General Cell Biology and Biochemistry Review

Comprehensive vocabulary flashcards covering Cell Biology and Molecular Cell Composition: historical cell theory, biological domains and kingdoms, viruses and subviral agents, biological membranes, transport mechanisms, the cytoskeleton, the cytosol, and biological macromolecules.

Fibrillar Theory

A 16th-century biological doctrine formulated by Gabriele Falloppio and Jean Fernel asserting that all human tissues and organs are fundamentally composed of elemental fibers.

Spontaneous Generation

The ancient hypothesis that living organisms can emerge directly from non-living matter, historically accepted for lower organisms by Aristotle and Needham, but refuted by Francesco Redi and Louis Pasteur.

Omnis Cellula e Cellula

The Latin aphorism coined by Rudolf Virchow in 1855 stating that every cell arises exclusively from the division of a pre-existing cell, forming the third postulate of classical cell theory.

Cell Theory (Classical Postulates)

The biological doctrine establishing that: 1) all living organisms consist of one or more cells; 2) the cell is the structural and functional unit of life (Schleiden & Schwann, 1838–1839); and 3) all cells arise from pre-existing cells (Virchow, 1855/1858).

Syncytium

A multinucleated cellular organization formed by the cytoplasmic fusion of multiple uninucleated cells, representing a structural exception to standard individual cell organization.

Coenocyte (Plasmodium)

A multinucleated cell resulting from multiple successive nuclear divisions (mitosis) occurring without intervening cytokinesis.

Three-Domain System

A biological classification model established by Carl Woese in 1990 that divides cellular life into Archaea, Bacteria, and Eukarya based on $16\text{S}$ and $18\text{S}$ ribosomal RNA phylogenetic analysis.

Peptidoglycan (Murein)

A rigid bacterial cell wall polymer consisting of alternating linear chains of $N$-acetylglucosamine (NAG) and $N$-acetylmuramic acid (NAM) linked by $\beta(1\rightarrow 4)$ glycosidic bonds, cross-linked by tetrapeptide chains.

Gram-Positive vs. Gram-Negative Cell Wall

Gram-positive walls possess a thick peptidoglycan layer containing teichoic and lipoteichoic acids, whereas Gram-negative walls have a thin peptidoglycan layer enclosed within a periplasmic space and an outer membrane bearing lipopolysaccharides (LPS) and porins.

Mycoplasmas

Obligate parasitic or commensal prokaryotes characterized by extremely small size ($< 1\text{ }\beta\text{m}$), reduced genomes ($\text{approx } 670$ genes), total absence of a cell wall, and plasma membranes naturally stabilized by sterols.

Cyanobacteria

Photosynthetic prokaryotes measuring $5\text{--}20\text{ }\beta\text{m}$ that feature a Gram-negative cell wall architecture, internal thylakoid membranes with photosynthetic pigments, carboxysomes for $\text{CO}_2$ fixation, and the ability to fix atmospheric nitrogen.

Pseudopeptidoglycan (Pseudomurein)

An archaeal cell wall polymer formed by alternating $N$-acetylglucosamine (NAG) and $N$-acetyltalosaminuronic acid (NAT) linked by $\beta(1\rightarrow 3)$ glycosidic bonds, rendering it insensitive to lysozyme.

Archaeal Membrane Lipids

Membrane lipids composed of branched phytanol isoprene chains connected to L-glycerol via ether linkages, forming either bilayers or heat-resistant monolayers.

Methanogens

Strictly anaerobic Archaea inhabiting wetlands, deep sediments, and the digestive tracts of animals that generate methane ($\text{CH}_4$) as a metabolic byproduct.

Halophiles

Aerobic, heterotrophic Archaea that thrive exclusively in environments with saturated salt concentrations, such as salt lakes and coastal evaporation ponds.

Thermoacidophiles

Extremophilic Archaea with heat- and acid-stable enzymes that inhabit extremely hot, sulfur-rich environments ($\text{volcanic springs, hydrothermal vents}$) at low pH.

Baltimore Classification

A viral taxonomy system established in 1971 that categorizes viruses into 7 distinct groups based on their genome composition, strandedness, sense, and pathway utilized to synthesize mRNA.

Retrovirus

An enveloped, icosahedral Baltimore Group VI virus possessing a single-stranded positive-sense RNA genome that replicates through a double-stranded DNA intermediate integrated as a provirus using reverse transcriptase.

Lytic Cycle

A viral replication cycle in which viral genome entry and biosynthesis result in the assembly of new virions and the subsequent enzymatic destruction and lysis of the host cell.

Lysogenic Cycle

A viral replication cycle wherein the viral DNA integrates stably into the host cell chromosome (prophage/provirus), replicating passively alongside host division until an induction event triggers lysis.

Viroid

An infectious plant pathogen consisting solely of a naked, single-stranded circular RNA molecule ($250\text{--}400$ nucleotides) that lacks any protein coat and replicates within the host nucleus or chloroplasts.

Virusoid (Satelloid)

A small circular single-stranded RNA particle encapsidated within certain plant RNA viruses whose replication is obligately dependent on the presence of a helper coinfecting virus.

Prion (PrPSc)

An infectious, nucleic-acid-free protein agent that propagates by inducing the post-translational conformational conversion of cellular alpha-helical $\text{PrP}^\text{C}$ into protease-resistant, beta-sheet-rich $\text{PrP}^\text{Sc}$, leading to fatal spongiform encephalopathies.

Resting Membrane Potential

The steady-state electrical voltage difference across the plasma membrane maintained primarily by selective ion distribution, typically measured at $-60\text{ mV}$ in resting cells.

Simple Diffusion

The passive, non-carrier-mediated transport of small, nonpolar or uncharged molecules across the lipid bilayer moving down their concentration gradient without metabolic energy expenditure.

Osmosis

The passive net diffusion of water molecules across a selectively permeable membrane toward the region with a higher solute concentration.

Permeases

Multipass transmembrane carrier proteins that exhibit enzyme-like kinetics ($V_{\text{max}}$ and substrate specificity) to facilitate the passive transport of specific polar molecules across the membrane via alternating conformational changes.

Ion Channels

Multipass membrane proteins featuring an aqueous hydrophilic pore that permits rapid, passive transport of specific inorganic ions down their electrochemical gradient when opened by voltage, ligand, or mechanical stimuli.

Aquaporins

Channel-forming integral membrane proteins that provide permanently open aqueous pathways for the rapid, bidirectional diffusion of water across cellular membranes.

Sodium-Potassium Pump (Na+/K+-ATPase)

A P-type primary active transport enzyme that hydrolyzes one ATP molecule to actively pump $3\text{ Na}^+$ ions out of the cell and $2\text{ K}^+$ ions into the cell against their respective concentration gradients.

Secondary Active Transport

The transport of a solute against its electrochemical gradient powered not directly by ATP, but coupled to the downhill movement of a cotransported ion via symport or antiport.

Transcytosis

A vesicular transport process wherein macromolecules are internalized at one cell surface by endocytosis, shuttled intact through the cytoplasm, and secreted at the opposite membrane by exocytosis.

Regulated Exocytosis

A secretory vesicle release mechanism that remains dormant until triggered by a specific extracellular or intracellular stimulus, typically involving an elevation of cytosolic $\text{Ca}^{2+}$.

Microtubules

Hollow, cylindrical cytoskeletal fibers measuring $25\text{ nm}$ in outer diameter, composed of 13 parallel protofilaments assembled from alternating $\text{a}$- and $\beta$-tubulin heterodimers around a $14\text{-nm}$ central lumen.

Dynamic Instability

The rapid and stochastic transition of microtubule plus ends between persistent polymerization (rescue) and rapid depolymerization (catastrophe), governed by the presence or loss of a stabilizing GTP-cap.

Treadmilling

A dynamic steady-state behavior where cytoskeletal polymers maintain constant length by simultaneously adding subunits at the plus end while dissociating subunits at the minus end.

Microtubule-Organizing Center (MTOC)

A specialized subcellular region, such as the centrosome or basal body, containing $\beta$-tubulin ring complexes that nucleate microtubule polymerization and anchor minus ends.

Microtubule Motor Proteins

ATP-dependent motor enzymes that move processively along microtubules to transport cargoes; kinesins travel toward the plus end (anterograde), while dyneins move toward the minus end (retrograde).

Intermediate Filaments

Tough, unpolarized, apolar cytoskeletal polymers with a diameter of $8\text{--}12\text{ nm}$ assembled from staggered tetramers that provide structural tensile strength and resist mechanical stress without requiring nucleotide triphosphate hydrolysis.

Keratins

A diverse class of intermediate filament proteins found in epithelial cells that associate with desmosomes and hemidesmosomes to provide epithelial mechanical integrity.

Nuclear Lamins

Intermediate filament proteins (types A, B, and C) forming a two-dimensional supporting fibrous meshwork beneath the inner nuclear envelope that reversibly depolymerizes during mitosis via phosphorylation.

Microfilaments (Actin Filaments)

Two-stranded helical cytoskeletal polymers measuring $7\text{ nm}$ in diameter composed of globular G-actin monomers that hydrolyze bound ATP upon assembly into F-actin.

Cell Cortex

A dense, specialized network of microfilaments and associated crosslinking proteins localized directly beneath the plasma membrane that determines cell surface shape and drives cell locomotion.

Septins

GTP-binding cytoskeletal proteins that assemble into non-polarized rod complexes (tetramers, hexamers, or octamers), functioning as diffusion barriers in membrane compartmentalization and assisting in cytokinesis.

FtsZ

A prokaryotic tubulin homolog that polymerizes at the midcell into the contractile Z-ring required for cell division and cytokinesis in bacteria, chloroplasts, and mitochondria.

ParM

An actin-like bacterial filament protein that undergoes symmetrical, ATP-driven polymerization to push replicated low-copy plasmids to opposite cellular poles prior to bacterial division.

Cytosol (Hyaloplasm)

The aqueous, structureless colloidal ground substance of the cytoplasm occupying $50\text{--}80\%$ of cellular volume, composed of $70\text{--}80\%$ water, ions, metabolites, and enzymes.

Sol-Gel Transformation

The reversible physical transition of the cytosol between an inner, fluid, low-viscosity sol state and an outer, firm, cortical gel state driven by cytoskeletal polymerization and depolymerization.

Cytoplasmic Inclusions

Non-membrane-bound, insoluble accumulations of stored metabolic reserves, pigments, or crystals lying suspended directly within the cytosol.

Volutin Granules

Dense prokaryotic cytoplasmic inclusion bodies composed of polymerized metaphosphate (polyphosphate) used for energy and phosphate storage.

Bioelements

The chemical elements essential for the constitution of living matter, categorized by abundance into primary ($\text{C, H, O, N, P, S}$), secondary ($\text{Ca, Na, K, Mg, Cl}$), and trace oligoelements.

Hydrogen Bond (Water)

An electrostatic attraction between the electropositive hydrogen atom of one water molecule and the electronegative oxygen atom of an adjacent water molecule, imparting water with high cohesion, high boiling point, and elevated specific heat.

O-Glycosidic Bond

The covalent ether bond formed by a condensation reaction between the anomeric hydroxyl group of one monosaccharide and a hydroxyl group of an adjacent molecule, releasing a water molecule.

Glycogen

A highly branched homopolysaccharide of glucose utilized for carbohydrate storage in animal liver and muscle, containing linear $\text{a}(1\rightarrow 4)$ glycosidic bonds and $\text{a}(1\rightarrow 6)$ branch points.

Cellulose

An unbranched structural homopolysaccharide of plant cell walls formed by repeating D-glucose units linked by $\beta(1\rightarrow 4)$ glycosidic bonds arranged into rigid parallel microfibrils.

Chitin

A linear, unbranched structural homopolysaccharide composed of $N$-acetyl-D-glucosamine monomers joined by $\beta(1\rightarrow 4)$ glycosidic bonds, forming fungal cell walls and arthropod exoskeletons.

Saturated vs. Unsaturated Fatty Acids

Saturated fatty acids contain only single carbon-carbon bonds and pack tightly as solids at room temperature, while unsaturated fatty acids possess one or more cis double bonds that induce kinks and maintain liquidity.

Acylglycerols (Neutral Fats)

Saponifiable lipids formed by the esterification of glycerol with 1, 2, or 3 fatty acid chains, functioning as primary uncharged hydrophobic metabolic energy stores.

Waxes

Esters synthesized from a long-chain fatty acid ($14\text{--}36$ carbons) and a high-molecular-weight monohydroxy fatty alcohol ($16\text{--}30$ carbons), possessing higher melting points than triglycerides and functioning as protective waterproof coatings.

Glycerophospholipids

Amphipathic membrane lipids consisting of a phosphatidic acid core (glycerol esterified to two fatty acid chains and a phosphate group) linked to a polar head group such as choline, ethanolamine, or serine.

Sphingolipids

Amphipathic membrane lipids built upon a ceramide backbone (the amino alcohol sphingosine linked via an amide bond to a fatty acid), categorized into sphingomyelins, cerebrosides, and gangliosides.

Terpenes (Isoprenoids)

Non-saponifiable lipids constructed from multiples of five-carbon isoprene units ($\text{C}_5\text{H}_8$), functioning as pigments, lipid-soluble vitamins ($\text{A, E, K}$), essential oils, and rubber.

Steroids

Non-saponifiable lipids characterized by a tetracyclic hydrocarbon core of four fused rings (cyclopentanoperhydrophenanthrene), encompassing cholesterol, bile acids, and steroid hormones.

Eicosanoids

Locally active 20-carbon fatty acid signaling derivatives including prostaglandins, thromboxanes, and leukotrienes that mediate inflammation, blood clotting, and smooth muscle contractions.

Peptide Bond

A covalent amide bond formed by a dehydration condensation reaction between the $\text{a}$-carboxyl group of one amino acid and the $\text{a}$-amino group of another, forming the protein backbone.

Protein Secondary Structure

The regular, local spatial conformation of a polypeptide backbone stabilized by periodic hydrogen bonding between carbonyl oxygens and amide hydrogens, primarily occurring as $\text{a}$-helices and $\beta$-pleated sheets.

Protein Denaturation

The loss of native secondary, tertiary, and quaternary protein architecture without breaking covalent peptide bonds, triggered by heat, extreme pH, or chemical denaturants, leading to loss of biological activity.

Heteroproteins (Conjugated Proteins)

Proteins composed of a polypeptide chain combined with a non-protein prosthetic group, such as glycoproteins (carbohydrate), lipoproteins (lipid), phosphoproteins (phosphate), or chromoproteins like hemoglobin (heme group).

Enzymes

Globular protein biocatalysts that accelerate chemical reactions by lowering their activation energy without being consumed or altering overall thermodynamic equilibrium.

Phosphodiester Bond

The strong covalent linkage in nucleic acids connecting the $3'$ hydroxyl group of one pentose sugar to the $5'$ hydroxyl group of the adjacent pentose via an intermediate phosphate group.

DNA Double Helix (B-DNA Dimensions)

A right-handed antiparallel double-stranded nucleic acid duplex stabilized by complementary base pairs ($\text{A}=\text{T}$, $\text{G}\equiv\text{C}$) exhibiting a uniform diameter of $20\text{ Å}$, a helical pitch of $34\text{ Å}$ per turn, and a base-pair distance of $3.4\text{ Å}$.

Nucleosome

The primary structural unit of eukaryotic chromatin compaction, consisting of approximately 147 base pairs of DNA wound around an octameric histone core ($\text{two each of H2A, H2B, H3, and H4}$).

Fluid Mosaic Model

The molecular membrane structural model proposed by Singer and Nicolson in 1972 describing biological membranes as dynamic, two-dimensional fluids of oriented amphipathic lipid bilayers in which integral and peripheral proteins are embedded and diffuse laterally.

Flip-Flop (Transverse Diffusion)

The spontaneous translocation of a membrane lipid molecule from one monolayer leaflet to the opposite monolayer leaflet, occurring very infrequently ($< 1\text{ time per month}$) due to the thermodynamic barrier of moving polar head groups through the hydrophobic core.

Transition Temperature (Tm) and Cholesterol

The phase change threshold of lipid bilayers from a rigid gel to a fluid liquid; cholesterol serves as a bidirectional fluidity buffer by decreasing fluidity at temperatures above $T_m$ and preventing tight packing/gelation at temperatures below $T_m$.

Membrane Asymmetry

The unequal structural distribution of lipids and proteins between membrane leaflets; in eukaryotic plasma membranes, phosphatidylcholine and sphingomyelin predominate in the exoplasmic leaflet, whereas phosphatidylethanolamine, phosphatidylinositol, and negatively charged phosphatidylserine reside in the cytosolic leaflet.

Glycocalyx

A carbohydrate-rich protective outer cell-coat consisting of the branched oligosaccharide and polysaccharide chains of membrane glycolipids, transmembrane glycoproteins, and proteoglycans exposed on the external leaflet.