Gene Regulation
Work out what changed: transcription, RNA processing, RNA stability, translation, or protein stability.
What to do when the question looks unfamiliar
- Step 1Locate the step: DNA → new RNA → mature mRNA → new protein.
- Step 2Check whether the measurement is production, amount present, or loss over time.
- Step 3Use a control or second measurement to rule out another explanation.
Talon’s rule: “It affects gene expression” tells me roughly as much as “something happened.” Name the step.
Turn genes up or down at the DNA level
Promoters help recruit transcription machinery. Activators and repressors affect how often transcription starts. An enhancer is a DNA sequence that can influence transcription from a distance through DNA looping.
Chromatin accessibility affects whether transcription machinery can reach DNA. Many cells have essentially the same genome but express different sets of genes. That difference helps explain why a neuron and a muscle cell behave differently.
In a bacterial operon, genes can share a promoter and be transcribed together. In the lac example, lactose-derived inducer reduces repression, and low glucose permits stronger activation. Follow the condition and the regulator before predicting transcription.
Cap, splice, tail: how pre-mRNA becomes mature mRNA
A 5′ cap helps protect the transcript and recruit translation initiation machinery. In most eukaryotic protein-coding transcripts, cleavage at the 3′ processing site creates the end where a poly-A tail is added. The tail generally helps stabilize the RNA.
Splicing removes introns and joins exons. Alternative splicing can keep different exons from the same precursor: exon 1–2–3 and exon 1–3 are different mature transcripts from the same gene. A changed coding region can yield a different protein isoform; a changed untranslated region may instead change RNA regulation.
Three different things people mean by “cutting RNA”
Read the evidence around the cut: does the result have a new exon junction, a properly finished 3′ end, or fewer intact target transcripts?
| Process | What changes | Typical outcome |
|---|---|---|
| Splicing | Introns are removed and exons are joined. | Mature RNA; alternate exon choices can change the isoform. |
| 3′-end processing | Pre-mRNA is cut at a processing site and the new end receives a poly-A tail. | A properly finished mRNA end. |
| Small-RNA-directed slicing | A guide RNA pairs with a complementary target mRNA; a protein such as AGO2 cuts it in a slicing pathway. | The cut message cannot produce a full-length protein and fragments are degraded. |
Use measurements to locate the change
New RNA production down suggests a transcription effect. New RNA unchanged but a shorter mRNA half-life points to faster RNA loss. A lower total mRNA level by itself cannot distinguish those explanations.
Same mature mRNA but less new protein suggests reduced translation. If new protein production is unchanged while existing protein disappears faster, reduced protein stability fits better. Measure the process before naming it.
A small RNA guides a silencing complex by base pairing. siRNA can direct cleavage of a highly complementary target; many animal miRNAs instead reduce translation and promote destabilization without directly slicing the target. On an AP question, use the mechanism given in the prompt.
AP Topics 6.3, 6.5, and 6.6 cover RNA processing and regulation. The cut-site examples help you apply those ideas to a specific mechanism.