Comprehensive Biology: Cell Biology, Membrane Transport, Bioenergetics, and Cytoskeletal Dynamics

Comprehensive vocabulary review flashcards covering cell structure, viral biology, membrane composition and transport, bioenergetics, intracellular trafficking pathways, the cytoskeleton, molecular motors, and nuclear organization.

Prokaryotic Cell

A single-celled organism measuring $1\text{--}10\,\mu\text{m}$ that lacks a membrane-bound nucleus and organelles, contains small ribosomes, reproduces asexually, and holds its genetic material as circular DNA (plasmid) within a nucleoid region.

Eukaryotic Cell

A unicellular or multicellular organism typically measuring $10\text{--}100\,\mu\text{m}$ that possesses a membrane-bound nucleus, complex organelles, large ribosomes, and genetic material organized into linear chromosomes.

Virion

An inanimate viral particle existing outside a host cell, consisting of a protein capsid enclosing a small genome of DNA or RNA that encodes up to a few hundred genes.

Capsid

The external protein capsule or shell that encloses and protects the viral genetic material.

Bacteriophage

A virus that infects bacteria, typically featuring a specialized structure consisting of a capsid head, collar, sheath, baseplate, spikes, and tail fibers.

Influenza Virus

An enveloped RNA virus featuring a host-derived lipid envelope embedded with surface glycoprotein spikes, specifically haemagglutinin and neuraminidase (sialidase), alongside ion channels.

Host Range

The specific spectrum of host species and cell types that a virus can bind to via cell-surface proteins and enter, classified as narrow (such as human influenza infecting respiratory epithelial cells) or wide (such as rabies infecting dogs, bats, foxes, raccoons, and humans).

Lytic Infection

A viral infection pathway in which the virus commandeers host cell machinery to synthesize viral components and assemble progeny particles, ultimately causing the rupture and death of the host cell.

Non-Lytic Infection

An integrative or lysogenic viral infection mode wherein viral genetic material integrates into the host genome as a provirus, allowing the host cell to survive, often with impaired function.

Provirus

Viral DNA that has integrated directly into the host cell chromosomal genome during a non-lytic (integrative) infection cycle.

Plasma Membrane

A trilaminar biological barrier measuring roughly $6\,\text{nm}$ thick composed of an amphipathic phospholipid bilayer that encloses the cell, regulates substance transport, responds to external stimuli, and mediates cell interactions.

Amphipathic

Describing a chemical property of molecules containing both hydrophilic (polar) and hydrophobic (non-polar) regions, causing phospholipids to spontaneously arrange into bilayers with tails sequestered away from water.

Phospholipid

The fundamental amphipathic building block of biological membranes, consisting of a glycerol backbone linked to two hydrophobic fatty acyl chains and a hydrophilic head group linked via a phosphate residue.

Fluid Mosaic Model

The structural model describing biological membranes as a fluid bilayer where lipids freely diffuse laterally within leaflets while diverse proteins, cholesterol, and carbohydrates penetrate or associate with the lipid plane.

Transition Temperature

The specific temperature at which a biological membrane transitions between a rigid, ordered crystalline gel state and a fluid liquid crystal state.

Cholesterol

An amphipathic sterol lipid that modulates membrane fluidity by packing tightly with phospholipids, decreasing fluidity in a liquid crystal membrane and increasing fluidity in a crystalline gel membrane.

Integral Membrane Protein

A protein that permanently spans the lipid bilayer (transmembrane protein), commonly functioning as an ion channel, nutrient transporter, receptor, or cell-cell junction.

Peripheral Membrane Protein

A protein that associates non-covalently with the polar surfaces of the lipid bilayer or with integral proteins, located on either the cytoplasmic or extracellular face of the membrane.

Lipid-Anchored Protein

A membrane protein situated on the membrane surface that is covalently tethered to a lipid molecule embedded within the phospholipid bilayer.

Simple Diffusion

A passive, downhill transport mechanism allowing very small, uncharged molecules such as $\text{O}_2$, $\text{CO}_2$, and $\text{NO}$ to pass directly across the hydrophobic core of the lipid bilayer without energy or transporter assistance.

Ion Channel

A multi-subunit integral membrane protein forming an aqueous, selective pore that allows small charged ions ($\text{Na}^+$, $\text{K}^+$, $\text{Ca}^{2+}$, $\text{Cl}^-$) to diffuse passively down their electrochemical gradients.

Voltage-Gated Channel

An ion channel that opens or closes in response to changes in electrical potential (voltage) across the biological membrane.

Ligand-Gated Channel

An ion channel that undergoes a conformational opening or closing upon the binding of a specific chemical molecule (ligand) to its receptor site.

Facilitated Diffusion

A carrier-mediated passive transport mechanism in which a solute binds to a facilitative transporter, inducing a conformational change that moves the molecule down its concentration gradient without requiring energy.

Uniporter

A membrane carrier protein that transports a single solute species across the bilayer down its concentration gradient.

Symporter

A cotransport protein that moves two distinct molecular species across the membrane simultaneously in the exact same direction.

Antiporter

A cotransport carrier that utilizes the favorable concentration gradient of one solute to drive the transport of a second solute across the membrane in the opposite direction.

Active Transport

The carrier-mediated movement of solutes across a membrane against their concentration gradient, powered by the input of cellular energy such as ATP hydrolysis.

Sodium-Potassium Pump

An ATP-dependent active transporter that maintains cellular ion gradients by pumping $3\,\text{Na}^+$ out of the cell and $2\,\text{K}^+$ into the cell for each molecule of ATP hydrolyzed.

Signal Transduction

The multi-stage cellular communication process wherein extracellular ligand binding to a receptor induces conformational changes that trigger intracellular second messenger cascades, producing a specific cellular response.

Second Messenger

An intracellular signaling substance (such as $\text{cAMP}$, $\text{Ca}^{2+}$, or G-proteins) that relays and amplifies signals received at cell-surface receptors to initiate an internal molecular phosphorylation cascade.

Extracellular Matrix (ECM)

A complex network of secreted macromolecules—including collagens, proteoglycans, glycosaminoglycans, and glycoproteins—that provides shape, bulk, and structural strength to animal tissues and binds surface receptors to guide cellular behavior.

Integrin

A transmembrane anchor protein that serves at the cell surface as a receptor for extracellular matrix components, physically linking the ECM to the internal cytoskeleton and transducing extracellular cues into intracellular signals.

Plant Cell Wall

A rigid protective structure situated exterior to the plant plasma membrane composed of cellulose, hemicellulose, pectin, and lignin that provides mechanical support, withstands turgor pressure, and defends against pathogens.

Mitochondrion

A double-membrane organelle responsible for aerobic cellular respiration and ATP synthesis, consisting of an outer membrane, an intermembrane space, folded inner membrane cristae, and a protein-rich matrix containing mitochondrial ribosomes and circular DNA.

Substrate-Level Phosphorylation

The direct enzymatic formation of ATP from ADP coupled to the hydrolysis of an organic high-energy metabolic intermediate, responsible for about $12\%$ of total ATP generated during cellular respiration (in glycolysis and the Krebs cycle).

Oxidative Phosphorylation

The indirect synthesis of ATP powered by an electrochemical proton gradient established by Complexes I–IV of the electron transport chain, generating roughly $88\%$ of total cellular ATP in animal cells.

Electron Transport Chain (ETC)

A series of multi-protein complexes (Complexes I–IV) and electron shuttles (CoQ, Cytochrome c) embedded within the inner mitochondrial membrane that transfer electrons from $\text{NADH}$ and $\text{FADH}_2$ to molecular oxygen while pumping protons ($\text{H}^+$) into the intermembrane space.

Apoptosis

A genetically programmed form of cell death characterized by cell shrinkage, plasma membrane blebbing, nuclear and DNA fragmentation, detachment from surrounding cells, and engulfment by phagocytes without causing inflammation.

Intrinsic Pathway of Apoptosis

The mitochondrial-driven apoptotic pathway activated by intracellular cellular damage, wherein pro-apoptotic proteins BAX and BAK permeabilize the outer mitochondrial membrane to leak cytochrome c into the cytoplasm.

Cytochrome c

A mitochondrial electron transfer protein that, upon release into the cytosol following mitochondrial membrane permeabilization, binds Apaf-1 and procaspase-9 to initiate apoptosis.

Caspases

A family of cysteine protease enzymes acting as initiators and executioners that systematically cleave essential cellular targets to dismantle the cell during apoptosis.

Endomembrane System

A coordinated network of internal eukaryotic membranes and organelles—including the ER, Golgi apparatus, endosomes, and lysosomes—that collaborate to synthesize, modify, package, and transport lipids and proteins.

Rough Endoplasmic Reticulum (RER)

A ribosome-studded organelle continuous with the outer nuclear membrane that executes membrane phospholipid synthesis, cotranslational protein translocation, chaperone-mediated protein folding, and protein glycosylation.

Smooth Endoplasmic Reticulum (SER)

A ribosome-free region of the endoplasmic reticulum that serves as the primary site of lipid synthesis, steroid hormone production, metabolic detoxification, and intracellular $\text{Ca}^{2+}$ sequestration.

Signal Sequence

A stretch of consecutive hydrophobic amino acids located at the amino-terminus (N-terminus) of a nascent polypeptide that directs the translating ribosome to dock onto the RER translocon.

Signal Recognition Particle (SRP)

A cytosolic ribonucleoprotein complex that binds the nascent N-terminal signal sequence emerging from a ribosome, halts translation, and docks the translation complex onto the SRP receptor on the ER membrane.

Translocon

An aqueous protein channel in the RER membrane that associates with docked ribosomes to thread nascent polypeptide chains directly into the ER lumen or bilayer.

BiP

An ER-resident molecular chaperone that binds incoming nascent polypeptides within the ER lumen to assist in proper protein folding and quality control.

Signal-Anchor Sequence

An internal hydrophobic amino acid sequence within a nascent membrane protein that halts translocon passage, causing the channel to laterally release the segment to embed as a permanent transmembrane alpha helix.

TOM Complex

The Translocase of the Outer Mitochondrial Membrane that recognizes post-translationally synthesized proteins in the cytosol and mediates their translocation across the outer mitochondrial membrane.

Anterograde Transport

Directional vesicular movement through the endomembrane system progressing forward from the ER toward the cis-Golgi network, across Golgi cisternae, and out toward the trans-Golgi network and plasma membrane.

Retrograde Transport

The backward trafficking of vesicles from the Golgi apparatus to the ER, or from distal (trans) to proximal (cis) Golgi cisternae, to retrieve and recycle resident compartment proteins and membrane lipids.

Cisternal Maturation

The dynamic mechanism of Golgi trafficking in which individual cisternae physically progress and mature from cis to medial to trans structures while their specific resident enzymes are continually recycled backward via retrograde vesicles.

Constitutive Secretion

The continuous, unregulated default exocytic pathway present in all eukaryotic cells that supplies newly synthesized membrane lipids, membrane proteins, and extracellular matrix components (such as collagen) to the cell surface.

Regulated Secretion

An exocytic pathway found in specialized secretory, neuronal, or endocrine cells where cargo proteins are stored in concentrated dense-core secretory granules and discharged only upon receipt of an external stimulus or elevation in cytosolic $\text{Ca}^{2+}$.

Exocytosis

The cellular process by which an intracellular vesicle fuses with the plasma membrane, releasing its luminal cargo into the extracellular fluid while integrating its membrane components into the cell surface.

Endocytosis

The cellular uptake pathway in which patches of the plasma membrane invaginate and bud inward to capture extracellular fluid, macromolecules, and cell-surface receptors within endocytic vesicles.

COPII Coat

A multi-protein vesicle coat complex whose assembly is initiated by the GTPase Sar1 to bud transport vesicles mediating forward (anterograde) movement from the ER to the cis-Golgi network.

COPI Coat

A protein coat that shapes vesicles mediating backward (retrograde) transport from the Golgi apparatus back to the rough ER and between Golgi cisternae.

Clathrin Coat

A polygonal protein coat lattice that drives vesicle budding from the trans-Golgi network, endosomal compartments, and the plasma membrane during receptor-mediated endocytosis.

SNARE Complex

A four-helix bundle formed by the specific pairing of a vesicle-associated v-SNARE with target membrane t-SNARE proteins, bringing opposing lipid bilayers into close apposition to drive membrane fusion.

Lysosome

A membrane-enclosed digestive organelle measuring $25\,\text{nm}$ to $1\,\mu\text{m}$ maintaining an internal $\text{pH}$ of $4.6$ via a vacuolar $\text{H}^+\text{-ATPase}$ proton pump, housing acid hydrolases to degrade macromolecules, endocytosed cargo, and worn-out organelles.

Autophagy

The normal catabolic disassembly of unnecessary or damaged cellular components, wherein an ER-derived isolation membrane (phagophore) engulfs target organelles to form a double-membrane autophagosome that fuses with a lysosome to generate an autolysosome.

Phagocytosis

A specialized endocytic process whereby a phagocytic cell extends pseudopods to engulf large particulate matter or pathogens into a phagosome, which subsequently fuses with lysosomes for enzymatic degradation.

Plant Vacuole

A large fluid-filled, membrane-enclosed plant organelle occupying up to $90\%$ of cellular volume that regulates cytoplasmic $\text{pH}$, generates hydrostatic turgor pressure for mechanical rigidity, and carries out intracellular acid hydrolysis at $\text{pH}\;5.0$.

Microtubules

Rigid, hollow cytoskeletal cylinders measuring approximately $25\,\text{nm}$ in outer diameter, built from 13 parallel protofilaments of $\alpha$-tubulin and $\beta$-tubulin heterodimers that possess intrinsic polarity with a fast-growing plus (+$) end and a slow-growing minus (-$$) end.

Axonemal Microtubules

Highly organized, stable microtubule doublet arrays anchored to basal bodies that form the central structural and motile core of eukaryotic cilia and flagella.

Microfilaments

Thin, polar cytoskeletal filaments measuring roughly $7\,\text{nm}$ in diameter formed by the head-to-tail helical polymerization of globular actin (G-actin) into filamentous actin (F-actin), functioning in cell motility, cytokinesis, and short-range transport.

Treadmilling

The dynamic steady-state behavior of polar actin microfilaments where ATP-bound G-actin monomers continuously add to the plus (+$) end while ADP-bound subunits dissociate from the minus (-$$) end at equivalent rates.

Intermediate Filaments

Tough, non-polar cytoskeletal fibers with an average diameter of $8\text{--}10\,\text{nm}$ formed from staggered anti-parallel tetramers of coiled-coil protein dimers that provide high tensile mechanical strength without supporting motor-based transport.

Microtubule-Organizing Centre (MTOC)

The specialized eukaryotic cellular structure (such as the centrosome or cilium basal body) that nucleates microtubule growth and anchors their minus ($-$) ends.

Kinesin

An ATP-dependent motor protein superfamily that moves processively toward the plus ($$+$) end of microtubules, driving anterograde transport of secretory vesicles and organelles outward toward the cell periphery.

Dynein

A minus-end-directed microtubule motor protein that hydrolyzes ATP to power retrograde transport of endosomes, lysosomes, and cargo inward toward the cell center or MTOC.

Myosin

A superfamily of actin-dependent motor proteins (including conventional Myosin II and unconventional Myosins) that hydrolyze ATP to move predominantly toward the plus ($$+$) end of microfilaments to power muscle contraction and short-range cargo transport.

Nuclear Envelope

A double-membrane barrier enclosing the eukaryotic nucleus composed of an outer nuclear membrane (studded with ribosomes and continuous with the RER) and an inner nuclear membrane separated by a lumen and perforated by nuclear pores.

Nuclear Lamina

A dense fibrous meshwork of intermediate filaments (lamins and keratins) lining the inner nuclear membrane that provides mechanical scaffolding to the nuclear envelope and anchors chromatin.

Nuclear Pore Complex (NPC)

An octagonal supramolecular complex of nucleoporin proteins spanning both membranes of the nuclear envelope that permits rapid passive diffusion of molecules $\le 40\,\text{kDa}$ while regulating the active transport of larger cargo.

Nuclear Localization Signal (NLS)

A specific sequence of positively charged basic amino acids within a protein that directs its regulated import through the nuclear pore complex into the nucleoplasm.

Nucleolus

The prominent, non-membrane-bound subnuclear compartment of eukaryotic cells dedicated to the transcription of ribosomal RNA (rRNA), rRNA processing, and the assembly of 40S and 60S ribosomal subunits.

Porin

An aqueous channel-forming integral protein in the outer mitochondrial membrane that renders it permeable to the passive diffusion of small metabolites and ions.

Sar1

A small regulatory GTP-binding protein that binds the ER donor membrane upon GTP loading to initiate the assembly of the COPII coat complex during transport vesicle budding.

Tau

A non-motor microtubule-associated protein (MAP) that binds, stabilizes, and organizes parallel microtubule arrays within neuronal axons.

Capping Protein

A cytoskeletal regulatory protein that specifically binds to the plus ($$+$) end of an actin filament to block the addition or loss of actin subunits.

Calvin Cycle

The light-independent metabolic pathway located in the chloroplast stroma that consumes ATP and $\text{NADPH}$ to synthesize carbohydrates from $\text{CO}_2$.

Differentiation

The developmental specialization process whereby an unspecialized cell acquires distinct morphological, biochemical, and functional characteristics tailored to a specific biological role.