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Cell Physiology: From Basics to Clinical Application

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1. The Cell: Overview and Structural Organization

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2. Organelles and Their Functions

Nucleus

• Largest organelle (2-20 µm diameter); stores, replicates, and reads genetic information
• Bounded by double nuclear membrane with nuclear pore complexes (NPC) - each NPC is ~120 nm and controls selective import/export of RNA, proteins, and ions
• Contains chromatin (DNA + histone proteins) and the nucleolus (site of rRNA synthesis and ribosome assembly)
• The nuclear lamina (intermediate filaments) provides structural scaffolding - mutation in lamin A/C causes Hutchinson-Gilford progeria and several cardiomyopathies (laminopathies)

Endoplasmic Reticulum (ER)

• Rough ER: studded with ribosomes; site of synthesis of secretory, membrane, and lysosomal proteins; adds N-linked glycans
• Smooth ER: lipid synthesis, steroid hormone production, drug detoxification (cytochrome P450 enzymes), and calcium storage
• The ER lumen is a major Ca²⁺ reservoir - a Ca²⁺-ATPase (SERCA pump) actively sequesters Ca²⁺ from cytoplasm into ER lumen. This stored Ca²⁺ is released in response to IP₃ and plays a major role in intracellular signaling
• Clinical: In heart failure, downregulation of SERCA2a reduces SR Ca²⁺ loading, impairing contractile force. Gene therapy targeting SERCA2a has been an area of investigation

Golgi Complex

• Stack of flattened saccules (cisternae) - functions as the cell's "post office"
• Processes, sorts, and targets newly synthesized proteins to their correct subcellular destinations (plasma membrane, lysosomes, secretion)
• Adds O-linked glycans and processes N-linked glycans further
• Clinical: I-cell disease (mucolipidosis II) - lysosomal enzymes are misrouted to the extracellular space instead of lysosomes, causing lysosomal storage

Mitochondrion

• "Balloon within a balloon" - outer membrane and inner membrane create two compartments: intermembrane space and matrix
• Inner membrane is thrown into folds called cristae, dramatically increasing surface area for oxidative phosphorylation
• Site of: Krebs (TCA) cycle, beta-oxidation of fatty acids, electron transport chain, ATP synthesis
• Contains its own DNA (mtDNA) - maternally inherited; encodes 13 proteins, 22 tRNAs, 2 rRNAs
• Produces ~36 ATP per glucose molecule (vs. only 2 by glycolysis)
• Clinical: Mitochondrial diseases (MELAS, MERRF, Leber hereditary optic neuropathy) arise from mtDNA mutations; tissues with highest energy demand (CNS, muscle, heart) are most affected. Metformin acts in part by inhibiting mitochondrial Complex I

Lysosomes

• Membrane-enclosed bags of ~50 hydrolytic enzymes (acid hydrolases) that function at pH ~5
• The vacuolar H⁺-ATPase acidifies the lysosomal lumen
• Digest macromolecules via: endocytosis (receptor-mediated, phagocytosis, pinocytosis), autophagy
• Clinical: Lysosomal storage diseases - Gaucher's (glucocerebrosidase deficiency), Niemann-Pick (sphingomyelinase deficiency), Tay-Sachs (hexosaminidase A deficiency), Pompe's (acid maltase/alpha-glucosidase deficiency). All cause accumulation of undegraded substrates

Cytoskeleton

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3. The Cell Membrane

Structure: Fluid Mosaic Model

• The lipid bilayer is not miscible with extra- or intracellular fluid - it is a hydrophobic barrier to water-soluble substances
• Lipid-soluble substances (O₂, CO₂, steroid hormones, fatty acids, ethanol) cross by simple diffusion directly through the bilayer
• The bilayer is not static - lipids diffuse laterally (flip-flop between leaflets is rare and requires flippases)
• Cholesterol intercalates between phospholipids, regulating fluidity: prevents crystallization at low temperatures and prevents excess fluidity at high temperatures. It also organizes lipid rafts - microdomains enriched in cholesterol and sphingolipids that concentrate signaling proteins

Membrane Proteins

• Integral (intrinsic) proteins: span the bilayer (transmembrane proteins); include ion channels, carrier proteins, receptors, enzymes
• Peripheral (extrinsic) proteins: attached to the cytoplasmic face by electrostatic interactions; include cytoskeletal anchors
• Channel proteins: aqueous pores allowing selective passage of water (aquaporins) or ions. They do NOT use energy
• Carrier proteins (transporters): bind the substrate, change conformation, and release it on the other side. Can be passive (facilitated diffusion) or active

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4. Membrane Transport

A. Passive Transport (No Energy Required)

• Movement of molecules down their concentration gradient (from high to low)
• Net flux is proportional to the concentration difference and the membrane's permeability to that molecule
• Fick's law of diffusion: Flux = P × A × ΔC (where P = permeability coefficient, A = area, ΔC = concentration gradient)
• Applies to: O₂, CO₂, N₂, steroid hormones, fatty acids, very small uncharged polar molecules (water crosses slowly this way)

• Down the concentration gradient, but via a protein carrier or channel
• Saturable (Michaelis-Menten kinetics), inhibitable by structural analogs
• Examples: GLUT1 (erythrocyte glucose transporter), GLUT2 (liver/pancreatic beta-cell), GLUT4 (insulin-regulated, in muscle and fat)
• Clinical: GLUT1 deficiency syndrome (De Vivo disease) - seizures, developmental delay; treated with ketogenic diet

• Movement of water across a semipermeable membrane from low-solute to high-solute concentration
• Osmolarity of body fluids = ~300 mOsm/L (plasma ~1 mOsm/L higher than interstitial fluid due to plasma proteins)
• Effective osmolarity (tonicity) is what determines cell volume changes:
  • Isotonic (0.9% NaCl) - no cell volume change
  • Hypotonic - cells swell (may lyse = hemolysis)
  • Hypertonic - cells shrink (crenation)
• Clinical: Hyponatremia causes cerebral edema (cells swell); severe hyponatremia (Na⁺ <120 mEq/L) causes seizures and herniation. Rapid correction risks osmotic demyelination syndrome (central pontine myelinolysis)

B. Active Transport (Energy Required)

• Na⁺-K⁺-ATPase (Sodium-Potassium Pump): the most important pump in animal cells
  • Pumps 3 Na⁺ OUT and 2 K⁺ IN per ATP hydrolyzed
  • Creates and maintains: Na⁺ outside = 142 mEq/L, Na⁺ inside = 14 mEq/L; K⁺ inside = 140 mEq/L, K⁺ outside = 4 mEq/L
  • Is electrogenic (net loss of 1 positive charge per cycle) - directly contributes ~-3 mV to the resting membrane potential
  • Essential for: maintaining cell volume, resting membrane potential, and as the energy source for secondary active transport
  • Clinical: Digoxin inhibits Na⁺-K⁺-ATPase → increases intracellular Na⁺ → reduces Na⁺/Ca²⁺ exchanger activity → increases intracellular Ca²⁺ → positive inotropy. Hyperkalemia inhibits the pump. Ouabain is a classic Na⁺-K⁺-ATPase inhibitor used in research
• Ca²⁺-ATPase (PMCA, SERCA): pump Ca²⁺ out of cytoplasm
• H⁺-K⁺-ATPase: in gastric parietal cells - target of proton pump inhibitors (omeprazole, pantoprazole)

• Cotransport (symport): Na⁺ moves with the solute in the same direction. Example: SGLT1/2 (Na⁺-glucose co-transport in the gut and kidney)
  • Clinical: SGLT2 inhibitors (gliflozins - empagliflozin, dapagliflozin) block glucose reabsorption in proximal tubule; used in T2DM, heart failure, and CKD
• Countertransport (antiport): Na⁺ moves in as another ion moves out. Example: Na⁺/Ca²⁺ exchanger (NCX), Na⁺/H⁺ exchanger (NHE)
  • Clinical: NHE1 inhibition is a target for cardioprotection in ischemia-reperfusion

• Endocytosis: receptor-mediated (clathrin-coated pits, e.g., LDL receptor), phagocytosis, pinocytosis, caveolae-mediated
• Exocytosis: secretory vesicles fuse with plasma membrane; regulated by Ca²⁺ (neurotransmitter release, insulin secretion)
• Clinical: Familial hypercholesterolemia - defective LDL receptor leads to impaired receptor-mediated endocytosis of LDL → markedly elevated LDL-C and premature atherosclerosis

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5. Resting Membrane Potential

• High K⁺ inside / low K⁺ outside
• Low Na⁺ inside / high Na⁺ outside
• Negative organic anions (proteins, phosphates) trapped inside

• Resting membrane is far more permeable to K⁺ and Cl⁻ than to Na⁺ or Ca²⁺
• K⁺ leaks out through K⁺ "leak" channels (tandem-pore domain channels) down its concentration gradient, leaving negative charges behind → interior becomes negative
• The K⁺ equilibrium potential (EK) = -94 mV (Nernst equation with 35:1 K⁺ inside/outside ratio)
• Na⁺ has a small opposing inward leak, so Vm (-70 mV) is slightly less negative than pure EK

E = (RT/zF) × ln([ion]outside / [ion]inside) At 37°C: E = (61.5/z) × log([ion]o / [ion]i)

Em = (gK/gT)·EK + (gNa/gT)·ENa + (gCl/gT)·ECl + (gCa/gT)·ECa

1. Direct (small): electrogenic contribution (-3 mV) from 3Na out / 2K in
2. Indirect (major): maintains the K⁺ concentration gradient that drives the K⁺ diffusion potential

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6. Action Potentials

Properties

• Stereotypical size and shape - same amplitude each time for a given cell type
• All-or-none: either reaches threshold and fires fully, or does not fire at all
• Propagation: nondecremental - the amplitude does not decrease along the axon
• Threshold: typically ~-55 mV (about 15 mV depolarization from rest)

Phases of a Nerve Action Potential (Hodgkin-Huxley model)

Refractory Periods

• Absolute refractory period (ARP): During depolarization and early repolarization; Na⁺ channels are in the inactivated state and cannot re-open regardless of stimulus strength. Prevents re-excitation and ensures unidirectional propagation
• Relative refractory period (RRP): After ARP; some Na⁺ channels have recovered but membrane is hyperpolarized; a suprathreshold stimulus can elicit an action potential but it will be smaller

Propagation and Conduction Velocity

• At each point, the local current from an active segment depolarizes adjacent membrane to threshold
• Myelinated axons: saltatory conduction - action potential "jumps" from node of Ranvier to node; much faster
• Factors increasing conduction velocity: myelination (most important), larger axon diameter, higher temperature
• Clinical: Multiple sclerosis - demyelination slows or blocks conduction velocity. Sodium channel blocker local anesthetics (lidocaine, bupivacaine) - block the inactivated state of Na⁺ channels; preferentially affect rapidly firing pain fibers

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7. Cell Signaling and Signal Transduction

Modes of Cell-to-Cell Communication

Types of Receptors

• Receptor IS the channel - binding opens the channel directly
• Fastest response (milliseconds)
• Examples: nicotinic ACh receptor (opens Na⁺/K⁺ channel), GABA-A receptor (opens Cl⁻ channel), NMDA/AMPA glutamate receptors
• Clinical: Benzodiazepines potentiate GABA-A (increase frequency of Cl⁻ channel opening); barbiturates increase duration; used as anxiolytics and for seizures. Myasthenia gravis - autoantibodies against nicotinic ACh receptors at NMJ

• Largest family of cell-surface receptors (~800 in humans); 7 transmembrane domains (serpentine receptors)
• Coupled to heterotrimeric G proteins (Gα, Gβ, Gγ)
• Ligand binding → G protein activation (GDP → GTP exchange on Gα) → Gα and Gβγ dissociate and activate effectors
• Major subtypes:

• cAMP activates protein kinase A (PKA) → phosphorylates downstream targets
• IP₃ triggers Ca²⁺ release from ER; DAG activates protein kinase C (PKC)
• Clinical: Cholera toxin ADP-ribosylates Gsα → constitutive activation → massive ↑cAMP in intestinal epithelium → Cl⁻ secretion and profuse watery diarrhea. Pertussis toxin ADP-ribosylates Giα → blocks inhibitory signaling. Many drugs target GPCRs: β-blockers, ACE inhibitors (indirectly), opioids (μ-receptor, Gi-coupled), statins' pleiotropic effects

• Ligand binding → receptor dimerization → autophosphorylation of tyrosine residues → activation of downstream cascades (RAS-MAPK, PI3K-Akt, PLC-γ)
• Examples: insulin receptor (heterotetrameric, but same principle), EGF receptor, PDGF receptor, VEGF receptor
• RAS-MAPK pathway: growth, proliferation
• PI3K-Akt-mTOR pathway: survival, protein synthesis, metabolism
• Clinical: RAS mutations are found in ~30% of human cancers (KRAS in pancreatic cancer, colorectal cancer, lung adenocarcinoma) - constitutively active RTK downstream signaling. Imatinib (Gleevec) inhibits BCR-ABL tyrosine kinase in CML. Trastuzumab (Herceptin) targets HER2/neu RTK in breast cancer. Insulin resistance in Type 2 diabetes involves defective downstream insulin receptor signaling (IRS-1 and PI3K pathway)

• For hydrophobic ligands that cross the membrane (steroid hormones, thyroid hormones, vitamin D, retinoids)
• Ligand binding → receptor dimerization → translocation to nucleus → binding to hormone response elements (HREs) in DNA → regulate gene transcription (hours-days)
• Clinical: Glucocorticoid receptors: cortisol/dexamethasone → anti-inflammatory gene expression; Androgen receptors: testosterone/DHT → prostate cancer; Thyroid hormone receptor mutations → resistance to thyroid hormone (Refetoff syndrome)

• Formed by connexins; allow direct passage of ions and small molecules (<1200 Da) including Ca²⁺ and cAMP between adjacent cells
• Regulated by intracellular Ca²⁺, pH, and Vm - elevated Ca²⁺ closes gap junctions (protective in ischemia)
• Clinical: Connexin 26 (GJB2) mutations are the most common cause of hereditary non-syndromic sensorineural hearing loss. Gap junctions are critical for cardiac electrical conduction

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8. Cell Cycle and Proliferation

Phases

Cyclin-CDK Control

• Cyclin D/CDK4,6 phosphorylate Retinoblastoma protein (pRb)
• Phospho-pRb releases E2F transcription factor → activates genes for S phase entry
• CDK inhibitors (CKIs) act as brakes: p21 (WAF1), p27 (KIP1), p16 (INK4a) inhibit CDK activity
• p53 (the "guardian of the genome") - activated by DNA damage → induces p21 → cell cycle arrest. If damage is irreparable → p53 triggers apoptosis. Clinical: p53 is mutated in >50% of human cancers (Li-Fraumeni syndrome = germline p53 mutation). CDK4/6 inhibitors (palbociclib, ribociclib, abemaciclib) are used in HR+/HER2- breast cancer

DNA Repair

• G1/S checkpoint: detects unreplicated DNA damage; p53-p21 axis
• Intra-S checkpoint: slows replication if damage detected
• G2/M checkpoint: ensures DNA is fully replicated before mitosis
• Repair mechanisms: nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), homologous recombination (HR), non-homologous end joining (NHEJ)
• Clinical: BRCA1/BRCA2 mutations impair HR → increased breast/ovarian cancer risk. Lynch syndrome = defective MMR genes (MLH1, MSH2, MSH6) → hereditary colorectal cancer. Xeroderma pigmentosum = defective NER → extreme UV sensitivity and skin cancer

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9. Apoptosis (Programmed Cell Death)

Comparison: Apoptosis vs. Necrosis

Pathways

• Triggered by internal stress: DNA damage, hypoxia, ER stress, growth factor withdrawal
• Pro-apoptotic Bcl-2 family proteins (Bax, Bak, Bad, Bid) permeabilize the outer mitochondrial membrane
• Cytochrome c leaks into cytosol → forms the apoptosome with Apaf-1 and procaspase-9 → activates caspase-9 → activates executioner caspases (caspase-3, -6, -7)
• Anti-apoptotic proteins Bcl-2 and Bcl-xL block this by preventing cytochrome c release
• Clinical: Chronic lymphocytic leukemia (CLL) and follicular lymphoma overexpress Bcl-2 (t(14;18) translocation in follicular lymphoma). Venetoclax is a BH3-mimetic that inhibits Bcl-2, restoring apoptosis in CLL

• Triggered by external death signals: FasL binding Fas (CD95), TRAIL binding DR4/DR5, TNF binding TNFR1
• Receptor activation → DISC (death-inducing signaling complex) formation → caspase-8 activation → executioner caspases
• Clinical: The extrinsic pathway is exploited by cytotoxic T lymphocytes (CTLs) via FasL-Fas interaction and perforin/granzyme mechanisms to kill virus-infected or cancer cells. Autoimmune lymphoproliferative syndrome (ALPS) = defective Fas-mediated apoptosis → lymphoproliferation

Morphological Features of Apoptosis

1. DNA fragmentation by Ca²⁺/Mg²⁺-dependent endonucleases → oligonucleosomal "ladder" on gel electrophoresis
2. Cell volume decreases; cytoskeletal reorganization
3. Membrane blebbing
4. Chromatin condensation and nuclear fragmentation
5. Cell breaks into membrane-bound apoptotic bodies that are phagocytosed by macrophages or neighboring cells

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10. Cellular Homeostasis: Integrated Clinical Correlations

Ischemia-Reperfusion Injury

Ion Channel Channelopathies

Cellular Edema vs. Vasogenic Edema

• Cytotoxic edema: failure of Na⁺-K⁺-ATPase (ischemia, hypoxia) → intracellular Na⁺ accumulation → osmotic water entry → cell swells; BBB is intact
• Vasogenic edema: BBB disruption → protein-rich fluid leaks into brain interstitium; Na⁺-K⁺-ATPase still functional

Pharmacological Targets Rooted in Cell Physiology

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Summary: The Cell in One Framework

STRUCTURE → FUNCTION → PHYSIOLOGY → PATHOLOGY → PHARMACOLOGY

Lipid bilayer    →  Barrier/permeability  →  Selective ion gradients  →  Channelopathies    →  Na⁺ channel blockers
Na⁺-K⁺-ATPase   →  Ion gradient engine   →  Resting membrane Vm     →  Ischemic injury     →  Digoxin, ouabain
Voltage-gated    →  Action potential      →  Neural/muscle signals    →  LQT, epilepsy       →  Lidocaine, anticonvulsants
ion channels
GPCRs / RTKs     →  Signal transduction   →  Hormone responses        →  Cancer, diabetes    →  β-blockers, imatinib
Cyclin-CDKs      →  Cell cycle            →  Proliferation control    →  Cancer              →  Palbociclib
Caspases / Bcl-2 →  Apoptosis             →  Tissue homeostasis       →  Lymphoma, CLL       →  Venetoclax
Lysosomes        →  Macromolecule digestion→  Cellular recycling      →  Storage diseases    →  ERT (Gaucher, Pompe)

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• Medical Physiology (Boron & Boulpaep), Chapters 2-3 - Organelles, Signal Transduction
• Guyton and Hall Textbook of Medical Physiology, Chapters 4-5 - Membrane Transport, Resting Membrane Potential
• Costanzo Physiology 7th Edition, Chapter 1 - Resting Potential, Action Potentials
• Schwartz's Principles of Surgery 11th Ed., Chapter 15 - Cell Cycle, Apoptosis, Signal Transduction
• Histology: A Text and Atlas (Ross & Pawlina) - Apoptosis morphology