🧬Biochemistry Unit 20 – Biochemical Signaling

Key Concepts and Terminology

• Biochemical signaling involves communication between cells through chemical messengers (ligands) that bind to specific receptors on target cells
• Ligands include hormones, neurotransmitters, growth factors, and cytokines which are released by signaling cells and travel through extracellular space or bloodstream to reach target cells
• Receptors are protein molecules located on the cell surface or within the cell that specifically recognize and bind to ligands
• Signal transduction refers to the process by which a receptor converts the extracellular signal into an intracellular response through a series of biochemical reactions
• Signaling pathways are cascades of molecular interactions and reactions that relay the signal from the receptor to effector molecules within the cell
• Effector molecules are proteins, enzymes, or transcription factors that ultimately bring about the cellular response to the signal
• Cellular responses can include changes in gene expression, metabolism, secretion, contraction, or differentiation depending on the type of cell and signal received
• Feedback mechanisms involve the regulation of signaling pathways by the cellular response itself or by other molecules to maintain homeostasis and prevent excessive or prolonged signaling

Types of Signaling Molecules

• Hormones are signaling molecules secreted by endocrine glands into the bloodstream that act on target cells distant from their site of production (insulin, estrogen)
• Neurotransmitters are chemical messengers released by neurons into synapses that bind to receptors on postsynaptic cells to transmit nerve impulses (acetylcholine, dopamine)
• Growth factors are polypeptides that stimulate cell growth, proliferation, and differentiation by binding to specific receptors on target cells (epidermal growth factor, nerve growth factor)
• Cytokines are small proteins secreted by immune cells that regulate immune responses, inflammation, and hematopoiesis (interleukins, interferons)
• Eicosanoids are lipid-derived signaling molecules that act locally on neighboring cells and include prostaglandins, thromboxanes, and leukotrienes (prostaglandin E2)
• Nitric oxide (NO) is a gaseous signaling molecule that diffuses through cell membranes and activates guanylyl cyclase to produce cGMP, regulating vascular tone and neurotransmission
• Peptide hormones are short chains of amino acids that bind to cell surface receptors and include hypothalamic releasing hormones, pituitary hormones, and gastrointestinal hormones (vasopressin, oxytocin)
• Steroid hormones are lipid-soluble molecules derived from cholesterol that diffuse through the cell membrane and bind to intracellular receptors, regulating gene expression (cortisol, testosterone)

Cell Membrane Receptors

• G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors that consist of seven transmembrane domains and are coupled to heterotrimeric G proteins
• Upon ligand binding, GPCRs undergo a conformational change that activates the associated G protein, which then dissociates into $\alpha$ and $\beta\gamma$ subunits to initiate signaling cascades
• Receptor tyrosine kinases (RTKs) are cell surface receptors with an extracellular ligand-binding domain and an intracellular tyrosine kinase domain
• Ligand binding induces RTK dimerization and autophosphorylation, creating docking sites for adaptor proteins and initiating signaling pathways such as MAPK and PI3K/Akt
• Ion channel-coupled receptors are ligand-gated ion channels that open or close in response to ligand binding, allowing the flow of specific ions across the cell membrane (nicotinic acetylcholine receptor)
• Intracellular receptors are located within the cytoplasm or nucleus and bind to lipid-soluble signaling molecules that diffuse through the cell membrane
• Upon ligand binding, intracellular receptors undergo a conformational change that allows them to bind to specific DNA sequences and regulate gene transcription (steroid hormone receptors)
• Receptor desensitization occurs when prolonged or repeated exposure to a ligand leads to a decrease in the receptor's responsiveness to the ligand
  • This can involve receptor internalization, degradation, or uncoupling from signaling molecules to prevent overstimulation and maintain homeostasis

Signal Transduction Pathways

• cAMP pathway involves the activation of adenylyl cyclase by G$\alpha_s$ subunit, leading to the production of cAMP, which activates protein kinase A (PKA) to phosphorylate downstream targets
• Phospholipase C (PLC) pathway is initiated by the activation of PLC by G$\alpha_q$ subunit or RTKs, resulting in the hydrolysis of PIP2 into IP3 and DAG
  • IP3 triggers calcium release from the endoplasmic reticulum, while DAG activates protein kinase C (PKC) to phosphorylate target proteins
• Mitogen-activated protein kinase (MAPK) pathways are a series of serine/threonine kinases that are sequentially activated by phosphorylation, leading to the regulation of cell growth, differentiation, and survival
• Ras-Raf-MEK-ERK pathway is a well-characterized MAPK pathway that is activated by RTKs and involves the small GTPase Ras, which recruits and activates the kinase Raf, initiating the kinase cascade
• PI3K/Akt pathway is activated by RTKs and GPCRs and involves the production of PIP3 by PI3K, which recruits and activates the serine/threonine kinase Akt, regulating cell survival, metabolism, and growth
• JAK/STAT pathway is activated by cytokine receptors and involves the phosphorylation of JAK kinases, which then phosphorylate and activate STAT transcription factors, regulating gene expression
• TGF-$\beta$ pathway is initiated by the binding of TGF-$\beta$ family ligands to serine/threonine kinase receptors, leading to the phosphorylation and activation of Smad transcription factors
• Wnt pathway involves the binding of Wnt ligands to Frizzled receptors, leading to the stabilization of $\beta$-catenin, which translocates to the nucleus and regulates gene transcription

Second Messengers and Amplification

• Second messengers are small, diffusible molecules that are generated or released in response to receptor activation and amplify the signal within the cell
• Cyclic AMP (cAMP) is a second messenger produced by adenylyl cyclase in response to GPCR activation, which activates PKA to phosphorylate target proteins
• Calcium (Ca2+) is a ubiquitous second messenger that is released from the endoplasmic reticulum in response to IP3 production or enters the cell through ion channels
  • Ca2+ binds to and activates various proteins, including calmodulin, which regulates numerous cellular processes
• Diacylglycerol (DAG) is a lipid second messenger produced by PLC activation that recruits and activates PKC at the plasma membrane
• Inositol trisphosphate (IP3) is a second messenger produced by PLC activation that binds to IP3 receptors on the endoplasmic reticulum, triggering Ca2+ release
• Nitric oxide (NO) is a gaseous second messenger that activates guanylyl cyclase to produce cGMP, regulating vascular tone and neurotransmission
• Signal amplification occurs when a single ligand-receptor interaction leads to the generation of multiple second messenger molecules, amplifying the signal
  • For example, the activation of a single GPCR can lead to the production of hundreds of cAMP molecules, each capable of activating multiple PKA molecules
• Compartmentalization of signaling molecules and enzymes within the cell helps to ensure the specificity and efficiency of signal transduction by localizing the components of a pathway in close proximity

Cellular Responses to Signals

• Changes in gene expression occur when signaling pathways activate transcription factors that bind to specific DNA sequences and regulate the transcription of target genes
• Cell proliferation is stimulated by growth factors and mitogens that activate signaling pathways such as MAPK and PI3K/Akt, promoting cell cycle progression and division
• Cell differentiation is the process by which cells specialize and acquire specific functions in response to developmental signals and transcription factor activation
• Apoptosis, or programmed cell death, can be induced by signaling pathways in response to cellular stress, DNA damage, or developmental cues (Fas ligand, TNF-$\alpha$)
• Metabolic regulation involves the modulation of enzyme activity and gene expression in response to hormones and nutrient availability to maintain energy homeostasis (insulin signaling)
• Cytoskeletal reorganization and cell migration are regulated by signaling pathways that control actin polymerization and myosin contractility, enabling cell movement and shape changes
• Secretion of hormones, neurotransmitters, and other signaling molecules is triggered by calcium signaling and SNARE protein-mediated vesicle fusion
• Synaptic plasticity, or the strengthening or weakening of synaptic connections between neurons, is modulated by neurotransmitter signaling and is crucial for learning and memory

Regulation and Feedback Mechanisms

• Negative feedback occurs when the cellular response to a signal inhibits further signaling, maintaining homeostasis and preventing excessive or prolonged pathway activation
• Positive feedback occurs when the cellular response to a signal enhances further signaling, leading to an amplification of the response and a switch-like behavior
• Receptor desensitization involves the reduction of receptor responsiveness to a ligand due to prolonged or repeated exposure, preventing overstimulation
  • This can occur through receptor internalization, degradation, or uncoupling from signaling molecules
• Feedback inhibition of signaling enzymes by downstream products or effectors helps to terminate the signal and reset the pathway for future activation
• Crosstalk between signaling pathways allows for the integration of multiple signals and the fine-tuning of cellular responses based on the overall cellular context
• Spatial and temporal regulation of signaling molecules through compartmentalization, scaffolding proteins, and pulsatile release ensures the specificity and efficiency of signal transduction
• Protein phosphatases remove phosphate groups from signaling molecules, counteracting the effects of protein kinases and providing an additional layer of regulation
• Ubiquitination and proteasomal degradation of signaling components is a common mechanism for terminating signaling pathways and recycling proteins

Clinical and Practical Applications

• Mutations in signaling pathway components can lead to various diseases, including cancer, developmental disorders, and metabolic syndromes
• Oncogenic mutations in RTKs, Ras, or downstream kinases can result in constitutive activation of growth-promoting pathways, contributing to uncontrolled cell proliferation in cancer
• Targeted therapies, such as small molecule kinase inhibitors and monoclonal antibodies, are designed to specifically inhibit overactive signaling pathways in cancer and other diseases (imatinib, trastuzumab)
• Hormone replacement therapy is used to treat endocrine disorders and deficiencies by supplying exogenous hormones to restore signaling (insulin for diabetes, estrogen for menopause)
• Neuropharmacology involves the development of drugs that modulate neurotransmitter signaling to treat neurological and psychiatric disorders (SSRIs for depression, L-DOPA for Parkinson's disease)
• Genome editing techniques, such as CRISPR-Cas9, can be used to correct mutations in signaling pathway genes or to study the effects of specific gene knockouts on signaling and cellular responses
• Optogenetics and chemogenetics are research tools that allow for the precise spatial and temporal control of signaling pathways in living organisms using light-sensitive or designer receptors
• Synthetic biology approaches aim to engineer novel signaling pathways and cellular behaviors by combining modular signaling components and genetic circuits
• Understanding the evolutionary conservation and divergence of signaling pathways across species provides insights into the fundamental mechanisms of cell communication and the development of complex organisms