MBG111 L8-An Introduction to Metabolism PDF

4.10.2021 Figure 8.1 Chapter 8 An Introduction to Metabolism What causes these two squid to glow? 1 Overview: The Energy of Life The living cell is a miniature chemical factory where thousands of reactions occur...

4.10.2021 Figure 8.1 Chapter 8 An Introduction to Metabolism What causes these two squid to glow? 1 Overview: The Energy of Life The living cell is a miniature chemical factory where thousands of reactions occur The cell extracts energy and applies energy to perform work Some organisms even convert energy to light, as in bioluminescence © 2011 Pearson Education, Inc. 2 1  4.10.2021 Concept 8.1: An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics Metabolism is the totality of an organism’s chemical reactions Metabolism is an emergent property of life that arises from interactions between molecules within the cell © 2011 Pearson Education, Inc. 3 Organization of the Chemistry of Life into Metabolic Pathways A metabolic pathway begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Starting Product molecule © 2011 Pearson Education, Inc. 4 2  4.10.2021 Catabolic pathways release energy by breaking down complex molecules into simpler compounds Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism Anabolic pathways consume energy to build complex molecules from simpler ones The synthesis of protein from amino acids is an example of anabolism Bioenergetics is the study of how organisms manage their energy resources © 2011 Pearson Education, Inc. 5 Forms of Energy Energy is the capacity to cause change Energy exists in various forms, some of which can perform work Kinetic energy is energy associated with motion Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules Potential energy is energy that matter possesses because of its location or structure Chemical energy is potential energy available for release in a chemical reaction Energy can be converted from one form to another © 2011 Pearson Education, Inc. 6 3  4.10.2021 Figure 8.2 A diver has more potential Diving converts energy on the platform potential energy to than in the water. kinetic energy. Climbing up converts the kinetic A diver has less potential energy of muscle movement energy in the water to potential energy. than on the platform. 7 The Laws of Energy Transformation Thermodynamics is the study of energy transformations A isolated system, such as that approximated by liquid in a thermos, is isolated from its surroundings In an open system, energy and matter can be transferred between the system and its surroundings Organisms are open systems © 2011 Pearson Education, Inc. 8 4  4.10.2021 The First Law of Thermodynamics According to the first law of thermodynamics, the energy of the universe is constant – Energy can be transferred and transformed, but it cannot be created or destroyed The first law is also called the principle of conservation of energy © 2011 Pearson Education, Inc. 9 The Second Law of Thermodynamics During every energy transfer or transformation, some energy is unusable, and is often lost as heat According to the second law of thermodynamics – Every energy transfer or transformation increases the entropy (disorder) of the universe The evolution of more complex organisms does not violate the second law of thermodynamics Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases © 2011 Pearson Education, Inc. 10 5  4.10.2021 Figure 8.3 Heat Chemical energy (a) First law of thermodynamics (b) Second law of thermodynamics 11 Figure 8.4 12 6  4.10.2021 Concept 8.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously Biologists want to know which reactions occur spontaneously and which require input of energy To do so, they need to determine energy changes that occur in chemical reactions © 2011 Pearson Education, Inc. 13 Free-Energy Change, G A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), change in entropy (∆S), and temperature in Kelvin (T) ∆G = ∆H – T∆S Only processes with a negative ∆G are spontaneous Spontaneous processes can be harnessed to perform work © 2011 Pearson Education, Inc. 14 7  4.10.2021 Free Energy, Stability, and Equilibrium Free energy is a measure of a system’s instability, its tendency to change to a more stable state During a spontaneous change, free energy decreases and the stability of a system increases Equilibrium is a state of maximum stability A process is spontaneous and can perform work only when it is moving toward equilibrium © 2011 Pearson Education, Inc. 15 Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change More free energy (higher G) Less stable Greater work capacity In a spontaneous change The free energy of the system decreases (G  0) The system becomes more stable The released free energy can be harnessed to do work Less free energy (lower G) More stable Less work capacity (a) Gravitational motion (b) Diffusion (c) Chemical reaction 16 8  4.10.2021 Free Energy and Metabolism The concept of free energy can be applied to the chemistry of life’s processes Exergonic and Endergonic Reactions in Metabolism An exergonic reaction proceeds with a net release of free energy and is spontaneous An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous © 2011 Pearson Education, Inc. 17 Figure 8.6 (a) Exergonic reaction: energy released, spontaneous Reactants Amount of energy released Free energy (G  0) Energy Products Progress of the reaction (b) Endergonic reaction: energy required, nonspontaneous Products Amount of energy required Free energy (G  0) Energy Reactants Progress of the reaction 18 9  4.10.2021 Equilibrium and Metabolism Reactions in a closed system eventually reach equilibrium and then do no work Cells are not in equilibrium; they are open systems experiencing a constant flow of materials A defining feature of life is that metabolism is never at equilibrium A catabolic pathway in a cell releases free energy in a series of reactions Closed and open hydroelectric systems can serve as analogies © 2011 Pearson Education, Inc. 19 Figure 8.7 Water flowing downhill G  0 G = 0 turns a turbine that drives Equilibrium a generator providing electricity to a lightbulb, and work in but only until the system isolated and reaches equilibrium. open systems (a) An isolated hydroelectric system (b) An open hydro- Flowing water keeps electric system G  0 driving the generator because intake and outflow of water keep the system from reaching equilibrium. G  0 Cellular respiration is G  0 analogous to this system: G  0 Glucose is broken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for (c) A multistep open hydroelectric system the next, so no reaction reaches equilibrium. 20 10  4.10.2021 Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work – Chemical – Transport – Mechanical To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one Most energy coupling in cells is mediated by ATP © 2011 Pearson Education, Inc. 21 The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is the cell’s energy shuttle ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis Energy is released from ATP when the terminal phosphate bond is broken This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves © 2011 Pearson Education, Inc. 22 11  4.10.2021 Figure 8.8 Adenine Phosphate groups Ribose (a) The structure of ATP Adenosine triphosphate (ATP) Energy Inorganic Adenosine diphosphate (ADP) phosphate (b) The hydrolysis of ATP 23 How the Hydrolysis of ATP Performs Work The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant The recipient molecule is now called a phosphorylated intermediate © 2011 Pearson Education, Inc. 24 12  4.10.2021 How ATP drives chemical work: Energy coupling using ATP hydrolysis (a) Glutamic acid conversion NH3 NH2 Glu Glu GGlu = +3.4 kcal/mol to glutamine Glutamic Ammonia Glutamine acid (b) Conversion NH3 reaction coupled P 2 1 NH2 with ATP ADP ADP Pi hydrolysis Glu ATP Glu Glu Glutamic Phosphorylated Glutamine acid intermediate GGlu = +3.4 kcal/mol (c) Free-energy change for NH3 NH2 ATP ADP Pi coupled Glu Glu reaction GGlu = +3.4 kcal/mol GATP = −7.3 kcal/mol + GATP = −7.3 kcal/mol Net G = −3.9 kcal/mol 25 Figure 8.10 Transport protein Solute ATP ADP Pi P Pi Solute transported (a) Transport work: ATP phosphorylates transport proteins. Vesicle Cytoskeletal track ATP ADP Pi ATP Motor protein Protein and vesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed. 26 13  4.10.2021 The Regeneration of ATP ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP) The energy to phosphorylate ADP comes from catabolic reactions in the cell The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways © 2011 Pearson Education, Inc. 27 Figure 8.11 The ATP cycle ATP H2O Energy from Energy for cellular catabolism (exergonic, work (endergonic, energy-releasing ADP Pi energy-consuming processes) processes) 28 14  4.10.2021 Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barriers A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction An enzyme is a catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction © 2011 Pearson Education, Inc. 29 The Activation Energy Barrier Every chemical reaction between molecules involves bond breaking and bond forming The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA) Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings © 2011 Pearson Education, Inc. 30 15  4.10.2021 Figure 8.12 Energy profile of an exergonic reaction A B C D Transition state A B Free energy EA C D Reactants A B G  O C D Products Progress of the reaction 31 How Enzymes Lower the EA Barrier Enzymes catalyze reactions by lowering the EA barrier Enzymes do not affect the change in free energy (∆G); instead, they hasten reactions that would occur eventually © 2011 Pearson Education, Inc. 32 16  4.10.2021 Figure 8.13 The effect of an enzyme on activation energy Course of reaction EA without without enzyme enzyme EA with enzyme is lower Free energy Reactants Course of G is unaffected reaction by enzyme with enzyme Products Progress of the reaction 33 Substrate Specificity of Enzymes The reactant that an enzyme acts on is called the enzyme’s substrate The enzyme binds to its substrate, forming an enzyme-substrate complex The active site is the region on the enzyme where the substrate binds Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction © 2011 Pearson Education, Inc. 34 17  4.10.2021 Figure 8.14 Substrate Active site Enzyme Enzyme-substrate complex (a) (b) 35 Catalysis in the Enzyme’s Active Site In an enzymatic reaction, the substrate binds to the active site of the enzyme The active site can lower an EA barrier by – Orienting substrates correctly – Straining substrate bonds – Providing a favorable microenvironment – Covalently bonding to the substrate © 2011 Pearson Education, Inc. 36 18  4.10.2021 Figure 8.15-3 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 3 Active site can lower EA and speed up a reaction. 6 Active site is available for two new substrate molecules. Enzyme 5 Products are 4 Substrates are released. converted to products. Products 37 Effects of Local Conditions on Enzyme Activity An enzyme’s activity can be affected by – General environmental factors, such as temperature and pH – Chemicals that specifically influence the enzyme © 2011 Pearson Education, Inc. 38 19  4.10.2021 Effects of Temperature and pH Each enzyme has an optimal temperature in which it can function Each enzyme has an optimal pH in which it can function Optimal conditions favor the most active shape for the enzyme molecule © 2011 Pearson Education, Inc. 39 Figure 8.16 Optimal temperature for Optimal temperature for typical human enzyme (37°C) enzyme of thermophilic (heat-tolerant) Rate of reaction bacteria (77°C) 0 60 20 80 40 100 120 Temperature (°C) (a) Optimal temperature for two enzymes Optimal pH for pepsin Optimal pH for trypsin (stomach (intestinal enzyme) enzyme) Rate of reaction 0 1 5 2 3 4 6 7 8 9 10 pH (b) Optimal pH for two enzymes 40 20  4.10.2021 Cofactors Cofactors are nonprotein enzyme helpers Cofactors may be inorganic (such as a metal in ionic form) or organic An organic cofactor is called a coenzyme Coenzymes include vitamins © 2011 Pearson Education, Inc. 41 Enzyme Inhibitors Competitive inhibitors bind to the active site of an enzyme, competing with the substrate Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective Examples of inhibitors include toxins, poisons, pesticides, and antibiotics © 2011 Pearson Education, Inc. 42 21  4.10.2021 Figure 8.17 (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition Substrate Active site Competitive inhibitor Enzyme Noncompetitive inhibitor 43 The Evolution of Enzymes Enzymes are proteins encoded by genes Changes (mutations) in genes lead to changes in amino acid composition of an enzyme Altered amino acids in enzymes may alter their substrate specificity Under new environmental conditions a novel form of an enzyme might be favored © 2011 Pearson Education, Inc. 44 22  4.10.2021 Figure 8.18 Mimicking evolution of an enzyme with a new function Two changed amino acids were Active site found near the active site. Two changed amino acids Two changed amino acids were found in the active site. were found on the surface. After seven rounds of mutation and selection in a lab,the enzyme β-galactosidase evolved into an enzyme specialized for breaking down a sugar different from lactose. This ribbon model shows one subunit of the altered enzyme; six amino acids were different. 45 Concept 8.5: Regulation of enzyme activity helps control metabolism Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes © 2011 Pearson Education, Inc. 46 23  4.10.2021 Allosteric Regulation of Enzymes Allosteric regulation may either inhibit or stimulate an enzyme’s activity Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site © 2011 Pearson Education, Inc. 47 Allosteric Activation and Inhibition Most allosterically regulated enzymes are made from polypeptide subunits Each enzyme has active and inactive forms The binding of an activator stabilizes the active form of the enzyme The binding of an inhibitor stabilizes the inactive form of the enzyme © 2011 Pearson Education, Inc. 48 24  4.10.2021 Figure 8.19 (a) Allosteric activators and inhibitors (b) Cooperativity: another type of allosteric activation Allosteric enzyme Active site Substrate with four subunits (one of four) Regulatory site (one Activator Stabilized active of four) Inactive form Active form Stabilized active form form Oscillation Non- Inhibitor Inactive form Stabilized inactive functional active site form 49 Cooperativity is a form of allosteric regulation that can amplify enzyme activity One substrate molecule primes an enzyme to act on additional substrate molecules more readily Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site © 2011 Pearson Education, Inc. 50 25  4.10.2021 Identification of Allosteric Regulators Allosteric regulators are attractive drug candidates for enzyme regulation because of their specificity Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses © 2011 Pearson Education, Inc. 51 Figure 8.20 EXPERIMENT Caspase 1 Active Substrate site Are there allosteric inhibitors of SH SH caspase Known active form Active form can bind substrate enzymes? SH Allosteric binding site Allosteric Known inactive form Hypothesis: allosteric inhibitor inhibitor locks enzyme in inactive form RESULTS Caspase 1 X-ray diffraction analysis Inhibitor Active form Allosterically Inactive form inhibited form 52 26  4.10.2021 Feedback Inhibition In feedback inhibition, the end product of a metabolic pathway shuts down the pathway Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed © 2011 Pearson Education, Inc. 53 Figure 8.21 Initial substrate Feedback inhibition in Active site (threonine) isoleucine synthesis available Threonine in active site Enzyme 1 (threonine Isoleucine deaminase) used up by cell Intermediate A Active site of Feedback enzyme 1 is inhibition Enzyme 2 no longer able to catalyze the Intermediate B conversion of threonine to Enzyme 3 intermediate A; pathway is Intermediate C switched off. Isoleucine binds to Enzyme 4 allosteric site. Intermediate D Enzyme 5 End product (isoleucine) 54 27  4.10.2021 Specific Localization of Enzymes Within the Cell Structures within the cell help bring order to metabolic pathways Some enzymes act as structural components of membranes In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria © 2011 Pearson Education, Inc. 55 Figure 8.22 Mitochondria The matrix contains enzymes in solution that are involved in one stage of cellular respiration. Enzymes for another stage of cellular respiration are embedded in the inner membrane. 1 m 56 28