Biology - Cell Communication

Ligand

A small signaling molecule that sends a signal by binding specifically to a receptor protein.

Receptor

A protein in a target cell that binds a specific ligand to initiate a cellular response.

Signal Transduction Pathway

The sequence of molecular events that turns an extracellular chemical signal into a specific cellular response.

Effector

A target protein, such as an enzyme or transcription factor, that is activated or inactivated to produce the cellular response.

Intercellular Signaling

Communication that occurs between different cells.

Intracellular Signaling

Communication that takes place within a single cell.

Binding Affinity

A measurement of how tightly and strongly a ligand binds to its corresponding receptor.

Gap Junction

An animal cell channel formed by connexons (about $1.5\,\text{nm}$ wide) that allows small molecules and ions to pass directly between adjacent cells.

Connexon

A protein assembly in animal cells that forms half of a gap junction channel.

Plasmodesmata

Membrane-lined channels through plant cell walls with a lumen of about $6\,\text{nm}$ that connect adjacent plant cells and act like circulatory capillaries.

Desmotubule

A narrow tube of smooth endoplasmic reticulum running through the central channel of a plasmodesma.

Autocrine Signaling

A signaling mechanism in which a cell secretes a chemical messenger that binds to receptors on that same cell.

Juxtacrine Signaling

A signaling process that acts directly between adjacent cells in physical contact.

Paracrine Signaling

Local chemical signaling in which a ligand diffuses through the extracellular matrix to nearby cells, providing a fast and short-lived response.

Endocrine Signaling

Long-distance signaling where hormones are transported via blood or lymph to distant target cells, resulting in slower but longer-lasting responses.

Hormone

The chemical ligand utilized in endocrine signaling that travels through the bloodstream or lymph to distant cells.

Pheromone

A chemical signal released into the environment to communicate between different individual organisms of the same species.

Cell-Surface Receptor

A transmembrane protein consisting of an external ligand-binding domain, a hydrophobic membrane-spanning region, and an intracellular domain that binds water-soluble ligands.

Intracellular Receptor

A receptor located in the cytosol or nucleus that binds small, nonpolar ligands such as steroid hormones that diffuse across the plasma membrane.

Ligand-Gated Ion Channel

A cell-surface receptor that opens an ion channel pore upon ligand binding, allowing ions to flow down their electrochemical gradient.

Enzyme-Linked Receptor

A cell-surface receptor whose intracellular domain has enzymatic activity or activates an enzyme upon ligand binding.

Tyrosine Kinase Receptor

A dimerized enzyme-linked receptor that phosphorylates tyrosine residues on itself and target proteins (e.g., the insulin receptor).

G Protein-Linked Receptor (GPCR)

A cell-surface transmembrane receptor that activates a trimeric G protein upon ligand binding.

G Protein

A molecular switch protein composed of alpha ($\alpha$), beta ($\beta$), and gamma ($\gamma$) subunits that is active when bound to GTP and inactive when bound to GDP.

GTPase Activity

The intrinsic enzymatic ability of the G protein alpha ($\alpha$) subunit to hydrolyze bound GTP to GDP, turning the switch off.

Agonist (Mimetic)

A chemical substance that mimics the normal ligand by binding and activating a receptor.

Antagonist (Inhibitor)

A chemical substance that binds to a receptor and blocks its activation by the normal ligand.

Transcription Factor

A protein that regulates gene expression by binding to specific DNA sequences to turn transcription on or off.

Crosstalk

The interconnected interaction and communication between different signaling pathways.

Divergence

A signaling pattern in which a single pathway or signal branches out to activate multiple different cellular targets or pathways.

Convergence

A signaling pattern in which multiple distinct pathways share or meet at a common molecular target.

Signal Integration

The process of merging signals from two or more distinct receptors to produce a single coordinated cellular response.

Cascade

A series of linked sequential molecular events that amplifies an initial signal, provides precise regulation, and coordinates distinct responses.

Protein Kinase

An enzyme that transfers a phosphate group from ATP to specific amino acid residues (serine, threonine, or tyrosine) on target proteins.

Phosphorylation

The addition of a phosphate group to serine, threonine, or tyrosine residues on a protein, altering the protein's conformation and activity.

Amplification

The process wherein a single signaling molecule triggers the production or activation of many downstream molecules in a pathway.

Second Messenger

A small, non-protein, diffusible intracellular molecule (such as $\text{Ca}^{2+}$, cAMP, DAG, or $\text{IP}_3$) that relays and amplifies a signal inside the cell.

Cyclic AMP (cAMP)

A major second messenger synthesized from ATP by the enzyme adenylyl cyclase.

Adenylyl Cyclase

An enzyme that converts ATP into the second messenger cyclic AMP (cAMP).

Protein Kinase A (PKA)

A kinase enzyme that is directly activated by cyclic AMP (cAMP) during a signaling cascade.

Epinephrine

A hormone that binds to GPCRs in liver cells to trigger glycogen breakdown into glucose via a cAMP-dependent pathway.

Growth Factor (Mitogen)

A signaling molecule that binds protein kinase receptors to stimulate cell growth and mitosis.

Ras

A monomeric G protein (small GTPase) in cell growth signaling; mutations that lock it permanently bound to GTP cause continuous cell division in cancer.

Cancer

A disorder of the cell cycle characterized by uncontrolled cell division resulting from mutations in signaling genes.

Apoptosis

Programmed cell death (cellular suicide) in multicellular eukaryotes that safely removes damaged, cancerous, or unneeded cells.

Quorum Sensing

A density-dependent bacterial signaling mechanism in which gene expression is altered once the cell population reaches a specific threshold.

Autoinducer

A signaling molecule secreted by bacteria (such as acyl-homoserine lactones, or AHL) to monitor population density and coordinate group behavior.

Bioluminescence

The generation and emission of light by living organisms, such as Vibrio bacteria glowing at high population densities.

Photophore

A specialized light-producing organ, such as the one in the Hawaiian bobtail squid (Euprymna scolopes) housing symbiotic Vibrio fischeri.

Why do cells need signaling?

To receive stimuli from the environment and communicate with other cells.

What is a ligand?

A small signaling molecule that sends a signal by binding a specific receptor.

Who can respond to a signal?

Only cells with the matching receptor.

What is a signal transduction pathway?

The sequence of events from signal binding to cellular response.

Four basic parts of a pathway?

Signal, receptor, effector targets, response.

Gap junction vs plasmodesmata?

Animal channels of connexons (about 1.5 nm) vs plant channels through the cell wall with a desmotubule (about 6 nm).

What passes through gap junctions?

Small molecules and ions, not proteins.

Autocrine vs paracrine vs endocrine?

Same cell vs nearby cells by diffusion vs distant cells by blood or lymph.

Which signaling is fastest and shortest-lived?

Paracrine (endocrine is slower but longer-lasting).

What is a pheromone?

A signal between different organisms of the same species.

What happens when a ligand binds a receptor?

The receptor changes shape; binding is reversible and the ligand is unchanged.

Agonist vs antagonist?

Agonist mimics the ligand; antagonist blocks the receptor (caffeine blocks adenosine).

Which ligands use cell-surface receptors?

Large or polar water-soluble ligands (peptides, proteins, small polar molecules).

Which ligands use intracellular receptors?

Small nonpolar ligands such as steroid hormones.

What do intracellular receptors do after binding?

The complex goes to the nucleus and acts as a transcription factor.

Three parts of a cell-surface receptor?

External ligand-binding domain, membrane-spanning region, intracellular domain.

Three types of cell-surface receptors?

Ion channel-linked, enzyme-linked, G protein-linked.

Example of a ligand-gated ion channel?

The acetylcholine receptor (Na+ enters muscle cells).

What does the insulin receptor do?

Tyrosine kinase that phosphorylates itself and targets, raising glucose transporters in the membrane.

How does a G protein turn on?

Alpha subunit swaps GDP for GTP and splits from beta-gamma.

How does a G protein turn off?

Alpha hydrolyzes GTP to GDP and the subunits reassemble.

Divergence vs convergence?

One pathway branching to many targets vs many pathways sharing a target.

What is signal integration?

Merging signals from different receptors so several requirements are met before a response.

Why are cascades useful?

They amplify the signal and give precise control and varied responses.

What does a protein kinase do?

Adds phosphate to serine, threonine or tyrosine, changing a protein's shape and activity.

What is a second messenger?

A small, non-protein, diffusible molecule that relays and amplifies a signal (cAMP, Ca2+, DAG, IP3).

How is cAMP made?

Adenylyl cyclase converts ATP to cAMP.

Order of the epinephrine pathway in liver?

Epinephrine, GPCR, adenylyl cyclase, cAMP, protein kinase A, glycogen breakdown to glucose.

What do growth factors do?

Bind kinase receptors to stimulate cell growth and division.

What is wrong with mutant Ras?

Stuck bound to GTP, so the switch is always on and cells divide continuously.

What is apoptosis and why does it matter?

Programmed cell death that removes damaged, cancerous or unneeded cells and ends signaling.

What is quorum sensing?

Bacterial signaling that triggers gene expression at a threshold cell density.

What are autoinducers?

Signaling molecules bacteria secrete to communicate with their own kind (such as AHL).

Why do Vibrio glow only at high density?

Light is useful only in large numbers (milky sea, squid light organ).

What is the squid-Vibrio relationship?

Mutualistic symbiosis; bacterial glow hides the squid from predators below.