way to keep the direction straight: the mRNA is made 5′ to 3′, and it is later read 5′ to 3′. Same direction both times. The template strand runs the opposite way, because the two DNA strands are antiparallel — but you only need to state that, not draw it.
Termination: knowing when to stop
RNA polymerase keeps going until it reaches a terminator sequence in the DNA. That sequence triggers the enzyme to detach from the DNA and releases the finished RNA molecule. The DNA closes back into its double helix, unchanged and ready to be transcribed again.
Three stages, three triggers: a promoter to start, a template to follow, a terminator to finish.
Different cells, different genes switched on
Every cell in your body carries the same genes, yet a neurone and a liver cell could hardly be more different. The reason is that they transcribe different sets of genes.
Essential genes — the enzymes of respiration, for example — are transcribed in every cell, all the time.
Other genes are transcribed only when needed, and only at the level needed. The gene for rhodopsin is only expressed in the light-sensitive cells of the retina.
Both prokaryotes and eukaryotes control this using transcription factors and other proteins that bind to particular DNA sequences.
This control is what makes differentiation possible: cells become specialised because they permanently switch particular genes on and others off.
What all that non-coding DNA is doing
Only around 1.5% of the human genome codes for polypeptides. The rest is not junk — several parts of it are essential.
Non-coding sequence
What it does
Promoters
Binding site for RNA polymerase at the start of a gene
Enhancers and silencers
Regulatory sequences that increase or reduce transcription of a gene
tRNA and rRNA genes
Transcribed into functional RNA molecules that are never translated into protein
Introns
Non-coding sections inside genes; removed from the transcript before translation
Telomeres
Repeated sequences that cap and protect the ends of chromosomes during cell division
Telomeres in a bit more detail
Telomeres are repeated sequences at the ends of chromosomes. The repeats give a primer somewhere to bind at the very end of the molecule, so replication can be completed. Without them, chromosomes would lose real genes and become shorter with every division.
Telomeres still shorten as we age, largely because of oxidative damage inside cells. That shortening is accelerated by smoking, pollution, obesity, stress and a poor diet, and antioxidants in the diet are claimed to slow it down.
Be careful with the word “claimed” there. The link between dietary antioxidants and telomere length is not settled science, and IB likes students who can tell the difference between a claim and a conclusion.
Worked examples
WORKED EXAMPLE
Where does the next nucleotide join?
An mRNA molecule is being made. State which end of the growing molecule the next nucleotide is added to, and give the direction of synthesis.
Step 1: Recall how the enzyme works
RNA polymerase can only add to one end of a growing strand: the 3′ end.
Step 2: State the direction that produces
Adding to the 3′ end means the strand grows 5′ to 3′.
Added at the 3′ end; synthesis runs 5′ to 3′The template is read in the opposite direction, because the strands are antiparallel.
WORKED EXAMPLE
A mutation in a promoter
A mutation changes several bases in the promoter of a gene. The gene itself is unchanged, yet no protein is produced. Explain why.
Step 1: Identify what the promoter does
It is the binding site for transcription factors and RNA polymerase.
Step 2: Work out the consequence of changing it
The altered sequence means the proteins can no longer bind, so transcription cannot be initiated.
Step 3: Follow it through
No mRNA is made → nothing to translate → no polypeptide.
The gene is never transcribed, so no protein is madeA perfect gene is useless if the switch in front of it is broken.
WORKED EXAMPLE
Telomere shortening
A cell line has telomeres 10 000 base pairs long and loses 50 base pairs from each telomere every division. How many divisions can occur before the telomeres are used up?
Step 1: Set up the calculation
Divisions = total length ÷ loss per division
Step 2: Substitute10 000 ÷ 50 = 200200 divisionsAfter that, further divisions would start cutting into genes — which is exactly what telomeres exist to prevent.
💡 Exam tip
Name all three stages if the question says “outline transcription” at HL. Initiation, elongation, termination, each with its trigger.
Say the promoter is non-coding and not transcribed. It is a common one-mark point.
Get the direction right: nucleotides are added to the 3′ end, so synthesis is 5′ to 3′.
If a question mentions cells with identical DNA behaving differently, the answer involves transcription factors and differential gene expression.
For non-coding DNA, learn four examples with a function each — that covers most possible questions.
Use the figure 1.5% for the coding fraction of the human genome. Precise numbers earn marks.
⚠ Common mix-up
Thinking the promoter is transcribed. It is read as a signal, never copied into mRNA.
Saying nucleotides are added to the 5′ end. They are added to the 3′ end; the strand grows 5′ to 3′.
Calling non-coding DNA “junk”. Much of it regulates genes or is transcribed into tRNA and rRNA.
Confusing transcription factors with RNA polymerase. The factors help the enzyme bind; they do not build the RNA.
Muddling terminator with stop codon. A terminator sequence ends transcription in the DNA; a stop codon ends translation on the mRNA.
Saying telomeres stop cells ageing. They protect chromosome ends during replication; they still shorten over time.
Up next: Post-Transcriptional Modification — the transcript you have just made is not ready to use. Before it can leave the nucleus it needs a cap, a tail, and quite a lot cut out of the middle.
Want this explained one-to-one?
Book a free session with an experienced IB Biology tutor and get your trickiest topics made simple.
