Cell Biology: Membrane Dynamics, Transport, Bioenergetics, and Organelle Trafficking

Comprehensive vocabulary flashcards covering membrane structure, active and passive transport, glycolysis, the citric acid cycle, mitochondrial and chloroplast bioenergetics, photosynthesis, and intracellular protein trafficking and sorting across all 14 lecture sources.

Lipid Bilayer

The two-layered sheet of lipid molecules that forms the structural basis of all biological membranes, consisting of two opposed leaflets with hydrophobic hydrocarbon tails facing inward and hydrophilic ionic heads facing outward.

Amphipathic

The chemical property of molecules possessing both a hydrophilic (water-soluble/polar) region and a hydrophobic (water-insoluble/nonpolar) region, characteristic of membrane phospholipids, cholesterol, and detergents like SDS.

Micelle

A spherical lipid aggregate formed spontaneously in water by single-tailed amphipathic molecules, in which the hydrophobic tails cluster together in the interior to exclude water while hydrophilic heads face the surrounding aqueous environment.

Liposome

A hollow, spherical artificial vesicle enclosed by a continuous phospholipid bilayer, forming spontaneously in aqueous solutions to eliminate exposed hydrophobic edges in an energy-conserving manner.

Lateral Diffusion

The rapid two-dimensional movement of lipids and embedded proteins drifting sideways, forward, and backward within the plane of a single membrane leaflet.

Transverse Diffusion

The extremely rare movement (occurring naturally approximately once a month per lipid) in which a membrane lipid flips from one monolayer of the bilayer to the opposing monolayer.

Flippases

Membrane-bound active enzymes that catalyze transverse diffusion by selectively transferring flipped phospholipids back to their designated membrane face to maintain lipid bilayer asymmetry.

Membrane Fluidity

The ease of lateral movement of molecules within the lipid bilayer, determined primarily by temperature, hydrocarbon tail length, the degree of unsaturation (double bonds), and sterol content.

Cholesterol

A short, rigid, amphipathic sterol that constitutes approximately $20\%$ of the lipids in typical human plasma membranes, acting to fill spaces between kinked unsaturated phospholipid tails and stiffen the bilayer.

Bacteriorhodopsin

A light-driven transmembrane proton pump found in the archaeal extremophile Halobacterium halobium that harnesses energy from sunlight to pump protons ($H^+$) out of the cell to keep the internal pH neutral.

Retinal

A non-protein, light-absorbing purple cofactor bound in the center of bacteriorhodopsin that alters its conformation upon absorbing a single photon of light to mechanically translocate a proton across the membrane.

Cell Cortex

A supporting meshwork of fibrous proteins attached to the cytosolic surface of the plasma membrane via transmembrane proteins, providing structural stability, shape, and mechanical resilience to the fragile lipid film.

Spectrin

A long, flexible, rod-shaped protein that forms the primary filamentous structural scaffolding of the red blood cell cortex, mutations in which lead to cell shape defects and anemia.

Membrane Domains

Functionally and compositionally specialized regions of a biological membrane generated by confining specific proteins through intracellular cortex tethering, extracellular matrix binding, or physical diffusion barriers.

Glycocalyx

A protective, lubricated, and electronegative carbohydrate layer on the outer surface of animal cells formed by the oligosaccharide side chains of membrane glycolipids, glycoproteins, and proteoglycans.

Lectins

Specialized proteins that recognize and bind with high affinity to specific oligosaccharide chains on cell-surface glycoproteins and glycolipids, mediating cellular adhesion and recognition processes.

Transporter Proteins

Membrane transport proteins containing moving parts that undergo cyclical conformational changes to shuttle specific solutes across the lipid bilayer via high-specificity binding sites.

Channel Proteins

Transmembrane proteins that form continuous, open hydrophilic pores allowing specific inorganic ions or small solutes to passively diffuse across the membrane down their electrochemical gradient without major conformational shifts.

KIN Mnemonic

A memory aid indicating that potassium ($K^+$) is maintained at a significantly higher concentration inside ($\text{IN}$) the cell compared to outside the cell.

Electrochemical Gradient

The combined net driving force that determines the passive transport of an ion across a membrane, composed of its concentration (chemical) gradient and the electrical potential across the membrane.

Facilitated Diffusion

A form of passive transport in which polar or charged solutes cross the lipid bilayer down their concentration or electrochemical gradient with the assistance of specialized transport proteins without metabolic energy expenditure.

Active Transport

The movement of a solute across a biological membrane against its electrochemical or concentration gradient, requiring an input of energy such as ATP hydrolysis, light absorption, or ion coupling.

Coupled Transporters

Membrane transport proteins that link the thermodynamically favorable downhill flow of one solute along its gradient to the uphill movement of a co-transported solute against its gradient.

Symporter

A coupled co-transporter that moves two different solute species across the biological membrane simultaneously in the exact same physical direction.

Antiporter

A coupled co-transporter that moves two different solute species across the biological membrane simultaneously in opposite physical directions.

$Na^+-K^+$ Pump

An ATP-driven primary active transport pump ($Na^+/K^+\text{-ATPase}$) that hydrolyzes ATP to export three $Na^+$ ions and import two $K^+$ ions per cycle, consuming roughly $30\%$ of a cell's total ATP budget.

Aquaporins

Specialized transmembrane channel proteins that selectively accelerate the passive diffusion of water molecules across biological membranes during osmosis.

Membrane Potential

The electrical voltage difference generated across a biological membrane due to localized imbalances in positive and negative charges, typically measuring between $-20\,\text{mV}$ and $-200\,\text{mV}$ at rest inside the cell.

Voltage-Gated Channels

Ion channels whose probability of opening and closing is directly governed by changes in the electrical membrane potential sensed by specialized voltage-sensor domains within the protein.

Ligand-Gated Channels

Ion channels that open or close in response to the specific non-covalent binding of an extracellular or intracellular chemical messenger molecule.

Stress-Gated Channels

Mechanosensitive ion channels whose opening and closing states are regulated by physical mechanical tension, pressure, or movement applied to the membrane or protein.

Substrate-Level Phosphorylation

The enzymatic transfer of a high-energy phosphate group directly from a phosphorylated metabolic intermediate to ADP, producing ATP without requiring an electron transport chain.

Oxidative Phosphorylation

The membrane-bound process in which ATP is synthesized from ADP and inorganic phosphate using energy derived from the electron transport chain and a transmembrane electrochemical proton gradient.

Glycolysis

A ubiquitous ten-step cytosolic pathway that breaks down one molecule of six-carbon glucose into two molecules of three-carbon pyruvate, generating a net of $2\,\text{ATP}$ and $2\,\text{NADH}$ without consuming oxygen.

Hexokinase

The initial glycolytic enzyme that phosphorylates glucose using one molecule of ATP to yield glucose-6-phosphate, trapping the negatively charged sugar inside the cell.

Phosphofructokinase-1

The key irreversible, allosterically regulated enzyme of glycolysis that consumes ATP to convert fructose-6-phosphate into fructose-1,6-bisphosphate in step 3.

Aldolase

The glycolytic enzyme in step 4 that cleaves the six-carbon sugar fructose-1,6-bisphosphate into two distinct three-carbon phosphorylated sugars: dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P).

Glyceraldehyde-3-Phosphate Dehydrogenase

The enzyme in step 6 of glycolysis that oxidizes glyceraldehyde-3-phosphate, reduces $NAD^+$ to $\text{NADH}$, and attaches an inorganic phosphate to form 1,3-bisphosphoglycerate.

Pyruvate Kinase

The final irreversible enzyme of glycolysis in step 10 that transfers a high-energy phosphate from phosphoenolpyruvate (PEP) to ADP, forming pyruvate and ATP.

Fermentation

An anaerobic metabolic pathway that regenerates $NAD^+$ from $\text{NADH}$ in the absence of oxygen to sustain glycolysis, reducing pyruvate to lactate in human muscle or to ethanol and $CO_2$ in yeast.

Lactate Dehydrogenase

A reversible enzyme that reduces pyruvate into lactate while oxidizing $\text{NADH}$ to $NAD^+$ under anaerobic conditions, clinically elevated in tissue ischemia or myocardial infarction.

Pyruvate Dehydrogenase Complex

A giant multi-enzyme complex located in the mitochondrial matrix that oxidatively decarboxylates pyruvate into acetyl-CoA, generating $CO_2$ and $\text{NADH}$.

Citric Acid Cycle

An eight-step cyclic pathway in the mitochondrial matrix that completely oxidizes the acetyl group of acetyl-CoA into two molecules of $CO_2$, producing $3\,\text{NADH}$, $1\,\text{FADH}_2$, and $1\,\text{GTP/ATP}$ per turn.

Citrate Synthase

The initiating enzyme of the citric acid cycle that condenses four-carbon oxaloacetate (OAA) with two-carbon acetyl-CoA to synthesize six-carbon citrate, allosterically inhibited by ATP, $\text{NADH}$, and succinyl-CoA.

Aconitase

The citric acid cycle enzyme that isomerizes citrate into isocitrate, which is irreversibly blocked by fluorocitrate formed when cells encounter fluoroacetate (rat poison).

Isocitrate Dehydrogenase

The rate-limiting citric acid cycle enzyme that oxidatively decarboxylates isocitrate to five-carbon $\alpha$-ketoglutarate, producing $CO_2$ and $\text{NADH}$, stimulated by ADP and $Ca^{2+}$.

$\alpha$-Ketoglutarate Dehydrogenase Complex

The enzyme complex that converts $\alpha$-ketoglutarate to four-carbon succinyl-CoA, releasing $CO_2$ and producing $\text{NADH}$; mutant forms can produce 2-hydroxyglutarate to inhibit histone demethylases in gliomas.

Succinyl-CoA Synthetase

The citric acid cycle enzyme that cleaves the high-energy thioester bond of succinyl-CoA to produce succinate, coupling the reaction to the substrate-level phosphorylation of GDP to GTP (or ADP to ATP).

Succinate Dehydrogenase

An enzyme embedded in the inner mitochondrial membrane (also acting as Complex II of the electron transport chain) that oxidizes succinate to fumarate while reducing FAD to $FADH_2$.

Gluconeogenesis

An anabolic metabolic pathway that synthesizes glucose from pyruvate and other non-carbohydrate precursors, reversing glycolytic reactions by bypassing steps 1, 3, and 10 with specialized enzymes.

Glycogen

A branched intracellular glucose storage polymer stored primarily in the liver and skeletal muscle, mobilized into glucose-1-phosphate by glycogen phosphorylase between meals.

Cristae

Extensive invaginations of the inner mitochondrial membrane that substantially increase the total surface area available for oxidative phosphorylation complexes and ATP synthesis.

Porins

Large, channel-forming transport proteins located in the outer mitochondrial membrane that allow free permeability to solutes and metabolites of $5{,}000\,\text{Daltons}$ or less.

Complex I

The NADH dehydrogenase complex in the inner mitochondrial membrane that receives high-energy electrons from $\text{NADH}$, passes them to ubiquinone, and pumps protons ($H^+$) from the matrix to the intermembrane space.

Ubiquinone

A small, hydrophobic, non-protein mobile electron carrier dissolved within the lipid bilayer of the inner mitochondrial membrane that shuttles electrons from Complexes I and II to Complex III.

Complex III

The cytochrome c reductase complex of the electron transport chain that accepts electrons from reduced ubiquinol and transfers them to the mobile peripheral protein cytochrome c while pumping protons into the intermembrane space.

Cytochrome c

A water-soluble, heme-containing peripheral protein located in the intermembrane space that transports electrons from Complex III to Complex IV; its release into the cytosol triggers apoptosis.

Complex IV

The cytochrome c oxidase complex that uses a heme group and copper atom to transfer four electrons to molecular oxygen ($O_2$), forming two water molecules ($H_2O$) while pumping protons across the membrane.

Proton-Motive Force

The combined electrochemical proton gradient across the inner mitochondrial membrane consisting of a large membrane potential and a small pH gradient (such as pH $7.2$ in the intermembrane space vs. $7.9$ in the matrix).

ATP Synthase

A reversible rotary multi-subunit enzyme (Complex V) driven by protons flowing down their electrochemical gradient to catalyze the synthesis of ATP from ADP and inorganic phosphate via chemiosmosis.

Thylakoid

A flattened, disc-like membrane-bound sac inside a chloroplast arranged in stacks called grana, housing chlorophyll, photosystems, and electron transport chains that carry out the light reactions of photosynthesis.

Stroma

The large enzyme-filled fluid compartment of the chloroplast surrounding the thylakoids, homologous to the mitochondrial matrix, where carbon fixation reactions occur.

Chlorophyll

The principal light-absorbing photosynthetic pigment with a porphyrin ring that absorbs blue ($430\,\text{nm}$) and red ($660\,\text{nm}$) wavelengths of visible light while reflecting green light.

Antenna Complex

A cluster of light-harvesting pigment molecules within a photosystem that captures photon energy and funnels it via resonance energy transfer to a specialized photochemical reaction center.

Reaction Center

A transmembrane protein complex within a photosystem housing a chlorophyll special pair that converts absorbed light energy into chemical energy by transferring a high-energy electron to a mobile carrier.

Photosystem II

The first operational photosystem in noncyclic electron flow that absorbs light to extract electrons from water via a manganese-containing water-splitting complex, releasing molecular oxygen ($O_2$) and generating a proton gradient.

Photosystem I

A photosynthetic complex that captures light to energize electrons and transfer them via ferredoxin to $NADP^+$ reductase, producing NADPH on the stromal surface.

Rubisco

The slow-acting stromal enzyme that catalyzes the initial carbon-fixing step of the Calvin cycle, combining carbon dioxide ($CO_2$) with ribulose-1,5-bisphosphate to generate 3-phosphoglycerate.

Endomembrane System

An interconnected developmental and functional system of membrane-enclosed organelles—including the nuclear envelope, ER, Golgi, endosomes, and lysosomes—that exchange cargo via transport vesicles and evolved via plasma membrane invagination.

Nuclear Pore Complex

An elaborate aqueous transport portal spanning both bilayers of the nuclear envelope that freely allows small hydrophilic molecules to diffuse while selectively gating macromolecules carrying transport signals.

Signal Sequence

A continuous stretch of $15\text{ to }60$ amino acids within a protein that serves as an address label targeting the protein to its correct cellular compartment or organelle.

Nuclear Localization Sequence

A specific sorting signal rich in positively charged amino acids (such as lysine and arginine) that directs fully folded cytosolic proteins to bind nuclear transport receptors for import through the nuclear pore complex.

Signal Recognition Particle

A cytosolic ribonucleoprotein complex that recognizes and binds an ER signal sequence emerging from a translating ribosome, pauses elongation, and docks the ribosome onto an ER membrane SRP receptor.

Stop-Transfer Sequence

A hydrophobic segment within a translocating polypeptide chain that halts transfer across the ER translocation channel and anchors the protein in the lipid bilayer as a transmembrane segment.

Chaperone Proteins

Specialized helper proteins that monitor folding fidelity in the ER and other organelles, binding incompletely folded or misfolded proteins to assist proper folding and prevent premature transit.

Clathrin

A vesicle coat protein that polymerizes into a curved, three-legged basket-like lattice on the cytosolic face of membranes to mechanically sculpt budding transport vesicles during endocytosis and Golgi transport.

Dynamin

A small cytosolic GTPase that assembles as a ring around the invaginated neck of a budding clathrin-coated pit, constricting the neck to pinch off the membrane vesicle.

Adaptins

Coat adapter proteins that secure the outer clathrin coat to the vesicle membrane and selectively capture transmembrane cargo receptors bound to appropriate cargo molecules.

Rab Proteins

A family of small GTP-binding proteins displayed on transport vesicle surfaces that function as molecular return addresses, specifically bound by tethering proteins on the target membrane to ensure accurate docking.

SNARE Proteins

Complementary transmembrane proteins (v-SNAREs on vesicles and t-SNAREs on target membranes) that wind together into tight bundles to catalyze the fusion of the two lipid bilayers.

Glycosylation

The covalent addition and enzymatic processing of branched oligosaccharide trees to proteins, initiated in the ER lumen and further diversified within the Golgi apparatus.

ER Retention Signal

A specific four-amino-acid C-terminal sequence that prevents resident ER proteins (such as glycosylating enzymes) from leaving the endoplasmic reticulum or retrieves them from the cis-Golgi.

Cis Face

The entry face of the Golgi apparatus consisting of flattened cisternae oriented toward the endoplasmic reticulum, where incoming transport vesicles from the ER dock and fuse.

Trans Face

The exit face of the Golgi apparatus oriented toward the plasma membrane, where processed and sorted proteins bud off in transport vesicles destined for the cell surface, lysosomes, or secretory storage.

Constitutive Exocytosis

A constant, non-regulated secretion pathway operating in all eukaryotic cells that supplies freshly synthesized lipids and proteins to the plasma membrane and continuously discharges molecules into the extracellular space.

Regulated Exocytosis

A specialized secretion pathway in dedicated secretory cells (such as pancreatic or neuronal cells) where concentrated cargo molecules in secretory vesicles dock at the plasma membrane and await an extracellular stimulus before fusing.

Pinocytosis

A non-specific, constitutive form of endocytosis ('cell drinking') where small vesicles pinch inward from the plasma membrane to ingest extracellular fluid and dissolved solutes.

Phagocytosis

A specialized form of endocytosis ('cell eating') wherein large particles, debris, or whole microorganisms are engulfed by plasma membrane pseudopods to form large phagosomes.

Receptor-Mediated Endocytosis

A highly selective endocytic pathway wherein specific extracellular macromolecules (such as LDL-cholesterol or transferrin) bind cell-surface receptors and are concentrated into clathrin-coated pits for internalized transport.

Uniporter

A carrier protein that moves a single type of solute down its concentration or electrochemical gradient across a biological membrane (such as GLUT transporters or urea transporters).