Educerie · AP · Biology
AP Biology 6.6 Gene Expression and Cell Specialization
In one breath
- In eukaryotes, RNA polymerase starts a gene only after transcription factors bind its promoter, and activators bound to enhancers, which can lie far upstream or downstream, loop round to boost it; repressors bind DNA and block it.
- Each cell type makes its own combination of factors, so each expresses its own genes, makes its own products and does its own job, while keeping every gene.
- Deletion experiments with reporter genes show which sequences are needed where: no promoter, no expression; no enhancer, no boost in the cells that use it.
- Small RNAs such as microRNAs pair with particular mRNAs and lower the protein made from them, without touching the gene.
What you must be able to do
- Explain how transcription factors and RNA polymerase binding at promoters and enhancers starts transcription, and how negative regulators binding DNA block it, and how this changes phenotypePredict expression after a promoter or enhancer is deleted; say which cell types express a gene from the factors present in each
- Explain how gene regulation produces differential expression, different cell products and functions, and how small RNA molecules regulate expressionExplain how a muscle cell and a nerve cell differ with the same DNA; interpret an experiment where a small RNA reduces a protein
Once you have read the note, tick off each one you can do in Check your understanding.
In the exam. Section I multiple choice gives you a model of a gene with its promoter and enhancers, a table of which transcription factors are present in which cell types, or a reporter-gene experiment where pieces of DNA were deleted, and asks which cells express the gene or which sequence is needed. Small-RNA experiments appear too (protein falls while the gene is unchanged). In Section II, Interpreting and evaluating experimental results questions use deletion and reporter data, Analyze model or visual representation questions use drawn enhancer loops, and Conceptual analysis questions ask you to connect differential expression with a cell's function.
1Promoters, enhancers and transcription factors
A promoter is a sequence just upstream of a gene, close to the transcription start site, where RNA polymerase and a set of general transcription factors assemble. Without them, transcription does not begin.
An enhancer is a regulatory sequence that can increase transcription of a gene from a distance. Enhancers can be upstream or downstream of the start site, sometimes thousands of base pairs away, and even inside introns. Activator proteins, a kind of transcription factor, bind an enhancer; the DNA between the enhancer and the promoter bends into a loop, bringing the bound activators into contact with the proteins at the promoter. This helps RNA polymerase bind and start. Figure 1 shows the loop.
Two features make this system good at producing different cell types:
- A gene can have several enhancers, each bound by different activators. One enhancer might switch the gene on in the eye, another in the limb.
- A gene often needs a combination of factors. If a gene's enhancer needs activators A and B, only cells that make both will express it. A small number of factors, used in combinations, can specify many cell types.
2Negative regulation
Negative regulatory molecules inhibit expression by binding to DNA and blocking transcription. In eukaryotes, repressor proteins can bind sequences called silencers, or sit on the promoter, so that RNA polymerase or activators cannot bind. It is the same principle as the bacterial repressor on an operator (topic 6.5): a protein in the way stops the enzyme.
So whether a gene is transcribed in a given cell depends on the balance at its regulatory sequences: which activators are present to turn it on, and which repressors are present to keep it off.
A gene is transcribed in a cell only if that cell makes the transcription factors its promoter and enhancers need, and not the repressors that block it; that is why cells with the same DNA make different proteins.
3Differential expression makes specialised cells
Gene regulation results in differential gene expression: different cells transcribe different genes. That decides the products each cell makes and therefore its function.
| Cell | Some genes it expresses | What that lets it do |
|---|---|---|
| Red blood cell precursor | haemoglobin | carry oxygen |
| Pancreatic beta cell | insulin | regulate blood glucose |
| Skeletal muscle cell | actin and myosin in large amounts | contract |
| Nerve cell | particular ion channels and neurotransmitter enzymes | send signals |
All four have the haemoglobin gene, the insulin gene and the rest. A pancreatic beta cell does not express haemoglobin because it lacks the transcription factors that the haemoglobin gene's regulatory sequences need. Many genes, the housekeeping genes of topic 6.5, are expressed in all of them.
Worked example (invented data). A gene's enhancer needs activators P and Q together. Which cell types express it?
| Cell type | Makes P | Makes Q | Makes repressor R (binds the promoter) |
|---|---|---|---|
| 1 | yes | yes | no |
| 2 | yes | no | no |
| 3 | yes | yes | yes |
| 4 | no | yes | no |
- Type 1: both activators, no repressor. Expressed.
- Type 2: lacks Q. Not expressed.
- Type 3: both activators, but R blocks the promoter. Not expressed.
- Type 4: lacks P. Not expressed.
Only cell type 1 expresses the gene. The reasoning to write: the gene needs both activators bound at the enhancer, and no repressor at the promoter.
4Reading deletion experiments
Biologists find regulatory sequences by joining them to a reporter gene (one whose product is easy to measure, such as a fluorescent protein), deleting pieces, and measuring output.
An invented data set. A gene's upstream DNA has a promoter and two candidate enhancers, E1 and E2. Constructs are tested in liver cells and kidney cells.
| Construct | Liver (fluorescence) | Kidney (fluorescence) |
|---|---|---|
| Promoter + E1 + E2 | 820 | 790 |
| Promoter + E1 | 805 | 35 |
| Promoter + E2 | 40 | 770 |
| Promoter only | 30 | 28 |
| E1 + E2, no promoter | 0 | 0 |
- Claim: E1 drives expression in liver and E2 in kidney. Evidence: removing E2 barely changes liver output (820 to 805) but drops kidney output to 35; removing E1 drops liver output to 40 but leaves kidney output high (770). Reasoning: each enhancer is bound by activators that only one cell type makes.
- Claim: the promoter is required. Evidence: with no promoter, output is 0 in both. Reasoning: RNA polymerase and the general factors assemble at the promoter; enhancers only boost transcription that starts there.
- The promoter alone gives a low level (about 30), the background that enhancers raise.
5Small RNAs regulate expression
Regulation does not end at transcription. Certain small RNA molecules have roles in regulating gene expression. The best known are microRNAs: short RNAs, about 22 nucleotides, made from the cell's own genes. A microRNA, held in a protein complex, base-pairs with a complementary sequence in a target mRNA. Then the mRNA is either broken down or blocked so that ribosomes cannot translate it. Either way, less protein is made, even though the gene is still being transcribed.
What to look for in data: if a small RNA acts on an mRNA, the protein falls. The mRNA may fall too (if it is broken down) or stay the same (if translation is blocked). The DNA and the rate of transcription are unchanged. Because one small RNA can match many mRNAs, a single microRNA can turn down a whole group of genes, another way to coordinate them.
Practice questions
6 questions on this note, from easy to hard. Each one you get right lights a star of this topic's constellation.