Topic 8: Introduction to Metabolism PDF
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Neil Campbell and Jane Reece
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This document is a PowerPoint presentation on the topic of introduction to metabolism. It describes the laws of thermodynamics, ATP regeneration, enzyme activity, and feedback inhibition. It includes learning objectives, diagrams, and relevant biological concepts.
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Topic 8: Introduction to Metabolism Laws of Thermodynamics, ATP regeneration, Enzyme Activity, Feedback Inhibition PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings...
Topic 8: Introduction to Metabolism Laws of Thermodynamics, ATP regeneration, Enzyme Activity, Feedback Inhibition PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Learning objectives (LOBs) 1. Explain the thermodynamic laws and describe the concepts of endergonic and exergonic reactions. 2. Describe the structure, function, production and hydrolysis of ATP. 3. Define an enzyme and explain the regulation of enzymatic activity by allosteric regulation and negative feedback inhibition. 4. Describe the different types of enzyme inhibitors and their mode of action. Reading: Chapter 6, Campbell Biology Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Energy of Life All living organisms require energy in order to survive The sunlight is the source of energy on Earth The sunlight is used for synthesis of sugars through photosynthesis (by plants) Energy is transferred through metabolism The living cell is a miniature factory where thousands of reactions occur => Converts energy in many ways Example: some organisms convert energy to light (bioluminescence) Figure 6.1 Bioluminescence in fungi Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Energy flow on Earth Sun → Producers → Consumers, decomposers Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Μetabolism Metabolism is the totality of an organism’s chemical reactions through which: - Energy is stored (anabolic processes) - Energy is released (catabolic processes) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Metabolic Pathways A metabolic pathway has many steps that begin with a specific molecule and end with a product Each step is catalyzed by a specific enzyme Metabolic pathways are controlled according to cellular demands Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Starting Product molecule Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Catabolic pathways Break down complex molecules into simpler compounds Release energy Example: cellular respiration Respiration: catabolic pathway Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Anabolic pathways Synthesize complicated molecules from simpler ones Consume energy Example: photosynthesis, protein synthesis from aminoacids Photosynthesis: anabolic pathway Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Forms of Energy Energy: the capacity to cause change – Exists in various forms – Some forms of energy can perform work – Life depends on the cell’s ability to convert energy from one form to another Thermodynamics: The study of energy conversion from one form to another Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Forms of Energy Kinetic energy: energy associated with motion Heat (thermal energy): kinetic energy associated with random movement of atoms or molecules Potential (chemical) energy: – Energy stored due to the location or structure of matter – Includes chemical energy stored in molecular structure Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Laws of Thermodynamics First law: Energy can be transferred and transformed to other forms but cannot be created or destroyed Second law: Spontaneous changes that do not require outside energy (no energy consumption) increase the entropy (disorder) of the universe Heat co2 + H2O Figure 6.3 (a) First law of thermodynamics: (b) Second law of thermodynamics: Energy can be transferred or transformed but Every energy transfer or transformation increases the disorder (entropy) of the universe. Neither created nor destroyed. For example, disorder is added to the cheetah’s For example, the chemical (potential) energy surroundings in the form of heat and the small in food will be converted to the kinetic molecules that are the by-products Copyright energy ofEducation, © 2005 Pearson the cheetah’s Inc. publishing movement. as Benjamin Cummings of metabolism. Biological Order and Disorder Living organisms: – Increase the entropy of the universe by releasing energy – Decrease entropy and maintain order by consuming (using) energy Figure 6.4 Plant root tissue (ts) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Free Energy and Metabolism Organisms live by spending (consuming) free energy Free energy: a living system’s energy that can do work under cellular conditions The free-energy change (ΔG) of a reaction indicates whether the reaction occurs spontaneously or not ΔG = Gfinal - Ginitial Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exergonic and Endergonic Reactions in Metabolism Εxergonic reactions: – Spontaneous reactions – Free energy released→ ΔG < 0 (negative) – ΔG = Gfinal - Ginitial => Gfinal < Ginitial Reactants Amount of energy released Free energy (∆G 0 - ΔG = Gfinal - Ginitial => Gfinal > Ginitial Products Amount of energy Free energy required (∆G>0) Energy Reactants Progress of the reaction Figure 6.6 (b) Endergonic reaction: energy required Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Equilibrium and Metabolism Reactions in a closed system eventually reach equilibrium (ΔG = 0) Cells in our body are open systems with metabolic pathways of many stages: – Experience a constant flow of materials in and out => metabolic pathways do not reach equilibrium Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Structure of ATP ATP (adenosine triphosphate): - the cell’s energy shuttle (energy storage and transfer) - Nucleotide that stores energy in phosphate bonds - Function: Provides energy for cellular functions – energy rich => unstable → tends to break down NH2 Adenine ATP structure N C C N O O O HC CH C -O O O O CH2 O N N O - O - O - H H Phosphate groups H H Ribose Figure 6.8 OH OH Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ATP hydrolysis and regeneration (synthesis) ATP hydrolysis: ATP → ADP + Pi => energy release ATP synthesis: ADP + Pi → ATP => energy stored (in phosphate bonds) Adenosine triphosphate (ATP) ATP Energy stored Energy released Adenosine diphosphate Pi (ADP) ADP Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Energy coupling by ATP ATP powers cellular work by energy coupling Energy coupling: the use of an exergonic process to drive an endergonic one Three main kinds of endergonic cellular work (require energy input): – Mechanical – Transport – Chemical ATP – mediated energy coupling: - an endergonic process can by driven by the ATP hydrolysis (exergonic process) => ATP hydrolysis provides the energy required for the endergonic reaction to occur Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ATP hydrolysis Exergonic reaction: Energy is released from ATP when any of the 2 terminal phosphate bonds are broken P P P Adenosine triphosphate (ATP) H2O Figure 6.9 ∆G = - 7.3 kcal/mol P i + P P Energy Inorganic phosphate Adenosine diphosphate (ADP) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ATP hydrolysis: energy coupling Can be coupled to endergonic reactions Endergonic reaction: ∆G is positive, reaction is not spontaneous Figure 6.10 NH2 NH3 ∆G = +3.4 kcal/mol Glu + Glu Glutamic Ammonia Glutamine acid Exergonic reaction: ∆G is negative, reaction is spontaneous ATP + H2O ADP + P ∆G = - 7.3 kcal/mol Coupled reactions: Overall ∆G is negative; ∆G = –3.9 kcal/mol together, reactions are spontaneous Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cellular work types powered by ATP hydrolysis ATP drives endergonic reactions by phosphorylation (transfer of a phosphate to other molecules) P i P Motor protein Protein moved (a) Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP ATP + P i P P i Solute Solute transported (b) Transport work: ATP phosphorylates transport proteins P NH2 Glu + NH3 + P i Glu Reactants: Glutamic acid Product (glutamine) and ammonia made Figure 6.11 (c) Chemical work: ATP phosphorylates key reactants Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Regeneration (synthesis) of ATP Catabolic pathways: regeneration of ATP from ADP and Pi ATP synthesis from ATP hydrolysis to ADP + Pi requires energy ADP + Pi yields energy ATP catabolism anabolism Energy from catabolism Energy for cellular work (exergonic, energy yielding (endergonic, energy- processes) ADP + Pi consuming processes) Figure 6.12 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Photosynthesis and Cellular Respiration Photosynthesis: light CO2 + H20 energy C6H1206 + O2 Carbon dioxide water glucose oxygen Cellular respiration (aerobic): C6H1206 + Ο2 CO2 + H20 + ΑΤP Glucose oxygen carbon water energy dioxide Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Photosynthesis and Αerobic Respiration Molecule and energy exchange Photosynthesis Αerobic respiration (chloroplasts) (mitochondria) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enzymes Enzymes: catalytic proteins that speed up metabolic reactions by lowering energy barriers Catalyst: a chemical agent that speeds up a reaction without being consumed by the reaction CH2OH CH2OH CH2OH CH2OH O O O H O H H H H Sucrase H H H OH O H HO + H2O OH H OH H HO HO HO CH2OH CH2OH H OH OH H H OH OH H Sucrose Glucose Fructose C12H22O11 C6H12O6 C6H12O6 Example: sucrose hydrolysis by sucrase Sucrase: the enzyme that catalyzes sucrose hydrolysis Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Activation Barrier Chemical reactions between molecules involve the breaking and forming of bonds The activation energy, EA: – The initial amount of energy needed to start a chemical reaction – Needed to de-stabilize the structure of the reactants => they can react more easily – Often supplied in the form of heat from the surroundings in a system – Heat can increase the speed of molecules and cause them to collide more frequently Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The activation energy EA The energy profile for an exergonic reaction A B C D Transition state A B EA Free energy C D Reactants A B ∆G < O C D Products Progress of the reaction Figure 6.14 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The activation energy EA The energy profile for an endergonic reaction EA Progress of the reaction Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Energy profiles of exergonic vs endergonic reactions ENERGY RELEASED ENERGY ABSORBED Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings How Enzymes Lower the EA Barrier An enzyme catalyzes reactions: – By lowering the activation energy (EA) barrier => This speeds up the reaction – The enzyme does not affect whether the reaction will happen spontaneously or not (without the input of energy) – An enzyme will only speed up a reaction that would occur anyway Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The effect of an enzyme on the reaction rate Course of reaction EA without without enzyme enzyme EA with enzyme is lower Reactants Free energy Course of ∆G is unaffected reaction by enzyme with enzyme Products Progress of the reaction Figure 6.15 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Substrate Specificity of Enzymes Substrate: the reactant an enzyme acts on Example: sucrose is the substrate for sucrase The enzyme binds to its substrate forming an enzyme- substrate complex Substrate specificity: the enzyme will only recognize its specific substrates (and no other related compounds) The 3D enzyme shape determines its function (e.g. ionic interactions, H-bonds) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The active site The active site: the region on the enzyme where the substrate binds Induced fit of a substrate: enzyme changes shape upon substrate binding =>brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction Substrate Active site Enzyme Enzyme- substrate complex Figure 6.16 (a) The active site (b) Induced fit of the substrate Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The catalytic cycle of an enzyme 1 Substrates enter active site; enzyme changes shape so its active site 2 Substrates held in embraces the substrates (induced fit). active site by weak interactions, such as hydrogen bonds and ionic bonds. 3 Active site (and R groups of Substrates Enzyme-substrate its amino acids) can lower EA complex and speed up a reaction by acting as a template for substrate orientation, 6 Active site stressing the substrates Is available for and stabilizing the two new substrate transition state, molecules providing a favorable microenvironment, Enzyme participating directly in the catalytic reaction. 5 Products are Released. 4 Substrates are converted into Figure 6.17 Products products. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The catalytic cycle of sucrase Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enzymes reduce the activation energy barrier The active site can lower an EA barrier by: – Orienting substrates correctly – Straining substrate bonds – Providing a favorable microenvironment – Covalently bonding to the substrate Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Effects of Local Conditions on Enzyme Activity Enzymes are proteins => their activity is affected by several environmental factors Denaturation: the loss of a protein’s native conformation due to unravelling => loss of function Environmental factors that may affect enzyme activity: - pH - Temperature - Cofactors: non-protein enzyme helpers required for enzyme activity Inorganic cofactors: e.g. metal ions (e.g. Zn, Cu) Coenzymes: organic cofactors (e.g. vitamins) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Effects of Temperature and pH on enzyme activity Each enzyme has an optimal temperature in which it can function Optimal temperature for Optimal temperature for typical human enzyme enzyme of thermophilic enzyme Rate of reaction 0 20 40 80 100 Temperature (Cº) Figure 6.18 (a) Optimal temperature for two enzymes Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Effects of Temperature and pH on enzyme activity Each enzyme as an optimal pH in which it can function Optimal pH for pepsin Optimal pH (stomach enzyme) for trypsin (intestinal enzyme) Rate of reaction 0 1 2 3 4 5 6 7 8 9 pH (b) Optimal pH for two enzymes Figure 6.18 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enzyme Inhibitors: Irreversible vs Reversible inhibition Irreversible inhibitors: bind to an enzyme by covalent bonding => inhibition is irreversible - Examples: several toxins, antibiotics and poisons – Sarin, DDT, parathion: inhibit nervous system enzymes – Penicillin derivatives: inhibit the enzyme transpeptidase that synthesize the bacterial cell wall peptidoglycan Reversible inhibitors: bind to enzymes by weak bonds (non-covalent interactions: H-bonds, hydrophobic interactions and ionic bonds) => inhibition is reversible - 2 types of reversible inhibitors: 1. Competitive inhibitors 2. Non-competitive inhibitors Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enzyme Inhibitors: Reversible inhibition Competitive inhibitors: bind to the active site of an enzyme (weak binding) Compete with the substrate => inhibit substrate binding to the active site Substrate A substrate can Active site bind normally to the active site of an enzyme Enzyme Inhibition can (a) Normal binding be overcome A competitive by adding inhibitor mimics the Competitive excess substrate, competing inhibitor substrate for the active site Figure 6.19 (b) Competitive inhibition Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enzyme Inhibitors: Reversible inhibition Non-competitive inhibitors: bind to another part of an enzyme not to the active site Change the shape of the enzyme Inhibit the function of the enzyme A non-competitive inhibitor binds to the Inhibition cannot enzyme away from be overcome by the active site, altering the conformation of adding excess the enzyme so that its substrate active site no longer functions. Non-competitive inhibitor Figure 6.19 (c) Non-competitive inhibition Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Regulation of enzyme activity A cell’s metabolic pathways: – Must be tightly regulated – Pathways should be activated only when necessary – Achieved by regulation of enzyme function Two basic methods of enzyme regulation: 1. Regulation of enzyme production by regulation of gene expression 2. Regulation of enzyme activity by feedback inhibition (by allosteric regulation) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Fig. 18-2 Precursor Example: tryptophan Feedback inhibition biosynthesis pathway trpE gene Enzyme 1 trpD gene Regulation of gene expression Enzyme 2 trpC gene trpB gene Enzyme 3 trpA gene Tryptophan (a) Regulation of enzyme (b) Regulation of enzyme activity production (gene expression) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Feedback Inhibition In feedback inhibition: – The end product of a metabolic pathway inhibits the pathway – Role: prevents a cell from wasting chemical resources by synthesizing more product than is needed – Examples: Inhibition of catabolic pathways by ATP (ATP is the end product) Inhibition of anabolic pathways by their end product (e.g tryptophan synthesis pathway inhibition by tryptophan) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Feedback inhibition Example: isoleucine synthesis Initial substrate metabolic pathway (threonine) Active site Threonine available in active site Enzyme 1 (threonine Isoleucine deaminase) used up by cell Intermediate A Feedback Active site of enzyme 1 inhibition Enzyme 2 no longer binds Intermediate B threonine => pathway is switched off Enzyme 3 Isoleucine Intermediate C binds to Enzyme 4 allosteric site Intermediate D Enzyme 5 Figure 6.21 End product (isoleucine) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Allosteric Regulation of Enzymes Allosteric regulation: – A form of reversible modulation common in enzymes (and proteins) made from polypeptide subunits – can be positive (activation) or negative (inhibition) – a protein’s function (activity) at one site (active site) is affected by binding of a regulatory molecule usually (not always) at another site (regulatory site) – Regulatory molecules bind to regulatory sites via non-covalent binding interactions (similar to reversible non-competitive inhibitors) – Enzyme changes shape when regulatory molecules bind to specific sites, affecting their function – can be heterotropic (regulatory molecules bind to sites other than the active sites) or homotropic (regulatory molecule is the substrate and binds to active sites) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Heterotropic allosteric regulation: Allosteric Activation and Inhibition Allosteric activator Allosteric enzyme Active site with four subunits (one of four) Allosteric activators stabilize the active Regulatory form of the enzyme site (one of four) Activator Active form Stabilized active form Allosteric inhibitor Oscillation Allosteric inhibitors stabilize the inactive form of the enzyme Inhibitor Non-functional Inactive form Stabilized inactive Regulatory site is different active site form from active site (a) Allosteric activators and inhibitors. In the cell, activators and inhibitors Figure 6.20 dissociate when at low concentrations. The enzyme can then oscillate again. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Homotropic allosteric activation: Cooperativity Homotropic allosteric regulation: Binding of substrate to active site of one subunit locks all subunits into active conformation Cooperativity: special form of positive allosteric regulation (activation) that can amplify enzyme activity – Example: O2 binding to haemoglobin – The binding of substrate (oxygen) at one subunit increases the binding affinity of the other subunits (oxygen= allosteric activator) Substrate Allosteric activator is Figure 6.20 the substrate; locks all Regulatory site is the subunits into active active site conformation Inactive form Stabilized active form (b) Cooperativity: another type of allosteric activation. Note that the inactive form shown on the left oscillates back and forth with the active form when the active form is not stabilized by substrate. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cooperativity: oxygen binding to haemoglobin Haemoglobin oxygen-dissociation curve Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Allosteric regulation summary Allosteric inhibitors can be competitive or non- competitive inhibitors Heterotropic allosteric modulator (non-competitive inhibitors + activators): - a regulatory molecule that is NOT the enzyme's substrate - Example: - AMP is a heterotropic allosteric activator of PFK (phosphofructokinase= glycolysis enzyme) - CO2 is a heterotropic allosteric inhibitor (non- competitive inhibitor) of haemoglobin => reduces haemoglobin's affinity for oxygen => Oxygen is released in the tissues Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Allosteric regulation summary Homotropic allosteric modulator (competitive inhibitors + activators): - both a substrate for its target enzyme and a regulatory molecule of the enzyme's activity. - It is typically an activator of the enzyme (exception: CO for Hb). - Example: O2 and CO are homotropic allosteric modulators of haemoglobin. - O2 is an homotropic allosteric activator of haemoglobin - CO is a competitive inhibitor: binds to haemoglobin at the same site as the oxygen => has higher affinity for Hb than oxygen => does not allow oxygen to be released in tissues. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enzyme activity regulation Irreversible regulation Reversible regulation Covalent Non-covalent Allosteric regulation (a type of reversible regulation) Heterotropic Homotropic regulation regulation Heterotropic Heterotropic Homotropic Homotropic activation inhibition activation inhibition Includes Includes non-competitive competitive inhibitors inhibitors Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Specific Localization of Enzymes Within the Cell Enzymes participating in the same pathway are located close to each other Cellular enzymes may be: – grouped into complexes – incorporated into membranes – contained inside organelles Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Specific Localization of Enzymes Within the Cell Mitochondria, sites of cellular respiration Figure 6.22 1 µm Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Videos https://www.youtube.com/watch?v=lk0CU7LcJq0 https://www.youtube.com/watch?v=ueup2PTkFW8 https://www.youtube.com/watch?v=qHb7iieM2Ro https://www.youtube.com/watch?v=WAZXqhtduFw http://www.biologyinmotion.com/atp/index.html Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Summary Endergonic vs exergonic reactions. ATP: structure, function, production and hydrolysis Enzymes: active sites, substrates, catalytic cycle Regulation of enzymatic activity: - Regulation of gene expression (=> enzyme production) - Feedback inhibition (by allosteric regulation) - Allosteric regulation: heterotropic inhibition/activation vs homotropic activation (cooperativity) - Reversible inhibition: competitive vs non- competitive - Irreversible inhibition Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings SBA example In the following reaction, which molecule is the substrate? sucrase sucrose + H2O glucose + fructose A. Fructose B. Glucose C. Sucrase D. Sucrose E. Water Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings