Cellular Signaling Pathways

Why This Matters

Cellular signaling pathways are the molecular language cells use to communicate, and understanding them is central to biophysics because they reveal how physical and chemical forces translate into biological responses. You're being tested on the biophysical principles underlying these pathways—receptor-ligand binding kinetics, conformational changes, phosphorylation cascades, and ion flux dynamics. These concepts connect directly to thermodynamics, membrane biophysics, and protein structure-function relationships that appear throughout the course.

Don't just memorize pathway names and components. Know what biophysical mechanism each pathway exploits—whether it's conformational switching in G proteins, enzymatic amplification through kinase cascades, or rapid ion conductance changes. When you can explain why a pathway uses a particular strategy (speed vs. amplification vs. specificity), you're thinking like a biophysicist and preparing for the kinds of analysis questions that distinguish strong exam performances.

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Receptor-Mediated Conformational Switching

These pathways rely on ligand-induced conformational changes in membrane receptors to transmit signals across the plasma membrane. The binding event triggers structural rearrangements that propagate information without the signaling molecule ever entering the cell.

G Protein-Coupled Receptor (GPCR) Signaling

• Seven-transmembrane architecture—GPCRs span the membrane seven times, creating a structure where extracellular ligand binding induces intracellular conformational changes that activate heterotrimeric G proteins
• G proteins act as molecular switches—they cycle between GDP-bound (inactive) and GTP-bound (active) states, with GTPase activity providing built-in signal termination
• Signal amplification through effector diversity—a single activated receptor can activate multiple G proteins, which then regulate enzymes like adenylyl cyclase or phospholipase C

Receptor Tyrosine Kinase (RTK) Signaling

• Ligand-induced dimerization—RTK activation requires two receptor monomers to come together, bringing their intracellular kinase domains into proximity for trans-autophosphorylation
• Phosphotyrosine residues create docking sites—phosphorylated tyrosines recruit signaling proteins containing SH2 or PTB domains, enabling pathway specificity
• Dysregulation drives oncogenesis—mutations causing constitutive RTK activation are among the most common drivers of cancer, making this pathway a major therapeutic target

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Phosphorylation Cascade Amplification

These pathways use sequential kinase activation to amplify signals and integrate multiple inputs. Each phosphorylation step can activate many downstream targets, creating exponential signal amplification.

MAPK/ERK Pathway

• Three-tiered kinase cascade—the pathway follows a conserved structure: MAP3K → MAP2K → MAPK (specifically Raf → MEK → ERK), with each level amplifying the signal
• Activated by RTKs through Ras—the small GTPase Ras connects receptor activation to the cascade, acting as another molecular switch with intrinsic GTPase activity
• Nuclear translocation regulates transcription—phosphorylated ERK enters the nucleus to activate transcription factors controlling cell cycle progression and differentiation genes

PI3K-Akt Pathway

• Lipid second messengers—PI3K phosphorylates membrane phosphoinositides to generate $PIP_3$, which recruits Akt to the membrane through its PH domain
• Akt is a master regulator of cell survival—once activated by phosphorylation at Thr308 and Ser473, Akt phosphorylates dozens of substrates controlling apoptosis, metabolism, and growth
• PTEN provides negative regulation—this lipid phosphatase removes the 3' phosphate from $PIP_3$, and its loss is one of the most frequent events in human cancers

JAK-STAT Signaling Pathway

• Direct receptor-to-nucleus signaling—unlike MAPK or PI3K pathways, JAK-STAT provides a relatively direct route from cytokine receptors to gene transcription with fewer intermediate steps
• Receptor dimerization activates JAKs—cytokine binding brings receptor-associated JAKs together for trans-phosphorylation, which then creates STAT docking sites
• STAT dimerization enables DNA binding—phosphorylated STATs form dimers through reciprocal SH2-phosphotyrosine interactions, creating the functional transcription factor

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Second Messenger Systems

These pathways use small diffusible molecules to rapidly spread signals throughout the cell. Second messengers amplify signals and enable spatial distribution of information far from the original receptor.

cAMP Signaling Pathway

• Adenylyl cyclase generates cAMP from ATP—this enzyme is activated by $G_s$ proteins and inhibited by $G_i$ proteins, integrating multiple GPCR inputs into a single output
• PKA activation requires cAMP binding—protein kinase A exists as an inactive tetramer; cAMP binding to regulatory subunits releases active catalytic subunits
• Phosphodiesterases terminate signaling—these enzymes hydrolyze cAMP to AMP, and their activity determines signal duration (caffeine inhibits phosphodiesterases, prolonging cAMP signals)

Calcium Signaling

• Steep concentration gradient enables rapid signaling—cytosolic $Ca^{2+}$ is maintained at ~100 nM while extracellular and ER concentrations reach 1-2 mM, a 10,000-fold gradient
• Multiple release mechanisms—$Ca^{2+}$ enters through voltage-gated channels, ligand-gated channels, or is released from ER stores via $IP_3$ receptors or ryanodine receptors
• Calmodulin transduces calcium signals—this protein undergoes conformational changes upon binding four $Ca^{2+}$ ions, enabling it to activate CaM kinases and other effectors

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Rapid Ion Flux Signaling

This pathway exploits direct coupling between ligand binding and ion conductance for the fastest possible cellular responses. No enzymatic cascades or second messengers—just immediate changes in membrane potential.

Ion Channel-Linked Receptor Signaling

• Ligand-gated channels combine receptor and effector—the receptor itself is the ion channel, eliminating intermediate steps and enabling responses within microseconds to milliseconds
• Ion selectivity determines response type—channels selective for $Na^+$ or $Ca^{2+}$ cause depolarization (excitatory), while $Cl^-$ channels typically cause hyperpolarization (inhibitory)
• Desensitization limits signal duration—prolonged agonist exposure causes conformational changes that close the channel despite continued ligand binding, a built-in negative feedback mechanism

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Transcription Factor Activation Pathways

These pathways regulate gene expression by controlling transcription factor activity or localization. The endpoint is changed patterns of protein synthesis, making these pathways slower but capable of sustained cellular reprogramming.

Wnt Signaling Pathway

• β-catenin stability is the key regulated step—without Wnt, a destruction complex (APC, Axin, GSK3β) phosphorylates β-catenin, targeting it for ubiquitination and degradation
• Wnt binding inhibits the destruction complex—Frizzled receptor activation through Dishevelled prevents β-catenin phosphorylation, allowing it to accumulate and enter the nucleus
• TCF/LEF transcription factors require β-catenin—these DNA-binding proteins switch from repressors to activators when β-catenin binds, controlling developmental gene programs

NF-κB Signaling Pathway

• IκB sequesters NF-κB in the cytoplasm—this inhibitor masks the nuclear localization signal of NF-κB, keeping the transcription factor inactive under basal conditions
• IKK phosphorylates IκB for degradation—inflammatory signals activate the IκB kinase complex, which phosphorylates IκB and targets it for proteasomal degradation
• Rapid nuclear translocation follows IκB loss—freed NF-κB immediately enters the nucleus to activate genes for cytokines, chemokines, and anti-apoptotic proteins

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Quick Reference Table

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Self-Check Questions

1. Which two pathways both use GTPase proteins as molecular switches, and how do their GTPases differ in structure and regulation?

2. Compare the mechanisms by which cAMP and calcium function as second messengers. Why is calcium signaling faster, and what makes cAMP signaling more tunable?

3. If an FRQ asks you to explain signal amplification, which pathway would provide the best example of a multi-tiered kinase cascade, and how does each tier increase the signal?

4. Both Wnt and NF-κB pathways regulate transcription factor nuclear entry—contrast the mechanisms by which each pathway achieves this outcome.

5. A mutation causes a receptor tyrosine kinase to be constitutively active (always on, even without ligand). Which downstream pathways would be affected, and why does this commonly lead to cancer?