Metabolism Chapter 8 PDF

Chapter 8: An Introduction to Metabolism Campbell Biology, 12th Edition 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...

Chapter 8: An Introduction to Metabolism Campbell Biology, 12th Edition 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  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 Loading… Metabolism is an emergent property of life that arises from interactions between molecules within the cell 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 Starting Reaction 1 Loading… Reaction 2 Reaction 3 Product molecule  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. 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. 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. The Laws of Energy Transformation Thermodynamics is the study of energy transformations. A isolated system, is isolated from its surroundings Loading… In an open system, energy and matter can be transferred between the system and its surroundings Organisms are open systems 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 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  Heat Chemical energy (a) First law of thermodynamics (b) Second law of thermodynamics 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. 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. Free Energy and Metabolism The concept of free energy can be applied to the chemistry of life’s processes. 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 (a) Exergonic reaction: energy released, spontaneous Reactants Amount of energy released Fr ( G 0) ee en Energy er Products gy Progress of the reaction (b) Endergonic reaction: energy required, nonspontaneous Products Amount of energy Fr required ee ( G 0) en Energy er Reactants gy Progress of the reaction 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 feature of life is that metabolism is never at equilibrium. A catabolic pathway in a cell releases free energy in a series of reactions  This is closed system G 0 a G 0 until it it does work reaches the equilibrium and then it stops and does no work. (a) An isolated hydroelectric system (b) An open hydro- electric system G 0 system This is an open animals the time inhumans , it does work all because it experiences slow of materials a Constant and it never reaches G 0 G 0 equilibrium. G 0 (c) A multistep open hydroelectric system 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. 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.  Adenine Phosphate groups Ribose (a) The structure of ATP Adenosine triphosphate (ATP) Energy Inorganic Adenosine diphosphate (ADP) phosphate (b) The hydrolysis of ATP  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 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.  1 ATPytteen (a) Glutamic acid each nu conversion Glu NH3 Glu NH2 GGlu = +3.4 kcal/mol butle Kal/mal to glutamine 7 Glutamic Ammonia Glutamin acid e (b) Conversion NH3 reaction coupled 1 P 2 NH2 with ATP ATP ADP ADP Pi Glu Glu Glu hydrolysis Glutamic Phosphorylated Glutamin acid intermediate e GGlu = +3.4 kcal/mol (c) Free-energy NH3 NH2 change for ATP ADP Pi Glu Glu coupled reaction GGlu = +3.4 GATP = 7.3 kcal/mol + GATP = 7.3 kcal/mol kcal/mol Net G = 3.9 kcal/mol Exerganic  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.  Transport protein Solute ATP AD Pi P P Pi Solute transported (a) Transport work: ATP phosphorylates transport proteins. Vesicle Cytoskeletal track ATP AD Pi ATP P Motor protein Protein and vesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed. The Regeneration of ATP ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP). The energy toLoading… 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.  ATP H2 O Energy from Energy for cellular catabolism (exergonic, work (endergonic, energy-releasing ADP Pi energy-consuming processes) processes) 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.  Sucrase Sucrose Glucose Fructose (C12H22O11) (C6H12O6) (C6H12O6) 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.  A B C D Transition state Fr A B EA ee en C D er Reactants gy A B G O C D Products Progress of the reaction 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.  Course of reaction EA without without enzyme enzyme EA with enzyme is lower Fr Reactant ee s en er Course of G is unaffected gy reaction by enzyme with enzyme Products Progress of the reaction 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.  Substrate Active site Enzyme Enzyme-substrate complex (a) (b ) 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  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 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. 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.  Optimal temperature for Optimal temperature for typical human enzyme enzyme of thermophilic (37°C) R (heat-tolerant) at bacteria (77°C) e of re a ct io n 0 20 40 60 80 100 120 Temperature (a) Optimal temperature (°C) for two enzymes Optimal pH for pepsin Optimal pH for trypsin (stomach (intestinal enzyme) enzyme) R at e of re a ct io n 0 1 2 3 54 6 7 8 9 10 pH (b) Optimal pH for two enzymes 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. Enzyme Inhibitors 1. Competitive inhibitors bind to the active site of an enzyme, competing with the substrate. Normal substrate molecule and compete for admission into the active site. This kind of inhibition can be overcome by increasing the concentration of substrate so that as active sites become available.  - I - CUSTOM TEXT HERE Getting fi MAKE ART - JAN 15 2020 There : 2. Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective. Toxins and poisons are often irreversible enzyme inhibitors. An example is sarin, a nerve gas. This small molecule binds covalently to the R group on the amino acid serine, which is found in the active site of acetylcholinesterase, an enzyme important in the nervous system. SIGN HERE But Bal Rol Rat Du data Dat (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition Substrate Active site Competitive inhibitor Enzyme Noncompetitive inhibitor 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. 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. (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 of four) Activator Stabilized active Inactive form Active form Stabilized active form form Oscillation Non- Inhibitor functional Inactive form Stabilized inactive active site form  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. 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.  Initial substrate Active site (threonine) available Threonine in active site Enzyme 1 Isoleucine (threonine used up by deaminase) 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)