Signal Transduction Pathways: Study Guide (Biology 4.3)

From signal to response

In Topic 4.2 you met the parts of a signal transduction pathway. A ligand binds a receptor. The receptor changes shape. Relay proteins, second messengers such as cAMP and chains of protein kinases pass the message on, often amplifying it.

This topic asks two new questions:

1. What does the pathway actually make the cell do? The answer is a cellular response, and there are several kinds.
2. What happens if any part of the pathway changes? A mutation, a drug or a toxin can change one component. Because each component switches on the next, the effect spreads to every step downstream.

Four kinds of cellular response

Kind of response	What changes	Typical speed	Example
Change in protein activity	an enzyme, channel or transporter the cell already has is switched on or off, often by phosphorylation	seconds to minutes	epinephrine makes liver cells break down glycogen and release glucose
Change in gene expression	a transcription factor is activated, so some genes are transcribed more (or less) and new proteins are made	minutes to hours	yeast mating pheromones switch on mating genes
Change in phenotype	the new proteins change what the cell, tissue or organism looks like or does	hours to days	ethylene changes the enzymes in fruit cells so the fruit softens and ripens
Apoptosis	the cell activates enzymes that take it apart from the inside	hours	the tissue between developing fingers and toes is removed

The first two rows describe where the pathway acts. The last two describe outcomes that usually follow from changed gene expression. They overlap: a phenotype change nearly always rests on new proteins made after gene expression changes.

Changing what proteins already do

The fastest responses need no new proteins. A kinase adds a phosphate group to an enzyme, channel or transporter. Its shape changes and it becomes more (or less) active. In liver cells, the hormone epinephrine starts a cAMP pathway that ends by activating the enzyme that breaks glycogen into glucose. Glucose can be released into the blood within seconds, ready for a sudden burst of activity. Nothing new was made: an existing enzyme was switched on.

Changing gene expression

Slower responses end at a transcription factor, a protein that binds DNA and makes some genes more (or less) likely to be transcribed. New mRNA is made, then new proteins. Some examples:

• Yeast mating pheromones. A yeast cell releases a pheromone that binds receptors on yeast cells of the opposite mating type. The pathway switches on mating genes, so the receiving cell stops dividing and grows towards its partner.
• Cytokines. These signalling proteins of the immune system bind receptors on target cells and change gene expression so that the cells replicate and divide.
• Steroid hormones such as testosterone pass through the membrane and bind a receptor inside the cell. The hormone–receptor complex itself acts as a transcription factor.
• HOX genes code for transcription factors that, during embryonic development, tell cells which part of the body plan they belong to (head, thorax, tail and so on). Signals in the embryo control which HOX genes each cell expresses.

Changing phenotype

When new proteins are made, a cell can take on a new phenotype: a new structure, behaviour or function. In ripening fruit, the plant hormone ethylene changes the production of several enzymes. Some break down cell walls (the fruit softens), some convert starch to sugar (it sweetens) and some change pigments (it changes colour).

Bacteria show the same principle through quorum sensing. Each bacterium releases a small signal molecule, an autoinducer. With few cells, it diffuses away. As the population grows, the concentration rises. Above a threshold, the autoinducer binds a receptor protein inside the cells that acts as a transcription factor. New genes switch on and the whole population changes behaviour together. In the marine bacterium Aliivibrio fischeri, which lives in the light organ of the Hawaiian bobtail squid, quorum sensing switches on the genes for light production. Glowing only makes sense when there are enough bacteria for the light to be seen.

Apoptosis: a response that ends the cell

Some signals tell a cell to die in a controlled way. This is apoptosis, or programmed cell death. The pathway activates protein-digesting enzymes that break the cell down from the inside. The fragments are packaged in membrane and eaten by other cells, so no contents leak out and no inflammation results.

Apoptosis is not a failure; it shapes the body. In a human embryo the hands start as paddles. Cells between the future fingers receive signals and undergo apoptosis, which separates the digits. In chick embryos, experiments that disrupted a receptor in this signalling pathway stopped the apoptosis and gave webbed feet, rather like a duck’s. Apoptosis also removes cells that are damaged, infected or no longer needed.

When part of the pathway changes: mutations

A receptor is a protein with separate domains: a ligand-binding domain that recognises the signal and an intracellular domain that passes it on. Every relay protein and kinase is also a protein whose shape is set by a gene. A mutation can change the shape of any of them, and so change everything downstream of that point.

Two kinds of change cover most cases:

• Loss of function. The component can no longer be switched on, or cannot switch on the next one. The signal stops at that point. The response is missing or weak, even when plenty of ligand is present. Example: in androgen insensitivity, the gene for the receptor for testosterone is mutated. Testosterone levels can be normal or high, but target cells cannot respond, so body features that depend on that response do not develop.
• Gain of function (stuck on). The component is active without its normal input. The response happens all the time, even with no ligand. Example: the relay protein Ras passes growth signals from receptors to a kinase cascade that ends in cell division. Certain mutations stop Ras from switching itself off. Cells then divide without a growth signal. Such mutations are found in many human cancers.

Where the change is matters too. A change upstream (in the receptor) affects all branches that come after it. A change in one branch (say, a kinase that only leads to branch B in Figure 1) can leave the other branch working normally.

When chemicals interfere: activators and inhibitors

Chemicals made by other organisms, or by drug companies, can act at any point in Figure 1.

Point	Chemical effect	Result	Example
Receptor (1)	mimics the ligand and switches the receptor on	pathway activated	synthetic hormones
Receptor (1)	blocks the ligand-binding site without switching it on	pathway inhibited	1-methylcyclopropene blocks ethylene receptors, so stored fruit ripens later; beta blocker drugs block receptors for epinephrine in the heart
Relay protein (3)	locks it in the active state	pathway activated, cannot switch off	cholera toxin keeps a G protein active in gut cells, so cAMP stays high and the cells pump out chloride ions and water: severe diarrhoea
Kinase (4)	blocks the enzyme’s active site	pathway inhibited from that point on	some cancer drugs inhibit an overactive kinase
Enzyme that removes a second messenger	slows its removal	response lasts longer	predict it from the rule below

The logic is always the same. Ask: does the chemical make this component more or less active? Then follow the effect downstream, step by step, to the response.

Worked example 1: quorum sensing in a fictional bacterium

Question. A fictional marine bacterium, strain M, can glow. Researchers grew cultures to different densities and measured the light given out per cell (arbitrary units).

Cell density / 10⁷ cells mL⁻¹	0.5	1	2	4	8	16
Light per cell / a.u.	1.0	1.1	1.2	1.5	38	41

A second, fictional experiment gave these results:

Culture	Density / 10⁷ cells mL⁻¹	Light per cell / a.u.
Normal strain M + synthetic autoinducer	1	36
Mutant that cannot make autoinducer	16	1.2
Mutant that cannot make autoinducer + synthetic autoinducer	16	39
Mutant whose autoinducer receptor cannot bind it	16	1.1

(a) Describe the trend in the first table. (b) Use both experiments to justify the claim: “Light production is switched on by the autoinducer reaching a threshold, not by crowding itself.” (c) Name the kind of cellular response.

(a) Trend. From 0.5 to 4 × 10⁷ cells mL⁻¹ the density rises eightfold, but light per cell rises only from 1.0 to 1.5. Between 4 and 8 × 10⁷ it jumps from 1.5 to 38, about 25 times higher (38 ÷ 1.5 = 25.3). Above that it levels off (41 at 16 × 10⁷). The response is switch-like, with a threshold between 4 and 8 × 10⁷ cells mL⁻¹.

(b) Claim, evidence, reasoning.

1. Evidence 1: adding synthetic autoinducer to a low-density culture (1 × 10⁷) gave strong light (36), with no crowding.
2. Evidence 2: cells that cannot make autoinducer stay dark even at the highest density (1.2), but glow (39) when it is added.
3. Evidence 3: cells with a receptor that cannot bind autoinducer stay dark at high density (1.1).
4. Reasoning: light appears whenever enough autoinducer is present, whatever the density, and never when it is missing or cannot be detected. So crowding acts only by raising the autoinducer concentration. The receptor result shows the signal must bind its receptor to act, as in any signal transduction pathway.

(c) Kind of response. A change in gene expression (light-producing genes are switched on), which changes the population’s phenotype (it glows).

Check. Is the claim proven? The data strongly support it for strain M under lab conditions. A single culture per condition is a weakness; repeats would make the conclusion more secure.

Worked example 2: ordering a pathway with mutants and an inhibitor

Question. In a fictional cell line, growth factor G binds a receptor. The signal passes through relay protein R and then kinase K, and ends with cell division. Researchers measured the percentage of cells that divided in 24 hours.

Cells	Without G / %	With G / %
Normal	2	30
Mutant 1: receptor’s ligand-binding domain changed	2	3
Mutant 2: R stuck in its active state	29	31
Normal + kinase K inhibitor	2	3
Mutant 2 + kinase K inhibitor	2	3

(a) By how many times does G increase division in normal cells? (b) Explain the results for mutants 1 and 2. (c) Justify the claim that K acts after R. (d) Predict the result for a mutant whose receptor intracellular domain is stuck “on”, treated with the K inhibitor.

(a) 30 ÷ 2 = 15 times (an increase of 28 percentage points).

(b) Mutant 1 is a loss of function at the start of the pathway. G cannot bind, so the receptor never changes shape and nothing downstream is switched on: division stays at the background level (3%). Mutant 2 is a gain of function. R is active without any signal, so everything after R is switched on and cells divide (29%) even without G. Adding G changes little, because the pathway is already fully on from R onwards.

(c) The K inhibitor blocks division in mutant 2 (2–3%), even though R is stuck on. If K came before R, an active R would not need K and cells would still divide. Because blocking K stops the signal from an active R, K must be downstream of R.

(d) A receptor stuck “on” is upstream of both R and K. Blocking K still stops the signal, so division would stay at about 2–3%, with or without G.

Interpretation. Mutant 2 behaves like a cancer cell: it divides with no growth signal. The inhibitor result shows why drugs aimed at a step downstream of the faulty protein can still work.

Common misconceptions

• “Every response involves new genes being switched on.” Many fast responses only change the activity of proteins the cell already has.
• “Apoptosis is what happens when a cell is damaged and bursts.” That uncontrolled death is different. Apoptosis is an ordered, signal-driven process that the cell carries out on itself.
• “A mutation in the receptor only matters if it is in the binding site.” A change in the intracellular domain can stop it passing the signal on, or leave it permanently on.
• “A mutation always stops the pathway.” Gain-of-function mutations do the opposite: the response happens with no signal.
• “Adding more ligand will fix a receptor mutation.” If the ligand cannot bind, or the receptor cannot pass the signal on, extra ligand changes nothing.
• “Quorum sensing means bacteria count each other.” Each cell detects only the concentration of a chemical; the concentration rises with population density.
• “An inhibitor only affects the step it binds.” It affects every step after that point, because each step depends on the one before.

Where this leads

Next, Topic 4.4, Feedback, shows how the response to a signal can loop back to reduce or increase the signal itself, which is how the body keeps conditions steady. Pathways that control growth and division return in Topic 4.6, where faults in them lead to cancer. Test yourself now with the practice questions, then use the revision notes and the checklist to consolidate.