Cell Biology: Key Terms and Glossary

An acid hydrolase is a lysosomal digestive enzyme, such as a protease, nuclease, lipase, or glycosidase, that works best near pH 4.5–5 and is far less active at the near-neutral pH of the cytosol.

Akt, also called protein kinase B, is brought to the membrane by PIP₃ and activated there, after which it promotes survival by inhibiting pro-apoptotic proteins and promotes growth through mTOR signalling.

Amphipathic describes a molecule with a hydrophilic part and a hydrophobic part, the property that makes membrane lipids seal into bilayers rather than leave an edge of tails in water.

Anaphase A is the movement of separated chromatids towards the poles as kinetochore microtubules shorten, the chromatid staying attached while tubulin is lost at the kinetochore and the pole.

Anaphase B is the movement that pushes and pulls the spindle poles further apart, by sliding of overlapping interpolar microtubules and by traction on astral microtubules.

Anchorage dependence is the requirement that a normal cell be attached to extracellular matrix in order to proliferate and survive, a requirement transformed cells no longer show.

Annexin V binds phosphatidylserine once that lipid is on the outer leaflet, marking an apoptotic cell whose plasma membrane is still intact rather than one that has already ruptured.

Apoptosis is programmed, ATP-dependent cell death carried out by caspases, in which the cell shrinks and is parcelled into membrane-bounded bodies that phagocytes clear without inflammation because the contents do not spill.

The apoptosome is the cytosolic complex in which cytochrome c, together with dATP, drives Apaf-1 to oligomerise and recruit procaspase-9, starting the executioner caspases of the intrinsic pathway.

An apoptotic body is a membrane-bounded piece blebbed from an apoptotic cell, holding the contents in until a phagocyte engulfs it.

An aquaporin is a channel that passes water rapidly and excludes protons, which is how tissues that must move water quickly, such as kidney collecting duct and red blood cells, raise their permeability.

The axoneme is the microtubule core of a eukaryotic cilium or flagellum; in motile ones it is nine outer doublets around a central pair, and dynein arms on one doublet walk along the next.

The barbed end is the plus end of an actin filament, where subunits add faster than they do at the pointed end.

The basal lamina is the thin matrix under epithelia and around muscle cells, fat cells, and Schwann cells, built chiefly from perlecan, a proteoglycan that carries heparan sulphate, together with nidogen, laminin, and type IV collagen.

Bax is a pro-apoptotic effector that, with Bak, oligomerises in the mitochondrial outer membrane and lets cytochrome c out once anti-apoptotic proteins no longer hold the membrane closed.

Bi-orientation is stable attachment under tension to opposite spindle poles, of the two sister chromatids in mitosis and of the two homologues in a meiosis I bivalent.

A cadherin is a Ca2+-dependent adhesion protein that binds the same kind of cadherin on the neighbouring cell, classical cadherins at adherens junctions and desmosomal cadherins at desmosomes.

Calnexin is an ER chaperone that binds a glycoprotein while one glucose is still on its N-linked sugar, keeping the protein in a cycle that gives it further chances to fold.

A carrier binds its solute on one side of the membrane, changes shape, and releases it on the other without opening a continuous pore; the cycle is passive when cargo only moves downhill and is secondary active transport when a second solute's gradient pays for uphill cargo.

A caspase is a cysteine protease, stored as an inactive zymogen, that cuts proteins after aspartate residues; initiator caspases activate executioner caspases, and the extrinsic and intrinsic death pathways meet in this cascade.

Catalase is the peroxisomal enzyme that decomposes hydrogen peroxide, produced by the organelle's oxidases, into water and oxygen, keeping that oxidant inside the peroxisome.

The cell plate is the new cross-wall of a dividing plant cell, formed when Golgi-derived vesicles fuse at the midplane under the guidance of the phragmoplast, the route used because actin–myosin pinching cannot cleave a walled cell.

Cell theory holds that an organism is composed of cells and of materials those cells have made, that structure and function have the cell as their basic unit, and that a new cell appears only by division of a cell that already exists.

Cellulose supplies the tension-resisting rods of the plant primary wall: microfibrils of β-1,4-glucan extruded at the cell surface by cellulose-synthase complexes as those complexes move in the membrane.

The centrosome organises microtubules in a typical animal cell: a pair of centrioles lies in pericentriolar material, and γ-tubulin rings there seed microtubules with their minus ends at the centre. Flowering plants, and many fungi, assemble spindles without centrioles, so this organelle is not required for mitosis in every eukaryote.

A channel is a gated pore that lets ions or water move down their electrochemical gradient, much faster than a carrier, and it spends gradients rather than creating them.

Chemiosmosis is the coupling in which electron transport builds a proton gradient across a sealed membrane and the return of those protons through ATP synthase drives ATP synthesis.

A chiasma is the visible join left where crossing over has exchanged segments between non-sister chromatids, and with cohesin along the arms it holds homologues together until anaphase I.

Cisternal maturation is the account of Golgi transport, favoured for large cargo, in which a cisterna itself moves from the cis face towards the trans face and matures, while resident enzymes recycle backwards in vesicles.

Clathrin is the coat on vesicles leaving the trans-Golgi network for endosomes and on pits that take membrane into the cell from the surface, and it is not the COPI coat or the COPII coat.

A claudin is the principal transmembrane protein of a tight junction, sealing the space between epithelial cells and fencing the membrane so that apical proteins do not drift into the basolateral domain.

Cohesin is the complex that holds sister chromatids together along their length and at the centromere until separase cuts it.

Collagen is the main tensile protein of the animal extracellular matrix, a triple helix of Gly-X-Y chains whose proline hydroxylation needs vitamin C; fibrillar collagens pack into fibres, whereas type IV forms the network of the basal lamina.

The confocal pinhole is a small aperture placed conjugate to the focal plane, just before the detector, so that in-focus fluorescence passes and light from other depths is blocked; the optical section that results does not escape the diffraction limit.

A connexin is the protein from which a vertebrate gap junction is built: six subunits ring a connexon, connexons of two cells dock to open a shared pore, and that pore admits ions and metabolites only up to about 1,000 daltons.

Constitutive secretion is the default path leaving the trans-Golgi network, a steady flow of vesicles that delivers folded soluble proteins and ordinary membrane proteins to the cell surface without a storage step.

Contact inhibition is the restraint that makes an ordinary cell cease proliferation once it meets its neighbours; transformed cells lack the restraint and keep dividing in piles.

The contractile ring is a cortical belt of actin and myosin II, positioned in the plane of the old metaphase plate, whose constriction pinches an animal cell in two.

Cristae are the folds of the inner mitochondrial membrane that carry the respiratory chain and ATP synthase, and they are more extensive in tissues with a heavier respiratory demand.

Cyclin D is the G1 cyclin that, with CDK4 or CDK6, answers growth factors by beginning to phosphorylate Rb and thereby partly releasing E2F.

Differential centrifugation separates particles by pelleting time as the force is stepped up, so nuclei come down before mitochondria and microsomes later still, and each pellet is enriched rather than pure.

The diffraction limit is the smallest separation at which a microscope can show two objects as two, given by Abbe as d = λ/(2 NA) and about 0.2 µm for visible light with a high-NA lens.

Dolichol is the lipid in the ER membrane on which the precursor oligosaccharide of N-linked glycosylation is assembled before transfer to the protein.

A domain is one of the three primary divisions these notes use, Bacteria, Archaea, and Eukarya, set apart by membrane chemistry, the machinery that handles genetic information, and the presence or absence of a nucleus.

Dynamic instability is the behaviour of a microtubule that grows while a GTP cap protects the plus end and then shrinks abruptly if hydrolysis catches the tip and the protofilaments peel outwards.

Dynamin is the GTPase that polymerises around the neck of a clathrin-coated pit at the plasma membrane and pinches the vesicle free.

Dynein walks towards the minus end of a microtubule, returning axonal cargo to the cell body, and on the axoneme the same walking bends the cilium because the doublets are linked and cannot simply slide apart.

The early endosome is the first sorting station after endocytosis, held near pH 6 by a proton pump, where ligands such as LDL leave their receptors and the receptors can return to the cell surface.

Endocrine signalling sends a hormone through the bloodstream to act on target cells far from the cell that released it.

Endosymbiosis is the origin of mitochondria from an alphaproteobacterium and of chloroplasts from a later cyanobacterium, which is why both organelles keep a double membrane, a circular chromosome, and 70S ribosomes, divide by fission, and cannot be built from scratch by the host.

A eukaryote encloses its chromosomes in a nuclear envelope, partitions the cytoplasm with membrane-bounded organelles, and uses 80S ribosomes in the cytosol, with 70S ribosomes retained in mitochondria and chloroplasts.

Flow cytometry measures cells one by one as they pass a laser in a fine stream, taking forward and side scatter as rough measures of size and internal complexity and taking fluorescence from dyes or labelled antibodies.

The fluid mosaic, proposed by Singer and Nicolson in 1972, pictures the membrane as a two-dimensional liquid of lipids with proteins embedded in it rather than merely coating the surface; sideways diffusion is the default, and the cell halts selected proteins by linking them to the cytoskeleton or the matrix, or by a tight-junction fence.

A focal adhesion is the integrin junction that ties actin stress fibres to the extracellular matrix and that strengthens when force is applied across it.

Geminin blocks Cdt1, and thereby blocks any new loading of MCM helicase, from S phase onward; only when geminin is destroyed as mitosis ends, and CDK activity has fallen, can origins be licensed again.

Glutaraldehyde is a dialdehyde fixative used in electron microscopy because it ties proteins into a dense network; those same links usually destroy the epitopes antibodies need, so fluorescence microscopy generally chooses a milder fixative.

Gram-negative describes a bacterial envelope with a thin peptidoglycan layer plus an outer membrane that bears LPS, an architecture that does not retain the crystal-violet complex and so stains pink.

Gram-positive describes a bacterial envelope with a thick peptidoglycan wall and no outer membrane, an architecture that retains the crystal-violet complex and so stains purple.

A hemidesmosome is the stable junction that anchors intermediate filaments of an epithelium to the basal lamina through the integrin α6β4.

A hormone-response element is the DNA sequence bound by the intracellular receptor for a steroid, thyroid hormone, retinoic acid, or vitamin D after hormone binding, and that binding changes transcription of the associated genes.

Importin is the nuclear-import receptor, often importin β working with the adaptor importin α on a classical NLS, which ferries cargo through the pore and releases it when nuclear Ran-GTP binds.

Independent assortment means each bivalent at metaphase I can face either spindle pole without regard to the other bivalents, so maternal and paternal chromosomes can be packaged in 2ⁿ ways, n being the haploid number, even before crossing over adds further variety.

An integrin is a heterodimer of an α subunit and a β subunit that binds extracellular matrix outside the cell and the cytoskeleton inside, and that also reports attachment as information used in decisions to divide or to die.

Isopycnic centrifugation is spun long enough for every particle to settle at the gradient position that matches its own buoyant density, and once there it stays, so equal-density particles co-band even when their sizes differ.

Kinesin is a microtubule motor that in the usual case walks towards the plus end, which in an axon, where plus ends point away from the cell body, carries cargo out to the synapse.

The kinetochore is the protein machine built on the centromere that binds spindle microtubules and through which the chromosome is moved.

A lamellipodium is the broad protrusion at the leading edge of a crawling cell, pushed outwards by a branched actin network nucleated by Arp2/3.

The LDL receptor binds low-density lipoprotein in clathrin-coated pits, releases it in the early endosome, and returns to the plasma membrane while the lipoprotein goes on to the lysosome.

Leaflet asymmetry is the difference in lipid composition between the two faces of a bilayer: ATP-using flippases retain phosphatidylserine on the cytosolic face, and that same lipid on the external face is a signal, the one apoptotic cells display to phagocytes.

Licensing is the loading of inactive MCM helicase onto an origin in late mitosis and G1, while CDK activity is low, and that same high CDK activity later blocks a second loading so the origin fires only once per cycle.

Lignin is the phenolic polymer laid into secondary plant walls after growth has stopped, making those walls rigid and waterproof.

Mannose 6-phosphate is the tag added to lysosomal hydrolases in the cis-Golgi so a receptor in the trans-Golgi network can send them to endosomes, and if the tag is missing, as in I-cell disease, the hydrolases are secreted instead.

A MAP kinase is the last kinase in a three-kinase cascade; in the common growth-factor pathway that kinase is ERK, which phosphorylates cytosolic targets and transcription factors, including those that induce cyclin D.

A marker enzyme is an activity used to name the organelle enriched in a fraction: catalase points to peroxisomes, acid phosphatase to lysosomes, and cytochrome c oxidase to mitochondria.

Membrane potential is the voltage produced by unequal charge across the plasma membrane; in a resting animal cell it is typically about −40 to −90 mV, inside negative, largely because K+ leaves through open channels while the sodium pump continually restores the gradients that this leak spends.

The middle lamella is the pectin-rich layer that cements the walls of neighbouring plant cells to one another.

A model organism is a species chosen because a short generation time, tractable genetics, a transparent body, or a large cell makes a cell-biological question easier, while the shared core machinery lets the answer travel.

N-linked glycosylation attaches, during translocation, a preformed oligosaccharide from dolichol onto an Asn-X-Ser/Thr asparagine (X not proline) that faces the ER lumen, so cytosolic proteins do not receive this sugar.

Necrosis is uncontrolled death after acute injury, in which the cell swells, the plasma membrane ruptures, and the spilled contents inflame the surrounding tissue, and caspases are not the executors.

The Nernst potential is the membrane voltage at which the chemical gradient of one ion is balanced by the electrical force on that ion, about −90 mV for potassium in a typical animal cell.

The niche is the local set of neighbouring cells, matrix, and signals that keeps a stem cell from differentiating, so a daughter that leaves those cues specialises.

Nondisjunction is a failure of chromosomes to separate in meiosis, so a gamete gains or lacks a chromosome and fertilisation can produce aneuploidy such as trisomy 21.

The nuclear lamina is a mesh of lamin intermediate filaments lining the inner nuclear membrane, supporting the envelope and binding chromatin.

The nucleoid is the region of a prokaryotic cell that contains the chromosome, usually one circular DNA molecule compacted by supercoiling and nucleoid-associated proteins rather than by eukaryotic histone octamers, and it is not enclosed by a membrane.

The nucleolus is the nuclear factory assembled on the chromosomal repeats of ribosomal RNA genes, where that RNA is transcribed and processed and ribosomal subunits are built, becoming active only in the cytosol.

Numerical aperture, NA = n sin θ, increases with the refractive index n of the medium in front of the lens and with the angular width of the light cone the lens can collect, and this value, not magnification alone, fixes how fine a detail can be separated.

An oncogene is a hyperactive allele of a proto-oncogene, a normal gene whose product encourages division or survival, produced by mutation, extra copies, or a translocation; a single altered copy suffices because the new product is itself too active.

Osmium tetroxide binds unsaturated lipids during preparation for electron microscopy and adds electron density, which is why membranes appear as dark lines in the image.

Paracrine signalling is chemical communication through the extracellular fluid to nearby cells, and a chemical synapse is a fast, spatially private form of it.

Pectin is the group of acidic polysaccharides that gel with water in the plant wall and that make up much of the cement in the middle lamella.

Peptidoglycan, which archaea do not make, is the osmotic brace of most bacteria: glycan chains in which N-acetylglucosamine alternates with N-acetylmuramic acid, stitched by short peptides, so the wall rather than the plasma membrane takes the turgor load.

Phase contrast makes an unstained living cell visible by converting small delays in the light wave into brighter and darker regions, and thick objects are ringed by a glow that hides their edges.

Plasmodesmata are plasma-membrane-lined channels through plant cell walls, each with a tubule of endoplasmic reticulum inside, and they can pass some proteins and RNAs, a larger cargo than a gap junction allows.

The positive-inside rule is the tendency of positively charged flanks of a transmembrane helix to stay on the cytosolic side of the membrane, which helps set which way the protein faces.

Potency is the range of cell types a stem cell's progeny can still become, from totipotent cells that can make the embryo and the extra-embryonic tissues, through pluripotent and multipotent cells, to unipotent cells limited to one differentiated type.

Prokaryote names a grade of cell plan rather than one evolutionary lineage: archaea and bacteria, whose DNA occupies a nucleoid and which lack a nucleus together with mitochondria, chloroplasts, endoplasmic reticulum, and Golgi.

Protein kinase A is the kinase whose catalytic subunits are freed when cAMP binds the regulatory subunits, so a rise in cAMP is read as phosphorylation of metabolic enzymes and of transcription factors.

Protein kinase C is the kinase that DAG and Ca2+ turn on at the membrane, downstream of phospholipase C, in the control of short-term responses such as secretion and smooth-muscle contraction.

A proteoglycan is a core protein carrying long, negatively charged glycosaminoglycan chains that bind water and allow the extracellular matrix to resist compression.

The proton-motive force is the electrochemical proton gradient across a sealed energy-transducing membrane, the sum of a membrane potential and a pH difference, which ATP synthase uses to make ATP.

A Rab is a small GTPase particular to one vesicle or organelle population that, when GTP is bound, recruits tethering proteins and so holds the vesicle near the correct target membrane.

Ran is the small GTPase of nuclear transport, mostly Ran-GTP in the nucleus and mostly Ran-GDP in the cytosol, and that gradient is what drives import and export in opposite directions.

Ras is a small GTPase held at the membrane by a lipid anchor and loaded with GTP by Sos downstream of many growth-factor receptors; a mutation that stops GTP hydrolysis leaves it active without ligand and makes an oncogene of the normal gene.

Rate-zonal centrifugation separates particles by their speed of travel through a gradient and must be stopped while they are still moving, before they reach the positions of their buoyant densities.

A receptor tyrosine kinase, once its kinase domains are brought into contact, phosphorylates tyrosines on itself and so creates docking sites for SH2 proteins, rather than having to modify every downstream target directly. The insulin receptor is an exception to ligand-driven assembly: it is already a dimer held by disulphide bonds, and insulin switches it on by reshaping that dimer.

Regulated secretion stores selected products, among them insulin, digestive enzymes, and peptide neurotransmitters, in dense granules, and allows those granules to fuse at the cell surface only after a cue, most often a rise in cytosolic Ca2+.

The restriction point, called Start in yeast, is the late-G1 commitment of an animal cell: lose growth factors before it and the cell enters G0, lose them afterwards and the cycle still runs to the end.

Rho-family GTPases divide the actin jobs of crawling: Rac builds the branched sheet at the front of the cell, Cdc42 builds the thin filopodia that probe ahead, and Rho builds the stress fibres that pull.

Rough ER is the region of endoplasmic reticulum whose cytosolic face carries ribosomes, docked only while they are making a protein with an ER signal sequence, and it is the entrance to the secretory pathway.

Rubisco is the enzyme in the chloroplast stroma that adds CO₂ to ribulose 1,5-bisphosphate to fix carbon, and that also reacts with O₂, a reaction that starts photorespiration and wastes carbon.

The sarcomere is one repeating contractile segment of striated muscle: thin filaments of actin run from the Z disc with the barbed end at that disc, and thick filaments of myosin occupy the centre, the A band.

Secondary active transport drives a cargo up its electrochemical gradient by linking that movement to Na+ or H+ flowing down a gradient which a pump has already established.

Securin is the inhibitor that holds separase inactive until APC/C–Cdc20 has securin ubiquitinated and the proteasome has destroyed it.

Separase is the protease that cleaves cohesin once securin has been removed, and that cleavage lets sister chromatids part and begins anaphase.

Shugoshin protects centromeric cohesin from cleavage during meiosis I, so sister chromatids stay together when the homologues separate, and the protection is lifted for meiosis II.

A signal sequence is a short address in a polypeptide that a receptor at the destination compartment recognises; the common ER version is hydrophobic, sits at the N-terminus, and is cut off in the lumen, whereas a chain that carries no address remains cytosolic.

A sister chromatid is one of the two copies of a chromosome made by replication, kept paired with the other copy by cohesin until that cohesin is cleaved.

Sliding filament is the mechanism of muscle shortening in which actin and myosin filaments increase their overlap without themselves becoming shorter, which is why the A band stays the same length as the sarcomere shortens.

Smooth ER is the tubular, ribosome-free region of the endoplasmic reticulum, used for lipid synthesis, for cytochrome P450 detoxification, and for storage of Ca2+, including the sarcoplasmic reticulum of muscle.

The spindle-assembly checkpoint is the wait imposed by kinetochores that lack microtubules or tension, blocking Cdc20 so APC/C cannot start anaphase, and it is a surveillance pathway rather than the spindle itself.

The Stokes shift is the difference by which the light a fluorophore emits is of longer wavelength than the light it absorbed, letting a fluorescence microscope collect emission against a dark field.

A stop-transfer sequence is a hydrophobic stretch that slips sideways out of the Sec61 pore, remains in the membrane as a single spanning helix, and leaves the ribosome completing the rest of the chain on the cytosolic side.

A Svedberg (S) is 10⁻¹³ seconds, the unit of sedimentation coefficient, meaning how fast a particle moves in a unit centrifugal field in a stated solvent. Those values cannot be added, because the shape changes when parts join: ribosomal subunits of 40S and 60S sediment as an 80S ribosome, not as 100S.

Synapsis is the lengthwise pairing of homologous chromosomes during prophase I of meiosis, stabilised by the synaptonemal complex, a pairing mitosis does not perform.

The Tat pathway is the route across the thylakoid membrane that carries proteins already folded, recognised by a twin-arginine motif, unlike the Sec-type thylakoid route that threads unfolded chains.

A thylakoid is an internal membrane of the chloroplast, stacked in places as grana, on which the light reactions pump protons into the lumen so that ATP synthase can make ATP on the stromal side.

A transit peptide is the cleavable N-terminal signal that directs a nuclear-encoded protein into the chloroplast stroma; it is positively charged, as a mitochondrial presequence is, but chloroplast receptors distinguish the two.

Treadmilling is steady subunit flux through an actin filament when free monomers sit between the two ends' critical concentrations: addition wins at the barbed end and loss wins at the pointed end.

Troponin is the Ca2+-binding complex on the thin filament of striated muscle that, when Ca2+ binds, shifts tropomyosin and uncovers myosin-binding sites on actin. Smooth muscle has no troponin and switches myosin on by phosphorylation of its regulatory light chain instead.

A tumour suppressor encodes a brake on division or a promoter of repair or of apoptosis, Rb, p53, and PTEN being the examples to remember, and the brake usually fails only after both copies are gone.

The unfolded-protein response is how the ER sensors IRE1, PERK, and ATF6 answer a backlog of unfolded protein: bulk translation is slowed, more chaperones are made, and a stress that does not ease can push the cell into apoptosis.

Zellweger syndrome is a peroxisome-biogenesis disease caused by mutations in PEX genes: the enzymes are still made, but import fails and the organelle is empty or absent.