The Cell – Comprehensive Study Notes

Cell Theory

• All living things are composed of cells.
• Cells are the basic unit of all organisms.
• All cells arise from pre-existing cells.

Types of Cells

• Two major categories
  • Prokaryotic cells (prokaryotes).
  • Eukaryotic cells (eukaryotes).
• Defining features
  • Prokaryotes: lack a true, membrane-bound nucleus and other membrane-bound organelles.
  • Eukaryotes: possess a true nucleus and numerous membrane-bound organelles.

Prokaryotic Cells

• Size: $0.5-5\,\mu m$ diameter.
• Metabolic strategies
  • Photoautotroph: energy from light, carbon from $CO_2$.
  • Chemoautotroph: energy from chemical reactions, carbon from $CO_2$.
  • Photoheterotroph: energy from light, carbon from organic molecules.
  • Chemoheterotroph: energy and carbon from organic compounds.
• Structural components (example: Bacillus coagulans)
  • Pili – attachment.
  • Nucleoid – DNA region (circular, naked DNA).
  • Ribosomes – $70\,S$ ($18\,nm$).
  • Plasma membrane.
  • Cell wall – peptidoglycan.
  • Capsule – glycoprotein, jelly-like.
  • Flagella – locomotion organelles.

Eukaryotic Cells

• Size: $10-100\,\mu m$ diameter, generally larger than prokaryotes.
• Characteristics
  • DNA enclosed in a double-membrane nucleus; DNA linear, associated with proteins.
  • Cytoplasm between plasma membrane and nucleus.
  • Extensive internal membrane system; membrane-bound organelles.
• Surface-area-to-volume considerations
  • Plasma membrane supplies $O_2$, nutrients, removes waste.
  • As cell size ↑, volume grows faster than surface area → limits size.

Comparative Summary

• Cell wall: prokaryote – peptidoglycan; eukaryote – cellulose (plants) or chitin (fungi).
• Flagellum: prokaryote – simple, single filament; eukaryote – complex $9+2$ microtubule array.
• Ribosomes: prokaryote $70\,S$; eukaryote $80\,S$ ($22\,nm$).
• Organelles: prokaryote – few, none membrane-bound; eukaryote – many, some membrane-bound.
• Capsules & pili present only in some prokaryotes.

Microscopy & Cell Study Techniques

• Light Microscope (LM)
  • Magnification, resolution, contrast are key parameters.
  • Bright-field (stained/unstained), phase-contrast, DIC, fluorescence, confocal enhance visualization.
• Electron Microscopes
  • Transmission (TEM) – internal ultrastructure.
  • Scanning (SEM) – 3-D surface topology.
  • Cryo-EM – vitrified samples at very low $T$, near-native state; complements X-ray crystallography.
• Cell Fractionation
  • Homogenization → differential centrifugation.
  • $1{,}000\,g$ for $10\,min$ → nuclei/debris.
  • $20{,}000\,g$ for $20\,min$ → mitochondria/chloroplasts.
  • $80{,}000\,g$ for $60\,min$ → microsomes.
  • $150{,}000\,g$ for $3\,h$ → ribosomes.

Nucleus

• Enclosed by nuclear envelope (double membrane with pores).
• Contains chromosomes (DNA + protein = chromatin). Chromatin condenses to discrete chromosomes in division.
• Nucleolus = site of rRNA synthesis & ribosome assembly.

Ribosomes

• Sites of protein synthesis.
• Free ribosomes – cytosol proteins; bound ribosomes – attached to rough ER for secretory/membrane proteins.

Endomembrane System

• Components: nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, plasma membrane.
• Connected physically or via vesicles.

Endoplasmic Reticulum (ER)

• >$50\%$ of total membrane.
• Continuous with nuclear envelope.
• Smooth ER
  • Lipid synthesis.
  • Detoxification of drugs/poisons.
  • $Ca^{2+}$ storage.
• Rough ER
  • Bound ribosomes produce proteins → glycoproteins.
  • Distributes transport vesicles.
  • Membrane factory.

Golgi Apparatus

• Flattened cisternae; cis (receiving) and trans (shipping) faces.
• Modifies ER products, manufactures macromolecules, sorts & packages into vesicles.

Lysosomes

• Membranous sacs of hydrolytic enzymes.
• Intracellular digestion
  • Phagocytosis – food vacuole fuses with lysosome.
  • Autophagy – recycle own organelles.

Vacuoles

• Types
  • Food vacuoles (phagocytosis).
  • Contractile vacuoles – pump excess water (protists).
  • Central vacuole (plants) – stores organic compounds & water, maintains turgor.

Energy-Related Organelles

• Mitochondria
  • Double membrane; inner membrane folded into cristae.
  • Matrix contains DNA, ribosomes.
• Chloroplasts (a plastid type)
  • Double membrane; contain chlorophyll.
  • Internal: thylakoids arranged in grana ( $\approx 10-100$ thylakoids per granum ); stroma fluid; lamellae connect grana.
  • Each chloroplast: $40-60$ grana.
• Peroxisomes
  • Contain catalase; convert $H<em>2O</em>2 \rightarrow H<em>2O + O</em>2$.
  • Detoxify alcohol (liver).

Cytoskeleton

• Network providing structural support, organization, motility.

Microtubules (Tubulin polymers)

• Hollow $25\,nm$ diameter, $15\,nm$ lumen, wall $5\,nm$.
• Functions: cell shape, organelle transport, chromosome separation, cilia/flagella movement, compartmentalization.
• Cilia/flagella: $9$ doublets + $2$ singlets pattern; basal body $9$ triplets.

Microfilaments (Actin filaments)

• Two intertwined actin strands, $7\,nm$ diameter.
• Functions: tension bearing, cell shape, muscle contraction (with myosin), cleavage furrow, amoeboid movement, membrane invagination (endocytosis/exocytosis).

Intermediate Filaments

• Fibrous proteins (keratin family), $8-12\,nm$ diameter.
• Only in animals; maintain cell & nuclear shape, anchor organelles, form nuclear lamina.

Centrosome & Centrioles

• Centrosome = microtubule-organizing center in animals; pair of perpendicular centrioles.
• Plant cells have MTOCs but usually no centrioles.

Cell Wall (Plants, Algae, Fungi)

• Composition
  • Plants/algae: cellulose.
  • Fungi: chitin.
• Layers
  • Primary cell wall – thin, flexible, random cellulose microfibrils, abundant plasmodesmata.
  • Secondary cell wall – thicker, lignified, microfibrils in ordered layers between plasma membrane & primary wall.
• Functions: shape maintenance, mechanical strength, prevents lysis in hypotonic environments.
• Plasmodesmata: channels connecting cytoplasm of adjacent plant cells.

Plasma Membrane Structure & Fluidity

• Constituents: phospholipids (amphipathic), proteins (integral & peripheral), carbohydrates (glycolipids, glycoproteins), cholesterol.
• Fluid Mosaic Model – proteins float in lipid bilayer.
• Lateral movement common; flip-flop rare.
• Temperature effects
  • Cooler $T$ → membrane solidifies.
  • Unsaturated tails ↑ fluidity; saturated tails ↓.
  • Cholesterol buffers: restrains movement at warm $T$, prevents tight packing at cool $T$.
• Organisms adjust lipid composition (e.g., winter wheat ↑ unsaturated phospholipids in cold).

Membrane Proteins

• Integral (transmembrane) – penetrate hydrophobic core, α-helical stretches.
• Peripheral – loosely bound to surface.
• Six major functions
  1. Transport (channels, carriers, pumps).
  2. Enzymatic activity.
  3. Signal transduction (receptors).
  4. Cell-cell recognition (ID tags).
  5. Intercellular joining (junctions).
  6. Attachment to cytoskeleton & ECM.

Membrane Transport Mechanisms

Passive Transport

• No ATP; movement down concentration gradient.
• Simple Diffusion – hydrophobic molecules, small uncharged polar molecules.
• Facilitated Diffusion – via specific channel/carrier proteins (e.g., $Na^+, K^+$ at resting nerve cell; glucose in/out RBC).
• Osmosis – diffusion of free water.
  • Tonicity definitions
  • Isotonic: equal solute → no net water.
  • Hypertonic: outside solute > inside → cell shrinks.
  • Hypotonic: outside solute < inside → cell swells.
  • Cells without wall: risk lysis/shriveling; require osmoregulation (e.g., Paramecium contractile vacuole).
  • Plant cells: turgid (hypotonic), flaccid (isotonic), plasmolyzed (hypertonic).

Active Transport

• Moves substances against gradient; requires ATP & specific carrier (pump).
• Example: Sodium-Potassium Pump
  1. $3\,Na^+$ bind cytoplasmic side.
  2. ATP phosphorylates pump → conformational change.
  3. $Na^+$ released outside; $2\,K^+$ bind.
  4. Dephosphorylation restores original shape → $K^+$ released inside.
• Factors: temperature, $O_2$ supply, mitochondria number, membrane surface area, inhibitors.
• Other pumps
  • Proton pump (plants, fungi, bacteria) exports $H^+$, generating membrane potential.

Electrochemical Gradient & Membrane Potential

• Membrane potential (voltage) favors cation entry, anion exit.
• Electrochemical gradient = chemical + electrical forces.
• Electrogenic pumps create voltage (Na/K pump, proton pump).

Bulk Transport

• Requires ATP; transports large molecules via vesicles.

Exocytosis

• Vesicle fuses with membrane → releases contents (e.g., pancreatic insulin secretion).

Endocytosis

• Membrane forms vesicle to import substances.
• Phagocytosis – “cell eating”, forms food vacuole, lysosome fusion.
• Pinocytosis – “cell drinking”, nonspecific, coated vesicles.
• Receptor-mediated endocytosis – specific ligand binding in coated pits.

Intercellular Junctions (Animals)

• Tight Junctions: seal neighboring cells, prevent fluid leakage.
• Desmosomes: anchoring junctions, rivet cells; linked to intermediate filaments.
• Gap Junctions: communicating channels for ions, sugars, small molecules; analogous to plasmodesmata.

Biological Size Scale & Cell Diversity

• Sizes range from atoms $10^{-10}\,m$ to nerve cells >1\,m.
• Light microscope resolves down to $~200\,nm$; electron microscope down to <1\,nm.

Checkpoints & Applications

• Cell theory → evolutionary principle: continuity of life via cell division.
• Nuclear envelope & chromatin organization regulate gene expression (accessibility, transport through pores).
• Spraying water on supermarket produce: creates hypotonic environment → water enters plant cells → turgor pressure ↑ → leaves become crisp.

Ethical, Practical & Research Notes

• Cryo-EM pivotal in COVID-19 spike protein visualization, accelerating vaccine design.
• Green synthesis of biocompatible nanoparticles: interdisciplinary link with toxicology and cell biology.
• Laboratory standards: GLP, ISO $17025$ compliance in biocompatibility testing (speaker’s expertise).

Key Numerical & Unit References (compiled)

• Prokaryote diameter $0.5-5\,\mu m$; eukaryote $10-100\,\mu m$.
• Plasma membrane thickness $0.04\,\mu m$.
• Microtubule diameter $25\,nm$; microfilament $7\,nm$; intermediate filament $8-12\,nm$.
• Ribosome sizes: prokaryote $70\,S$ ($18\,nm$), eukaryote $80\,S$ ($22\,nm$).
• Differential centrifugation speeds: $1{,}000\,g$, $20{,}000\,g$, $80{,}000\,g$, $150{,}000\,g$.
• Sodium-Potassium pump stoichiometry: $3\,Na^+$ out/ $2\,K^+$ in per ATP.

Concept Integration & Real-World Relevance

• Surface-area limitations underpin multicellularity and organ development.
• Membrane fluidity adaptations explain cold-water fish survivability and winter crop resilience.
• Disruption of junctions (e.g., tight junction compromise) linked to diseases (leaky gut, metastasis).
• Targeting ion pumps and channels is central in pharmacology (cardiac glycosides, proton-pump inhibitors).