BIOLOGY. An Introduction to Metabolism CAMPBELL. Reece Urry Cain Wasserman Minorsky Jackson

Transcription

1 CAMPBELL BIOLOGY TENTH EDITION Reece Urry Cain Wasserman Minorsky Jackson 8 An Introduction to Metabolism Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick 2014 Pearson Education, Inc.

2 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 2014 Pearson Education, Inc. Figure 8.1

3 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 2014 Pearson Education, Inc.

4 The chemistry of life is organized into metabolic pathways A metabolic pathway begins with a specific molecule, which is then altered in a series of defined steps to form a specific product. A specific enzyme catalyzes each step of the pathway Pearson Education, Inc.

5 Two types of Metabolic Pathways 1. 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 2. 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 2014 Pearson Education, Inc.

6 Forms of Energy Energy is the capacity to cause change Energy exists in various forms, some of which can perform work. Two important forms of energy are 1. Kinetic energy is the energy associated with the relative motion of objects. Objects in motion can perform work by imparting motion to other matter. Heat or thermal energy is kinetic energy associated with the random movement of atoms or molecules. 2. Potential energy is the energy that matter possesses because of its location or structure. Water behind a dam possesses potential energy because of its altitude above sea level. Molecules possess potential energy because of the arrangement of their atoms. Chemical energy is a form of potential energy stored in molecules because of the arrangement of their atoms Pearson Education, Inc.

7 Energy Conversion Energy can be converted from one form to another. For example, as a boy climbs stairs to a diving platform, he is releasing chemical energy stored in his cells from the food he ate for lunch. The kinetic energy of his muscle movement is converted to potential energy as he climbs. As the boy dives, the potential energy is converted back to kinetic energy. Kinetic energy is transferred to the water as the boy enters it. Some energy is converted to heat due to friction Pearson Education, Inc.

8 Figure 8.2 A diver has more potential 1 energy on the platform than in the water. 3 Diving converts potential energy to kinetic energy. 2 Climbing up converts the kinetic energy of muscle movement to potential energy. 4 A diver has less potential energy in the water than on the platform.

9 The Laws of Energy Transformation Thermodynamics is the study of energy transformations A closed 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 living in open systems 2014 Pearson Education, Inc.

10 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 Plants do not produce energy; they transform light energy to chemical energy. During every transfer or transformation of energy, some energy is converted to heat, which is the energy associated with the random movement of atoms and molecules Pearson Education, Inc.

11 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 due to the loss of usable energy. By combination of both first and second law s quantity of energy will same but quality of energy will not same in the universe Pearson Education, Inc.

12 Figure 8.3 Entropy and Heat Heat Chemical energy (a) First law of thermodynamics (b) Second law of thermodynamics Much of the increased entropy of the universe takes the form of increasing heat, which is the energy of random molecular motion. In most energy transformations, some energy is converted at least partly to heat. Living cells unavoidably convert usable forms of energy to unusable heat. Only a small portion of the chemical energy from the cheetah s food is transferred to movement; it is lost as heat.

13 The word spontaneous describes a process that can occur without an input of energy For a process to occur spontaneously, without outside help in the form of energy input, it must increase the entropy of the universe. Spontaneous processes need not occur quickly. Some spontaneous processes are instantaneous, such as an explosion. Some are very slow, such as the rusting of an old car. A process that cannot occur on its own is said to be nonspontaneous; it will happen only if energy is added to the system. Water flows downhill spontaneously but moves uphill only with an input of energy, such as when a machine pumps the water against gravity. Here is another way to state the second law of thermodynamics: For a process to occur spontaneously, it must increase the entropy of the universe Pearson Education, Inc.

14 Biological Order and Disorder The structure of a multicellular body is organized and complex. However, an organism also takes in organized forms of matter and energy from its surroundings and replaces them with less ordered (unusable) forms. For example, an animal consumes organic molecules as food and catabolizes them to low-energy carbon dioxide and water. This increase in organization does not violate the second law of thermodynamics. The entropy of a particular system, such as an organism, may decrease as long as the total entropy of the universe the system plus its surroundings increases. Figure 8.4 Living systems increase the entropy of their surroundings, even though they create ordered structures from less ordered starting materials.

15 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 A living system s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell 2014 Pearson Education, Inc.

16 How can we determine which reactions occur spontaneously and which ones require an input of energy? The concept of free energy (symbolized by the letter G) is useful for measuring the spontaneity of a system. Free energy is the portion of a system s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell. The change in free energy, G, can be calculated for any specific chemical reaction with the formula G = H T S In this formula: H symbolizes the change in the system s total energy S is the change in the system s entropy T is the absolute temperature in Kelvin (K) units (K = C + 273). For a process to occur spontaneously, the system must give up total energy ([H] must decrease), give up order (TS must increase), or both. G must have a negative value ( G < 0) in order for a process to be spontaneous. Remember spontaneous processes do not require energy input from the outside

17 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 2014 Pearson Education, Inc.

18 Free energy, 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 Figure 8.5

19 Free energy, stability, work capacity, and spontaneous change Gravitational Motion is an unstable system. The diver is unstable on top of the platform. Once he jumps and gravity pulls him down into the water: He is more stable, has less free energy/work capacity This process will occur spontaneously. Diffusion is an unstable system. The concentrated dye is unstable (more likely to disperse) than when the dye is spread randomly in a solution.the dye molecules will randomly disperse: The dye becomes more stable, has less free energy/work capacity This process will occur spontaneously. Chemical reactions are unstable system. The polysaccharide molecule is unstable (more likely to break down) than when the polysaccharide is broken down into monosaccharides. The polysaccharide will be broke down: The polysaccharide becomes more stable, has less free energy/work capacity. This process will occur spontaneously.

20 Maximum Stability=Equilibrium Another term for a state of maximum stability is equilibrium. In a chemical reaction at equilibrium, the rates of forward and backward reactions are equal, and there is no change in the relative concentrations of products or reactants. At equilibrium, G = 0, and the system can do no work. A process is spontaneous and can perform work only when it is moving toward equilibrium. Movements away from equilibrium are nonspontaneous and require the addition of energy from an outside energy source (the surroundings).

21 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 2014 Pearson Education, Inc.

22 Exergonic Reactions in Metabolism An exergonic reaction proceeds with a net release of free energy and is spontaneous, G is (negative) Figure 8.6 The magnitude of G for an exergonic reaction represents the maximum amount of work the reaction can perform

23 Cellular Respiration is an example of Exergonic Reaction For the overall reaction of cellular respiration, C 6 H 12 O 6 + 6O 2 6CO 2 + 6H 2 O G = 686 kcal/mol. For each mole (180 g) of glucose broken down by respiration under standard conditions (1 M of each reactant and product, 25 C, ph 7), 686 kcal of energy are made available to do work in the cell. The products (6CO 2 and 6 H 2 O) have 686 kcal less free energy per mole than the reactants Pearson Education, Inc.

24 Endergonic Reactions in Metabolism An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous An endergonic reaction stores free energy in molecules, G is + (positive) Figure 8.6 The magnitude of G for an endergonic reaction represents the amount of energy required to drive the reaction.

25 Photosynthesis is an example of Endergonic Reaction If cellular respiration releases 686 kcal/mol, then photosynthesis, the reverse reaction, must require an equivalent investment of energy. 6CO 2 + 6H 2 O C 6 H 12 O 6 + 6O 2 G = +686 kcal/mol Photosynthesis is strongly endergonic, powered by the absorption of light energy Pearson Education, Inc.

26 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 cell continues to do work throughout its life. 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

27 Figure 8.7 G < 0 G = 0 Equilibrium and work in an isolated hydroelectric system

28 Figure 8.8 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: C 6 H 12 O 6 + 6O 2 6CO 2 + 6H 2 O Catabolic pathways in a cell release free energy in a series of reactions. Equilibrium is never reached because the products of one step in the series become reactants for the next reaction. Finally, waste products are expelled from the cell.

29 What keeps the sequence of reactions going? Glucose and Oxygen Fig. 8.8 Carbon Dioxide and Water The huge free energy difference between glucose and oxygen at the top of the energy hill and CO2 and H2O at the bottom of the hill. As long as cells have a steady supply of glucose (or other fuel sources) and waste products can be eliminated, a metabolic pathway will never reach equilibrium and the cell will be able to do the work necessary to live.

30 ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: 1. Chemical 2. Transport 3. 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 2014 Pearson Education, Inc.

31 The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is the cell s energy shuttle ATP is composed of ribose (a sugar), adenine (a purine- nitrogenous base), and three phosphate groups The bonds between the phosphate groups on ATP can be broken by hydrolysis. When the terminal phosphate bond is broken, a molecule of inorganic phosphate (HOPO 3 2-, abbreviated Pi here) leaves ATP, which then becomes adenosine diphosphate (ADP) and energy is released. This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves Hydrolysis of ATP- ATP + H 2 O ADP + Pi + Energy This reaction is exergonic and In cells, ΔG = -7.3 kcal Pearson Education, Inc.

32 Figure 8.9 Adenine Phosphate groups Ribose (a) The structure of ATP Adenosine triphosphate (ATP) Energy Inorganic phosphate Adenosine diphosphate (ADP) (b) The hydrolysis of ATP

33 How 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 hydrolysis of ATP is directly coupled to endergonic processes by the transfer of the phosphate group to another molecule. This recipient molecule is now phosphorylated (phosphorylated intermediate); it is more reactive (less stable) than the original unphosphorylated molecules. The key to coupling exergonic and endergonic reactions is the formation of a phosphorylated intermediate.

34 Figure 8.10 (a) Glutamic acid conversion to glutamine Glu Glutamic acid NH 3 NH 2 Glu Ammonia Glutamine G Glu = +3.4 kcal/mol (b) Conversion reaction coupled with ATP hydrolysis Glu ATP ADP NH 3 1 P 2 Glu NH 2 Glu ADP P i Glutamic acid Phosphorylated intermediate Glutamine G Glu = +3.4 kcal/mol (c) Free-energy change for coupled reaction Glu G Glu = +3.4 kcal/mol + G ATP = 7.3 kcal/mol NH 3 NH 2 ATP Glu G ATP = 7.3 kcal/mol ADP P i Net G = 3.9 kcal/mol How ATP Performs Work I. Glutamine Synthesis

35 Fig II. Transport and Mechanical Work

36 The Regeneration of ATP an Endergonic Process Fig 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 The chemical potential energy temporarily stored in ATP drives most cellular work 2014 Pearson Education, Inc.

37 Enzymes speed up metabolic reactions by lowering energy barriers Sucrase Sucrose (C 12 H 22 O 11 ) Glucose (C 6 H 12 O 6 ) Fructose (C 6 H 12 O 6 ) An enzyme is bio 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 No sucrase = years to hydrolyze With sucrase = seconds to hydrolyze 2014 Pearson Education, Inc.

38 The Activation Energy Barrier Every chemical reaction between molecules involves bond breaking and bond forming To reach a state at which bonds can break and reform, reactant molecules must absorb energy from their surroundings. When the new bonds of the product molecules form, energy is released as heat as the molecules assume stable shapes with lower energy. The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (E A ) Activation energy is often supplied in the form of heat from the surroundings AB + CD Figure 8.13 AC + BD

39 Figure 8.14 How Enzymes Lower the EA Barrier Enzymes catalyze reactions by lowering the EA barrier. Activation energy is the amount of energy necessary to push the reactants over an energy barrier so that the downhill part of the reaction can begin. Enzymes do not affect the change in free energy ( G); instead, they hasten reactions that would occur eventually. Free energy Course of reaction without enzyme Reactants Course of reaction with enzyme E A without enzyme Progress of the reaction E A with enzyme is lower G is unaffected by enzyme Products 2014 Pearson Education, Inc.

40 Enzymes are substrate specific The reactant that an enzyme acts on is the substrate. The enzyme binds to a substrate, or substrates, forming an enzyme-substrate complex. While the enzyme and substrate are bound, the catalytic action of the enzyme converts the substrate to the product or products. The reaction catalyzed by each enzyme is very specific. What accounts for enzyme-substrate recognition? The specificity of an enzyme results from its three-dimensional shape, which is a consequence of its amino acid sequence.

41 Figure 8.15 Active Site The active site of an enzyme is typically a pocket or groove on the surface of the protein where catalysis occurs. The active site is usually formed by only a few amino acids. The rest of the protein molecule provides a framework that determines the configuration of the active site. The specificity of an enzyme is due to the fit between the active site and the substrate. The active site is not a rigid receptacle for the substrate. As the substrate enters the active site, interactions between the chemical groups on the substrate and those on the R groups (side chains) of the amino acids of the protein cause the enzyme to change shape slightly. This change leads to an induced fit that brings the chemical groups of the active site into position to catalyze the reaction.

42 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 E A barrier by Orienting substrates correctly In reactions involving more than one reactant, the active site brings substrates together in the correct orientation for the reaction to proceed. Straining substrate bonds As the active site binds the substrate, the enzyme may stretch the substrate molecules toward their transition-state form, stressing and bending critical chemical bonds that must be broken during the reaction. Providing a favorable microenvironment An active site may be a pocket of low ph, facilitating H+ transfer to the substrate as a key step in catalyzing the reaction. Covalently bonding to the substrate Enzymes may briefly bind covalently to substrates.

43 1 Substrates enter active site; enzyme changes shape such that its active site enfolds the substrates (induced fit). 2 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. Substrates Enzyme-substrate complex 3 Active site can lower E A and speed up a reaction. 6 Active site is available for two new substrate molecules. Enzyme Figure Products are released. 4 Substrates are converted to products. Products Copyright 2014 Pearson Education, Inc.

44 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 Each enzyme works best at certain optimal conditions, which favor the most active 3-D conformation for the enzyme molecule.

45 A cell s physical and chemical environment affects enzyme activity Temperature has a major impact on reaction rate. Each enzyme has an optimal temperature that allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules. Most human enzymes have optimal temperatures of about 37 C. The thermophilic bacteria (heat-tolerant) that live in hot springs contain enzymes with optimal temperatures of 77 C or higher. Each enzyme has an optimal ph. This optimal ph falls between 6 and 8 for most enzymes. However, digestive enzymes-pepsin in the stomach are designed to work best at ph 2. Intestinal enzymes-trypsin have an optimal ph of Pearson Education, Inc.

46 Figure 8.17 Rate of reaction Optimal temperature for Optimal temperature for typical human enzyme (37 C) enzyme of thermophilic (heat-tolerant) bacteria (77 C) Temperature ( C) (a) Optimal temperature for two enzymes Rate of reaction Optimal ph for pepsin (stomach enzyme) Optimal ph for trypsin (intestinal enzyme) ph (b) Optimal ph for two enzymes

47 Cofactors Many enzymes require non-protein helpers, called cofactors, for catalytic activity. Cofactors bind permanently or reversibly to the enzyme. Some inorganic cofactors are zinc, iron, and copper in ionic form. Organic cofactors are called coenzymes. Most vitamins are coenzymes or the raw materials from which coenzymes are made.

48 Competitive Enzyme Inhibitors Certain chemicals selectively inhibit the action of specific enzymes. If inhibitors attach to the enzyme by covalent bonds, inhibition may be irreversible. If inhibitors bind by weak bonds, inhibition may be reversible. Some reversible inhibitors resemble the substrate and compete for binding to the active site. These molecules are called competitive inhibitors. Competitive inhibition can be overcome by increasing the concentration of the substrate Pearson Education, Inc. Figure 8.18

49 Examples of Enzyme inhibitors include toxins, poisons, pesticides, and antibiotics 1. Toxins and poisons are often irreversible enzyme inhibitors. Sarin is a nerve gas that binds covalently to the R group on the amino acid serine. Serine is found in the active site of acetylcholinesterase, an important nervous system enzyme. 2. DDT acts as a pesticide by inhibiting key enzymes in the nervous system of insects. 3. Penicillin blocks the active site of an enzyme that many bacteria use to make their cell walls.

50 Non-Competitive Enzyme Inhibitors Non-competitive inhibitors effect enzymatic reactions by binding to another part of the molecule. Binding by the inhibitor causes the enzyme to change shape, rendering the active site less effective at catalyzing the reaction. Figure Pearson Education, Inc.

51 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 2014 Pearson Education, Inc.

52 Two changed amino acids were found near the active site. Active site Figure 8.19 Two changed amino acids were found in the active site. Two changed amino acids were found on the surface. Mimicking evolution of an enzyme with a new function

53 Regulation of enzyme activity helps control metabolism Metabolic control often depends on allosteric regulation. Many molecules that naturally regulate enzyme activity behave like reversible noncompetitive inhibitors. In allosteric regulation, a protein s function at one site is affected by the binding of a regulatory molecule to a separate site. This regulation may result in either inhibition or stimulation of an enzyme s activity. 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

54 Most allosterically regulated enzymes are constructed of two or more polypeptide chains. Each subunit has its own active site. The complex oscillates between two shapes, one catalytically active and the other inactive. In the simplest case of allosteric regulation, an activating or inhibiting regulatory molecule binds to a regulatory site (sometimes called an allosteric site), often located where subunits join. The binding of an activator stabilizes the conformation that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme. Allosteric Regulation Figure 8.20

55 Allosteric Regulation By binding to key enzymes, the reactants and products of ATP hydrolysis play a major role in balancing the flow of traffic between anabolic and catabolic pathways. For example, ATP binds to several catabolic enzymes allosterically, inhibiting their activity by lowering their affinity for substrate. If ATP production exceeds demand, the excess ATP will allosterically inhibit catabolic enzymes. ADP functions as an activator of the same enzymes. If ATP production lags behind its use, ADP will accumulate, activate the exzymes that speed up catabolism. ATP and ADP also affect key enzymes in anabolic pathways.

56 Co-operativity Figure 8.20 In enzymes with multiple catalytic subunits, binding by a substrate to one active site by induced fit triggers the same favorable conformational changes at all other subunits. This mechanism, called cooperativity, amplifies the response of enzymes to substrates, priming the enzyme to accept additional substrates. The vertebrate oxygen-transport protein hemoglobin is a classic example of cooperativity. Hemoglobin is made up of four subunits, each with an oxygen-binding site. The binding of an oxygen molecule to each binding site increases the affinity for oxygen of the remaining binding sites. Under conditions of low oxygen, as in oxygen-deprived tissues, hemoglobin is less likely to bind oxygen and releases it where it is needed. When oxygen is at higher levels, as in the lungs or gills, the protein has a greater affinity for oxygen as more binding sites are filled Pearson Education, Inc.

57 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 Metabolic Regulation Feedback Inhibition 2014 Pearson Education, Inc. Figure. 8.21

58 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 2014 Pearson Education, Inc.

59 The cell is compartmentalized: The organization of cellular structures helps bring order to metabolic pathways. A team of enzymes for several steps of a metabolic pathway may be assembled as a multienzyme complex. The product from the first reaction becomes the substrate for an adjacent enzyme in the complex until the final product is released. Some enzymes and enzyme complexes have fixed locations within the cells as structural components of particular membranes. Others are confined within membrane-enclosed eukaryotic organelles. Metabolic Regulation Cellular Localization The matrix contains Enzymes involved in one stage of Cellular respiration The cristae inner membranes contain enzymes needed for another stage of Cellular respiration Figure Pearson Education, Inc.