Cell Biology: Cytoskeleton, Cell Motility, Adhesions, Cell Signaling, and Nuclear Structure

Comprehensive vocabulary flashcards covering cytoskeletal architecture (microtubules, microfilaments, intermediate filaments), molecular motor mechanisms, muscle contraction, cell junctions and ECM, GPCR and RTK signal transduction pathways, DNA structure, and nuclear organization.

Nucleosome Core Particle

The basic structural unit of chromatin consisting of a histone octamer (two $H2A\text{--}H2B$ dimers and two $H3\text{--}H4$ dimers) wrapped by approximately $146\,\text{bp}$ of DNA about $1.7$ times.

Histone H1

A linker histone not part of the octamer core that binds linker DNA between nucleosomes and facilitates the compaction of the $10\,\text{nm}$ chromatin fiber into the $30\,\text{nm}$ chromatin fiber.

Chromatin Packing Levels

The progressive compaction of genomic DNA from a $2\,\text{nm}$ DNA double helix into a $10\,\text{nm}$ 'beads-on-a-string' nucleosome fiber, a $30\,\text{nm}$ chromatin fiber, $300\,\text{nm}$ loops, $700\,\text{nm}$ heterochromatin, and ultimately a $1400\,\text{nm}$ mitotic chromosome.

Histone Code

The combinatorial pattern of specific covalent post-translational modifications (methylation, acetylation, phosphorylation, ubiquitination) on protruding histone amino-terminal tails that regulates transcriptional activity and chromatin structure.

Histone Acetyltransferases (HATs)

Enzymes that transfer acetyl groups to lysine residues on histone side chains, neutralizing positive charges, relaxing chromatin structure, and promoting transcriptional activation.

Histone Deacetylases (HDACs)

Enzymes that remove acetyl groups from histone amino-terminal tails, restoring positive charges, leading to tighter chromatin packing and transcriptional repression.

SWI/SNF Family

An ATP-dependent class of chromatin remodeling proteins that alters the position of nucleosomes along DNA by sliding or ejecting them, thereby increasing DNA accessibility.

Chromodomain vs. Bromodomain

Protein structural motifs where chromodomains recognize and bind methylated histones characteristic of compact chromatin, while bromodomains specifically bind acetylated histone lysines associated with open, transcriptionally active chromatin.

Constitutive Heterochromatin

Permanently compacted, transcriptionally silent chromatin that serves structural roles within chromosomes, exemplified by centromeres and telomeres.

Centromere

An internal, highly repetitive constitutive heterochromatin locus on each chromosome that maintains sister chromatid cohesion and serves as the assembly site for the kinetochore to attach spindle microtubules during mitosis and meiosis.

Telomere

A repetitive DNA structure located at the ends of linear eukaryotic chromosomes (having the conserved sequence $\text{TTAGGG}$ in all vertebrates) that protects chromosome termini from degradation and shortening during replication.

G Bands

Distinct, reproducible alternating light and dark bands visible on mitotic chromosomes under light microscopy produced by staining with Giemsa stain.

LINEs and SINEs

Classes of interspersed repeated transposable elements where LINEs (long interspersed nuclear elements) measure $6000\text{--}8000\,\text{bp}$ and encode transposition machinery, while SINEs (short interspersed nuclear elements) are under $500\,\text{bp}$ and rely on external enzymes (e.g., human Alu sequences, making up $10\%$ of the genome).

Nuclear Pore Complex (NPC)

A symmetrical macromolecular channel of approximately $120\,\text{nm}$ diameter composed of about $30$ distinct nucleoporins that spans the inner and outer nuclear membranes to mediate nucleocytoplasmic exchange.

Nuclear Localization Signal (NLS)

An amino acid targeting sequence ($8\text{--}30$ residues long, typically rich in basic residues lysine, arginine, and proline) on a cargo protein that directs its active import into the nucleus via importins.

Ran GTPase Cycle

A nucleocytoplasmic transport regulatory system maintained by a nuclear GEF (which loads GTP onto Ran) and a cytoplasmic GAP (which stimulates Ran GTP hydrolysis), governing cargo loading and release by importins and exportins.

Nuclear Lamina

A dense meshwork of intermediate filaments composed of lamins (classes A, B, and C) lining the nucleoplasmic face of the inner nuclear membrane that provides mechanical support to the nucleus.

Nucleolus

A prominent non-membrane-bound subnuclear compartment containing fibrils (transcription of rRNA genes) and granules (assembly of ribosomal RNA with ribosomal proteins into subunits).

Genetic Transformation

The permanent change in genotype and phenotype of a bacterium mediated by the direct uptake of foreign naked DNA, first demonstrated in Streptococcus pneumoniae by Frederick Griffith.

Avery-MacLeod-McCarty Experiment

The experimental demonstration that DNA is the transforming material of virulent bacteria, proven when transforming activity was destroyed exclusively by DNase, but not by proteases, RNase, or lipid/polysaccharide-degrading enzymes.

Chargaff's Rules

The biochemical observation that in all double-stranded cellular DNA, the stoichiometric molar ratio of adenine equals thymine ($A = T$) and guanine equals cytosine ($G = C$).

B-DNA

The predominant right-handed conformation of the DNA double helix in physiological conditions, featuring a diameter of $2\,\text{nm}$, a helical rise of $0.34\,\text{nm}$ per base pair, a pitch of $3.4\,\text{nm}$, and distinct major and minor grooves.

DNA Supercoiling

The twisting of the DNA double helix upon its own axis into higher-order tertiary coils, occurring as positive supercoiling (overtwisting in the same direction) or negative supercoiling (undertwisting in the opposite direction).

Topoisomerases

Enzymes that regulate DNA supercoiling; Type I topoisomerases produce transient single-strand breaks without ATP, whereas Type II topoisomerases (such as bacterial DNA gyrase) produce ATP-dependent double-strand breaks.

DNA Melting Temperature ($T_m$)

The precise temperature at which half of the maximum absorbance increase at $260\,\text{nm}$ is reached due to the thermal denaturation (unwinding) of double-stranded DNA into single strands, increasing linearly with $G + C$ content.

Fluorescent In Situ Hybridization (FISH)

A cytogenetic technique utilizing fluorescently labeled single-stranded DNA or RNA probes to hybridize to complementary target sequences in intact chromosomes or cells.

Microtubule

A hollow cylindrical cytoskeletal polymer with an outer diameter of $25\,\text{nm}$ and an inner diameter of $15\,\text{nm}$, typically composed of $13$ protofilaments of alternating $\alpha\beta$-tubulin heterodimers that utilize GTP and exhibit structural polarity.

Microtubule Treadmilling

A dynamic steady-state behavior occurring when free tubulin concentration is above the critical concentration for the plus end but below that for the minus end, resulting in net subunit addition at the plus end and simultaneous subunit loss at the minus end.

Dynamic Instability

The coexistence of growing and shrinking microtubules in the same population, governed by the presence of a GTP cap at the plus end: rapid depolymerization after cap loss is termed catastrophe, while transition back to growth is rescue.

Colchicine

An antimitotic plant alkaloid that binds to $\beta$-tubulin monomers, inhibiting microtubule assembly, promoting disassembly, and preventing mitotic spindle formation.

Taxol

An antimitotic chemotherapy drug (paclitaxel) that binds tightly to polymerized microtubules and stabilizes them, preventing spindle disassembly and arresting dividing cells in mitosis.

$\gamma$-Tubulin Ring Complex ($\gamma$-TuRC)

A ring-shaped protein complex found within the pericentriolar material of the centrosome that nucleates the polymerization of new microtubules, capping and anchoring their minus ends.

Microtubule-Associated Proteins (MAPs)

Cytoskeletal accessory proteins (such as Tau in axons and MAP2 in dendrites) that bind along microtubule walls at regular intervals to stabilize them and bundle them into organized parallel arrays.

EB1

A plus-end tracking protein (+-TIP) that binds selectively to growing microtubule plus ends, stabilizing them and reducing the likelihood of catastrophic depolymerization.

MCAK

Mitotic centromere-associated kinesin; a specialized kinesin-13 catastrophin that lacks motor translocation activity and instead induces microtubule depolymerization by destabilizing plus ends.

Microfilaments (F-Actin)

Cytoskeletal fibers measuring $7\,\text{nm}$ in diameter formed by the reversible ATP-dependent polymerization of globular G-actin monomers into two intertwined helical strands with barbed (plus) and pointed (minus) ends.

Thymosin $\beta 4$

An actin monomer-sequestering protein that binds free ATP-G-actin, preventing spontaneous microfilament assembly and maintaining a buffered cytosolic pool of unpolymerized actin.

Profilin

An actin-binding regulatory protein that competes with thymosin $\beta 4$ for binding to G-actin monomers, catalyzing ADP-to-ATP exchange and directing monomers to polymerize onto filament barbed ends.

CapZ and Tropomodulin

Filament-capping proteins where CapZ binds specifically to the barbed (plus) end of microfilaments to inhibit subunit turnover, while tropomodulin binds to the pointed (minus) end to prevent depolymerization.

Arp2/3 Complex

A multi-protein actin-nucleating complex activated by WASP or WAVE/Scar that binds to the side of preexisting microfilaments to initiate new actin branches at a $70^\circ$ angle.

Formins

Dimers of actin-nucleating and elongating proteins with flexible whiskers that capture profilin-actin complexes to promote the rapid assembly of unbranched, long actin filaments at the barbed end.

Rho Family GTPases

Monomeric G proteins (Rho, Rac, and Cdc42) acting as molecular switches for actin organization: activated Rho triggers stress fiber formation, activated Rac stimulates lamellipodial branched networks, and activated Cdc42 promotes filopodial parallel bundles.

Intermediate Filaments (IFs)

Tough, flexible cytoskeletal cords ($8\text{--}12\,\text{nm}$ diameter) assembled from anti-parallel fibrous tetramers into eight protofilaments that have no inherent structural polarity and do not bind nucleotides.

Kinesin-1

A plus-end directed, dimeric microtubule motor protein composed of two heavy chains with ATPase head domains and two light chains that drives processive anterograde fast axonal transport of vesicular cargo.

Cytoplasmic Dynein

A large, minus-end directed microtubule motor protein complex that associates with dynactin to transport vesicles and organelles in retrograde fast axonal transport toward the cell body/centrosome.

Axoneme

The central structural core of eukaryotic cilia and flagella containing an arrangement of nine outer doublet microtubules (composed of a complete 13-protofilament A tubule and an incomplete B tubule) surrounding a central microtubule pair ('$9 + 2$' pattern).

Nexin

An interdoublet protein linker in the axoneme that bridges adjacent outer doublets to restrain unrestrained microtubule sliding and convert dynein-generated shearing forces into axonemal bending.

Myosin II

A two-headed, plus-end-directed microfilament motor protein with two heavy chains, two essential light chains, and two regulatory light chains that self-assembles into bipolar thick filaments to drive muscle contraction and cytokinesis.

Sarcomere

The repeating contractile unit of a muscle myofibril delimited by two Z lines, consisting of an anisotropic dark A band, isotropic light I bands, a central H zone, and an M line.

Thin Filament

The microfilament-containing contractile element of striated muscle composed of F-actin intertwined with continuous strands of tropomyosin and calcium-sensitive troponin complexes (TnT, TnI, and TnC).

Cross-Bridge Cycle

The cyclical mechanical sequence in muscle contraction wherein ATP hydrolysis cocks the myosin head, cross-bridge formation occurs, inorganic phosphate release triggers the power stroke, and new ATP binding induces detachment from actin.

Myosin Light-Chain Kinase (MLCK)

An enzyme activated by $\text{Ca}^{2+}$-calmodulin in smooth muscle cells that phosphorylates the regulatory light chain of myosin II, inducing a conformational change that enables filament assembly and cross-bridge cycling.

Adherens Junction

An actin-anchored cell-cell adhesive junction prominent in epithelia that mediates continuous mechanical attachment via cadherin homophilic binding connected intracellularly to actin via $\beta$-catenin and $\alpha$-catenin.

Desmosome

A button-like cell-cell adhesive junction that confers high tensile strength to tissues by linking desmosomal cadherins (desmocollins and desmogleins) across a $25\text{--}35\,\text{nm}$ intercellular space to intermediate filaments via dense plaque proteins.

Tight Junction

An occluding junction formed by interlocking rows of claudins and occludins that seals adjacent epithelial cells together, creating a selective paracellular permeability barrier and preventing lateral diffusion of lipids and membrane proteins.

Gap Junction

A communicating junction formed by aligned hexameric cylindrical channels called connexons in adjacent membranes, establishing a continuous aqueous pore ($3\,\text{nm}$ wide) for the direct intercellular passage of ions and small molecules.

Collagen

The most abundant extracellular matrix structural glycoprotein in animals, synthesized as procollagen triple helices in the ER, cleaved by procollagen peptidase extracellularly, and assembled into staggered fibrils with a characteristic $67\,\text{nm}$ repeat pattern.

Proteoglycan

An extracellular matrix complex composed of numerous negatively charged glycosaminoglycan (GAG) chains (such as chondroitin sulfate or keratan sulfate) covalently linked along the length of a core protein, often anchored noncovalently to hyaluronate.

Fibronectin

A dimeric adhesive glycoprotein linked by two disulfide bonds at its C-termini that binds to cell surface integrins via an Arg-Gly-Asp (RGD) tripeptide sequence and simultaneously attaches to ECM components like collagen, heparin, and fibrin.

Integrin

A heterodimeric transmembrane cell surface receptor consisting of $\alpha$ and $\beta$ subunits that mechanically couples extracellular ligands (such as fibronectin or laminin) to the actin cytoskeleton at focal adhesions or to intermediate filaments at hemidesmosomes.

Focal Adhesion

A localized, dynamic multiprotein complex through which cultured or migrating non-epithelial cells attach to the extracellular matrix, containing clustered integrins connected to stress fiber actin bundles via talin, vinculin, and $\alpha$-actinin.

Hemidesmosome

A specialized adhesive structure in epithelial cells mediating stable anchorage to the underlying basal lamina, utilizing $\alpha_6\beta_4$ integrin and plectin-containing plaques to connect to intermediate filaments (keratin).

Plasmodesma

A membrane-lined cytoplasmic channel traversing the plant cell wall that contains a central tubular desmotubule derived from the endoplasmic reticulum and an annulus, permitting direct intercellular transport.

G Protein-Coupled Receptor (GPCR)

A major superfamily of cell-surface signaling receptors with seven transmembrane $\alpha$-helices, an extracellular ligand-binding domain, and cytosolic loops that interact with heterotrimeric G proteins.

Heterotrimeric G Protein

A membrane-associated molecular switch composed of $G_\alpha$, $G_\beta$, and $G_\gamma$ subunits: ligand-bound GPCR causes $G_\alpha$ to exchange GDP for GTP and dissociate from $G_{\beta\gamma}$, allowing both components to interact with downstream effectors.

Protein Kinase A (PKA)

A cAMP-dependent serine/threonine protein kinase consisting of two regulatory and two catalytic subunits; binding of four cyclic AMP molecules to the regulatory subunits causes dissociation and release of active catalytic monomers.

Phospholipase C (PLC)

An effector enzyme activated by $G_q$ or receptor tyrosine kinases that cleaves membrane phosphatidylinositol-4,5-bisphosphate ($\text{PIP}_2$) into the soluble second messenger inositol-1,4,5-trisphosphate ($\text{IP}_3$) and membrane-bound diacylglycerol (DAG).

Calmodulin

An ubiquitous intracellular calcium sensor protein shaped like an arm with two globular domains, each binding two $\text{Ca}^{2+}$ ions (four total), which undergoes a conformational change to bind and activate target enzymes such as MLCK.

Receptor Tyrosine Kinase (RTK)

A class of single-pass transmembrane cell-surface receptors whose intracellular domain has intrinsic tyrosine kinase activity that undergoes ligand-induced dimerization (or clustering) and cross-autophosphorylation.

SH2 Domain

A conserved protein domain (Src Homology 2) found in signaling adaptors like GRB2 and enzymes like $\text{PLC}_\gamma$ that specifically recognizes and binds phosphorylated tyrosine residues within defined amino acid motifs on activated RTKs.

Ras-MAPK Pathway

A canonical mitogenic signaling cascade wherein activated Ras-GTP recruits and activates Raf (a MAPKKK), which phosphorylates MEK (a MAPKK), which phosphorylates MAPK, which then translocates to the nucleus to phosphorylate transcription factors Jun and Ets.

Ste5

A yeast scaffolding protein that binds the components of the mating pheromone MAPK cascade into a organized signaling complex at the membrane upon recruitment by the activated $G_{\beta\gamma}$ subunit.