Cell Bio exam 3

Collagen alignment

Helps each tissue withstand its characteristic mechanical stresses, such as woven layers in skin and parallel bundles in tendons.

Fibroblasts and collagen

Attach to secreted collagen and exert traction, pulling and compacting fibrils into organized sheets or cables.

Skin collagen organization

Woven or alternating collagen layers that resist tension in multiple directions.

Tendon collagen organization

Parallel collagen bundles aligned with the main direction of tension.

Collagen (function)

Forms extracellular fibrils that provide tensile strength.

Fibronectin

Extracellular adhesive protein that links collagen to integrins.

Integrins

Transmembrane proteins that connect the extracellular matrix to intracellular actin filaments through adaptor proteins.

Reversible integrin attachments

Provide traction as cells attach, pull, and release during migration.

Integrin activation

Supports signaling in both directions across the membrane (inactive folded form vs active extended form).

Integrin defects

Can impair immune-cell migration or platelet adhesion, causing recurrent infections or excessive bleeding.

Glycosaminoglycans (GAGs)

Negatively charged polysaccharides made of repeating disaccharide units.

Proteoglycans

A core protein with attached GAG chains, often forming a bottlebrush-like structure.

Cartilage matrix

Abundant proteoglycans within a collagen network, forming a resilient matrix that resists compression.

Aggrecan

Cartilage proteoglycan that binds hyaluronan through link proteins to form large extracellular aggregates.

Why GAGs resist compression

Negative charges attract cations and draw in water, creating a hydrated gel that cushions tissues.

Other roles of proteoglycans

Regulate molecular filtration, growth-factor signaling, and cell migration through the ECM.

Apical surface

Epithelial surface that faces a lumen or the external environment.

Basal surface

Epithelial surface that attaches to the basal lamina.

Basal lamina

Thin ECM layer beneath the epithelium, made mainly of type IV collagen and laminin.

Underlying connective tissue

Provides structural support to the epithelium and often contains blood vessels that supply it.

Epithelial polarity

Allows directional functions such as absorption, secretion, and transport.

Tight junctions

Seal neighboring epithelial cells, restrict passage of water-soluble molecules between cells, and separate apical from basolateral membrane domains.

Claudins and occludins

Transmembrane proteins that form branching sealing strands of tight junctions.

Adherens junctions

Use cadherins and linker proteins to connect the actin networks of neighboring cells.

Adhesion belts

Continuous adherens junctions just below the tight junctions near the apical surface, linking contractile actin-myosin bundles across cells.

Epithelial folding by adhesion belts

Localized belt contraction bends a sheet into folds, tubes, cups, or vesicles (neural tube, lens vesicle).

Desmosomes

Cell-to-cell junctions that use cadherins to connect keratin intermediate filaments of adjacent cells and distribute tensile force.

Hemidesmosomes

Attach the basal surface of epithelial cells to the basal lamina using integrins that bind laminin and connect to keratin.

Gap junctions

Channels that let ions and small water-soluble molecules pass directly between neighboring cells' cytoplasms.

Cadherins

Adhesion proteins in adherens junctions and desmosomes that bind identical cadherins on adjacent cells.

Homophilic binding

Binding between identical molecules on neighboring cells (cadherin to cadherin), which requires extracellular Ca2+.

Cell-to-cell vs cell-to-matrix junctions

Cell-to-cell are tight, adherens, desmosomes, and gap junctions. Cell-to-basal lamina are hemidesmosomes (integrin based).

Lung-on-a-chip

Device that recreates the alveolar-capillary interface between lung airspaces and blood vessels.

Lung chip design

Two microchannels separated by a thin, porous, flexible PDMS membrane coated with ECM, with epithelial cells on one side and endothelial cells on the other.

Air-liquid interface in the chip

Air introduced above the epithelium while the vascular channel carries fluid, creating a physiological interface.

Breathing simulation in the chip

Vacuum applied to side chambers cyclically stretches and relaxes the tissues (5 to 15 percent strain).

Soft lithography

Technique used to create recessed microchannels within multiple PDMS layers of the chip.

Chip fabrication steps

Bond a 10 micrometer porous membrane between PDMS layers, then pump PDMS etchant through side channels to remove membrane and form vacuum chambers.

Barrier confirmation in lung chip

Continuous occludin (epithelium) and VE-cadherin (endothelium) junctions, plus near-physiological albumin permeability.

Effect of air exposure in lung chip

Increased surfactant production and a strengthened tissue barrier.

Effect of stretch on cells

Cells distort and align in the direction of applied force.

Lung chip inflammation pathway

Epithelial cytokines (TNF-alpha) activate endothelium, raising ICAM-1, which promotes neutrophil adhesion and migration into the alveolar space.

ICAM-1

Endothelial adhesion molecule that promotes immune-cell adhesion and migration from circulation into the alveolar space.

Neutrophil response on chip

Captured under flow, adhere, crawl to cell junctions, cross the barrier, migrate toward E. coli, and engulf the bacteria.

Breathing and silica nanoparticles

Cyclic strain alone has little effect but strongly amplifies nanoparticle-induced ICAM-1 expression and ROS production.

Strain and nanoparticle translocation

Breathing-like strain increased nanoparticle movement into the vascular channel more than fourfold while albumin transport stayed unchanged, so the barrier was not simply damaged.

N-acetylcysteine

Antioxidant that reduces strain-induced ROS and nanoparticle translocation.

Whole-lung validation of lung chip

In mouse lungs, cyclic breathing increased nanoparticle entry into circulation more than fivefold, matching chip predictions.

Limitations of lung chip

Simplified cellular composition, altered barrier thickness, and no alveolar macrophages.

Requirements to replace animal models

Human biological relevance, predictive accuracy against human data, reproducibility across experiments and labs, standardized protocols, and commercial manufacturing.

Organ chip validation example

Nearly 800 liver chips tested 27 known drugs with up to 87 percent sensitivity and 100 percent specificity.

Membrane-enclosed organelles

Occupy nearly half of a typical eukaryotic cell's volume.

ER surface area

The ER membrane network provides about 20 to 30 times more surface area than the plasma membrane.

Mitochondria in liver cells

About 22 percent of cell volume and roughly 1,700 per cell.

Differential centrifugation

Separates organelles by differences in size and density.

Origin of the nuclear envelope

Thought to arise from plasma membrane infoldings surrounding DNA, which also contributed to the endomembrane system.

Endomembrane system

ER, Golgi, endosomes, lysosomes, nuclear envelope, and plasma membrane, which exchange material by vesicular transport.

Mitochondria and chloroplasts origin

Arose from engulfed bacteria, are not part of the endomembrane system, and import most proteins through protein import machinery.

Nuclear localization signal (NLS)

Exposed signal that lets a protein be recognized by a cytosolic nuclear import receptor.

Nuclear import mechanism

Receptor-cargo complex binds cytosolic fibrils, passes through the gel-like pore meshwork, and releases cargo in the nucleus while the protein stays folded.

Cytosolic retention of a protein

A regulatory partner can mask the NLS or anchor the protein, and a signal can release the restraint to permit nuclear import.

Protein B experiment logic

Protein A is nuclear without protein B even with no hormone, so protein B retains A in the cytosol (by NLS masking or anchoring).

Outward secretory pathway

ER to Golgi to plasma membrane or lysosomes.

Inward endocytic pathway

Plasma membrane to early endosomes to late endosomes to lysosomes.

Vesicle targeting

Targeting proteins direct each vesicle to the appropriate target membrane, preserving organelle identity.

Membrane orientation in vesicular transport

Cytosolic face stays cytosolic and the lumenal face ends up as the extracellular face.

Golgi stack

Stack of 3 to 20 flattened cisternae with a cis face (ER-facing, entry) and trans face (exit).

Glycosylation order

Begins in the ER with a core oligosaccharide, then Golgi enzymes modify it in order ER, cis Golgi, central Golgi, trans Golgi.

Blocking an early glycosylation step

Can also prevent later sugar additions.

Exocytosis

Secretory vesicle membrane fuses with the plasma membrane, releasing soluble cargo outside and adding membrane to the cell surface.

Constitutive secretion

Unregulated exocytosis that needs no specific sorting signal.

Regulated secretion

Vesicles bud from the trans Golgi network, store concentrated cargo, and release it on an extracellular signal (for example insulin after high blood glucose).

Receptor-mediated endocytosis

Concentrates specific macromolecules in clathrin-coated vesicles via cell-surface receptors, over 1,000-fold more efficient than nonspecific pinocytosis.

LDL receptor trafficking

Endosomal acidification separates LDL from its receptor, the receptor recycles, and LDL goes to lysosomes where cholesterol is released.

Preventing LDL-receptor dissociation

Disrupts normal sorting and reduces delivery of LDL cholesterol for release and use.

Organelle import assay

Mix labeled proteins with isolated organelles, then use centrifugation and protease to test whether the protein is inside.

Protease protection logic

An intact membrane protects imported proteins from external protease, and adding detergent disrupts the membrane so they are digested.

Co-sedimentation limitation

Cannot distinguish proteins inside an organelle from those stuck to its surface.

Receptor expression and signaling

Types and amounts of receptors determine which signals a cell detects and how strongly it responds.

Signal combinations

Specific combinations promote survival, growth and division, or differentiation, and without survival signals most animal cells undergo apoptosis.

Gi and K+ channel in heart pacemaker cells

Acetylcholine activates a GPCR, Galpha-i exchanges GDP for GTP, and the Gbetagamma complex opens a K+ channel, slowing heart rate.

Ending G protein channel activation

GTP hydrolysis lets Galpha rejoin Gbetagamma, and delaying this step prolongs the response.

cAMP pathway

Active stimulatory Galpha turns on adenylyl cyclase, which converts ATP to cAMP.

Switching off Galpha

Galpha hydrolyzes GTP to GDP, and failure to do so prolongs adenylyl cyclase activation and cAMP production.

cAMP phosphodiesterase

Terminates the cAMP signal by hydrolyzing cAMP to AMP.

Mouse fur color prediction

Galpha that binds but cannot hydrolyze GTP gives prolonged cAMP and pigment signaling, so dark brown fur (like losing phosphodiesterase).

Nitric oxide (NO) signaling

Acetylcholine activates a Gq receptor in endothelium, IP3 raises Ca2+, NO synthase makes NO from arginine, and NO diffuses to smooth muscle.

NO action in smooth muscle

Activates guanylyl cyclase, which converts GTP to cGMP and causes relaxation.

cGMP level control

Production by guanylyl cyclase and breakdown by cGMP phosphodiesterase.

RTK activation

Ligand binding causes dimerization, kinase domains cross-phosphorylate tyrosines, and phosphotyrosines become docking sites for SH2-domain proteins.

Terminating RTK signaling

Tyrosine phosphatases remove phosphates, and receptor endocytosis targets receptors for degradation.

PI 3-kinase pathway

RTK recruits PI 3-kinase, which phosphorylates inositol phospholipids to create docking sites that recruit and activate Akt.

Akt and cell survival

Active Akt phosphorylates Bad, which releases active Bcl2 to inhibit apoptosis.

Unphosphorylated Bad

Binds and inhibits Bcl2, a protein that normally suppresses apoptosis.

Tor

Kinase activated through the RTK, PI 3-kinase, Akt pathway that increases cell size by stimulating protein synthesis and inhibiting degradation.

Rapamycin

Anticancer drug that suppresses cell growth by inhibiting Tor.

Phospholipase C

Activated by both GPCRs and RTKs, leading to Ca2+ release, calmodulin activation, and CaM-kinase activation.

Pathway ordering with Ras

If constitutively active Ras restores signaling in a protein X mutant, X is upstream of Ras. If signaling still needs protein Y, Y is downstream of Ras.

Intermediate filament structure

Two monomers form a coiled-coil dimer, two dimers form a staggered antiparallel tetramer (no polarity), and tetramers associate side by side into a rope-like filament about 10 nm wide.

Keratin intermediate filaments

Form strong flexible networks in epithelial cells anchored by desmosomes (cell to cell) and hemidesmosomes (to basal lamina).