SCIENCE Chapter 6 Energy and Life | COMPLETE Study Guide | Download To Score An A.

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Chapter 6: Energy of Life Concept 6.1 An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics 1. Metabolism – the totality of an organism’s chemical reac ... tions Organization of the Chemistry of Life into Metabolic Pathways 1. Metabolic Pathway A. Begins with a specific molecule, altered in a series of defined steps, resulting in a certain product B. There are mechanisms that regulate these enzymes, thus balancing metabolic supply and demand 2. Metabolism A. Manages the material and energy resources of the cell B. Catabolic pathways – release energy by breaking down complex molecules to simpler compounds 1) Cellular respiration C. Energy that was stored in the organic molecules become available to do the work of the cell, such as changing cell shape or transporting solutes D. Anabolic pathways – consume energy to build complicated molecules from simpler ones E. Energy released from the catabolic pathways can be stored and used in anabolic pathways Forms of Energy 1. Energy A. The capacity to cause change B. To move matter against opposing forces C. The ability to rearrange a collection of matter D. Exist in different forms E. Work of life depends on the ability of cells to transform energy from one form to another 2. Kinetic energy A. Energy associated with the relative motion of objects B. Moving objects can perform work by imparting motion to other patter 3. Thermal energy A. Kinetic energy associated with the random movement of atoms or molecules B. Thermal energy in transferring from one object to another is heat 4. Potential energy A. Energy that matter possesses because of its location or structure B. Example – water behind a dam possess energy because of tis altitude above sea level 5. Chemical energy A. The potential energy available for release in a chemical reation B. For example – glucose are high in chemical energy C. Conversion of energy – woman climbing the ladder to the diving platform is releasing chemical energy from the food she ate for lunch and using some of the energy to perform the work of climbing i. Kinetic energy of muscle movement is being transformed into potential energy due to her increasing height above the water ii. The men diving is converting his potential energy to kinetic energy, which is then transferred to the water as he enters it. The Laws of Energy Transformation 1. Thermodynamics – the study of the energy transformation that occur in a collection of matter 2. System – the matter under study A. Isolated system – unable to exchange either energy or matter with its surroundings B. Open system- energy and matter can be transferred between the system and its surrounding 3. Surrounding – rest of the universe, everything outside the system The First Law of Thermodynamics (principle of conservation of energy) 1. Energy of the universe is constant 2. Energy can be transferred and transformed, but it cannot be created or destroyed A. Electric company does not make energy but merely converts energy to a form that is convenient for us to use The Second Law of Thermodynamics 1. During every single energy transfer or transformation, some energy becomes unavailable to do work A. In most energy transformation, the more unstable forms of energy are at least partly converted to thermal energy and released as heat B. Example in Textbook p144: Only a small fraction of the chemical energy from food is transformed into the motion, most is lost in heat, which dissipates rapidly through the surroundings C. Every energy transfer or transformation increases the entropy of the universe 2. In carrying out chemical reactions that performs various types of work, living cells convert other forms of energy into heat A. The system can only be put to work when there is a temperature difference that result in thermal energy flowing as heat from a warmer location to a cooler one 1) If the temperature is uniform, the heat generated during a chemical reaction will simply warm a body of matter 3. The loss of usable energy as heat to the surrounding is that each energy transfer or transformation makes the universe more disordered 4. Entropy – measurement of molecular disorder or randomness A. The physical disintegration of a system’s organized structure is a good analogy for an increase in entropy 1) Example-gradual decay of an unmaintained building over time 2) Production of CO2 while breaking down food 5. Spontaneous process A. The process that can proceed without requiring an input of energy B. Spontaneous - energetically favorable 1) Example – explosion 6. Nonspontaneous A. A process that on its own, will lead to a decrease in entropy B. Happen only if energy is supplied C. Example – pumping water up against gravity D. A nonspontaneous process leads to an increase in the entropy of the universe as a whole Biological Order and Disorder 1. Cells create ordered structures from less organized starting materials A. Complex organisms evolved from simpler ancestors B. Green algae to flowering plants 2. An organism also takes in organized form of matter and energy from the surroundings and replaces them with less ordered forms A. An animal obtains starch, proteins and other complex molecules from food, breaks down during catabolic pathways and releases carbon dioxide and water (small molecules that possess less chemical energy than the food B. On a larger scale, energy flows into most ecosystems in the form of light and exits in the form of heat 1) The entropy of a particular system, such as an organism, may actually decrease as long as the total entropy of the university (the system plus its surroundings) increase Concept 6.2 The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously Free-Energy Change, ΔG 1. The portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system 2. The change in free energy equation ΔG = ΔH - TΔS A. The equation uses only properties of the system itself B. ΔH the change in the system’s enthalpy C. ΔS the change in the system’s entropy D. ΔT the absolute temperature in Kelvin E. We can measure ΔG for any reaction 1) We can then predict whether the process will be spontaneous 2) Experiments have shown only processes with a negative ΔG are spontaneous 3) ΔH must be negative in order for ΔG to be negative, or TΔS must be positive, or both F. Every spontaneous process decreases the system’s free energy, processes that have a positive or zero ΔG are never spontaneous Free Energy, Stability and Equilibrium 1. ΔG = G final state – G initial state A. ΔG can only be negative when the process involves a loss of free energy during the change from initial to final state B. The system in its final state is less likely to change and more stable because it has less free energy 2. Free energy A. A measure of a system’s instability – tendency to change to a more stable state 1) Unless something prevents it, each of these systems will move toward greater stability 3. Equilibrium A. As a reaction proceeds towards equilibrium, the free energy of the mixture of reactants and products decreases B. Free energy increases when a reaction is somehow pushed away from equilibrium, perhaps by removing some of the products C. For a system at equilibrium, G is at its lowest possible value in the system 1) Any change in equilibrium will have a positive ΔG and will not be spontaneous 2) Therefore, systems never spontaneously move away from equilibrium i. It can do no work since a system at equilibrium cannot spontaneously change ii. It can perform work only if it is moving towards equilibrium Free Energy Metabolism Exergonic and Endergonic Reactions in Metabolism 1. Exergonic reaction A. Proceeds with a net release of free energy, occur spontaneously B. ΔG is negative C. The magnitude of ΔG represents the maximum amount of work the reaction can perform 1) The greater the decrease in free energy, the greater the amount of work that can be done D. The breaking of bonds does not release energy but requires energy 1) Energy stored in bonds represents the potential energy that can be released when new bonds are formed after the original bonds break 2. Endergonic reaction A. Absorbs free energy from its surrounding B. Essentially stores free energy in molecules, ΔG is positive C. Nonspontaneous D. Magnitude of ΔG is the quantity of energy required to drive the reaction E. Example – downhill is exergonic, reverse uphill is endergonic 1) However, a reversible process cannot be downhill in both directions 2) For example – plants capture light convert its energy to chemical energy to assemble glucose molecules Equilibrium and Metabolism 1. The chemical reactions of metabolism are reversible and would reach equilibrium if they occurred in the isolation of a test tube A. A cell that has reached metabolic equilibrium is dead. However, metabolism as a whole is never at equilibrium is a defining feature of life 1) Constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium 2) Cells continue to do work throughout its life 3) The key to maintaining lack of equilibrium is that the product of a reaction does not accumulate but instead becomes a reactant in the next step, waste products are expelled from the cell 4) Overall sequence of reactions is kept going by the huge free-energy difference between glucose and oxygen i. Glucose and oxygen at the top of the energy hill ii. Carbon dioxide and water at the downhill iii. Equilibrium is never reached as long as the cells have a steady supply of glucose or other fuels and oxygen and are able to expel waste products to the surrounding Concept 6.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions 1. Three main kinds of work for cells: A. Chemical work – the pushing of endergonic reactions that would not occur spontaneously 1) Examples – synthesis of polymers from monomers B. Transport work – the pumping of substances across membranes against the direction of spontaneous movement C. Mechanical work – such as the beating of cilia, the contraction of muscle cells and the movement of chromosomes during cellular production D. Energy coupling 1) The key feature which cells manage their energy resources 2) The use of an exer The Structure and Hydrolysis of ATP 1. Contains sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups 2. One of the nucleoside triphosphates used to make RNA 3. Bonds between the phosphate groups of ATP can be broken by hydrolysis A. A molecule of inorganic phosphate leaves the ATP, which becomes ADP B. In the cell, conditions do not conform to standard conditions because reactant and product concentration differ from 1 M C. The phosphate bonds of ATP are sometimes referred to as high-energy phosphate bonds D. The release of energy during the hydrolysis of ATP comes from the chemical change of the system to a state of lower free energy, not from the phosphate bonds themselves 4. Useful to the cell because the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver A. All three phosphate groups are negatively charged B. When they are crowded together, their mutual repulsion contributes to the instability of this region of the ATP molecule 1) The triphosphate tail of ATP is the chemical equivalent of a compressed spring How the Hydrolysis of ATP Performs Work 1. The process of shivering uses ATP hydrolysis during muscle contraction to warm the body. A. The generation of heat is an inefficient use of valuable energy B. The cell’s proteins harness the energy released during ATP hydrolysis in several ways to perform chemical, transport and mechanical work 2. The cell is able to use the energy released by ATP hydrolysis directly to drive chemical reactions that are endergonic A. If the ΔG of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, two reactions can be coupled so that the coupled reactions overall are exergonic 1) Involves phosphorylation – The transfer of a phosphate group from ATP to some other molecule, such as an reactant 2) The recipient molecule with the phosphate group covalently bonded is called phosphorylated intermediate – key to coupling exergonic and endergonic reactions i. More reactive than the original unphosphorylated molecule 3. Transport and mechanical work in the cell are nearly always powered by the hydrolysis of ATP A. ATP hydrolysis leads to a change in a protein’s shape and often its ability to bind another molecule B. Sometimes occurs via a phosphorylated intermediate C. In the case of mechanical work involving motor proteins, a fibrous network in the cytoplasm, a cycle occurs in which ATP is fist bound noncovalently to the motor protein D. ATP is hydrolyzed, releasing ADP and P E. Another ATP molecule can then bind F. The motor protein changes in shape and ability to bind the cytoskeleton at each stage, resulting in movement of the protein along the cytoskeletal track G. Phosphorylation and dephosphorylation promote crucial protein shape changes during many other important cellular processes as well The Regeneration of ATP 1. ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP 2. The free energy required to phosphate ADP comes from exergonic breakdown reactions in the cell – the ATP cycle A. This process couples the cell’s energy-yielding (exergonic)processes to the energy consuming (endergonic) ones at an astonishing pace 3. The regeneration of ATP is necessary endergonic since both directions of a reversible process cannot be downhill 4. Free energy must be spent to form ATP from ADP and P 5. Catabolic (exergonic) pathways provide the energy for the endergonic process of making ATP 5. Concept 6.4 Enzymes speed up metabolic reactions by lowering energy barriers 1. A spontaneous chemical reaction occurs without any requirement for outside energy but may occur so slowly that it is imperceptible A. With the addition of enzyme, a solution of sucrose dissolved in sterile water can be hydrolyzed within seconds 2. Enzyme A. A macromolecule that acts as a catalyst – a chemical agent that speeds up a reaction without being consumed by the reaction B. Without the regulation of enzymes, the pathways of metabolism would become extremely congested since many chemical reactions would take too long The Activation Energy Barrier 1. Every chemical reaction between molecules involves both bond breaking and bond forming 2. Changing one molecule into another generally involves contorting the starting molecule into a highly unstable state before the reaction can proceed A. To reach the contorted state where bonds can change, reactant molecules must absorb energy from their surroundings B. When the new bonds of the product molecules form, energy is released as heat and the molecules return to stable shapes with lower energy than the contorted state 3. Free energy of activation/activation energy A. The amount of energy needed to push the reactants to the top of an energy barrier (or uphill) so that the “downhill” part can begin B. Often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings 1) Absorption accelerates the reactant molecule so they collide more often and forcefully 2) Absorption also agitates the atoms within the molecules, making the breakage of bonds more likely C. When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition – transition state D. Activation energy provides a barrier that determine the rate of the reaction 1) The reactant must absorb enough energy to reach the top of the activation energy barrier before the reaction can occur 2) In most cases, the activation energy is so high and the transition state is reached so rarely that the reaction will hardly proceed at all i. Reaction will occur at a noticeable rate only if energy is provided, usually heat ii. For example – only when the spark plugs fire in an automobile engine can there be the explosive release of energy that pushes the pistons How Enzymes Speed Up Reactions 1. Although heat can increase the rate of a reaction by allowing reactants to attain the transition state more often, it would not work well in biological system A. High temperature denatures proteins and kills cells B. Heat would speed up all reactions, mot just the one needed 2. Catalysis – a process by which a catalyst selectively speeds up a reaction without itself being consumed 3. An enzyme catalyzes a reaction by lowering the activation energy EA barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperature 4. An enzyme cannot change the ΔG for a reaction, it cannot make an endergonic reaction exergonic A. Enzymes can hasten a reaction that would eventually occur, which enables the cell to have a dynamic metabolism, routing chemicals smoothly through metabolic pathways B. Enzymes are specific for the reactions they catalyze, can recognize its specific substrate even among closely related compounds 1) The specificity results from its shapes Substrate Specificity of enzymes 1. Substrate – the reactant any enzyme acts on 2. Enzyme binds to its substrate, forming an enzyme- substrate complex A. The catalytic action of the enzyme converts the substrate to the product 3. Most end in -ase 4. Active site A. The region where the catalyst occurs 1) A pocket or groove on the surface of the enzyme where catalysis occurs B. Formed by only a few of the enzyme’s amino acids, the rest of the protein molecule providing a framework that determines the shape of the active site C. The specificity of an enzyme is attributed to a complementary fit between the shape of tis active site and the shape of the substrate 5. The enzyme and the active site is not fixed in shape A. The enzyme changes shape slightly due to the interactions between the substrate’s chemical groups and chemical groups on the side chains of the amino acids that form the active sites B. The shape change makes the active site fit even more snugly around the substrate C. Induced fit 1) Tightening of the binding after initial contact 2) Brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction Catalysis in the Enzyme’s Active Site 1. The entire enzymatic reactions cycle occurs very quickly 2. The enzymes emerge from the reaction in their original form A. Very small amount of enzyme can have a huge metabolic impact by functioning over and over again in catalytic cycles 3. Enzymes can catalyze reversible metabolic reactions both ways (forward and backward, depending on which direction has a ΔG A. Mainly determined by the relative concentrations of reactants and products B. Net effect is always in the direction of equilibrium 4. Enzymes use a variety of mechanisms that lower activation energy and speed up a reaction A. When there are two more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them B. As the active site of an enzyme clutches the bound substrates, the enzyme may stretch the substrate molecules toward their transition state form, stressing and bending critical chemical bonds to be broken during the reaction C. The active site may also provide a microenvironment that is more conducive to a particular type of reaction than the solution itself would be without the enzyme D. Amino acids in the active site directly participate in the chemical reaction 1) It sometimes even involves brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme 5. The rate at which a particular amount of enzyme converts substrate to product is party a function of the initial concentration of the substrate A. The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules B. There is a limit to how fast the reaction can be pushed by adding more substrate to a fixed concentration of enzyme C. At some point, the concentration of substrate will be high enough that all enzyme molecules will have their active sites engaged 1) At this substrate concentration, the enzyme is saturated and the ate of the reaction is determined by the speed at which the active site converts substate to product D. When an enzyme population is saturated, the only way to increase the rate is to add more enzyme Effects of Local Conditions on Enzyme Activity Effects of Temperature and pH 1. Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because the substrates collide with active sites more frequently when the molecules more rapidly A. Above that temperature, the speed of the enzymatic reaction drops shortly B. The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds and other weak interactions that stabilize the active shape of the enzyme, the protein molecule eventually denatures 2. Each enzyme has an optimal temperature at which its reaction rate is greatest A. The temperature allows the greatest number of molecular collision and the fastest conversion of the reactants to product molecules 3. Each enzyme also has a pH at which it is most active A. Most optimal pH value for most enzymes 6-8 Cofactors 1. Nonprotein helpers for catalytic activity, often for chemical processes like electron transfers that cannot be easily carried out by the amino acids in proteins 2. Bound tightly to the enzyme as a permanent residents, or loosely and reversibly along with the substrate 3. Some or inorganic – zinc, iron, and copper 4. Coenzyme – organic cofactor Enzyme Inhibitors/Competitive Inhibitors 1. Reduce the productivity of enzymes by blocking substrates from entering active sites 2. They can be overcome by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry Noncompetitive Inhibitors 1. Do not compete directly with the substrate to bind to the enzyme at the active site 2. They impede enzymatic reactions by binding to another part of the enzyme 3. Cause the enzyme molecule to change its shape in such a way that the active site becomes much less effective at catalyzing the conversion of substrate to product Examples 1. Irreversible enzyme inhibitors – Toxins, poisons, pesticides 2. Antibiotics are inhibitors of specific enzymes in bacteria – penicillin blocks the active site of an enzyme that many bacteria use to make walls Concept 6.5 Regulation of enzyme activity helps control metabolism Allosteric Activation and Inhibition 1. Allosteric regulation A. A protein at one site is affected by the binding of a regulatory molecule to a separate site B. Result in either inhibition or stimulation of an enzyme’s activity C. Most are constructed from two or more subunits, each composed of a polypeptide chain with its own active site D. The entire complex oscillates between two different shapes, one catalytically active and the other inactive 2. An activating or inhibiting regulatory molecule binds to a regulatory site (allosteric site) , often where the subunits join A. The binding of an activator to a regulatory site stabilizes the shape that has functional active sites B. The binding of an inhibitor stabilizes the inactive form of the enzyme 3. The subunits of an allosteric enzyme fit together in such a way that a shape change in one subunit is transmitted to all others 4. Through the interaction, a single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits 5. Fluctuating concentrations of regulators can cause a sophisticated pattern of response in the activity of cellular enzymes A. The products of ATP hydrolysis play a complex role in balancing the flow of traffic between anabolic and catabolic pathways by their effects on key enzymes B. ATP binds to several catabolic enzymes allosterically, lowering their affinity for substrate and thus inhibiting their activity C. ADP functions as an activator of the same enzyme D. If ATP production lags behind its use, ADP accumulates and activates the enzymes that speed up catabolism, producing more ATP E. If the supply exceeds demand, catabolism slows .own as ATP molecules accumulate and bind to the same enzyme, inhibiting them 6. Other kind of allosteric activation A. Cooperativity - substrate molecule binding to one active site in a multsubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites B. Amplifies the response of enzymes to substrates C. It is considered allosteric regulation because its binding affects catalysis in another active site D. Hemoglobin – cooperativity for several reasons 1) Made up of 4 subunits, each with an oxygen- binding site 2) The binding of an oxygen molecule to one binding site increases the affinity for oxygen of the remaining binding sites 3) Thus, where oxygen is at high level, hemoglobin’s affinity for oxygen increases as more binding sites are filled 4) When oxygen is deprived, the release of each oxygen molecule decreases the oxygen affinity of the other binding sites, resulting in the release oxygen where it is most needed Feedback Inhibition 1. Allosteric inhibition of an enzyme in an ATP- generating pathway by ATP itself 2. A metabolic pathway is halted by the inhibitory binding of tis end product to an enzyme that acts early in the pathway Localization of Enzymes Within the Cell 1. The cell is compartmentalized, and cellular structures help bring order to metabolic pathways 2. In some instances, a team of enzymes for several steps of a metabolic pathway are assembled into a multienzyme complex 3. The arrangements facilitate series of reactions [Show More]

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