Cell biology

Archaeon

Microscopic organism that is a member of one of the two divisions of prokaryotes; often found in hostile environments such as hot springs or concentrated brine. (*See also* bacterium.)

Bacterium

Microscopic organism that is a member of one of the two divisions of prokaryotes; some species cause disease. The term is sometimes used to refer to any prokaryotic microorganism, although the world of prokaryotes also includes archaea, which are only distantly related to each other. (*See also* archaeon.)

Cell

The basic unit from which a living organism is made; an aqueous solution of chemicals, enclosed by a membrane, that has an ability to self-replicate.

Chloroplast

Specialized organelle in algae and plants that contains chlorophyll and serves as the site for photosynthesis.

Chromosom

Long, threadlike structure composed of DNA and proteins that carries the genetic information of an organism; becomes visible as a distinct entity when a plant or animal cell prepares to divide.

Cytoplasm

Contents of a cell that are contained within its plasma membrane but, in the case of eukaryotic cells, outside the nucleus.

Cytoskeleton

System of protein filaments in the cytoplasm of a eukaryotic cell that gives the cell shape and the capacity for directed movement. Its most abundant components are actin filaments, microtubules, and intermediate filaments.

Cytosol

Contents of the main compartment of the cytoplasm, excluding membrane-enclosed organelles such as endoplasmic reticulum and mitochondria. The cell fraction remaining after membranes, cytoskeletal components, and other organelles have been removed.

DNA

Double-stranded polynucleotide formed from two separate chains of covalently linked deoxyribonucleotide units. It serves as the cell’s store of genetic information that is transmitted from generation to generation.

Electron microscope

Instrument that illuminates a specimen using beams of electrons to reveal and magnify the structures of very small objects, such as organelles and large molecules.

Endoplasmic reticulum (ER)

Labyrinthine membrane-enclosed compartment in the cytoplasm of eukaryotic cells where lipids and proteins are made.

Eukaryote

An organism whose cells have a distinct nucleus and cytoplasm.

Evolution

Process of gradual modification and adaptation that occurs in living organisms over generations.

Fluorescence microscope

Instrument used to visualize a specimen that has been labeled with a fluorescent dye; samples are illuminated with a wavelength of light that excites the dye, causing it to fluoresce.

Genome

The total genetic information carried by all the chromosomes of a cell or organism; in humans, the total number of nucleotide pairs in the 22 autosomes plus the X and Y chromosomes.

Golgi apparatus

Membrane-enclosed organelle in eukaryotic cells that modifies the proteins and lipids made in the endoplasmic reticulum and sorts them for transport to other sites.

Homologous

Describes genes, chromosomes, or any structures that are similar because of their common evolutionary origin. Can also refer to similarities between protein sequences or nucleic acid sequences.

Micrometer

Unit of length equal to one millionth (10^–6) of a meter or 10^–4 centimeter.

Microscope

Instrument for viewing extremely small objects. Some use a focused beam of visible light and are used to examine cells and organelles. Others use a beam of electrons and can be used to examine objects as small as individual molecules.

Mitochondrion

Membrane-enclosed organelle, about the size of a bacterium, that carries out oxidative phosphorylation and produces most of the ATP in eukaryotic cells.

Model organism

A living thing selected for intensive study as a representative of a large group of species. Examples include the mouse (representing mammals), the yeast *Saccharomyces cerevisiae* (representing a unicellular eukaryote), and *Escherichia coli* (representing bacteria).

Nucleus

In biology, refers to the prominent, rounded structure that contains the DNA of a eukaryotic cell. In chemistry, refers to the dense, positively charged center of an atom.

Organelle

A discrete structure or subcompartment of a eukaryotic cell that is specialized to carry out a particular function. Examples include mitochondria and the Golgi apparatus.

Photosynthesis

The process by which plants, algae, and some bacteria use the energy of sunlight to drive the synthesis of organic molecules from carbon dioxide and water.

Plasma membrane

The protein-containing lipid bilayer that surrounds a living cell.

Prokaryote

Major category of living cells distinguished by the absence of a nucleus; includes the archaea and the eubacteria (commonly called bacteria).

Protein

Macromolecule built from amino acids that provides cells with their shape and structure and performs most of their activities.

Protozoan

A free-living, nonphotosynthetic, single-celled, motile eukaryote.

Ribosome

Large macromolecular complex, composed of RNAs and proteins, that translates a messenger RNA into a polypeptide chain.

RNA

Molecule produced by the transcription of DNA; usually single-stranded, it is a polynucleotide composed of covalently linked ribonucleotide subunits. Serves a variety of informational, structural, catalytic, and regulatory functions in cells.

Amphipathic

Having both hydrophobic and hydrophilic regions, as in a phospholipid or a detergent molecule.

Bacteriorhodopsin

Pigmented protein found in abundance in the plasma membrane of the salt-loving archaeon *Halobacterium halobium*; pumps protons out of the cell, fueled by light energy.

Cell cortex

Specialized layer of cytoplasm on the inner face of the plasma membrane. In animal cells, it is rich in actin filaments that govern cell shape and drive cell movement.

Cholesterol

Short, rigid lipid molecule present in large amounts in the plasma membranes of animal cells, where it makes the lipid bilayer less flexible.

Detergent

Soapy substance used to solubilize lipids and membrane proteins.

Fat droplet

Large cluster of hydrophobic fats or oils that forms inside the cells.

Glycocalyx

Protective layer of carbohydrates on the outside surface of the plasma membrane formed by the sugar residues of membrane glycoproteins, proteoglycans, and glycolipids.

Lipid bilayer

Thin pair of closely juxtaposed sheets, composed mainly of phospholipid molecules, that forms the structural basis for all cell membranes.

Membrane domain

Functionally and structurally specialized region in the membrane of a cell or organelle; typically characterized by the presence of specific proteins.

Membrane protein

A protein associated with the lipid bilayer of a cell membrane.

Phosphatidylcholine

Common phospholipid present in abundance in most cell membranes; uses choline attached to a phosphate as its head group.

Phospholipid

A major type of lipid molecule in many cell membranes. Generally composed of two fatty acid tails linked to one of a variety of phosphate-containing polar groups.

Plasma membrane

The protein-containing lipid bilayer that surrounds a living cell.

Saturated

Describes an organic molecule that contains a full complement of hydrogen; in other words, no double or triple carbon–carbon bonds.

Unsaturated

Describes an organic molecule that contains one or more double or triple bonds between its carbon atoms.

Autophagy

Mechanism by which a cell "eats itself," digesting molecules and organelles that are damaged or obsolete.

Clathrin

Protein that makes up the coat of a type of transport vesicle that buds from either the Golgi apparatus (on the outward secretory pathway) or from the plasma membrane (on the inward endocytic pathway).

Coated vesicle

Small membrane-enclosed sac that wears a distinctive layer of proteins on its cytosolic surface. It is formed by pinching-off of a protein-coated region of cell membrane.

Endocytosis

Process by which cells take in materials through an invagination of the plasma membrane, which surrounds the ingested material in a membrane-enclosed vesicle. (*See also* pinocytosis and phagocytosis.)

Endomembrane system

Interconnected network of membrane-enclosed organelles in a eukaryotic cell; includes the endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes, and endosomes.

Endosome

Membrane-enclosed compartment of a eukaryotic cell through which material ingested by endocytosis passes on its way to lysosomes.

Exocytosis

Process by which most molecules are secreted from a eukaryotic cell. These molecules are packaged in membrane-enclosed vesicles that fuse with the plasma membrane, releasing their contents to the outside.

Lysosome

Membrane-enclosed organelle that breaks down worn-out proteins and organelles and other waste materials, as well as molecules taken up by endocytosis; contains digestive enzymes that are typically most active at the acid pH found inside these organelles.

Membrane-enclosed organelle

Any organelle in a eukaryotic cell that is surrounded by a lipid bilayer—for example, the endoplasmic reticulum, Golgi apparatus, and lysosome.

Nuclear envelope

Double membrane surrounding the nucleus. Consists of outer and inner membranes, perforated by nuclear pores.

Nuclear pore

Channel through which selected large molecules move between the nucleus and the cytoplasm.

Peroxisome

Small membrane-enclosed organelle that contains enzymes that degrade lipids and destroy toxins.

Phagocytic cell

A cell such as a macrophage or neutrophil that is specialized to take up particles and microorganisms by phagocytosis.

Phagocytosis

The process by which particulate material is engulfed ("eaten") by a cell. Prominent in predatory cells, such as *Amoeba proteus*, and in cells of the vertebrate immune system, such as macrophages.

Pinocytosis

Type of endocytosis in which soluble materials are taken up from the environment and incorporated into vesicles for digestion. (Literally, "cell drinking.")

Rab protein

One of a family of small GTP-binding proteins present on the surfaces of transport vesicles and organelles that serves as a molecular marker to help ensure that transport vesicles fuse only with the correct membrane.

Receptor-mediated endocytosis

Mechanism of selective uptake of material by animal cells in which a macromolecule binds to a receptor in the plasma membrane and enters the cell in a clathrin-coated vesicle.

Rough endoplasmic reticulum

Region of the endoplasmic reticulum associated with ribosomes and involved in the synthesis of secreted and membrane-bound proteins.

Secretion

Production and release of a substance from a cell.

Secretory vesicle

Membrane-enclosed organelle in which molecules destined for secretion are stored prior to release.

Signal sequence

Amino acid sequence that directs a protein to a specific location in the cell, such as the nucleus or mitochondria.

SNARE

One of a family of membrane proteins responsible for the selective fusion of vesicles with a target membrane inside the cell.

Tethering protein

Filamentous transmembrane protein involved in the docking of transport vesicles to target membranes.

Transport vesicle

Membrane vesicle that carries proteins from one intracellular compartment to another—for example, from the endoplasmic reticulum to the Golgi apparatus.

Unfolded protein response (UPR)

Molecular program triggered by the accumulation of misfolded proteins in the endoplasmic reticulum. Allows cells to expand the endoplasmic reticulum and produce more of the molecular machinery needed to restore proper protein folding and processing.

Vesicular transport

Movement of material between organelles in the eukaryotic cell via membrane-enclosed vesicles.

Adaptation

Adjustment of sensitivity following repeated stimulation; allows a cell or organism to register small changes in a signal despite a high background level of stimulation.

Adenylyl cyclase

Enzyme that catalyzes the formation of cyclic AMP from ATP; an important component in some intracellular signaling pathways.

Ca2+/calmodulin-dependent protein kinase (CaM-kinase)

Enzyme that phosphorylates target proteins in response to an increase in Ca2+ ion concentration through its interaction with the Ca2+-binding protein calmodulin.

Calmodulin

Small Ca2+-binding protein that modifies the activity of many target proteins in response to changes in Ca2+ concentration.

Cell signaling

The molecular mechanisms by which cells detect and respond to external stimuli and send messages to other cells.

Cyclic AMP

Small intracellular signaling molecule generated from ATP in response to hormonal stimulation of cell-surface receptors.

Cyclic-AMP-dependent protein kinase (PKA)

Enzyme that phosphorylates target proteins in response to a rise in intracellular cyclic AMP concentration.

Diacylglycerol (DAG)

Small messenger molecule produced by the cleavage of membrane inositol phospholipids in response to extracellular signals. Helps activate protein kinase C.

Enzyme-coupled receptor

Transmembrane protein that, when stimulated by the binding of a ligand, activates an intracellular enzyme (either a separate enzyme or part of the receptor itself).

Extracellular signal molecule

Any molecule present outside the cell that can elicit a response inside the cell when the molecule binds to a receptor.

G protein

A membrane-bound GTP-binding protein involved in intracellular signaling; composed of three subunits, this intermediary is usually activated by the binding of a hormone or other ligand to a transmembrane receptor.

G-protein-coupled receptor (GPCR)

Cell-surface receptor that associates with an intracellular trimeric GTP-binding protein (G protein) after activation by an extracellular ligand. These receptors are embedded in the membrane by seven transmembrane α helices.

GTP-binding protein

Intracellular signaling protein whose activity is determined by its association with either GTP or GDP. Includes both trimeric G proteins and monomeric GTPases, such as Ras.

Hormone

Extracellular signal molecule that is secreted and transported via the bloodstream (in animals) or the sap (in plants) to target tissues on which it exerts a specific effect.

Inositol 1,4,5-trisphosphate (IP3)

Small intracellular signaling molecule that triggers the release of Ca2+ from the endoplasmic reticulum into the cytosol; produced when a signal molecule activates a membrane-bound protein called phospholipase C.

Inositol phospholipid

Minor lipid component of plasma membranes that plays a part in signal transduction in eukaryotic cells; cleavage yields two small messenger molecules, IP3 and diacylglycerol.

Iintracellular signaling pathway

A set of proteins and small-molecule second messengers that interact with each other to relay a signal from the cell membrane to its final destination in the cytoplasm or nucleus.

Ion-channel-coupled receptor

Transmembrane receptor protein or protein complex that opens in response to the binding of a ligand to its external face, allowing the passage of a specific inorganic ion.

Local mediator

Secreted signal molecule that acts at a short range on adjacent cells.

MAP kinase

Mitogen-activated protein kinase. Signaling molecule that is the final kinase in a three-kinase sequence called the MAP-kinase signaling module.

MAP-kinase signaling module

Set of three functionally interlinked protein kinases that allows cells to respond to extracellular signal molecules that stimulate proliferation; includes a mitogen-activated protein kinase (MAP kinase), a MAP kinase kinase, and a MAP kinase kinase kinase.

Molecular switch

Intracellular signaling protein that toggles between an active and inactive state in response to receiving a signal.

Monomeric GTPase

Small, single-subunit GTP-binding protein. Proteins of this family, such as Ras and Rho, are part of many different signaling pathways.

Neurotransmitter

Small signaling molecule secreted by a nerve cell at a synapse to transmit information to a postsynaptic cell. Examples include acetylcholine, glutamate, GABA, and glycine.

Nitric oxide (NO)

Locally acting gaseous signal molecule that diffuses across cell membranes to affect the activity of intracellular proteins.

Nuclear receptor

Protein inside a eukaryotic cell that, on binding to a signal molecule, enters the nucleus and regulates transcription.

Phosphoinositide 3-kinase (PI 3-kinase)

Enzyme that phosphorylates inositol phospholipids in the plasma membrane, which generates docking sites for intracellular signaling proteins that promote cell growth and survival.

Phospholipase C

Enzyme associated with the plasma membrane that generates two small messenger molecules in response to activation.

Protein kinase

Enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein.