Cell Biology: Microscopy, Membrane Transport, Organelles, and Membrane Structure

Comprehensive vocabulary flashcards covering microscopy principles, membrane transport systems, eukaryotic organelles, endomembrane trafficking, and membrane lipid/protein biochemistry.

Resolution (Resolving Power)

The minimum distance two separate points can be apart and still be distinguished as distinct objects in a microscope.

Abbé Equation

The mathematical formula $r = \frac{0.61\lambda}{NA} = \frac{0.61\lambda}{n \sin(\alpha)}$, where $r$ is resolution limit, $\lambda$ is illumination wavelength, $n$ is refractive index, and $\alpha$ is angular aperture.

Numerical Aperture ($NA$)

A dimensionless number representing the light-gathering capacity of a microscope lens, defined by the formula $NA = n \sin(\alpha)$.

Angular Aperture ($\alpha$)

The half-angle of the maximum cone of light rays that can enter the objective lens from a focal point on the specimen.

Phase-Contrast Microscopy

A light microscopy method that converts invisible phase differences caused by variations in sample thickness and refractive index into visible alterations in image brightness to examine living, unstained cells.

Differential Interference Contrast (DIC) Microscopy

A light microscopy technique that uses optical modifications based on phase shifts to produce a shadow-casting, three-dimensional visual effect with apparent relief.

Laser Scanning Confocal Microscopy

A fluorescence imaging technique that uses a focused laser beam and confocal pinholes to reject out-of-focus light, allowing optical sectioning and three-dimensional reconstruction of thick specimens.

Direct Immunofluorescence

A staining method where a fluorophore is coupled directly to a primary antibody that selectively targets and binds an antigen of interest.

Indirect Immunofluorescence

A detection method in which an unlabeled primary antibody binds a target molecule and is subsequently recognized by fluorophore-conjugated secondary antibodies, providing signal amplification.

Green Fluorescent Protein (GFP)

A $27\,\text{kDa}$ naturally fluorescent protein discovered by Osamu Shimomura in the jellyfish Aequorea victoria, genetically fused to target proteins to monitor subcellular localization and dynamic processes in living cells.

Fluorescence Recovery After Photobleaching (FRAP)

An experimental technique where a defined cellular region is bleached with intense laser light to quantify the rate of lateral diffusion as unbleached fluorescent molecules return into the bleached area.

Fluorescence Resonance Energy Transfer (FRET)

A technique measuring non-radiative energy transfer between two fluorophores positioned within $10\,\text{nm}$ of each other to assess whether two molecules are directly touching or interacting.

Transmission Electron Microscopy (TEM)

An electron microscopy method in which an electron beam is transmitted through ultra-thin, heavy metal-stained specimen sections to produce high-resolution internal images with a practical resolution limit of $\sim 0.3\,\text{nm}$.

Scanning Electron Microscopy (SEM)

An electron microscopy method that yields three-dimensional architectural images of specimen surfaces by detecting secondary electrons deflected from intact, unsectioned samples.

Cryo-Electron Microscopy (Cryo-EM)

A specialized electron microscopy technique used to solve high-resolution structures of biological macromolecules rapidly frozen in vitreous ice without chemical fixation or heavy metal stains.

Partition Coefficient

A physical measurement of solute polarity and lipid solubility; higher partition coefficients correspond to greater nonpolar character and more rapid penetration through lipid bilayers.

Osmosis

The passive net movement of water across a semipermeable membrane from a region of lower solute concentration to a region of higher solute concentration.

Plasmolysis

The phenomenon in plant cells placed in hypertonic solutions where water exits by osmosis, causing protoplast shrinkage and loss of internal turgor pressure.

Aquaporin

A tetrameric transmembrane channel protein featuring a narrow $0.3\,\text{nm}$ water-selective pore lined with conserved hydrophilic residues that conducts billions of water molecules per second.

Porin

A transmembrane transport protein composed of an antiparallel $\beta$-barrel forming a wide, water-filled pore that allows non-specific passive diffusion of small hydrophilic molecules across outer membranes of bacteria, mitochondria, and chloroplasts.

Electrochemical Gradient

The combined driving force governing the movement of a charged solute across a membrane, comprising both the chemical concentration gradient and the electrical membrane potential difference.

Selectivity Filter (Ion Channel)

A narrow constriction within an ion channel lined with backbone carbonyl oxygens perfectly spaced to coordinate dehydrated ions of a specific atomic radius, compensating for the energetic cost of dehydration.

Ball-and-Chain Inactivation

A structural gating mechanism in voltage-gated ion channels where a flexible cytoplasmic peptide domain acts as a tethered ball that blocks the channel pore shortly after opening.

GLUT1

A ubiquitous mammalian uniporter carrier protein that facilitates the passive, bidirectional diffusion of D-glucose across plasma membranes using an alternating conformation mechanism.

$Na^+/K^+$ ATPase

A P-class primary active transport pump that hydrolyzes ATP to export $3\,Na^+$ ions and import $2\,K^+$ ions per cycle against their electrochemical gradients, maintaining cellular osmotic balance and resting membrane potential.

V-Type ATPase

A multi-subunit primary active transporter located in endomembrane organelles (lysosomes, endosomes, vacuoles, and secretory vesicles) that uses ATP hydrolysis to pump protons ($H^+$) into the lumen.

F-Type ATPase (ATP Synthase)

A reversible proton-translocating rotary motor located in bacterial plasma membranes, inner mitochondrial membranes, and chloroplast thylakoids that uses an electrochemical proton gradient to generate ATP from $ADP$ and $P_i$.

ABC Transporters

A large superfamily of primary active transport proteins containing two transmembrane domains and two conserved cytosolic ATP-binding cassettes that utilize ATP hydrolysis to translocate nutrients, lipids, and xenobiotics.

Multidrug Resistance (MDR) Transporter

A clinically relevant ABC-type efflux pump that uses ATP hydrolysis to pump diverse, chemically dissimilar hydrophobic drugs out of cancer cells or bacteria, conferring drug resistance.

Secondary Active Transport

The endergonic movement of a solute against its electrochemical gradient coupled directly to the exergonic flow of a driving ion (commonly $Na^+$ or $H^+$) down its gradient.

Symporter

A membrane cotransporter that couples the movement of one solute down its electrochemical gradient to the movement of a second solute in the same direction across the membrane.

Antiporter

A membrane cotransporter that facilitates the coupled exchange of two different molecules or ions across the membrane in opposite directions.

Nuclear Envelope

A dual-membrane barrier surrounding the eukaryotic nucleus consisting of an inner nuclear membrane and an outer nuclear membrane that is continuous with the rough endoplasmic reticulum.

Nucleolus

A prominent non-membrane-bound nuclear subcompartment where ribosomal RNA (rRNA) is transcribed and processed, and ribosomal subunits are assembled.

Rough Endoplasmic Reticulum (RER)

A network of flattened, ribosome-studded membranous cisternae continuous with the nuclear envelope, serving as the primary site for the translation, translocation, and initial folding of endomembrane and secretory proteins.

Smooth Endoplasmic Reticulum (SER)

A tubular, ribosome-free network of cytoplasmic membranes dedicated to the synthesis of lipids and steroid hormones, detoxification of organic compounds, and storage of calcium ions.

Sarcoplasmic Reticulum (SR)

A specialized smooth endoplasmic reticulum in muscle cells whose membrane is largely composed of $Ca^{2+}$ ATPase pumps, functioning as an intracellular calcium reservoir that controls contraction.

Cis Golgi Network (CGN)

The entry face of the Golgi complex that receives transition transport vesicles from the rough ER and directs proteins forward into the Golgi stack or back to the ER.

Trans Golgi Network (TGN)

The major sorting station at the exit face of the Golgi complex where fully glycosylated proteins are packaged into vesicles directed toward the plasma membrane, endosomes, or lysosomes.

Lysosome

A single-membrane digestive organelle containing approximately 50 acid hydrolases maintained at an acidic pH by internal V-class $H^+$ pumps to degrade biological macromolecules.

Autophagy

An intracellular degradation pathway in which damaged organelles or cytoplasmic portions are sequestered within a double-membrane autophagosome that fuses with a lysosome for digestion.

Peroxisome

A single-membrane metabolic organelle not derived from the endomembrane system that carries out the oxidative breakdown of fatty acids ($>12$ carbons) using oxidases and eliminates toxic hydrogen peroxide via catalase.

Cristae

Extensive invaginations of the inner mitochondrial membrane that project into the matrix, housing the electron transport complexes and ATP synthase machinery.

Thylakoids

Flattened membranous sacs within chloroplasts arranged in stacks called grana, containing chlorophyll pigments, reaction centers, and electron transport proteins for light-dependent reactions.

Tonoplast

The single membrane surrounding the central vacuole in plant cells, containing active transporters that accumulate solutes to drive water entry and maintain turgor pressure.

Endosymbiont Theory

The evolutionary model proposing that mitochondria and chloroplasts originated from free-living aerobic and photosynthetic bacteria that were engulfed by ancestral eukaryotic cells through phagocytosis.

Phosphoglycerides

The predominant structural lipids in biological membranes, built upon a glycerol-3-phosphate backbone esterified to two fatty acid tails and a polar head group.

Sphingolipids

Membrane lipids derived from the amino alcohol sphingosine coupled to a fatty acid via an amide bond to form ceramide, lacking a glycerol backbone.

Sphingomyelin (SM)

A phospholipid sphingolipid composed of ceramide linked to a phosphocholine head group, particularly abundant in animal plasma membranes and the myelin sheath.

Glycolipids

Lipids modified with carbohydrate chains residing exclusively in the exoplasmic leaflet of the plasma membrane, formed in the Golgi lumen and involved in cell-cell recognition and protection.

Sterols

Amphipathic membrane lipids containing a characteristic four-ring hydrocarbon skeleton, represented by cholesterol in animals, ergosterol in fungi, and stigmasterol in plants.

Amphipathic

The chemical property of having both a hydrophilic, water-soluble polar region and a hydrophobic, water-insoluble nonpolar region within the same molecule.

Micelle

A spherical monolayer formed in aqueous solutions by wedge-shaped amphipathic lipids whose polar head cross-sectional area exceeds that of their single hydrocarbon tail.

Liposome

A synthetic spherical vesicle consisting of an aqueous core bounded by a closed lipid bilayer, self-assembled in vitro to investigate membrane proteins and deliver drugs.

Phosphatidylserine (PS)

A negatively charged phosphoglyceride normally restricted to the cytoplasmic leaflet that flips to the outer leaflet during apoptosis to signal phagocytosis.

Integral Membrane Proteins

Proteins that penetrate into or span the hydrophobic interior of the lipid bilayer, typically utilizing one or more hydrophobic $\alpha$-helices or $\beta$-barrels to form stable van der Waals contacts with lipid tails.

Peripheral Membrane Proteins

Proteins associated with either membrane surface via weak non-covalent interactions with lipid polar heads or integral membrane proteins, extractable by changes in pH or ionic strength.

Lipid-Anchored Membrane Proteins

Proteins located entirely on the surface of a membrane leaflet that are covalently linked to an embedded lipid group such as a fatty acid, prenyl group, or glycolipid.

Acylation

A post-translational covalent attachment of a fatty acid chain (such as a 14-carbon myristoyl group via an amide link or a 16-carbon palmitoyl group via a thioester link) to anchor a cytosolic protein to the inner leaflet.

Prenylation

The covalent addition of an isoprenoid lipid group (a 15-carbon farnesyl or 20-carbon geranylgeranyl group) via a thioether bond to a C-terminal cysteine residue of a cytosolic protein.

GPI Anchor

A glycosylphosphatidylinositol lipid structure attached to the C-terminus of proteins in the ER lumen, anchoring them exclusively to the exoplasmic leaflet of the plasma membrane.

Hydropathy Plot

A quantitative diagram plotting the free energy of transfer (hydropathy index) of sequential amino acid segments from nonpolar to aqueous environments, identifying hydrophobic transmembrane spans of $20\text{--}30$ residues.

Transition Temperature ($T_m$)

The critical temperature at which a lipid bilayer transitions between a rigid, ordered gel state and a fluid, disordered liquid-crystalline state.

Fluidity Buffer

The function of cholesterol in preventing hydrocarbon chains from packing tightly at low temperatures while restricting their excessive motion and mobility at high temperatures.

Lipid Rafts

Dynamic, transient membrane microdomains enriched in cholesterol, sphingolipids with long saturated chains, and GPI-anchored proteins that are $1\text{--}2\,\text{nm}$ thicker and less fluid than the surrounding bilayer.

Transverse Diffusion (Flip-Flop)

The thermodynamically unfavorable movement of a phospholipid molecule from one leaflet of a bilayer to the opposite leaflet, an event that occurs very slowly ($\sim 10^5\,\text{s}$) without enzyme catalysis.

Flippase

An ATP-dependent membrane enzyme that selectively translocates specific phospholipids between leaflets to generate and preserve lipid bilayer asymmetry.

Erythrocyte Membrane Skeleton

A two-dimensional filamentous protein network on the cytoplasmic surface of red blood cells composed of spectrin tetramers linked to actin and anchored via ankyrin to Band 3 to provide mechanical elasticity.