Glossary

Every field has its jargon, and the cell's is thicker than most. These are the words you'll meet across the concept and pattern pages, from Adaptation to the adaptation loop. Each entry is short on purpose, and where a concept page covers the idea properly we point you to it.

Adaptation: The slow return of a cell's response to its starting level while a signal stays on. In E. coli, kinase activity drops when attractant arrives and then climbs back over several minutes, so the cell can respond to the next change. See C5.
Adaptation precision: Activity after adapting divided by activity before the stimulus, where 1 means the return is perfect. Experiments measure it on different outputs, such as tumbling or kinase activity, so be careful when you compare values from different studies.
Attractant: A chemical that a cell swims toward, such as the amino acid aspartate. When it binds a receptor in E. coli, it lowers CheA activity and the cell tumbles less.
Brownian motion: The random jiggling of small objects caused by collisions with the molecules around them. At bacterial scale it turns a cell's heading within seconds, so a cell can't keep a straight course for long.
CheA: The kinase that sits behind the chemotaxis receptors and phosphorylates CheY. Attractant binding lowers its activity, which is the fast first step of the response.
CheB: The enzyme that removes methyl groups from receptors. In the model analysed by Yi and colleagues it works only on active receptors, and that's what lets the adaptation loop settle at one fixed level.
CheR: The enzyme that adds methyl groups to receptors, pushing them toward their active state. Cells without CheR can't adapt, as Alon and colleagues found.
CheW: A partner protein that links CheA to the receptors in the receptor cluster.
CheY and CheY-P: CheY is a small messenger protein that CheA phosphorylates. The phosphorylated form, CheY-P, pushes the flagellar motor toward tumbling, so less CheY-P means longer runs.
Chemotaxis: Movement guided by chemicals, toward attractants and away from repellents. Bacterial chemotaxis in E. coli is the main example on this site.
Coefficient of variation: The standard deviation of a set of measurements divided by their mean. It gives a size-free measure of how much individuals differ, for example in resting kinase activity from cell to cell.
Diffusion: The spreading of molecules by random motion. At the scale of a bacterium, this is how molecules reach the cell's surface.
Dynamic range: The span of input levels that produce a response. Adaptation widens it in E. coli by resetting the receptors each time the background changes. See C6.
Escherichia coli (E. coli): A rod-shaped gut bacterium about 2 micrometers long. Its chemotaxis system is one of the best-studied signaling systems in biology, which is why so many of our pages start from it.
Evidence tag: A small label on a claim saying what supports it: observed, inferred or modeled. Grading claims by evidence says what each one means.
Flagellar motor: The rotary motor at the base of each bacterial flagellum, about 45 nm across and driven by ions flowing across the membrane. The direction it turns decides whether the cell runs or tumbles. See C2.
Gain: How much a pathway's output changes for a small change in its input. A high-gain pathway turns a small signal into a large response. See C6.
History-dependence: When a cell's present response depends on conditions it met before. It's a weaker claim than memory, and the site keeps the two apart. See D1.
Integral feedback: A control scheme that keeps a running total of how far an output has been from its target and pushes against that total. The system can come to rest only at the target, which is why Yi and colleagues used it to explain exact adaptation.
Kinase: An enzyme that attaches a phosphate group to another molecule, often switching that molecule on or off. CheA is the kinase in bacterial chemotaxis.
MeAsp: Alpha-methyl-aspartate, a lab attractant related to aspartate. Experimenters like it because it gives cells a clean, controlled attractant step.
Memory: On this site, a narrower claim than history-dependence: a stored cell state carries the past forward and changes later behavior in a testable way. Whether receptor methylation qualifies is an open question, and we don't know the answer. See D1.
Methylation: The addition of methyl groups to a molecule. In chemotaxis, CheR methylates receptors and CheB demethylates them, and the methylation level is the slow dial that resets the receptors.
Noise: Random fluctuation in a signal. A cell counts molecules that arrive at random times, so any count over a short window varies, and averaging for longer helps, at the cost of speed. See B2.
Phosphorylation: The attachment of a phosphate group to a protein, a common way cells switch proteins on or off. CheA phosphorylates CheY to make CheY-P.
Receptor: A protein, usually in the membrane, that turns a molecular encounter at the cell surface into a change inside the cell. See C1.
Receptor cluster: A large, ordered array of chemotaxis receptors together with CheA and CheW, gathered at the cell poles. Clusters amplify small changes in attractant concentration.
Repellent: A chemical that a cell swims away from. It acts in the opposite direction to an attractant, raising tumbling.
Reynolds number: A number comparing inertial forces to viscous forces in a moving fluid. For a bacterium it is tiny, so inertia is negligible and the cell stops almost at once when it stops swimming - no coasting. See B1.
Run: A stretch of fairly straight swimming by E. coli. Runs get longer when the cell is moving up an attractant gradient, which biases its path toward the source. See C3.
Speed-accuracy tradeoff: Averaging a noisy signal for longer makes the estimate more accurate and the response slower. Berg and Purcell worked out how this limits molecular sensing.
Temporal comparison: Detecting a gradient by comparing the current signal with the signal a few seconds earlier. Swimming turns a difference in space into a change over time that the cell can detect. See C4.
Tumble: A brief, disorderly change of direction between runs that sends the cell off in a new random direction. CheY-P makes tumbles more frequent.