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An Introduction to Metabolism

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1 An Introduction to Metabolism
Chapter 8 An Introduction to Metabolism

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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

3 Concept 8.1: Metabolism Metabolism is the totality of an organism’s chemical reactions An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics Metabolism is an emergent property of life that arises from interactions between molecules within the cell A metabolic pathway begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme Bioenergetics is the study of how organisms manage their energy resources Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

4 Starting molecule Product
Fig. 8-UN1 Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Starting molecule Product

5 Catabolism and Anabolism
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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

6 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

7 Fig. 8-2 A diver has more potential energy on the platform than in the water. Diving converts potential energy to kinetic energy. Figure 8.2 Transformations between potential and kinetic energy Climbing up converts the kinetic energy of muscle movement to potential energy. A diver has less potential energy in the water than on the platform.

8 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 open systems Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

9 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

10 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

11 (a) First law of thermodynamics (b) Second law of thermodynamics
Fig. 8-3 Heat CO2 + Chemical energy H2O Living cells unavoidably convert organized forms of energy to heat Spontaneous processes occur without energy input; they can happen quickly or slowly For a process to occur without energy input, it must increase the entropy of the universe (a) First law of thermodynamics (b) Second law of thermodynamics

12 Biological Order and Disorder
Cells create ordered structures from less ordered materials Organisms also replace ordered forms of matter and energy with less ordered forms Energy flows into an ecosystem in the form of light and exits in the form of heat 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

13 Concept 8.2: Free-Energy Change, G
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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

14 Only processes with a negative ∆G are spontaneous
Free-Energy Change, G 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 G  system’s quantity of free energy H  system’s total energy T  absolute temperature in Kelvin S  system’s total entropy So, for a process to occur spontaneously, the system must either give up energy (decrease H), give up order (increase S), or both. The change in G must be negative. In other words, nature runs downhill in the sense of a loss of useful energy – the capacity to perform work. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

15 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

16 Unstable systems (top diagrams) are rich in “free” energy.
Fig. 8-5 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 Unstable systems (top diagrams) are rich in “free” energy. They have a tendency to change spontaneously to a more stable state (bottom)…and it is possible to harness this “downhill” change to perform work. (a) Gravitational motion (b) Diffusion (c) Chemical reaction

17 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

18 Progress of the reaction
Fig. 8-6 Reactants Amount of energy released (∆G < 0) Energy Free energy Products Progress of the reaction (a) Exergonic reaction: energy released Products Exergonic Reaction: ΔG < 0 Reaction proceeds with a net RELEASE of free energy…these reactions occur spontaneously. Endergonic Reaction: ΔG > 0 Reaction proceeds with an ABSORPTION of free energy…these reactions are not spontaneous. Amount of energy required (∆G > 0) Energy Free energy Reactants Progress of the reaction (b) Endergonic reaction: energy required

19 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

20 Fig. 8-7 ∆G < 0 ∆G = 0 (a) An isolated hydroelectric system (b) An open hydroelectric system ∆G < 0 Flowing water drives the generator only until the system reaches equilibrium (CLOSED) Flowing water keeps driving the generator because intake and outflow of water keep the system from reaching equilibrium (OPEN) Cellular respiration is analogouos to part c. 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 the next, so no reaction ever reaches equilibrium ∆G < 0 ∆G < 0 ∆G < 0 (c) A multistep open hydroelectric system

21 Concept 8.3: ATP & Energy Coupling
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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

22 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

23 H2O P P P Adenosine triphosphate (ATP) P + P P + Energy
Fig. 8-9 P P P Adenosine triphosphate (ATP) H2O 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 P + P P + Energy i Inorganic phosphate Adenosine diphosphate (ADP)

24 Overall, the coupled reactions are exergonic
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 exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

25 ∆G = +3.4 kcal/mol Glutamic acid Ammonia Glutamine
Fig. 8-10 NH2 NH3 + ∆G = +3.4 kcal/mol Glu Glu Glutamic acid Ammonia Glutamine (a) Endergonic reaction 1 ATP phosphorylates glutamic acid, making the amino acid less stable. P + ATP + ADP Glu Glu NH2 P 2 Ammonia displaces the phosphate group, forming glutamine. NH3 + + P i Glu Glu Figure 8.10 How ATP drives chemical work: Energy coupling using ATP hydrolysis (b) Coupled with ATP hydrolysis, an exergonic reaction (c) Overall free-energy change

26 The recipient molecule is now phosphorylated
Phosphorylation ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant The recipient molecule is now phosphorylated Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

27 Membrane protein Solute Solute transported Vesicle Cytoskeletal track
Fig. 8-11 Membrane protein P P i Solute Solute transported (a) Transport work: ATP phosphorylates transport proteins ADP ATP + P i Vesicle Cytoskeletal track Figure 8.11 How ATP drives transport and mechanical work ATP Motor protein Protein moved (b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzed

28 + H2O Energy for cellular work (endergonic, energy-consuming
Fig. 8-12 ATP + H2O Energy from catabolism (exergonic, energy-releasing processes) Energy for cellular work (endergonic, energy-consuming processes) 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 chemical potential energy temporarily stored in ATP drives most cellular work ADP + P i

29 Enzymes speed up metabolic reactions by lowering energy barriers.
Concept 8.4: Enzymes 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

30 Sucrose (C12H22O11) Sucrase Glucose (C6H12O6) Fructose (C6H12O6)
Fig. 8-13 Sucrose (C12H22O11) Sucrase Figure 8.13 Example of an enzyme-catalyzed reaction: hydrolysis of sucrose by sucrase Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction A solution of sucrose dissolved in sterile water will sit for years at room temp with no appreciable hydrolysis occurring….BUT, if add SUCRASE (an enzyme), the sucrose will be converted in seconds… Glucose (C6H12O6) Fructose (C6H12O6)

31 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 heat from the surroundings Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

32 Progress of the reaction
Fig. 8-14 A B C D Transition state A B EA C D Free energy Reactants A B Figure 8.14 Energy profile of an exergonic reaction Uphill - Reactants A & B must absorb enough energy from the surroundings to surmount the hill of activation energy and reach the unstable transition state. Downhill – Bonds break, and new bonds form. Energy is released to surroundings during this process (EXERGONIC - ∆G negative) – products have less energy than reactants. THIS IS WITH NO ENZYME ACTIVITY!!! ∆G < O C D Products Progress of the reaction

33 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

34 Progress of the reaction
Fig. 8-15 Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Free energy Course of reaction with enzyme ∆G is unaffected by enzyme Without affecting the free-energy change (∆G) for the reaction, an enzyme speeds the reaction up by lowering the activation energy required to start the reaction. Black Curve – shows course of reaction w/out enzyme. Red Curve – shows course of reaction with enzyme. ENZYMES ARE NOT USED UP DURING THESE PROCESSES! Products Progress of the reaction

35 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 Rate of conversion of substrate into new products depends on initial concentration of substrate! But there is a limit to total speed of reaction – all enzyme molecules may be working (saturated), so only way to increase reaction speed is to ADD MORE ENZYME! So…to speed up reaction…add MORE substrate or add more enzyme!!! Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

36 Substrate Active site Enzyme Enzyme-substrate complex (a) (b)
Fig. 8-16 Substrate Active site The specificity of an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substrate. Active site of enzyme can be seen in computer model as groove on surface of protein (blue) On entering the active site, the substrate (red) induces a change in the shape of the protein that causes the active site to embrace the substrate. Enzyme Enzyme-substrate complex (a) (b)

37 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

38 Fig. 8-17 Substrates enter active site; enzyme changes shape such that its active site enfolds the substrates (induced fit). 1 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. 2 Substrates Enzyme-substrate complex Active site can lower EA and speed up a reaction. 3 Active site is available for two new substrate molecules. 6 Enzyme 5 Products are released. Substrates are converted to products. 4 Products

39 An enzyme’s activity can be affected by
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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

40 Optimal temperature for typical human enzyme Optimal temperature for
Fig. 8-18 Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria Rate of reaction 20 40 60 80 100 Temperature (ºC) (a) Optimal temperature for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Each enzyme has an optimal temperature in which it can function Each enzyme has an optimal pH in which it can function Rate of reaction 1 2 3 4 5 6 7 8 9 10 pH (b) Optimal pH for two enzymes

41 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

42 Enzyme Inhibitors http://bcs. whfreeman
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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

43 Fig. 8-19 Substrate Active site Competitive inhibitor Enzyme Figure 8.19 Inhibition of enzyme activity Noncompetitive inhibitor (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition (b) Competitive Inhibition: Mimics the substrate and competes for the active site (c) Noncompetitive Inhibition: Binds to the enzyme at a location away from the active site, but alters the shape of the enzyme so that the active site is no longer fully functional.

44 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

45 Allosteric Regulation of Enzymes http://bcs. whfreeman
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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

46 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

47 Each enzyme has active and inactive forms
Fig. 8-20 Allosteric enyzme with four subunits Active site (one of four) Regulatory site (one of four) Activator Active form Stabilized active form Oscillation Non- functional active site Inhibitor Inactive form Stabilized inactive form 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 Substrate Inactive form Stabilized active form (b) Cooperativity: another type of allosteric activation

48 Stabilized active form
Fig. 8-20a Allosteric enzyme with four subunits Active site (one of four) Regulatory site (one of four) Activator Active form Stabilized active form Oscillation Allosteric regulation is the term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme’s activity. MOST ALLOSTERICALLY REGULATED ENZYMES ARE CONSTRUCTED FROM 2 OR MORE POLYPEPTIDE CHAINS: The enzyme oscillates between 2 conformational states, one active and the other inactive. Remote (away) from the active sites are the allosteric sites, specific receptors for regulators of the enzyme, which may be an activator or an inhibitor. b) Here we see the opposing affects of an allosteric activator and an allosteric inhibitor on the conformation of all four subunits of enzyme. Non- functional active site Inhibitor Inactive form Stabilized inactive form (a) Allosteric activators and inhibitors

49 Cooperativity Cooperativity is a form of allosteric regulation that can amplify enzyme activity In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

50 Feedback Inhibition http://highered. mcgraw-hill
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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

51 Fig. 8-22 Initial substrate (threonine) Active site available Threonine in active site Enzyme 1 (threonine deaminase) Isoleucine used up by cell Intermediate A Feedback inhibition Enzyme 2 Active site of enzyme 1 no longer binds threonine; pathway is switched off. Intermediate B Enzyme 3 Intermediate C Figure 8.22 Feedback inhibition in isoleucine synthesis Isoleucine binds to allosteric site Enzyme 4 Intermediate D Enzyme 5 End product (isoleucine)

52 Fig. 8-23 Mitochondria 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 1 µm

53 You should now be able to:
Distinguish between the following pairs of terms: catabolic and anabolic pathways; kinetic and potential energy; open and closed systems; exergonic and endergonic reactions In your own words, explain the second law of thermodynamics and explain why it is not violated by living organisms Explain in general terms how cells obtain the energy to do cellular work Explain how ATP performs cellular work Explain why an investment of activation energy is necessary to initiate a spontaneous reaction Describe the mechanisms by which enzymes lower activation energy Describe how allosteric regulators may inhibit or stimulate the activity of an enzyme Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings


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