Cell Biology: Comprehensive Lecture Review

Comprehensive practice flashcards reviewing the seven core cell biology lectures: Cell Introduction & Microscopy, Biological Membranes, The Nucleus & Endomembrane System, Cell Junctions & Adhesion, Extracellular Matrix, The Cytoskeleton, and The Cell Cycle.

Who coined the term 'cell' in 1665 after examining cork tissue under a microscope, and in which publication did this work appear?

Robert Hooke coined the term in his 1665 publication Micrographia.

What are the typical magnification ranges for standard light microscopes compared to electron microscopes?

Light microscopes typically magnify from $\times 40$ to $\times 1000$, whereas electron microscopes can achieve magnifications of up to around $\times 1{,}000{,}000$.

How does resolution differ from magnification in microscopy?

Magnification makes a specimen appear larger, whereas resolution is the capacity to distinguish two closely spaced objects as separate and distinct entities.

What is the defining optical property of a fluorophore in fluorescence microscopy?

A fluorophore is a molecule that absorbs light at a shorter excitation wavelength and emits light at a longer wavelength.

What is the primary difference in image generation between a Transmission Electron Microscope (TEM) and a Scanning Electron Microscope (SEM)?

A TEM transmits electrons directly through a thin specimen to create a 2D projection, whereas an SEM sweeps electrons across the surface to produce a 3D surface image.

What are the typical size ranges of prokaryotic cells compared to eukaryotic cells?

Prokaryotic cells typically range from $1\,\mu\text{m}$ to $10\,\mu\text{m}$ in diameter or length, whereas eukaryotic cells typically range from $10\,\mu\text{m}$ to $100\,\mu\text{m}$.

What specialized internal membrane system allows certain photosynthetic prokaryotes, such as cyanobacteria, to perform photosynthesis?

The thylakoid membrane.

Which eukaryotic organelles are surrounded by a double membrane (two lipid bilayers)?

The nucleus, mitochondria, and chloroplasts.

What is the function of the enzyme catalase found inside peroxisomes?

Catalase breaks down toxic hydrogen peroxide ($H_2O_2$), which is generated by peroxisomal oxidation reactions, into water and molecular oxygen.

What are the three major molecular constituents of biological membranes and their approximate percentages by weight?

Lipids ($22\%$ to $79\%$), proteins ($18\%$ to $78\%$), and carbohydrates ($0\%$ to $10\%$).

Why is the formation of a phospholipid bilayer in water energetically favorable?

Phospholipids are amphipathic; their hydrophilic heads form hydrogen bonds with water, while their hydrophobic fatty acid tails interact with each other in the interior to exclude water.

What structural backbone replaces glycerol in the membrane phospholipid sphingomyelin?

Sphingosine, an $18$-carbon amino alcohol.

What four types of phospholipid movements occur within biological membranes, and which is extremely rare without enzyme catalysis?

Lateral diffusion, rotation, flexion, and flip-flop; flip-flop between leaflets is extremely rare without catalytic enzymes.

How does cholesterol regulate membrane fluidity across different temperatures?

At higher temperatures, cholesterol restricts excessive phospholipid movement to reduce fluidity; at lower temperatures, it prevents tight packing of fatty acid tails to inhibit solidification.

How do peripheral membrane proteins differ from integral membrane proteins in their membrane attachment?

Integral membrane proteins possess hydrophobic domains that span or embed into the lipid bilayer, whereas peripheral membrane proteins lack exposed hydrophobic regions and associate non-covalently with integral proteins or membrane lipid heads.

In the asymmetric plasma membrane, which phospholipids and glycolipids are predominantly found in the extracellular leaflet versus the cytoplasmic leaflet?

The extracellular leaflet contains phosphatidylcholine (PC), sphingomyelin (SM), and glycolipids; the cytoplasmic leaflet contains phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylinositol (PI).

What intermediate filament proteins constitute the nuclear lamina, and what is its primary function?

Lamins (Lamin A, Lamin B, and Lamin C); they form a supportive fibrous meshwork beneath the inner nuclear membrane to maintain nuclear shape and structure.

What group of genetic diseases is caused by mutations in lamin genes, and which syndrome causes premature aging?

Laminopathies; Hutchinson-Gilford Progeria Syndrome causes premature aging.

Which targeting sequences and transport receptors direct proteins into and out of the nucleus through the nuclear pore complex?

A nuclear localization signal (NLS) is recognized by importin for import into the nucleus, and a nuclear export signal (NES) is recognized by exportin for export to the cytoplasm, both coordinated by the GTPase Ran.

How do euchromatin and heterochromatin differ in condensation, nuclear staining, and transcriptional activity?

Euchromatin is loosely packed, lightly stained, and transcriptionally active; heterochromatin is tightly packed, darkly stained, and transcriptionally inactive.

What specific functions take place within the nucleolus of a eukaryotic cell?

Ribosomal RNA (rRNA) is transcribed and processed, and combines with imported ribosomal proteins to assemble the small and large ribosomal subunits.

What enzyme deficiency causes Glycogen Storage Disease type 1a (GSD-1a), and what clinical manifestations result?

A deficiency in Glucose-6-phosphatase; it causes glycogen buildup in the liver, hepatomegaly, and severe hypoglycemia.

What is the function of the signal recognition particle (SRP) in directing nascent polypeptides to the rough endoplasmic reticulum?

SRP binds the N-terminal hydrophobic signal sequence emerging from a cytosolic ribosome and targets the ribosome-polypeptide complex to an SRP receptor in the rough ER membrane.

What key post-translational modifications occur to newly synthesized proteins within the lumen of the rough ER?

Cleavage of the signal sequence, assisted protein folding, N-linked glycosylation, and the formation of disulfide bonds between cysteine residues.

How do the cis face and trans face of the Golgi apparatus differ functionally?

The cis face faces the rough ER and receives incoming transport vesicles, whereas the trans face sorts, packages, and buds off vesicles destined for the plasma membrane, secretory vesicles, or lysosomes.

What biochemical defect underlies Tay-Sachs disease, and what is the pathological outcome?

A deficiency of a lysosomal enzyme prevents the degradation of ganglioside lipids, resulting in ganglioside accumulation in brain cells, progressive neurodegeneration, blindness, deafness, and early childhood death.

What distinguishes homotypic cell adhesion from heterotypic cell adhesion?

Homotypic adhesion occurs between identical cell types, whereas heterotypic adhesion occurs between cells of different types.

What is cell polarity in an epithelial monolayer, and what are its three primary surfaces?

The asymmetric structural and functional organization of the cell surface into an apical membrane (facing the lumen), a lateral membrane (contacting neighboring cells), and a basal membrane (anchoring to the basement membrane).

Which transmembrane and scaffolding proteins form tight junctions, and what are the primary roles of these junctions?

Transmembrane proteins claudins, occludin, and junctional adhesion molecules (JAMs) linked via the scaffolding protein ZO-1 to the actin cytoskeleton; they prevent diffusion of membrane proteins to maintain polarity and regulate paracellular transport.

What CAMs and cytoplasmic adaptor proteins form adherens junctions, and which cytoskeletal element do they anchor?

Cadherins (calcium-dependent CAMs) interact homophilically in the extracellular space and bind intracellular adaptor proteins called catenins, which attach to actin filaments.

What transmembrane proteins and plaque adaptors make up desmosomes, and which cytoskeletal filament provides their tensile strength?

Desmoglein and desmocollin (cadherins) anchored to a dense cytoplasmic plaque (containing plakoglobin, plakophilin, and desmoplakin), which connects directly to keratin intermediate filaments.

What structural unit forms a gap junction channel, and what size limit restricts molecular passage through it?

Six connexin proteins form a cylindrical hemichannel called a connexon; two aligned connexons form an intercellular channel permeable to inorganic ions and small metabolites up to approximately $1200\,\text{Da}$.

What are the five consecutive stages of leukocyte extravasation during inflammation?

1. Rolling (selectins binding carbohydrate ligands); 2. Activation (chemokine signaling); 3. Firm adhesion (activated integrins binding ICAM-1/VCAM-1); 4. Diapedesis; 5. Migration into tissues.

What repeating amino acid motif characterizes collagen alpha chains, and why is glycine strictly required at every third residue?

The Gly-X-Y repeat (where X is often proline and Y is often hydroxyproline); glycine is the smallest amino acid and is required to fit inside the tightly packed core of the triple helix.

Why is vitamin C essential for collagen structural stability, and what condition occurs in its absence?

Vitamin C is an essential cofactor for prolyl and lysyl hydroxylases that generate hydroxyproline and hydroxylysine; its deficiency impairs hydrogen bonding in the triple helix, causing scurvy.

What are the four primary functional classes of collagen, and which collagen types exemplify them?

Fibril-forming (Type I), fibril-associated/FACIT (Type IX), network-forming (Type IV), and transmembrane (Type XVII).

How does cell-surface traction mediate the assembly of soluble fibronectin dimers into insoluble ECM fibrils?

Integrins on the cell surface bind fibronectin, and intracellular actomyosin contractions apply mechanical tension, unfolding the fibronectin dimer to expose cryptic binding sites that promote fibrillogenesis.

What are the two structural components of elastic fibres, and what functional roles do their hydrophobic versus hydrophilic regions play?

An elastin core surrounded by a fibrillin-rich microfibrillar sheath; hydrophobic regions give elastin elasticity and recoil by adopting alternative conformations, while hydrophilic lysine-rich regions form covalent cross-links for tensile strength.

What is the structural distinction between typical proteoglycans and hyaluronan (hyaluronic acid)?

Proteoglycans consist of glycosaminoglycan (GAG) chains covalently linked to a central core protein; hyaluronan is an exceptionally long, non-sulfated GAG that exists independently without covalent attachment to a core protein.

How do hemidesmosomes and focal adhesions differ in their intracellular cytoskeletal attachments and primary ECM ligands?

Hemidesmosomes anchor intermediate filaments (keratin) via integrin $\alpha_6\beta_4$ to laminin in the basal lamina, whereas focal adhesions anchor actin microfilaments via integrins to fibronectin to mediate dynamic migration and signaling.

What are the four principal molecular constituents of the basal lamina?

Type IV collagen, laminin, nidogen (entactin), and heparan sulfate proteoglycans (such as perlecan).

What nucleotide bound states distinguish monomeric G-actin from polymerized F-actin?

Free G-actin monomers predominantly bind ATP, whereas F-actin subunits within the microfilament hydrolyze ATP and become bound to ADP.

What three distinct kinetic phases characterize in vitro actin microfilament assembly?

1. Nucleation (formation of a stable actin trimer nucleus); 2. Elongation (rapid subunit addition at both ends); 3. Steady state (equilibrium between addition and dissociation).

What is actin treadmilling, and at which ends of the filament do net polymerization and depolymerization occur?

Treadmilling is the steady-state dynamic flux where G-actin-ATP monomers add preferentially to the barbed (+ or plus) end while G-actin-ADP subunits dissociate from the pointed (- or minus) end at identical rates, maintaining a constant overall filament length.

How is a eukaryotic microtubule assembled, what is its outer diameter, and what are its constituent subunits?

A microtubule is a stiff, hollow cylinder measuring $25\,\text{nm}$ in outer diameter, composed of $13$ parallel protofilaments formed by alternating $\alpha$- and $\beta$-tubulin heterodimers.

What is dynamic instability in microtubules, and what nucleotide state of the tubulin dimer dictates the presence of a GTP cap?

Dynamic instability is the stochastic switching between growth and shrinkage; a GTP cap composed of GTP-bound $\beta$-tubulin stabilizes the plus end in a straight conformation, whereas GTP hydrolysis to GDP causes conformational strain, curvature, and rapid catastrophe upon cap loss.

Which molecular motor proteins travel along microtubules, and in which direction do they move relative to microtubule polarity?

Kinesins move toward the plus (+) end (anterograde), whereas dyneins move toward the minus (-) end (retrograde).

Why do mature intermediate filaments lack structural polarity compared to actin filaments and microtubules?

Intermediate filament monomers form parallel coiled-coil dimers, which then associate in an antiparallel, staggered orientation to generate symmetric tetramers that possess identical ends.

Which specific intermediate filament proteins are expressed in epithelial cells, mesenchymal cells, muscle cells, and astrocytes?

Epithelial cells express keratins (Classes I and II); mesenchymal cells express vimentin; muscle cells express desmin; and astrocytes express glial fibrillary acidic protein (GFAP).

What two functional chromosomal loci control the replication cycle during prokaryotic binary fission?

The origin of replication (ori), where DNA replication begins, and the termination of replication site (ter), where replication ends.

What are the four defined phases of the eukaryotic cell cycle, and which comprise interphase?

The four phases are G1, S, G2, and M; interphase consists of G1, S, and G2.

How does the cellular DNA content change between the G1 phase and the G2 phase of the eukaryotic cell cycle?

In G1, the cell is diploid ($2n$); during S phase, DNA replication doubles the genome content to $4n$, which is maintained throughout G2 until cytokinesis.

How do cyclins activate cyclin-dependent kinases (CDKs) to regulate cell cycle progression?

CDKs are constitutively expressed but inactive alone; cyclin binding induces a conformational change exposing the catalytic active site of the CDK, allowing it to phosphorylate specific protein substrates using ATP.

What is the biochemical mechanism by which G1/S cyclin-CDK complexes drive cells past the restriction point (R)?

The G1/S cyclin-CDK complex phosphorylates the retinoblastoma protein (RB), inducing a conformational change that inactivates RB and relieves its transcriptional inhibition of S-phase entry.

What is the sequential order of cyclin-CDK complexes that regulate cell cycle progression from G1 to M phase (mnemonic DEAB)?

Cyclin D-Cdk4 (G1 progression), Cyclin E-Cdk2 (G1/S transition), Cyclin A-Cdk2 (S-phase replication), and Cyclin B-Cdk1 (M-phase mitosis).

How does the tumor suppressor p53 initiate cell cycle arrest in response to DNA damage?

DNA damage stabilizes p53, which induces the expression of the CDK inhibitor p21 ($21\,\text{kDa}$); p21 binds directly to G1/S cyclin-CDK complexes, inhibiting their catalytic activity and arresting the cell cycle.

What extrinsic signaling molecule released by blood platelets stimulates adjacent skin cells to enter the cell cycle during wound repair?

Platelet-derived growth factor (PDGF).