Key Idea: Topic D2.2 answers one big question: if almost every cell in your body carries the same DNA, why are a neuron, a muscle cell and a skin cell so different? The answer is gene expression β a gene being transcribed and translated into a product. Each cell type switches different genes ON and OFF, so it builds a different set of proteins. The cell's identity is its pattern of expression, not its DNA. From there the topic builds up the controls: transcription factors that switch genes on or off; epigenetic tags (DNA methylation and histone modification) that lock a pattern in without touching the bases; how the environment can leave epigenetic marks that are sometimes inherited; and finally how an epigenetic change differs from a mutation β plus how expression is measured. It is an HL-only topic, tested mainly on Paper 1 (MCQs) and Paper 2 (short 'explain how a gene is switched on/off' answers).
𧬠Gene expression & why cells differ (4.5.1)
Gene expression means a gene is used β it is transcribed into mRNA and that mRNA is translated into a protein (its product). A gene that is not expressed sits silent. Almost all of your cells contain the same complete genome, yet they differ because each type expresses a different subset of genes. A pancreas Ξ²-cell expresses the insulin gene; a red-blood-cell precursor expresses the haemoglobin gene; a neuron expresses genes for ion channels. Different genes expressed β different proteins built β different cell. This is the foundation of differentiation: as a cell develops it commits to a stable expression pattern.
Gene expression = turning a gene into a product. The base sequence is transcribed into mRNA, then translated at the ribosome into a polypeptide that folds into a protein. A muscle cell and a nerve cell carry the SAME genome but EXPRESS different genes, so they build different proteins β which is why they look and behave so differently.
π Interactive diagram
Explore the labelled diagram, charts and maps for this topic in study mode.
| Question | Answer in one line |
|---|---|
| Do a skin cell and a white blood cell have the same genes? | Yes β almost every body cell carries the same complete genome. |
| Then why are they so different? | They express different subsets of those genes, so they make different proteins. |
| What is 'gene expression'? | A gene being transcribed and translated into a functional product (usually a protein). |
| What decides which genes a cell expresses? | Its type, its position, signals it receives, and its history β set up during development and tuned by regulation. |
Same DNA in every cell; different genes switched on. Cells differ not because they have different genes, but because they express different ones.
ποΈ Regulation of transcription (4.5.2)
The main place a cell controls a gene is at transcription β deciding whether the gene gets copied into mRNA at all. The controllers are transcription factors: proteins that bind specific regulatory DNA sequences near a gene. An activator transcription factor helps RNA polymerase bind the promoter and start transcription, switching the gene ON (more mRNA, more protein). A repressor does the opposite β it blocks the polymerase or the activators, switching the gene OFF. Because different cells contain different transcription factors, the same gene can be ON in one cell type and OFF in another, all from one shared genome.
Two switches on the same DNA. TOP β a transcription factor binds a regulatory sequence and lets RNA polymerase settle on the promoter, so the gene is transcribed (gene ON). BOTTOM β methyl groups (CHβ) and tightly packed DNA/histones block the polymerase, so no mRNA is made (gene OFF, silenced). The base sequence is identical in both β only the regulation differs.
π Interactive diagram
Explore the labelled diagram, charts and maps for this topic in study mode.
| Regulator | What it is | Effect on transcription |
|---|---|---|
| Activator (transcription factor) | A protein that binds a regulatory DNA sequence near a gene | Recruits / stabilises RNA polymerase at the promoter β gene switched ON (more mRNA) |
| Repressor (transcription factor) | A protein that binds DNA at or near the gene | Blocks RNA polymerase or the activators β gene switched OFF (less / no mRNA) |
| Promoter | The DNA region just upstream of a gene | Where RNA polymerase binds to start transcription β not a protein itself |
Key Idea: Activator β gene ON. It helps RNA polymerase bind the promoter β more mRNA. Repressor β gene OFF. It blocks transcription β less / no mRNA. Both are transcription factors (proteins) that bind regulatory DNA sequences β they do not change the gene's bases, only whether it is read.
π·οΈ Epigenetics β methylation & histone modification (4.5.3)
Epigenetic changes alter whether a gene is expressed without changing the DNA base sequence. They are chemical tags laid on top of the genome ('epi-' = above). Two main types: DNA methylation β small methyl (CHβ) groups are added to bases (cytosines) in a gene's control region. Heavy methylation usually silences the gene: it packs the DNA tightly and keeps RNA polymerase out. Histone modification β DNA is wound around histone proteins. Tags such as acetyl groups on the histone tails loosen the winding so the gene is accessible (ON), while removing them or adding other marks tightens it so the gene is hidden (OFF). Together these tags set a stable, cell-specific expression pattern.
| Epigenetic change | What happens to the DNA / histones | Usual effect on the gene |
|---|---|---|
| DNA methylation | Methyl (CHβ) groups are added to cytosine bases in the gene's control region | Usually silences the gene (heavy methylation β OFF) |
| Histone modification | Chemical tags (e.g. acetyl groups) added to histone tails change how tightly DNA is wound | Loose packing β gene accessible / ON; tight packing β gene hidden / OFF |
Methylation = Muted gene (CHβ tags pack the DNA away β OFF). Acetylation of histones = Accessible gene (loosens the packing β ON). Neither touches the base sequence β that is what makes them epigenetic, not mutations.
π Environmental influence & epigenetic inheritance (4.5.4)
Epigenetic tags are not fixed at birth β the environment can add or remove them. Things like diet, stress, toxins and smoking can change a cell's methylation pattern, switching genes on or off in response to what the body experiences. This is one way identical twins (same DNA) can grow apart over a lifetime: their epigenomes drift differently. Most marks are reset when gametes form, but some survive and are passed to offspring β this is epigenetic inheritance. A famine experienced by one generation, for example, has been linked to altered gene regulation in their grandchildren. So a trait can be inherited without any change to the DNA sequence β the heritable thing is the pattern of tags.
The chain: environment β epigenome β phenotype
- An environmental factor (diet, stress, a toxin) reaches the cell.
- It triggers adding or removing methyl / histone tags at certain genes.
- Those genes are now expressed more or less β the protein output changes.
- The cell's (and sometimes the body's) phenotype shifts, with the DNA sequence unchanged.
- If the marks escape resetting in gametes, the change can be passed to offspring (epigenetic inheritance).
The key claim to be able to state: the environment can change gene expression β and sometimes that change is inherited β all without altering the DNA base sequence. This is exactly what separates epigenetics from classical genetics.
π Mutations vs epigenetic change; measuring expression (4.5.5)
It is easy to confuse a mutation with an epigenetic change because both can alter how a cell behaves β but they are fundamentally different. A mutation changes the DNA base sequence itself; it is permanent and may change the protein the gene codes for. An epigenetic change leaves the bases untouched and instead changes whether the gene is read β and it is reversible. Mutations are inherited permanently; epigenetic marks are inherited only sometimes. Measuring expression asks 'how active is this gene right now?'. Because expression means transcription + translation, you measure the amount of mRNA (how much the gene is being transcribed) or the amount of protein (the final product). More mRNA / more protein = the gene is being expressed more strongly.
| Feature | Mutation | Epigenetic change |
|---|---|---|
| What changes | The base sequence of the DNA itself | Tags ON the DNA / histones β the base sequence is unchanged |
| Reversible? | No (not normally) β it is a permanent sequence change | Yes β methylation and histone tags can be added or removed |
| How it affects a gene | May alter the protein's amino-acid sequence | Alters whether the gene is expressed, not the protein's code |
| Inherited? | Yes, if in gametes β passed on permanently | Sometimes β some marks survive into offspring (epigenetic inheritance) |
| To measure... | You look at... | Common method (idea, not detail) |
|---|---|---|
| Whether a gene is expressed | The amount of its mRNA in the cell | Detect / count the gene's mRNA β more mRNA = gene more active |
| How much protein is made | The amount of the protein itself | Detect the protein with a labelled antibody or marker |
| Which genes a methyl pattern silences | Where methyl groups sit on the genome | Compare methylation patterns between cell types or conditions |
Key Idea: Mutation = the SEQUENCE changes (a permanent change to the bases). Epigenetic change = the SWITCHES change (tags on/off the same, unchanged bases β reversible). If an exam describes a base being swapped, deleted or inserted β mutation. If it describes methyl groups or histone tags turning a gene on/off β epigenetic.
βοΈ Worked examples
IB-style question β two cells, one genome
A pancreas cell makes insulin but a skin cell does not, even though both contain the insulin gene. Explain how this is possible. [3]
Model answer:
Same genome. Both cells contain the same complete DNA, including the insulin gene β having the gene is not the same as using it.
Different expression. The insulin gene is expressed (transcribed and translated) in the pancreas cell but is switched off in the skin cell.
How it is switched. In the pancreas cell the right transcription factors are present to switch the gene on; in the skin cell the gene is kept off (e.g. repressed or epigenetically silenced), so no insulin protein is made. (1 mark: same genome; 1 mark: different genes expressed; 1 mark: control via transcription factors / regulation.)
Both cells carry the same genome including the insulin gene, but cells differ by which genes they express; the pancreas cell expresses (transcribes and translates) the insulin gene because the right transcription factors switch it on, while in the skin cell that gene is switched off, so no insulin is made.
IB-style question β switching a gene off without changing its DNA
Describe one way a gene can be switched off without altering its base sequence, and state why this is called an epigenetic change. [3]
Model answer:
Name the mechanism. Methyl (CHβ) groups are added to the DNA in the gene's control region (DNA methylation) β or histones are modified so the DNA is packed tightly.
Effect. The tightly packed / methylated DNA stops RNA polymerase binding, so the gene is not transcribed β no mRNA, no protein. The gene is silenced.
Why 'epigenetic'. The base sequence is unchanged β only a reversible chemical tag has been added on top of the DNA. A change in expression without a change in the sequence is, by definition, epigenetic (not a mutation). (1 mark: methylation / histone modification; 1 mark: blocks transcription β gene off; 1 mark: sequence unchanged so epigenetic.)
Adding methyl groups to the DNA (or modifying histones to pack the DNA tightly) blocks RNA polymerase so the gene is not transcribed and is switched off; because the base sequence itself is unchanged and the tag is reversible, this is an epigenetic change rather than a mutation.
IB-style question β mutation or epigenetic change?
Two changes are observed in a gene's behaviour. In change A a single DNA base is replaced; in change B a methyl group is added to the gene's promoter and later removed. Classify each change and justify your answer. [4]
Model answer:
Change A is a mutation. A base has been replaced, so the DNA base sequence itself has changed β this is a mutation.
It is permanent. A sequence change like this is not normally reversible and could alter the protein the gene codes for.
Change B is an epigenetic change. A methyl group is added then removed β the base sequence is never altered, only a tag on top of it.
It is reversible. Because the tag can be added and taken off, the gene's expression changes back and forth while the sequence stays the same β the hallmark of an epigenetic change. (1 mark each: A = mutation; A = sequence changed; B = epigenetic; B = sequence unchanged / reversible.)
Change A is a mutation because a base is replaced, so the DNA base sequence itself is altered (permanent). Change B is an epigenetic change because a methyl group is added and removed without altering the base sequence, so it is reversible β the gene's expression changes but its code does not.
β Quick self-check
Tap each card to check yourself.
Why do cells with the same genome look and behave differently? Because they express different subsets of their genes. Each cell type transcribes and translates a different set of genes, so it builds different proteins β its identity is its expression pattern, not its DNA.
How does a transcription factor switch a gene ON? An activator transcription factor binds a regulatory DNA sequence and helps RNA polymerase bind the promoter, so the gene is transcribed into mRNA (more protein). A repressor does the opposite and switches it OFF.
What is DNA methylation and what does it do? Methyl (CH3) groups are added to bases in a gene's control region; this usually silences the gene by packing the DNA tightly so RNA polymerase cannot transcribe it. The base sequence is unchanged.
How do histone modifications affect expression? Tags like acetyl groups on histone tails loosen the DNA winding so a gene is accessible (ON); removing them tightens the winding so the gene is hidden (OFF).
Can the environment change gene expression, and can it be inherited? Yes β diet, stress and toxins can add or remove epigenetic tags, changing expression without altering the DNA sequence. Some marks escape resetting in gametes and are passed to offspring (epigenetic inheritance).
What is the difference between a mutation and an epigenetic change? A mutation changes the DNA base sequence (permanent, may change the protein). An epigenetic change leaves the sequence untouched and instead switches the gene on/off using reversible tags.
How do you measure how strongly a gene is expressed? Measure the amount of its mRNA (transcription) or the amount of its protein (the final product). More mRNA / more protein means the gene is being expressed more strongly.
Exam Tips
- Master idea of the whole topic: almost all cells share the same genome; they differ because they EXPRESS different genes. 'Same DNA, different switches.'
- Gene expression = transcription + translation. A gene being 'expressed' means it is being read into mRNA and made into protein.
- Transcription factors: activator β helps RNA polymerase bind the promoter β gene ON (more mRNA); repressor β blocks it β gene OFF. Both are proteins binding regulatory DNA.
- Epigenetics changes expression WITHOUT changing the base sequence. DNA methylation (CH3) usually silences a gene; histone acetylation usually loosens DNA so a gene is ON.
- Memory hook: Methylation = Muted; histone Acetylation = Accessible. Neither alters the bases.
- The environment (diet, stress, toxins) can add/remove epigenetic tags; some survive into gametes, so a trait can be inherited with no DNA-sequence change (epigenetic inheritance).
- Mutation vs epigenetic: a mutation changes the SEQUENCE (permanent); an epigenetic change flips the SWITCHES on the same unchanged bases (reversible). Read the stem for which one is described.
- To measure expression, measure the mRNA level (how much it is transcribed) or the protein level (the final product) β more = expressed more strongly.