Revise Gene expression for IB Biology (D2.2)

Gene expression is the process by which the information in a gene is used to make a functional product, usually a protein. The crucial idea for D2.2 is that expression is regulated: a gene that is being transcribed is 'switched on' and its product is made, while a gene that is not transcribed is 'switched off' and makes nothing, even though it is still physically present in the cell. This on/off control matters because a cell would waste enormous resources — and could not specialise — if it made every possible protein at once. Instead each cell expresses only the genes whose products it actually needs. Note the careful wording: a cell can carry a gene and still not express it. 'Having the gene' and 'making the protein' are not the same thing.

The main point at which a gene is switched on or off is transcription — the making of RNA from the DNA template. Two players control it. The promoter is a short non-coding DNA sequence just before the gene; it is the site where the transcription machinery assembles and it marks where transcription begins. Transcription factors are proteins that bind to the promoter (and to other regulatory sequences) and determine whether RNA polymerase can start transcribing. Some transcription factors promote transcription (switching a gene on or turning it up), while others repress it (switching a gene off or turning it down). Because transcription factors are proteins, and different cells contain different sets of them, the same promoter can be active in one cell type and silent in another. Keep the categories straight: promoters are DNA sequences; transcription factors are proteins that bind them.

Because a cell's set of active transcription factors and its epigenetic marks determine which genes are switched on, different cell types express different subsets of the same genome. This is called differential gene expression, and it is the answer to the classic puzzle: if all my cells share one identical genome, why are they so different? A pancreatic beta cell switches on the insulin gene and makes insulin; a neuron keeps the insulin gene switched off but switches on genes for neurotransmitter handling. Neither cell has different genes — they read different parts of the same genome. Cell specialisation (differentiation) is therefore the visible result of differential gene expression: as a cell commits to a type, it stably switches on the genes for that role and switches off the rest.

A phenotype is not fixed by the genotype alone: the environment can change which genes are expressed. Temperature, light and chemicals (including diet and hormones) all act as signals that alter transcription, so the same genotype can produce different phenotypes in different conditions. The classic example is the coat colour of the Himalayan rabbit. It carries an allele for tyrosinase, the enzyme needed to make the dark pigment melanin, but this version of the enzyme is temperature-sensitive: it is active only at cooler temperatures. In the warm core of the body the pigment pathway is effectively switched off and the fur grows pale; in the cool extremities — ears, nose, paws — the enzyme is active, so those regions grow dark fur. The genome is identical across the whole animal; the environment (temperature) decides where the gene's product is functional. Other examples include light triggering flowering genes in plants, and dietary chemicals altering expression in developing organisms.

Epigenetics is the study of heritable changes in gene expression that occur WITHOUT any change to the DNA base sequence. This definition is the single most important line in the topic: the DNA text is left completely unchanged; what changes is how that text is read — which genes are switched on or off. Two overview mechanisms are required. In DNA methylation, methyl groups (–CH₃) are added to cytosine bases, often in a gene's promoter; heavy methylation there typically silences the gene by blocking the transcription machinery from binding. In histone modification, chemical tags are added to the histone proteins that DNA is wrapped around: some tags loosen the packaging so genes become accessible and can be expressed, while others tighten it so genes are silenced. In neither case is a single DNA base altered — which is exactly why these changes are epigenetic and not mutations.

Two further features make epigenetics powerful. First, epigenetic marks can be influenced by the environment: temperature, diet, stress and chemicals can add or remove methylation and histone tags, changing which genes are expressed without touching the sequence. Second, these marks are heritable — they are copied when a cell divides (so a silenced gene stays silenced in daughter cells), and some marks are even passed from parent to offspring, so an environmentally triggered change in expression can sometimes be inherited. Because the sequence is untouched, many epigenetic marks are also reversible, letting expression patterns respond to changing conditions.

D2.2 'explain' questions are marked analytically: each distinct valid biological point is worth one mark, up to the total available. Method/idea marks (M) credit correct reasoning, answer marks (A) credit a correct named conclusion or example, and error-carried-forward (ECF) means a slip early on does not cost later marks that follow correctly from it. Equivalent correct wording is accepted. Study how each mark below is tied to a specific, named idea, not to loose phrasing.

Gene regulation is the thread running through the rest of D. Differential gene expression underlies development and the specialisation of stem cells; environmental and epigenetic control connects to how phenotypes vary within a population and how organisms respond to their surroundings. Once you can say clearly that genes are switched on and off, that transcription factors and promoters do the switching, and that epigenetic marks change expression without changing the sequence, you have the framework for the whole continuity-and-change unit.