Chapter 8 An Introduction to Metabolism AP Biology

Chapter 8: An Introduction to Metabolism AP Biology

Overview: The Energy of Life Living cell = miniature chemical factory where thousands of reactions occur Cell extracts energy applies it to perform work Some organisms convert energy light, bioluminescence

Concept 8. 1: An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics Metabolism: totality of organism’s chemical reactions an emergent property of life that arises from interactions between molecules within the cell Organization of the Chemistry of Life into Metabolic Pathways Metabolic pathway: begins with specific molecule and ends with a product Each step catalyzed by a specific enzyme

Organization of the Chemistry of Life into Metabolic Pathways Catabolic pathways: release energy by breaking down complex molecules into simpler compounds Anabolic pathways: consume energy to build complex molecules from simpler ones Ex: Cellular respiration= the breakdown of glucose in the presence of oxygen Ex: synthesis of protein from amino acids Bioenergetics: study of how organisms manage their energy resources

Forms of Energy: the capacity to cause change exists in various forms, some can perform work Kinetic energy: energy associated with motion Heat (thermal energy): kinetic energy associated with random movement of atoms or molecules Potential energy: energy that matter possesses because of its location or structure Chemical energy: potential energy available for release in a chemical reaction Energy can be converted from one form to another

The Laws of Energy Transformation Thermodynamics: study of energy transformations Closed system: isolated from surroundings Ex: Liquid in a thermos Open system: energy and matter can be transferred between system and surroundings Ex: Organisms! Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Thermodynamics First law of thermodynamics: energy of universe is constant: – Energy can be transferred and transformed, but it cannot be created nor destroyed Also called the principle of conservation of energy

Thermodynamics Second law of thermodynamics: during every energy transfer or transformation, some energy is unusable, and is often lost as heat Every energy transfer or transformation increases the entropy (disorder) of the universe Living cells unavoidably convert organized energy forms heat Spontaneous processes occur without energy input quickly or slowly For a process to occur without energy input, it must increase the entropy of universe

Fig. 8 -3 Heat Chemical energy (a) First law of thermodynamics CO 2 + H 2 O (b) Second law of thermodynamics

Biological Order and Disorder Cells create ordered structures from less ordered materials Organisms replace ordered forms of matter and energy with less ordered forms Energy: Evolution of more complex organisms does not violate the second law of thermodynamics Flows into an ecosystem as light Exits as heat Explain this. Why not? Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 8 -4 Root of buttercup plant; As open system, plants can increase their order as long as order of surroundings decrease 50 µm

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 THUS! they need to determine energy changes that occur in chemical reactions

Free-Energy Change, G Free energy: energy that can do work when temperature and pressure are uniform like in a living cell Change in free energy (∆G) during a process is related to change in enthalpy/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 Can you think of one? Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Free Energy, Stability, and Equilibrium Free energy: measure of system’s instability or tendency to change to more stable state During spontaneous change: free energy decreases stability of system increases Equilibrium: state of maximum stability A process is spontaneous and can perform work only when it is moving toward equilibrium

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 (a) Gravitational motion (b) Diffusion (c) Chemical reaction

Fig. 8 -5 a • 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

Fig. 8 -5 b Spontaneous change (a) Gravitational motion Spontaneous change (b) Diffusion Spontaneous change (c) Chemical reaction

Free Energy and Metabolism Concept of free energy can be applied to chemistry of life’s processes Exergonic reaction: net release of free energy; spontaneous Endergonic reaction: absorbs free energy from its surroundings; nonspontaneous

Fig. 8 -6 a Free energy Reactants Amount of energy released (∆G < 0) Energy Products Progress of the reaction (a) Exergonic reaction: energy released

Fig. 8 -6 b Free energy Products Energy Reactants Progress of the reaction (b) Endergonic reaction: energy required Amount of energy required (∆G > 0)

Equilibrium and Metabolism Reactions in closed system eventually reach equilibrium and then do no work Cells not in equilibrium; they are open systems with constant flow of materials Defining feature of life = metabolism is never at equilibrium Catabolic pathway: releases free energy in a series of reactions Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 8 -7 ∆G < 0 ∆G = 0 (a) An isolated hydroelectric system (b) An open hydroelectric system ∆G < 0 (c) A multistep open hydroelectric system

Fig. 8 -7 a ∆G < 0 (a) An isolated hydroelectric system ∆G = 0

Fig. 8 -7 b ∆G < 0 (b) An open hydroelectric system

Fig. 8 -7 c ∆G < 0 (c) A multistep open hydroelectric system

Concept 8. 3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions Cell does three main kinds of work: Chemical Transport Mechanical Cells manage energy resources by energy coupling the use of an exergonic process to drive an endergonic one Most energy coupling in cells mediated by ATP Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

The Structure and Hydrolysis of ATP (adenosine triphosphate): cell’s energy shuttle ATP is composed of : ribose (a sugar) adenine (a nitrogenous base) three phosphate groups Bonds between phosphate groups of ATP’s tail can be broken by hydrolysis Energy released from ATP when terminal phosphate bond broken comes from chemical change to a state of lower free energy, not from the phosphate bonds themselves

How ATP Performs Work Three types of cellular work (mechanical, transport, and chemical) powered by the hydrolysis of ATP In cell energy from exergonic reaction of ATP hydrolysis can be used to drive a endergonic reaction Overall: coupled reactions are exergonic ATP drives endergonic reactions by phosphorylation transferring a phosphate group to some other molecule, such as a reactant recipient molecule is now phosphorylated

Fig. 8 -10 NH 2 Glutamic acid NH 3 + ∆G = +3. 4 kcal/mol Glu Ammonia Glutamine (a) Endergonic reaction 1 ATP phosphorylates glutamic acid, making the amino acid less stable. P + Glu ATP Glu + ADP NH 2 2 Ammonia displaces the phosphate group, forming glutamine. P Glu + NH 3 Glu + Pi (b) Coupled with ATP hydrolysis, an exergonic reaction (c) Overall free-energy change

The Regeneration of ATP renewable resource that is regenerated by addition of phosphate group to adenosine diphosphate (ADP) Energy to phosphorylate ADP comes from catabolic reactions in the cell Chemical potential energy temporarily stored in ATP drives most cellular work Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Concept 8. 4: Enzymes speed up metabolic reactions by lowering energy barriers Catalyst: chemical agent that speeds up a reaction without being consumed by the reaction Enzyme: catalytic protein Enzyme-catalyzed reaction Ex: Hydrolysis of sucrose by enzyme sucrase Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

The Activation Energy Barrier Every chemical reaction between molecules involves bond breaking AND bond forming Free energy of activation, or activation energy (EA): initial energy needed to start chemical reaction often supplied in form of heat from the surroundings

How Enzymes Lower the EA Barrier Enzymes catalyze reactions by lowering EA barrier Enzymes do not affect change in free energy (∆G); instead, they hasten reactions that would occur eventually

Substrate Specificity of Enzymes Substrate: reactant that an enzyme acts on Enzyme-substrate complex: formed when enzyme binds to its substrate Active site: region on the enzyme where the substrate binds Induced fit of substrate brings chemical groups of active site into positions that enhance their ability to catalyze the reaction

Catalysis in the Enzyme’s Active Site In enzymatic reaction the substrate binds to the active site of the enzyme Active site can lower an EA barrier by Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Covalently bonding to the substrate

Fig. 8 -17 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 6 Active site is available for two new substrate molecules. Enzyme 5 Products are released. 4 Substrates are converted to products. Products 3 Active site can lower EA and speed up a reaction.

Effects of Local Conditions on Enzyme Activity Enzyme’s activity can be affected by General environmental factors Temperature p. H Chemicals that specifically influence enzyme

Fig. 8 -18 Rate of reaction Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria 40 60 80 Temperature (ºC) (a) Optimal temperature for two enzymes 0 20 Rate of reaction Optimal p. H for pepsin (stomach enzyme) 4 5 p. H (b) Optimal p. H for two enzymes 0 1 2 3 100 Optimal p. H for trypsin (intestinal enzyme) 6 7 8 9 10

Cofactors Cofactors: nonprotein enzyme helpers may be inorganic (such as a metal in ionic form) or organic Coenzyme: organic cofactor include vitamins Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Enzyme Inhibitors Competitive inhibitors: bind to active site of enzyme, competing with the substrate Noncompetitive inhibitors: bind to another part of enzyme, causing enzyme to change shape and making active site less effective Examples: toxins, poisons, pesticides, and antibiotics

Fig. 8 -19 Substrate Active site Competitive inhibitor Enzyme Noncompetitive inhibitor (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition

Concept 8. 5: Regulation of enzyme activity helps control metabolism Chemical chaos would result if cell’s metabolic pathways were not tightly regulated Cell does this by: 1. 2. switching on/off genes that encode specific enzymes regulating the activity of enzymes Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Allosteric Regulation of Enzymes Allosteric regulation may either inhibit or stimulate an enzyme’s activity occurs when a regulatory molecule binds to protein at one site and affects the protein’s function at another site

Allosteric Activation and Inhibition Most allosterically regulated enzymes made from polypeptide subunits Each enzyme has active and inactive forms Binding of activator stabilizes the active form of the enzyme Binding of inhibitor stabilizes the inactive form of the enzyme Cooperativity: form of allosteric regulation that can amplify enzyme activity binding by substrate to one active site stabilizes favorable conformational changes at all other subunits

Fig. 8 -20 a Allosteric enzyme with four subunits Regulatory site (one of four) Active site (one of four) Activator Active form Stabilized active form Oscillation Non. Inhibitor Inactive form functional active site (a) Allosteric activators and inhibitors Stabilized inactive form

Fig. 8 -20 b Substrate Inactive form Stabilized active form (b) Cooperativity: another type of allosteric activation

Identification of Allosteric Regulators Allosteric regulators = attractive drug candidates for enzyme regulation Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses

Fig. 8 -21 a EXPERIMENT Caspase 1 Active site Substrate SH Known active form SH Allosteric binding site Allosteric Known inactive form inhibitor SH Active form can bind substrate S–S Hypothesis: allosteric inhibitor locks enzyme in inactive form

Fig. 8 -21 b RESULTS Caspase 1 Active form Inhibitor Allosterically Inactive form inhibited form

Feedback Inhibition Feedback inhibition: end product of a metabolic pathway shuts down the pathway Prevents cell from wasting chemical resources by synthesizing more product than needed

Specific Localization of Enzymes Within the Cell Structures within cell help bring order to metabolic pathways Some enzymes act as structural components of membranes In eukaryotic cells, some enzymes reside in specific organelles Ex: enzymes for cellular respiration located in mitochondria Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

You should now be able to: 1. Distinguish between the following pairs of terms: 1. 2. 3. 4. 5. 6. 7. 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

Fig. 8 -UN 2 Free energy Course of reaction without enzyme EA with enzyme is lower Reactants Course of reaction with enzyme ∆G is unaffected by enzyme Products Progress of the reaction