Chapter 2 Bioenergetic and Metabolism PDF

2. BIOENERGETICS AND METABOLISM BIOCHEMISTRY II Moeurng Sreylak  CONTENTS I. Introduction to Bioenergetic and metabolism II. Bioenergetics and Thermodynamics III. Chemical Logic and Common Biochemical Reactions IV. Regulation of Metabolic pathways  I. Int...

2. BIOENERGETICS AND METABOLISM BIOCHEMISTRY II Moeurng Sreylak  CONTENTS I. Introduction to Bioenergetic and metabolism II. Bioenergetics and Thermodynamics III. Chemical Logic and Common Biochemical Reactions IV. Regulation of Metabolic pathways  I. Introduction to Bioenergetics and Metabolisms 3 What is BIOENERGETICS Bioenergetics is the study of the transformation of energy in living organisms. It focuses on how cells convert energy from one form to another, particularly in the context of cellular respiration and photosynthesis. These processes involve the production and utilization of ATP (adenosine triphosphate)  I. Introduction to Bioenergetics and Metabolisms 4 What is Metabolism Every enzyme-catalyzed reaction and reaction sequence serves an important role in an organism’s physiology: to (1) obtain chemical energy (2) convert nutrient molecules into the cell’s own characteristic molecules, including precursors of macromolecules; (3) polymerize monomeric precursors into macromolecules: proteins, nucleic acids, and polysaccharides; (4) synthesize and degrade biomolecules required for specialized cellular functions, such as membrane lipids, intracellular messengers, and pigments.  I. Introduction to Bioenergetics and Metabolisms 5 Metabolism refers to chemical reactions in organisms that enable them to grow, reproduce, maintain their structures, and respond to their environments. These reactions can be categorized into two types: 1.Catabolism: The breakdown of molecules to obtain energy. For example, the breakdown of carbohydrates into glucose, which is used by cells to produce ATP (the energy currency of the cell). 2.Anabolism: The synthesis of all compounds needed by cells. This process builds up larger molecules from smaller ones, such as the formation of proteins from amino acids. I. Introduction to Bioenergetics and Metabolisms 6  I. Introduction to Bioenergetics and Metabolisms 7 Some metabolic pathways are linear, and some are branched, yielding multiple useful end products from a single precursor or converting several starting materials into a single product.  I. Introduction to Bioenergetics and Metabolisms 8 There are 3 types of Metabolic partway Presentation title 9  I. Introduction to Bioenergetics and Metabolisms 10 (a) Converging Catabolism: Catabolism involves the breakdown of large, complex molecules (like starch, glycogen, sucrose, fatty acids, and amino acids) into simpler forms. In this diagram, carbohydrates (starch, glycogen, sucrose), proteins (represented by amino acids like alanine, serine, leucine, isoleucine, phenylalanine), and lipids (fatty acids) are all broken down through various pathways. All of these breakdown processes converge at acetyl-CoA, a key molecule in metabolism, which enters the citric acid (Krebs) cycle.  I. Introduction to Bioenergetics and Metabolisms Presentation title 11 (b) Diverging Anabolism: Anabolism involves the synthesis of complex molecules from simpler ones, requiring energy. In this section, acetyl-CoA acts as a building block for the synthesis of various complex molecules, such as: Fatty acids and their derivatives (triacylglycerols, phospholipids).  I. Introduction to Bioenergetics and Metabolisms 12 (c) Cyclic Pathway: The diagram also highlights the Krebs (citric acid) cycle, a cyclic metabolic pathway. Acetyl-CoA enters this cycle and reacts with oxaloacetate to produce citrate, which is further processed, releasing carbon dioxide (CO₂), and regenerating oxaloacetate for the next cycle.  I. Introduction to Bioenergetics and Metabolisms Presentation title 13 Summary ✓ Converging catabolism breaks down various nutrients (carbohydrates, proteins, fats) into a common molecule, acetyl-CoA. ✓ Diverging anabolism uses acetyl-CoA to synthesize essential complex molecules. ✓ The cyclic pathway (Krebs cycle) generates energy by processing acetyl-CoA, releasing CO₂, and regenerating oxaloacetate.  II. Bioenergetics and Thermodynamics 14 Bioenergetics in action is cellular respiration. During this process, cells convert the chemical energy stored in glucose into adenosine triphosphate (ATP), which the cell can use to perform various types of work. Ex. Melting Ice: Ice has a highly ordered structure, and as it melts, the molecules move into a more disordered state Biological Energy Transformations Obey the Laws of Thermodynamics (liquid water), increasing entropy. 1. The First Law of Thermodynamics states that energy is conserved: it cannot be created or destroyed but only transformed or transferred. 2. The Second Law of Thermodynamics states that the entropy, or disorder, of the universe tends to increase in all natural processes. Thus, while energy remains constant, systems evolve toward greater entropy.  II. Bioenergetics and Thermodynamics 15 ▪ Living organisms preserve their internal order by taking from their surroundings free energy in the form of nutrients or sunlight, and returning to their surroundings an equal amount of energy as heat and entropy. ▪ Cells are isothermal systems — they function at essentially constant temperature (and also function at constant pressure). ▪ Heat flow is not a source of energy for cells, because heat can do work only as it passes to a zone or an object at a lower. II. Bioenergetics and Thermodynamics 16 ▪ The standard transformed free-energy change, ΔG’o, is a physical constant that is characteristic for a given reaction and can be calculated from the equilibrium constant for the reaction: Δ G’o = - RT ln Keq. ▪ The actual free-energy change, ΔG, is a variable that depends on ΔG’o and on the concentrations of reactants and products: ΔG= ΔG’o + RT ln ([products]/[reactants])  II. Bioenergetics and Thermodynamics 17 Standard Free-Energy Change Is Directly Related to the Equilibrium Constant The composition of a reacting system (a mixture of chemical reactants and products) tends to continue changing until equilibrium is reached. the equilibrium constant is given by: The concentrations of reactants and products at equilibrium define the equilibrium constant, Keq Where a, b, c, and d are the number of molecules of A, B, C, and D participating,  18 WORKED EXAMPLE 13-1 Calculation of ΔG′° Example  19 Calculation of ΔG′° Home-work  20 Homework  21 III. Chemical Logic and Common Biochemical Reactions In biochemistry, chemical logic refers to the underlying principles and patterns that govern biochemical reactions. It’s the logic behind how cells organize, control, and link reactions to sustain life. This includes understanding why certain pathways are efficient, how energy is managed, and how reactions are coupled for efficiency. 1. Oxidation-Reduction (Redox) Reactions: These 2. Group Transfer Reactions: In these reactions, involve the transfer of electrons between molecules. functional groups like phosphate, methyl, or acyl Redox reactions are crucial for cellular respiration groups are transferred between molecules. For and energy production, as they drive the electron example, ATP transfers its phosphate group to other transport chain in mitochondria. molecules, activating them for various cellular processes. An oxidation-reduction reaction. Shown here is the oxidation of lactate to pyruvate.  III. Chemical Logic and Common Biochemical Reactions 22 3. Hydrolysis and Condensation Reactions: Hydrolysis breaks bonds by adding water, while condensation forms bonds by removing water. Hydrolysis is common in digestion, breaking down polymers into monomers. Condensation reaction  23 III. Chemical Logic and Common Biochemical Reactions 4. Isomerization Reactions: The molecule's functional groups or bonds are rearranged to create a new structural isomer. Isomerization is essential in pathways like glycolysis, where glucose is converted into various isomeric forms for efficient energy extraction. A. Glucose Fructose (via Glucose-6-Phosphate and Fructose-6-Phosphate)Enzyme: Phosphoglucose isomerase. ▪ Glucose, a six-carbon sugar (C6H12O6), is a key molecule in energy metabolism. ▪ Its isomerization into different forms facilitates its role in glycolysis, the citric acid cycle, and other metabolic pathways. ▪ The process involves reversible chemical reactions that rearrange glucose into structural or functional isomers.  III. Chemical Logic and Common Biochemical Reactions 24 5. Ligase Reactions: ▪ Ligase enzymes catalyze the joining (ligation) of two molecules, typically involving the formation of a covalent bond. ▪ These reactions require energy, usually derived from ATP or a similar high-energy molecule. DNA Ligase Reaction:Function: Seals nicks in the sugar-phosphate backbone of DNA. IV. Regulation of Metabolic Pathways 25 Metabolic regulation is one of the most remarkable features of living organisms. Of the thousands of enzyme- catalyzed reactions that can take place in a cell. Metabolism as a three-dimensional meshwork. A typical eukaryotic cell has the capacity to make about 30,000 different proteins, which catalyze thousands of different reactions involving many hundreds of metabolites, most shared by more than one “pathway.”  IV. Regulation of Metabolic Pathways 26 Cells and Organisms Maintain a Dynamic Steady State Living cells and organisms maintain internal stability while continuously exchanging materials and energy with their environment. This is a critical aspect of life, allowing organisms to adapt to changes and sustain their functions over time. Ex: Glucose Catabolic Direction: Glucose is broken down via pathways like glycolysis and the citric acid cycle to generate ATP, which powers cellular functions and counters entropy (the natural tendency toward disorder). Anabolic Direction: Glucose is used to synthesize essential molecules (e.g., glycogen for energy storage or intermediates for nucleotides and amino acids).  IV. Regulation of Metabolic Pathways 27 Maintaining a dynamic steady state ensures survival by protecting cells and organisms from external and internal perturbations, such as environmental changes or cellular damage. Glucose in homeostasis For example, changes in v1 for the entry of glucose from various sources into the blood are balanced by changes in v2 for the uptake of glucose from the blood into various tissues, so the concentration of glucose in the blood ([S]) is held nearly constant at 5 mM. This is homeostasis for blood glucose. The failure of homeostatic mechanisms is o×en at the root of human disease.  28 IV. Regulation of Metabolic Pathways Cells must tightly regulate certain reactions to maintain their internal balance. Equilibrium in Reactions: ATP breaking down into ADP and Pi). If these reactions were allowed to reach equilibrium, their products (like fructose 1,6-bisphosphate or ADP) could accumulate in dangerously high concentrations. Osmotic ImbalanceF1,6BP is a highly charged molecule and could contribute to osmotic stress if present in high concentrations. This could lead to water influx, swelling, and damage to the cell.  29 2. Major Pathway Categories a) Carbohydrate Metabolism (Blue)Involves pathways like glycolysis, gluconeogenesis, and the citric acid cycle. Central to energy production, providing ATP and metabolic intermediates. b) Lipid Metabolism (Green)Includes fatty acid synthesis, β-oxidation, and cholesterol metabolism.Critical for energy storage and membrane formation. c) Energy Metabolism (Teal)Encompasses oxidative phosphorylation and ATP generation.Directly tied to mitochondrial function and cellular energy demands. d) Amino Acid Metabolism (Purple)Covers the synthesis and breakdown of amino acids.Links to protein synthesis and nitrogen metabolism. e) Nucleotide Metabolism (Red)Involves the synthesis and degradation of nucleotides (DNA/RNA building blocks).Supports genetic information processing and energy transfer (ATP, GTP). f) Glycan Biosynthesis and Metabolism (Light Blue)Relates to the synthesis of glycans, important for cell signaling and structural integrity.g) Metabolism of Cofactors and Vitamins (Orange)Involves processing essential molecules like vitamins, necessary for enzymatic functions. h) Biosynthesis of Secondary Metabolites (Pink)Produces compounds like alkaloids, flavonoids, and terpenes, often involved in defense and signaling. i) Biodegradation of Xenobiotics (Gray)Handles the breakdown of foreign substances and toxins 30