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An Introduction to Metabolism

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1 An Introduction to Metabolism
Chapter 8 An Introduction to Metabolism

2 Fig. 8-1 Figure 8.1 What causes the bioluminescence in these fungi?

3 I. Metabolism The totality of an organism’s chemical reactions

4 Begins with a specific molecule and ends with a product
II. Metabolic Pathways Begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme Enzyme 1 Enzyme 2 Enzyme 3 D C B A

5 Catabolic pathways: release energy, break down molecules
Ex. Cellular respiration - breakdown of glucose with oxygen

6 Anabolic pathways: consume energy, build complex molecules
Ex. Synthesis of protein from amino acids

7 III. Forms of Energy (E) Energy = capacity to cause change
Kinetic E = E from motion Heat (thermal E) = KE from random movement of atoms or molecules Potential E = E because of location or structure Chemical E = PE available for release in a reaction Energy can be converted from one form to another

8 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.

9 IV. The Laws of Energy Transformation
Thermodynamics = the study of energy transformations Closed system = isolated from surroundings Open system = energy and matter can be transferred between system and surroundings Organisms = open systems

10 A. The First Law of Thermodynamics
Energy of the universe is constant: – Energy can be transferred and transformed, but it cannot be created or destroyed Principle of conservation of energy

11 B. The Second Law of Thermodynamics
During every energy transfer or transformation, some energy is unusable, and is lost as heat – Every energy transfer or transformation increases the entropy (disorder) of the universe Chemical energy Heat CO2 H2O

12 V. Free-Energy Change, G
Free energy = available energy to do work when temp and pressure are uniform

13 Change in free energy (∆G) during a process is related to the change in enthalpy (change in total energy (∆H)), change in entropy (disorder (∆S)), and temp in Kelvin (T): ∆G = ∆H – T∆S Only processes with a negative ∆G are spontaneous and can be harnessed to do work Free Energy Bozeman

14 VI. Free Energy and Metabolism
Exergonic reaction proceeds with a net release of free energy (ΔG < 0) and is spontaneous Endergonic reaction absorbs free energy from its surroundings (ΔG > 0) and is nonspontaneous

15 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 Amount of energy required (∆G > 0) Figure 8.6 Free energy changes (ΔG) in exergonic and endergonic reactions Energy Free energy Reactants Progress of the reaction (b) Endergonic reaction: energy required

16 A. 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

17 (a) An isolated hydroelectric system
Fig. 8-7a ∆G < 0 ∆G = 0 Figure 8.7a Equilibrium and work in isolated and open systems (a) An isolated hydroelectric system

18 (b) An open hydroelectric system
Fig. 8-7b ∆G < 0 Figure 8.7b Equilibrium and work in isolated and open systems (b) An open hydroelectric system

19 (c) A multistep open hydroelectric system
Fig. 8-7c ∆G < 0 ∆G < 0 ∆G < 0 Figure 8.7c Equilibrium and work in isolated and open systems (c) A multistep open hydroelectric system

20 VIII. Structure and Hydrolysis of ATP
ATP (adenosine triphosphate) is the cell’s energy shuttle ATP = ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups ATP Overview - Bozeman For the Cell Biology Video Space Filling Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.

21 Bonds between the phosphate groups can be broken by hydrolysis (releasing energy)
This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves For the Cell Biology Video Stick Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.

22 H2O P P P Adenosine triphosphate (ATP) P + P P + Energy
Fig. 8-9 P P P Adenosine triphosphate (ATP) H2O Figure 8.9 The hydrolysis of ATP P + P P + Energy i Inorganic phosphate Adenosine diphosphate (ADP)

23 X. How ATP Performs Work ATP powers 3 types of cellular work (mechanical, transport, and chemical) Energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction (energy coupling) Overall, coupled reactions are exergonic ATP drives endergonic reactions by transferring a phosphate group to some other molecule (phosphorylation)

24 ∆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

25 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

26 XI. The Regeneration of ATP
ATP is regenerated by addition of a phosphate group to adenosine diphosphate (ADP) The energy comes from catabolic reactions in the cell The chemical PE temporarily stored in ATP drives most cellular work

27 + 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) Figure 8.12 The ATP cycle ADP + P i

28 XII. Activation Energy Initial E needed to start a chemical reaction is the free energy of activation, or activation energy (EA) Activation energy is often supplied from heat

29 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 ∆G < O C D Products Progress of the reaction

30 XIII. Enzymes Lower the EA
Enzymes catalyze reactions by lowering the EA Enzymes do not affect the change in free energy (∆G); they hasten reactions that would occur eventually

31 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 Figure 8.15 The effect of an enzyme on activation energy Products Progress of the reaction

32 XIV. Substrate Specificity of Enzymes
substrate = reactant that an enzyme acts on enzyme-substrate complex = enzyme binding to its substrate Active site = region on enzyme where the substrate binds Induced fit = brings chemical groups of active site into positions that enhance their ability to catalyze the reaction Enzyme Overview - Bozeman For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.

33 Substrate Active site Enzyme Enzyme-substrate complex (a) (b)
Fig. 8-16 Substrate Active site Figure 8.16 Induced fit between an enzyme and its substrate Enzyme Enzyme-substrate complex (a) (b)

34 XV. Enzyme’s Active Site
The active site can lower an EA barrier by Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Covalently bonding to the substrate

35 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 Figure 8.17 The active site and catalytic cycle of an enzyme Enzyme 5 Products are released. Substrates are converted to products. 4 Products

36 XVI. Effects on Enzyme Activity
An enzyme’s activity can be affected by Each enzyme has optimum Temp and pH Chemicals that influence the enzyme (cofactors and inhibitors)

37 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) Figure 8.18 Environmental factors affecting enzyme activity Rate of reaction 1 2 3 4 5 6 7 8 9 10 pH (b) Optimal pH for two enzymes

38 A. Cofactors Nonprotein enzyme helpers May be inorganic (such as a metal in ionic form) or organic Coenzyme = organic cofactor (vitamins)

39 B. Enzyme Inhibitors Competitive inhibitors bind to active site of enzyme, competing w/ substrate Noncompetitive inhibitors bind to another part of enzyme, causing enzyme to change shape and making active site less effective Ex. toxins, poisons, pesticides, and antibiotics

40 Noncompetitive inhibitor
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

41 XVII. Allosteric Regulation of Enzymes
Allosteric regulation = inhibit or stimulate an enzyme’s activity Occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site

42 A Allosteric Activation and Inhibition
Most allosterically regulated enzymes are made from polypeptide subunits Each enzyme has active (activator stabilizes) and inactive (inhibitor stabilizes) forms

43 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 Figure 8.20a Allosteric regulation of enzyme activity Non- functional active site Inhibitor Inactive form Stabilized inactive form (a) Allosteric activators and inhibitors

44 Cooperativity = form of allosteric regulation that can amplify enzyme activity
Binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

45 (b) Cooperativity: another type of allosteric activation
Fig. 8-20b Substrate Inactive form Stabilized active form Figure 8.20b Allosteric regulation of enzyme activity (b) Cooperativity: another type of allosteric activation

46 B. Feedback Inhibition End product of a metabolic pathway shuts down the pathway Prevents cell from wasting chemical resources by making more product than needed Biochemical Pathway (no inhibition) Feedback Inhibition of Biochemical Pathways

47 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 Isoleucine binds to allosteric site Figure 8.22 Feedback inhibition in isoleucine synthesis Enzyme 4 Intermediate D Enzyme 5 End product (isoleucine)

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