🔬Biological Chemistry I Unit 15 – Metabolism and Signaling Pathway Integration

Key Concepts and Definitions

• Metabolism encompasses all chemical reactions involved in maintaining the living state of cells and organisms
• Anabolism constructs molecules from smaller units (requires energy input)
• Catabolism breaks down molecules into smaller units (releases energy)
• Metabolic pathways are series of enzymatic reactions that convert an initial substrate into a final product
  • Pathways can be linear, cyclic, or branched
  • Examples include glycolysis (linear) and the citric acid cycle (cyclic)
• Enzymes are protein catalysts that lower the activation energy of reactions without being consumed
  • Enzymes are highly specific to their substrates and reactions
• Cofactors are non-protein molecules required for enzyme function (metal ions, coenzymes)
• Signaling molecules are chemicals that transmit messages between cells or within a cell
  • Examples include hormones (insulin), neurotransmitters (dopamine), and growth factors (EGF)
• Receptors are proteins that bind to signaling molecules and initiate cellular responses

Metabolic Pathways Overview

• Glycolysis breaks down glucose into pyruvate in the cytosol (anaerobic)
  • Produces 2 ATP and 2 NADH per glucose molecule
• Citric acid cycle (Krebs cycle) oxidizes acetyl-CoA to CO2 in the mitochondrial matrix
  • Generates 3 NADH, 1 FADH2, and 1 GTP per acetyl-CoA
• Oxidative phosphorylation produces ATP using the electron transport chain and chemiosmosis
  • NADH and FADH2 from glycolysis and the citric acid cycle donate electrons to the ETC
• Pentose phosphate pathway generates NADPH and ribose-5-phosphate for biosynthesis
• Fatty acid synthesis builds long-chain fatty acids from acetyl-CoA (requires NADPH)
• Beta-oxidation breaks down fatty acids into acetyl-CoA units in the mitochondria
• Amino acid metabolism involves the synthesis and degradation of amino acids
  • Excess amino acids can be converted to glucose (glucogenic) or ketone bodies (ketogenic)

Energy Production and ATP

• ATP (adenosine triphosphate) is the primary energy currency of the cell
  • Consists of adenosine, ribose, and three phosphate groups
  • Hydrolysis of ATP to ADP + Pi releases energy for cellular processes
• ATP is produced through substrate-level phosphorylation and oxidative phosphorylation
  • Substrate-level phosphorylation directly transfers a phosphate group from a high-energy intermediate to ADP (examples: glycolysis, citric acid cycle)
  • Oxidative phosphorylation uses the proton gradient generated by the electron transport chain to drive ATP synthesis
• The electron transport chain (ETC) is a series of protein complexes in the inner mitochondrial membrane
  • Electrons from NADH and FADH2 are passed through the complexes, releasing energy to pump protons into the intermembrane space
• Chemiosmosis is the process by which the proton gradient drives ATP synthesis
  • Protons flow back into the matrix through ATP synthase, causing it to rotate and catalyze ATP formation
• The total ATP yield per glucose molecule is approximately 30-32 ATP (including ATP from glycolysis, citric acid cycle, and oxidative phosphorylation)

Signaling Molecules and Receptors

• Signaling molecules can be classified based on their chemical structure and function
  • Peptide hormones (insulin), steroid hormones (estrogen), amino acid derivatives (epinephrine), and gases (nitric oxide)
• Receptors can be categorized by their location and mechanism of action
  • Cell surface receptors (G protein-coupled receptors, receptor tyrosine kinases)
  • Intracellular receptors (nuclear receptors, cytoplasmic receptors)
• G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors
  • Consist of seven transmembrane domains and interact with heterotrimeric G proteins
  • Ligand binding induces a conformational change that activates the G protein, which then modulates the activity of effector proteins (enzymes or ion channels)
• Receptor tyrosine kinases (RTKs) are cell surface receptors with intrinsic enzymatic activity
  • Ligand binding induces receptor dimerization and autophosphorylation, creating docking sites for signaling proteins
• Nuclear receptors are intracellular receptors that directly regulate gene expression
  • Ligand binding causes the receptor to translocate to the nucleus and bind to specific DNA sequences, modulating transcription of target genes

Intracellular Signaling Cascades

• Signaling cascades amplify and propagate signals from the receptor to the final cellular response
• The cAMP/PKA pathway is activated by GPCRs coupled to Gs proteins
  • Activated Gs stimulates adenylyl cyclase to produce cAMP, which activates protein kinase A (PKA)
  • PKA phosphorylates various target proteins, modulating their activity
• The phospholipase C (PLC) pathway is activated by GPCRs coupled to Gq proteins
  • Activated Gq stimulates PLC to cleave PIP2 into IP3 and DAG
  • IP3 triggers calcium release from the endoplasmic reticulum, while DAG activates protein kinase C (PKC)
• The MAPK (mitogen-activated protein kinase) pathway is a common downstream effector of many receptors
  • Consists of a three-tiered kinase cascade (MAPKKK, MAPKK, MAPK) that amplifies the signal
  • Activated MAPKs can phosphorylate transcription factors, regulating gene expression
• The PI3K/Akt pathway is involved in cell survival, growth, and metabolism
  • Receptor activation recruits PI3K to the membrane, where it converts PIP2 to PIP3
  • PIP3 recruits Akt (protein kinase B) to the membrane, leading to its activation by phosphorylation

Pathway Integration and Regulation

• Metabolic pathways are regulated to maintain homeostasis and respond to cellular needs
• Allosteric regulation involves the binding of effectors to enzymes at sites other than the active site
  • Allosteric activators (AMP for glycogen phosphorylase) and inhibitors (ATP for phosphofructokinase) modulate enzyme activity
• Covalent modification, such as phosphorylation, can alter enzyme activity
  • Example: Glycogen synthase is inactivated by phosphorylation and activated by dephosphorylation
• Hormonal regulation allows for the coordination of metabolic activities across tissues
  • Insulin promotes glucose uptake and storage (glycogenesis) while suppressing glucose production (gluconeogenesis)
  • Glucagon stimulates glucose production (glycogenolysis and gluconeogenesis) during fasting
• Transcriptional regulation controls the expression of metabolic enzymes
  • The transcription factor SREBP (sterol regulatory element-binding protein) regulates the expression of genes involved in lipid synthesis
• Feedback inhibition is a common mechanism for regulating pathway flux
  • The end product of a pathway inhibits the activity of an earlier enzyme in the pathway (example: ATP inhibits phosphofructokinase in glycolysis)

Metabolic Disorders and Diseases

• Inborn errors of metabolism are genetic disorders caused by defects in metabolic enzymes
  • Phenylketonuria (PKU) is caused by a deficiency in phenylalanine hydroxylase, leading to the accumulation of phenylalanine
  • Galactosemia is caused by a deficiency in enzymes involved in galactose metabolism, resulting in the accumulation of toxic metabolites
• Diabetes mellitus is a group of metabolic disorders characterized by hyperglycemia
  • Type 1 diabetes is caused by autoimmune destruction of pancreatic beta cells, leading to insulin deficiency
  • Type 2 diabetes is characterized by insulin resistance and impaired insulin secretion
• Obesity is a complex metabolic disorder influenced by genetic, environmental, and behavioral factors
  • Associated with an increased risk of developing type 2 diabetes, cardiovascular disease, and certain cancers
• Metabolic syndrome is a cluster of conditions that increase the risk of heart disease, stroke, and diabetes
  • Includes abdominal obesity, high blood pressure, high blood sugar, high triglycerides, and low HDL cholesterol
• Cancer cells exhibit altered metabolism to support their rapid growth and proliferation
  • The Warburg effect describes the increased reliance of cancer cells on aerobic glycolysis for energy production

Lab Techniques and Applications

• Enzyme assays measure the activity of enzymes by monitoring the formation of products or the disappearance of substrates
  • Spectrophotometric assays detect changes in absorbance (example: measuring NADH production at 340 nm)
  • Fluorometric assays detect changes in fluorescence (example: using fluorescent substrates or coupled reactions)
• Metabolomics is the study of the complete set of small-molecule metabolites in a biological system
  • Mass spectrometry (MS) and nuclear magnetic resonance (NMR) are common techniques for metabolite detection and quantification
• Isotope labeling allows for the tracking of metabolic fluxes and the identification of pathway intermediates
  • Stable isotopes (13C, 15N) are used to label substrates, and their incorporation into metabolites is measured
• Metabolic flux analysis (MFA) is a computational approach to quantify the rates of metabolic reactions in a network
  • Uses data from isotope labeling experiments and stoichiometric models to estimate fluxes
• Genome-scale metabolic models (GEMs) are mathematical representations of an organism's metabolic network
  • Integrate genomic, biochemical, and physiological data to predict metabolic capabilities and guide metabolic engineering efforts
• High-throughput screening (HTS) is used to identify compounds that modulate the activity of metabolic enzymes or pathways
  • Automated assays are performed on large libraries of small molecules to identify potential drug candidates or tool compounds