Energy Transformations and Enzymes AP Bio Chapter 6

The reactions of a cell either consume or release energy. Metabolism – totality of an organism’s chemical processes Controlled by enzymes – biological catalysts that lower energy barriers and speed up metabolic processes

Each step is catalyzed by a specific enzyme A metabolic pathway begins with a specific molecule and ends with a product. Each step is catalyzed by a specific enzyme Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

Types of pathways Catabolic pathways – break down complex molecules; release energy Anabolic pathways – require energy to combine simpler molecules to make complex ones; requires energy. Bioenergetics – how organisms manage their energy resources

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Energy Potential – energy matter possesses The capacity to cause change Energy exists in various forms, some of which can perform work. Kinetic – energy of motion Potential – energy matter possesses because of its location or structure

A diver has more potential energy on the platform than in the water. 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.

In molecules, the Potential Energy is the energy stored in the bonds.

KE is also random movement of atoms or molecules as in thermal energy (heat)

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

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

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 The quantity of energy is constant but not the quality!

Living cells unavoidably convert organized forms of energy to heat Fig. 8-3 Living cells unavoidably convert organized forms of energy to heat Heat CO2 + Chemical energy H2O Figure 8.3 The two laws of thermodynamics (a) First law of thermodynamics (b) Second law of thermodynamics

Biological Order and Disorder Cells create ordered structures from less ordered materials 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

LIFE REQUIRES FREE ENERGY!

Free-Energy Change, G A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell. The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Gibbs Free Energy ∆G = ∆H – T∆S The change in free energy (∆G) during a process is related to the change in enthalpy, or (∆H), change in entropy (∆S), and temperature in Kelvin (T).

ΔH ENTHALPY – heat content of molecule (total PE in its bonds) It is a measure of the total energy there NegativeΔ H – releases heat; exothermic Positive Δ H – absorbs heat; endothermic Spontaneous reactions have - Δ H

Δ S ENTROPY (disorder) S final state – S initial state Spontaneous reactions have + Δ S

Temp necessary due to more KE of molecules, disrupting order T (temperature 0K) Temp necessary due to more KE of molecules, disrupting order Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

(a) Gravitational motion (b) Diffusion (c) Chemical reaction Fig. 8-5b Spontaneous change Spontaneous change Spontaneous change Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change (a) Gravitational motion (b) Diffusion (c) Chemical reaction

In summary ∆G < 0, spontaneous, exergonic, net release of free energy ∆G > 0, endergonic, not spontaneous, absorbs free energy ∆G = 0, equilibrium (bad for cells)

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!

Closed and open hydroelectric systems can serve as analogies Fig. 8-7 ∆G < 0 ∆G = 0 A catabolic pathway in a cell releases free energy in a series of reactions Closed and open hydroelectric systems can serve as analogies (a) An isolated hydroelectric system ∆G < 0 (b) An open hydroelectric system Figure 8.7 Equilibrium and work in isolated and open systems ∆G < 0 ∆G < 0 ∆G < 0 (c) A multistep open hydroelectric system

Exergonic and Endergonic Reactions in Metabolism …one more time…. 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

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

Exergonic reaction

Endergonic reaction- energy absorbing

To provide energy for endergonic reactions, coupled reactions pair exergonic reactions with endergonic reactions

System with High Free En. Low Free En. Stability Spontaneous Equilibrium Work Capacity

System with High Free En. Low Free En. Stability low high Spontaneous Equilibrium Work Capacity

System with High Free En. Low Free En. Stability low high Spontaneous Change will be change will not be Equilibrium Work Capacity

System with High Free En. Low Free En. Stability low high Spontaneous Change will be change will not be Equilibrium moves toward Is at Work Capacity

System with High Free En. Low Free En. Stability low high Spontaneous Change will be change will not be Equilibrium moves toward Is at Work Capacity

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

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

In cell, the source of energy for work is ATP. ATP is a nucleoside triphosphate. Nucleoside = adenosine = adenine (purine) + ribose 3 Phosphate groups

Adenine Phosphate groups Ribose Fig. 8-8 Adenine Phosphate groups Figure 8.8 The structure of adenosine triphosphate (ATP) Ribose

Energy is released from ATP when the terminal phosphate bond is broken 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 For the Cell Biology Video Stick Model of ATP (Adenosine Triphosphate), go to Animation and Video Files. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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)

The Phosphate that is removed can be bonded to another molecule and make that molecule more reactive. That molecule is PHOSPHORYLATED. This is a coupled reaction.

ATP = ADP + P + energy (-7kcal) ATP = ADP + P + energy (-7kcal). Energy transfer occurs by a coupled reaction Example : Phosphocreatine stores high energy bonds in skeletal muscle ATP = ADP + P + energy (-

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

∆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

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

ADP can be regenerated. By cellular respiration from the breakdown (catabolism) of food By light in photosynthesis

+ 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

Why do dinoflagellates glow? 2 https://www.bing.com/videos/search?q=dinoflagellates+glowing+video&ru=%2fsearch%3fq%3ddinoflagellates%2bglowing%2bvideo%26src%3dIE-SearchBox%26FORM%3dIENTTR%26conversationid%3d&mmscn=vwrc&view=detail&mid=086651D5544CE857CB99086651D5544CE857CB99&rvsmid=E44BCCC26FFC6BE2D4B1E44BCCC26FFC6BE2D4B1&FORM=VDRVRV 1 https://www.bing.com/videos/search?q=dinoflagellates+glowing+video&ru=%2fsearch%3fq%3ddinoflagellates%2bglowing%2bvideo%26src%3dIE-SearchBox%26FORM%3dIENTTR%26conversationid%3d&view=detail&mid=7844038A3F8BA148D7597844038A3F8BA148D759&&mmscn=vwrc&FORM=VDRVRV

It is a chemical reaction involving, you got it…… ENZYMES

Enzyme- Luciferase Substrates- luciferin and oxygen Product: oxyluciferin

Enzymes Speed up reactions Lower activation energy – EA energy absorbed by reactants to reach an unstable transition state (bonds fragile); may be supplied by heat Activation energy barrier – necessary to keep energy-rich molecules from decomposing spontaneously

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

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

Properties of enzymes Are proteins Are specific for the substrate (what they work on) which is determined by 3-D shape. They bind at the active site. The substrate induces the enzyme to change shape. INDUCED FIT May have “ase” name endings, may be named for substrate they work on

Or, it can go the other way, two substrates can be combined to make a product.

Enzymes can be used over and over! They are not changed in the reaction.

The active site can lower an EA barrier by Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Covalently bonding to the substrate

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)

Substrates enter active site; enzyme 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

Ex: Hydrolase – hydrolytic (catabolic) Isomerase – rearrangment of atoms

Effects of Temperature and pH Each enzyme has an optimal temperature optimal pH in which it can function Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

Enzyme Inhibitors 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

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

Allosteric Regulation of Enzymes Allosteric regulation can also activate 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

Allosteric Activators And Inhibitors Fig. 8-20 Allosteric enyzme with four subunits Active site (one of four) Allosteric Activators And Inhibitors Regulatory site (one of four) Activator Active form Stabilized active form Oscillation Non- functional active site Inhibitor Inactive form Stabilized inactive form Figure 8.20 Allosteric regulation of enzyme activity (a) Allosteric activators and inhibitors Substrate Inactive form Stabilized active form (b) Cooperativity: another type of allosteric activation

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

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

(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

Identification of Allosteric Regulators Allosteric regulators are attractive drug candidates for enzyme regulation Ex - Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

EXPERIMENT Allosteric binding site Allosteric inhibitor Caspase 1 Fig. 8-21a EXPERIMENT Caspase 1 Active site Substrate SH SH Known active form Active form can bind substrate Figure 8.21 Are there allosteric inhibitors of caspase enzymes? Allosteric binding site SH S–S Allosteric inhibitor Known inactive form Hypothesis: allosteric inhibitor locks enzyme in inactive form

RESULTS Caspase 1 Inhibitor Active form Allosterically inhibited form Fig. 8-21b RESULTS Caspase 1 Inhibitor Figure 8.21 Are there allosteric inhibitors of caspase enzymes? Active form Allosterically inhibited form Inactive form

Cofactors and Coenzymes also help regulate enzyme action Holoenzyme- An apoenzyme together with its cofactor. A holoenzyme is complete and catalytically active. Most cofactors are not covalently bound but instead are tightly bound. An apoenzyme is an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor. Both cofactors and coenzymes help to complete the structure of a conjugated enzyme, forming a holoenzyme.

Enzyme activity can be determined by Amount of substrate – faster up to a limit when substrate gives out Temperature – faster up to optimal temp, then slows. High temp may denature (unravel protein). pH – most work at 6 – 8 Cofactors – small nonproteins that bind to the active site - inorganic Zn, Cu, Co Coenzymes organic molecules (vitamins) Presence of inhibitors

Feedback Inhibition 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

Figure 8.22 Feedback inhibition in isoleucine synthesis Enzyme 4 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)

Specific Localization of Enzymes Within the Cell Some enzymes act as structural components of membranes In eukaryotic cells, some enzymes reside in specific organelles; for example, lysosomes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Back to the dinoflagellates….enzymes are located in scintillons.