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Chapter 8: An Introduction to

1. Energy & Chemical Reactions 2. ATP 3. Enzymes & Metabolic Pathways

1. Energy & Chemical Reactions

Chapter Reading – pp. 142-148

2 Basic Forms of Energy Kinetic Energy (KE) • energy in motion or “released” energy: • heat (molecular motion) • electric current* (flow of charged particles)

• light energy* (radiation of photons)

• mechanical energy* (structural movement)

• chemical energy* (breaking covalent bonds, flow from high to low concentration)

*forms of KE cells use to “do things”

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Potential Energy (PE) • stored energy (i.e., not yet released):

A diver has more potential Diving converts energy on the platform potential energy to than in the water. kinetic energy. • gravitational potential

• chemical bonds*

• chemical gradients*, charge gradients*

*sources of PE Climbing up converts the kinetic A diver has less potential energy of muscle movement energy in the water cells rely on to potential energy. than on the platform.

Illustration of Kinetic & Potential Energy

KE highest at b, lowest at a & c

PE highest at a & c, lowest at b

Laws of Energy Transformation st 1 Law of Thermodynamics “Energy is neither created Principle of Conservation of Energy: nor destroyed, but may be converted to other forms.”

Heat CO2 + Chemical energy H2O

(a) First law of thermodynamics (b) Second law of thermodynamics

nd 2 Law of Thermodynamics “Every energy transfer or • every energy conversion results in transformation increases the a loss of usable energy as HEAT of the universe.”

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Chemical Free Energy Gibb’s Free Energy (G) = “chemical PE”

DG = Gproducts - Greactants Negative DG: • “loss” of chemical PE (e.g., respiration) • net release of KE (for or to raise temperature) Positive DG: • “gain” of chemical PE (e.g., photosynthesis) • requires input of KE (e.g., sunlight) DG = 0: • system is at equilibrium

Examples of Spontaneous Changes in Free Energy

• More free energy (higher G) • Less stable • Greater work capacity

In a spontaneous change • The free energy of the system decreases (DG  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)

• in each case DG is negative and PE decreases

Exergonic Reactions Reactants Amount of energy released • net release of energy (∆G < 0) (DG is negative) Energy Products • loss of PE Free energy Progress of the reaction (a) : energy released

Endergonic Reactions Products

Amount of energy • net consumption of required (∆G > 0) energy Energy

(DG is positive) Reactants Free energy

• gain of PE Progress of the reaction (b) Endergonic reaction: energy required

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Activation Energy (EA) Whether endergonic or exergonic, all chemical reactions require some energy input for the reaction to proceed – the A B activation C D energy (EA) Transition state

A B EA • all reactions require C D some sort of “spark” Reactants A B ∆G < O C D • this is why sources of chemical PE are Products “stable” Progress of the reaction

Mechanical Model of

The upright bottle falling over is analogous to an exergonic reaction, yet it still requires some energy input for the bottle to tip over.

2. ATP

Chapter Reading – pp. 148-151

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ATP – an Ideal Cellular Fuel • useable amount of energy (DG -7.3 kcal/mole) • stable, soluble in water (negatively charged)

• terminal phospho- anhydride bond easily broken

ATP Hydrolysis • exergonic cleavage of terminal phospho-anhydride bond

P P P

Adenosine triphosphate (ATP)

H2O

DG -7.3 kcal/mole)

P + P P i + Energy

Inorganic phosphate Adenosine diphosphate (ADP)

The ATP Cycle

ATP + H2O

Energy from Energy for cellular catabolism (exergonic, work (endergonic, energy-releasing energy-consuming processes) ADP + P i processes)

Exergonic processes (e.g., cellular respiration) provide energy for the endergonic synthesis of ATP, whereas ATP hydrolysis releases energy that can be used for other endergonic activities…

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Examples of ATP-powered “Work”

Membrane protein

P P i Solute Solute transported (a) Transport work: ATP phosphorylates transport proteins ADP ATP + P i Vesicle Cytoskeletal track

ATP

Motor protein Protein moved (b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzed

Coupling of Biochemical Reactions Exergonic reactions fuel (provide energy for) endergonic reactions in cells (i.e, they are “coupled”)

• breakdown of exergonic glucose fuels endergonic ATP production exergonic endergonic • ATP hydrolysis fuels most cellular activities

Example of Coupling w/ ATP Hydrolysis (a) Glutamic acid NH3 NH2 conversion DGGlu = +3.4 kcal/mol to glutamine Glu Glu Glutamic Ammonia Glutamine acid

(b) Conversion NH3 reaction coupled 1 P 2 with ATP ADP NH2 ADP ATP P i hydrolysis Glu Glu Glu Glutamic Phosphorylated Glutamine acid intermediate

DGGlu = +3.4 kcal/mol

(c) Free-energy NH3 NH2 change for ATP ADP P i coupled Glu Glu reaction DGGlu = +3.4 kcal/mol DGATP = 7.3 kcal/mol + DGATP = 7.3 kcal/mol

Net DG = 3.9 kcal/mol

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3. Enzymes & Metabolic Pathways

Chapter Reading – pp. 142, 151-159

Enzymes are Biological Catalysts

Biochemical reactions such as the one below will not occur spontaneously without a catalyst:

Sucrase

Sucrose Glucose Fructose

(C12H22O11) (C6H12O6) (C6H12O6)

Enzymes are biological catalysts made of protein or RNA that determine when reactions occur. • the production and regulation of enzymes give a cell complete control over all of the biochemical reactions that occur within the cell

Enzymes Lower Activation Energy

Course of reaction EA without without enzyme enzyme EA with enzyme is lower Reactants

Course of DG is unaffected reaction by enzyme

with enzyme Free energy Free

Products

Progress of the reaction

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Enzymes physically bind Substrates Substrate The “fit” of substrate into active site is Active sites highly specific and due to molecular complementarity

Enzyme Enzyme-substrate complex • complementary in Substrate physical shape (“hand in glove”) Active site • complementary in chemical properties (attraction between opposite charges, Enzyme Enzyme-substrate complex hydrophobic regions)

The Catalytic Cycle of Enzymes

1 Enzyme available with empty active • every enzyme has a site unique substrate & Active site Substrate thus catalyzes a (sucrose) specific reaction 2 Substrate binds to enzyme with induced fit

Enzyme Glucose (sucrase)

Fructose • cells produce 1000s of different H2O enzymes, all of 4 Products are released which are proteins 3 Substrate is encoded by a converted to particular gene products

Factors effecting Enzyme Activity

Optimal temperature for Optimal temperature for typical human enzyme enzyme of thermophilic (heat-tolerant) Optimal temperature bacteria and pH for a given enzyme depend on the environment in which

Rate of reaction of Rate it normally functions 0 20 40 60 80 100 Temperature (ºC) (a) Optimal temperature for two enzymes

Optimal pH for pepsin Optimal pH (stomach enzyme) for trypsin Deviation from the (intestinal enzyme) optimal conditions can result in denaturation and loss of enzyme

activity Rate of reaction of Rate 0 1 2 3 4 5 6 7 8 9 10 pH (b) Optimal pH for two enzymes

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Enzyme Regulation

Substrate

Active site Competitive inhibitor

Enzyme

Noncompetitive inhibitor

(a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition

Enzymes can be regulated by inhibitors in two general ways: 1) Competition between inhibitor & substrate for active site 2) Remotely inducing the active site to change shape

Competitive Enzyme Inhibition Substrate Competitive Competitive inhibitor inhibition involves binding of an inhibitor to Enzyme the active site

• inhibitor must be reversible to be able Reversible Substrate competitive to regulate in inhibitor response to concentration

Increase in substrate irreversible inhibitors concentration Enzyme essentially poison the enzyme

Allosteric Enzyme Regulation

Substrate Allosteric Distorted regulation Active site Enzyme active site involves the binding of a

substance to Allosteric site an enzyme Allosteric Allosteric inhibition inhibitor outside the (non-competitive) active site Substrate Distorted Active site • induces change active site in shape of active site

Allosteric site • must be Allosteric activator reversible Allosteric activation

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Cooperativity With many multimeric enzymes, the binding of substrate to one active site can stabilize the “active conformation” of other active sites, thus increasing the frequency with which they bind substrate.

Substrate • this is a type of allosteric regulation since active sites are regulated in a

Inactive form Stabilized active non-competitive form manner (b) Cooperativity: another type of allosteric activation

Metabolic Pathways Most biological processes, whether anabolic (building) or catabolic (breaking down), require a series of chemical reactions (i.e., a pathway)

Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Starting molecule

• each step in a is catalyzed by a specific enzyme • a missing or inactive enzyme can prematurely shut down a metabolic pathway, leading to the accumulation of potentially dangerous intermediates

Initial substrate (threonine) Feedback Active site available Threonine in active site Inhibition

Enzyme 1 (threonine The end-products of Isoleucine deaminase) used up by metabolic pathways can cell be important reversible Intermediate A Feedback enzyme inhibitors inhibition Enzyme 2 Active site of enzyme 1 no st longer binds Intermediate B • inhibit 1 enzyme, turn threonine; pathway is pathway “off” switched off. Enzyme 3

Intermediate C low [inhibitor] = pathway ON Isoleucine binds to Enzyme 4 allosteric high [inhibitor] = pathway OFF site Intermediate D • can be competitive or Enzyme 5 allosteric inhibition

End product • important way of regulating (isoleucine) end-product levels

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Key Terms for Chapter 8

• kinetic, potential energy, free energy

• endergonic, exergonic, coupling of reactions

• activation energy

• enzyme, catalyst • substrate, active site, molecular complementarity • competitive, noncompetitive, feedback inhibition • allosteric, cooperative regulation Relevant • reversible vs irreversible Chapter Questions 1-7

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