Biochemistry 7 - METABOLISM I PDF

Introduction to metabolism Key principles: Although thousands of different chemical reactions occur in the biosphere, most of them fall within a small set of reaction types ATP is the universal energy currency in living organisms Oxidation-reduction reactions ind...

Introduction to metabolism Key principles: Although thousands of different chemical reactions occur in the biosphere, most of them fall within a small set of reaction types ATP is the universal energy currency in living organisms Oxidation-reduction reactions indirectly provide much of the energy needed to make ATP To respond to changes in external circumstances, cells must regulate enzyme activities Metabolic pathways The biochemical reactions in the living cell – metabolism, are organised into metabolic pathways These pathways have dedicated purposes: Extraction of energy Storage of fuels Synthesis of important building blocks Elimination of waste materials The pathways can be represented as a map: Follow the fate of metabolites and building blocks Identify enzymes that act on these metabolites Identify points and agents of regulation Identify sources of metabolic diseases The relationship between catabolic and anabolic pathways Catabolism – the degradative phase of metabolism Releases energy Extracts energy from nutrients Anabolism (biosynthesis) – the building phase of metabolism Requires energy Uses E to synthesise biomolecules Connection between catabolic and anabolic pathways CP converge AP diverge  Chemical logic and common biochemical reactions Biochemical reactions occur in repeating patterns Involve interactions between nucleophiles and electrophiles Nucleophiles – functional groups rich in and capable of donating electrons Combine with and give up electrons to electrophiles Electrophiles – electron-deficient functional groups that seek electrons Carbon can act as either a nucleophile or electrophile 5 general categories of reactions in living cells: Reactions that make or break carbon-carbon bonds Internal rearrangements, isomerizations, and eliminations Free-radical reactions Group transfers Redox Homolytic and Heterolytic cleavage Homolytic cleavage – cleavage of a covalent bond where each atom leaves the bond as a radical, carrying on unpaired electron Heteroclytic cleavage – cleavage of a covalent bond where one atom retains both bonding electrons More common Kinases, phosphorylases and phosphatases Kinases – transfer a phosphoryl group from ATP to an acceptor molecule Catalyze a phosphorylation reaction Phospohrylases – catalyze a displacement reaction where phosphate attacks and becomes covalently attached at the point of bond breakage (addition of a phosphate group from Pi + H) Catalyze a phosphorolytic reaction Phosphatases – catalyse the removal of a phosphoryl group from a phosphate ester Catalyze dephosphorylation reactions Phosphorylation Synthases, Synthetases, Ligases, and Lyases Synthases – catalyse condensation reactions in which no nucleotide triphosphate is required (no need for ATP or GTP) Synthetases – catalyse condensation reactions that require a nucleotide triphosphate (ATP or GTP) Ligases – catalyse condensation reactions in which two atoms are joined using ATP or another energy source Lyases – catalyse cleavages or additions in which electronic rearrangements occur Oxidases and Oxygenases, dehydrogenases Oxidases – catalyse biological oxidation reactions where oxygen is the electron acceptor, and oxygen does not appear in the oxidized product Oxyganases - catalyse biological oxidation reactions where oxygen is the electron acceptor and oxygen does appear in the oxidized product Monooxygenases – one O atom is incorporated into the product Dioxygenases – two O atoms are incorporated in the product Dehydrogenases – catalyse redox reactions in which NAD+ is the electron acceptor, and molecular oxygen is not involved Redox Reactions: Oxidation and Reduction The transfer of electrons during chemical reactions releases energy stored in organic molecules This released energy is ultimately used to synthesize ATP Chemical reactions that transfer electrons between reactants are called oxidation-reduction reactions, or redox reactions In oxidation, a substance loses electrons or is oxidized In reduction, a substance gains electrons or is reduced (the amount of positive charge is reduced) Conjugate redox pair Oxidation of Organic Fuel Molecules During Cellular Respiration During cellular respiration, the fuel (such as glucose) is oxidized, and O2 is reduced The special role of ATP ATP is the chemical link between catabolism and anabolism Energy obtained from catabolism of nutrient molecules is used to make ATP from ADP and Pi The exergonic conversion of ATP to ADP and Pi or AMP and PPi is coupled to many endergonic reactions and processes The free energy change for ATP hydrolysis is large and negative For most enzymes that utilize ATP – the true substrate is MgATP2- ATP provides energy by group transfers, not by simple hydrolysis First step – transfer of part of the ATP molecule to a substrate molecule or to an amino acid residue, activating it Second step – displacement of the phosphate-containing moiety, generating Pi, PPi, or AMP as the leaving group Phosphate compounds with High energy of hydrolysis donate their phosporyl group Any phosphorylated compound can be synthesized by coupling the synthesis to the breakdown of another phosphorylated compound with a more negative energy of hydrolysis PEP - Phosphoenolpyruvate (2-phosphoenolpyruvate, PEP) is the carboxylic acid derived from the enol of pyruvate and phosphate Assembly of informational macromolecules requires energy Through group transfer reactions, ATP provides the energy for: The synthesis of informational macromolecules (DNA, RNA, protein) The transport of molecules and ions across membranes against gradients Through hydrolysis, ATP provides the energy for muscle contraction Adenylate kinase – lowers the ADP concentration and replenishes ATP during periods of intense demand for ATP (guanylate kinase – GTP) Creatine kinase – uses the phosphocreatine reservoir to replenish ATP at a rapid rate Stepwise Energy Harvest via NAD+ and the Electron Transport Chain In cellular respiration, glucose and other organic molecules are broken down in a series of steps Electrons from organic compounds are usually first transferred to NAD+, a coenzyme (nicotinamide adenine dinucleotide) As an electron acceptor, NAD+ functions as an oxidizing agent during cellular respiration Each NADH (the reduced form of NAD+) represents stored energy that is used to synthesize ATP NAD+ helps convert food to energy works as a shuttle bus, transferring electrons from one molecule to another  NADH passes the electrons to the electron transport chain Unlike an uncontrolled reaction, the electron transport chain passes electrons in a series of steps instead of one explosive reaction O2 pulls electrons down the chain in an energy-yielding tumble The energy yielded is used to regenerate ATP A few types of Coenzymes and Proteins serve as universal electron carriers Derived from vitamin Niacin B3 (nicotinic acid) and Tryptophan (AA) NAD - nikotinamid adenine dinukleotide NADP -….phosphate Flavin nucleotides – derived from the vitamin riboflavin B2 FMN - flavin mononucleotide FAD – flavin adenine dinucleotide water-soluble coenzymes that undergo reversible oxidation and reduction in many of the electron transfer reactions NAD and NADP are freely diffusible FMN and FAD are usually enzyme-bound Oxidation is often synonymous with dehydrogenation Dehydrogenation – a reaction where a compound loses two electrons and 2 hydrogen ions Catalyzed by dehydrogenases Electrons are transferred from the electron donor to the electron acceptor Directly as electrons As hydrogen atoms As a hydride ion (hydrogen with electron pair) Through direct combination with oxygen Metabolism The flow of metabolites through pathways is regulated to maintain homeostasis Sometimes, the levels of required metabolites must be altered very rapidly Need to increase the capacity of glycolysis during action Need to reduce the capacity of glycolysis after the action Need to increase the capacity of gluconeogenesis after successful action In many cases, the ultimate products of metabolic pathways directly or indirectly inhibit their own biosynthetic pathways Pathways are inextricably intertwined with all the other cellular pathways in a multidimensional network of reactions Metabolic regulation – processes that serve to maintain homeostasis at the molecular level Metabolic control – processes that lead to a change in the output of a metabolic pathway over time  ATP and AMP are key cellular regulators Adenylate kinase – catalyses the production of AMP in the reaction: 2 ADP → AMP + ATP AMP-activated protein kinase (AMPK) – responds to a decrease in the ATP/AMP ratio by phosphorylating key proteins and regulating their activities (metabolic control) A 10% decrease in ATP can greatly affect the activity of ATP utilizing enzymes and leads to a dramatic increase in AMP AMPK enzyme adenosine monophosphate- activated protein kinase Energy sensor Master regulator of energy metabolism largely to activate glucose and fatty acid uptake and oxidation when cellular energy is low  Cellular Respiration and Fermentation Living cells require energy from outside sources – we need energy! Some animals, such as the chimpanzee, obtain energy by eating plants, and some animals feed on other organisms that eat plants  Overview: Life is work Energy flows into an ecosystem as sunlight and leaves as heat Photosynthesis generates O2 and organic molecules, which are used in cellular respiration Cells use chemical energy stored in organic molecules to regenerate ATP, which powers work  Light energy ECOSYSTEM Photosynthesis in chloroplasts CO2 + H2O Organic + O2 molecules Cellular respiration in mitochondria ATP powers ATP most cellular work Heat energy Catabolic Pathways and Production of ATP The breakdown of organic molecules is exergonic Fermentation is a partial degradation of sugars that occurs without O2 Aerobic respiration consumes organic molecules and O2 and yields ATP Anaerobic respiration is similar to aerobic respiration but consumes compounds other than O2 Cellular respiration includes both aerobic and anaerobic respiration but is often used to refer to aerobic respiration Although carbohydrates, fats, and proteins are all consumed as fuel, it is helpful to trace cellular respiration with the sugar glucose C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + Energy (ATP + heat) Glucose The Stages of Cellular Respiration: A Preview Harvesting of energy from glucose has three stages Glycolysis (breaks down glucose into two molecules of pyruvate) The citric acid cycle (completes the breakdown of glucose) Oxidative phosphorylation (accounts for most of the ATP synthesis) 1. Glycolysis Glycolysis (“splitting of sugar”) breaks down glucose into two molecules of pyruvate in a series of enzyme- catalyzed reactions Some free energy is conserved as ATP and NADH Glycolysis occurs in the cytoplasm and has two major phases Energy investment phase Energy payoff phase Glycolysis occurs whether or not O2 is present = ANAEROBIC Noteworthy chemical transformations of glycolysis 1. Degradation of the carbon skeleton of glucose to yield pyruvate 2. Phosphorylation of ADP to ATP by compounds with high phosphoryl group transfer potential, formed during glycolysis 3. Transfer of a hydride ion to NAD+, forming NADH Glycolysis is irreversible (but we have gluconeogenesis) Negative delta g (free energy) - spontaneous Pyruvate is a high-energy molecule 2 fates: aerobic (oxidative reactions) and anaerobic (reduction to lactate or ethanol) Also can provide the carbon skeleton for alanine synthesis or fatty acid synthesis ATP yield during glycolysis Importance of phosphorylated intermediates All nine intermediates are phosphorylated Functions of the phosphoryl groups: Prevent glycolytic intermediates from leaving the cell Serve as essential components in the enzymatic conservation of metabolic energy Lower the activation energy and increase the specificity of the enzymatic reactions  Investment phase – 5 step (preparatory phase) PFK1 catalyzes the transfer of P from ATP Irreversible under intracellular conditions 1st committed step (Allosteric regulation) Activity increases when ATP supply is depleted Mg2+ or ADP and AMP accumulate Hexokinase activates glucose by phosphorylating at C-6 ATP serves as the phosphoryl donor Hexokinase require Mg2+ Irreversible under intracellular conditions Humans encode 4 hexokinases (I to IV) that catalyse the same reaction Isozymes – two or more enzymes that catalyse the same reaction but are encoded by different genes  Payoff phase – 5 step (2x) Each of the two molecules of glyceraldehyde-3-phosphate undergoes oxidation at C1  The 10 step summary of glycolysis To remember: Glycolysis occurs in the cytoplasm Glucose is converted to pyruvate, which will then move on to the next step of cellular respiration Anaerobic respiration and fermentation Enable cells to produce ATP without the use of oxygen Most cellular respiration requires O2 to produce ATP Without O2, the electron transport chain will cease to operate In that case, glycolysis couples with fermentation or anaerobic respiration to produce ATP  Anaerobic respiration uses an electron transport chain with a final electron acceptor other than O2, for example sulfate Fermentation uses substrate-level phosphorylation instead of an electron transport chain to generate ATP Types of fermentation Fermentation consists of glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis Two common types are alcohol fermentation and lactic acid fermentation  Regeneration of NAD+ To be used again in glycolysis Pyruvate takes the H+ reduced In alcohol fermentation, pyruvate is converted to ethanol in two steps, with the first releasing CO2 Alcohol fermentation by yeast is used in brewing, winemaking, and baking Lactic acid fermentation In lactic acid fermentation, pyruvate is reduced by NADH, forming lactate as an end product, with no release of CO2 Lactic acid fermentation by some fungi and bacteria is used to make cheese and yogurt Human muscle cells use lactic acid? fermentation to generate ATP when O2 is scarce  When animal tissues cannot be supplied with sufficient oxygen to support aerobic oxidation of the pyruvate and NADH produced in glycolysis, NAD+ is regenerated from NADH by the reduction of pyruvate to lactate The reduction of pyruvate in this pathway is catalyzed by lactate dehydrogenase In glycolysis, dehydrogenation of the two molecules of glyceraldehyde 3- phosphate derived from each molecule of glucose converts two molecules of NAD+ to two of NADH Because the reduction of two molecules of pyruvate to two of lactate regenerates two molecules of NAD+ , there is no net change in NAD+ or NADH Summary: Fates of Pyruvate under Anaerobic Conditions: Fermentation The NADH formed in glycolysis must be recycled to regenerate NAD+ , which is required as an electron acceptor in the first step of the payoff phase Under aerobic conditions, electrons pass from NADH to O2 in mitochondrial respiration Under anaerobic or hypoxic conditions, many organisms regenerate NAD+ by transferring electrons from NADH to pyruvate, forming lactate Other organisms, such as yeast, regenerate NAD+ by reducing pyruvate to ethanol and CO2 In these anaerobic processes (fermentations), there is no net oxidation or reduction of the carbons of glucose A variety of microorganisms can ferment sugar in fresh foods, resulting in changes in pH, taste, and texture, and preserving food from spoilage.