Signal Lab: a cell signalling simulation for IB C2.1 and AP Unit 4

Lock & ligand

A receptor is a protein with a binding site for one specific signalling chemical: its ligand. Choose a receptor, choose a ligand, then play with concentration and affinity.

RECEPTOR

LIGAND

LIGAND CONCENTRATION

AFFINITY · K_d

lower K_d = tighter binding

MISSIONS

KEY IDEAS

The binding site's shape and chemistry are complementary to one ligand: others don't fit.
Binding is reversible: ligands bind and let go, so the % occupied depends on concentration.
K_d is the concentration that fills half the receptors. High affinity = low K_d.
Binding changes the receptor's shape: that is what switches the signal on.

IB C2.1.2 C2.1.14AP 4.1 · 4.5

Quorum sensing

Vibrio fischeri only glows when there are enough of them. Each cell releases an autoinducer; when it builds up past a threshold, every cell switches on its light genes at once.

ENVIRONMENT

AUTOINDUCER MADE PER CELL

POSITIVE FEEDBACK (AUTOINDUCER BOOSTS ITS OWN SYNTHESIS)

MISSIONS

HOW IT WORKS

LuxI makes the autoinducer (an AHL), which diffuses freely out of, and into, every cell.
More cells in a confined space → autoinducer concentration rises.
Above threshold it binds LuxR, an intracellular receptor that switches on the lux genes: luciferase → light.
lux genes include luxI, so more autoinducer is made: positive feedback locks the glow on.
The Hawaiian bobtail squid uses the light as camouflage against moonlight.

IB C2.1.3 C2.1.4AP 4.1

Signal sorter

Classify each signalling chemical twice: by what job it does and by what kind of molecule it is. Practise at your own pace, or go for a 60-second rapid round.

Score 0Streak 0∞

–

1 · FUNCTIONAL CATEGORY

2 · CHEMICAL GROUP

HormonesSecreted by endocrine glands into the blood. Travel far, act on distant targets, effects can last hours.

NeurotransmittersReleased by neurons into a synapse. Diffuse ~20 nm to the next cell. Fast, short-lived, very local.

CytokinesSmall proteins released by cells (especially immune cells) to act on nearby cells, coordinating immune responses.

Calcium ionsSignal inside cells: a rise in cytoplasmic Ca²⁺ triggers events such as neurotransmitter release and muscle contraction.

Why so many different molecules? Each ligand needs its own receptor shape, so chemical variety lets a body send many separate messages at once without crosstalk. Different chemistry also means different behaviour: small amines and amino acids are made and recycled fast; proteins can be highly specific; lipid-soluble steroids can enter cells and act on genes.

MISSIONS

CHEMICAL GROUPS

Hormones: amines (adrenaline, thyroxine), proteins/peptides (insulin, ADH), steroids (oestradiol, testosterone).
Neurotransmitters: amino acids (glutamate, GABA), peptides (endorphins), amines (dopamine, serotonin) and nitric oxide, a gas.
Some molecules do two jobs: adrenaline is a hormone and a neurotransmitter.

IB C2.1.5AP 4.1

Near & far

Neurotransmitters just diffuse across a gap. Hormones hitch a ride in the blood. Drag the distance and race them to find out why.

DISTANCE TO TARGET

	Neurotransmitter	Hormone
Released by	A neuron, into a synapse	An endocrine gland, into the blood
Travels by	Diffusion across the ~20 nm synaptic gap	The blood system, then diffusion out of capillaries
Effect	Localized: one target cell	Distant: every cell with the receptor, anywhere in the body
Speed & duration	Milliseconds; removed quickly	Seconds to hours; can last much longer

MISSIONS

THE PHYSICS

Diffusion time grows with the square of distance (t ≈ x² ÷ 2D). Double the distance, four times the wait. Brilliant over nanometres, hopeless over metres, so long-distance signals need the circulation.

IB C2.1.6 C2.1.7 C2.1.12AP 4.2

Inside or outside?

Pick a ligand and predict where its receptor is. Hydrophilic ligands can't cross the membrane; hydrophobic ones slip straight through.

LIGAND

THIS CELL HAS RECEPTORS FOR

YOUR PREDICTION

Choose a ligand, make a prediction, then send it.

MISSIONS

TWO KINDS OF RECEPTOR

Transmembrane: for hydrophilic ligands that stay outside. Hydrophobic amino acids sit in the bilayer; hydrophilic ones face the water on each side.
Intracellular: in the cytoplasm or nucleus, for hydrophobic ligands (steroids) that cross the membrane.
Activated steroid receptors bind specific DNA sequences and promote transcription of target genes.

IB C2.1.7–C2.1.11AP 4.2 · 4.3 · 4.4

Pathway workshop

Three transmembrane receptors, three ways to relay a message inside. Fire them, amplify them, then sabotage them.

ACETYLCHOLINE RELEASED

ACETYLCHOLINESTERASE

NAME THE HORMONE

HORMONE MOLECULES BOUND

SABOTAGE (AP 4.4)

INSULIN IN BLOOD

RECEPTOR

MISSIONS

RECEPTION → TRANSDUCTION → RESPONSE

ACh receptor: binding opens a channel in the receptor; Na⁺ diffuses in, the membrane depolarises.
Adrenaline: receptor activates a G protein → adenylyl cyclase → cAMP, the second messenger → kinases → glycogen broken down to glucose.
Insulin: binding makes the receptor phosphorylate tyrosines inside the cell → a sequence of reactions → vesicles carry GLUT4 transporters to the membrane.
Each step can activate many molecules at the next: amplification.

IB C2.1.13 C2.1.14AP 4.5

Feedback loops

Negative feedback cancels a change. Positive feedback amplifies it until something ends the loop. Run both, then control the endometrium with progesterone.

RESPONSE STRENGTH

HYPOTHALAMUS SENSITIVITY TO OESTRADIOL

PROGESTERONE

MISSIONS

TWO KINDS OF FEEDBACK

Negative: the output reduces the stimulus → stability around a set point (insulin lowers blood glucose).
Positive: the output increases the stimulus → a rapid build-up that must be ended by another event (oestradiol → GnRH → LH surge → ovulation).
Oestradiol acts on hypothalamus cells that secrete GnRH; progesterone acts on endometrium cells, maintaining the thickened lining.

IB C2.1 AP Unit 4

Exam check

Score 0 / 0