Energy, Catalysis, and Energy, Catalysis, and BiosynthesisBiosynthesis

The Chemistry & Physics of LifeThe Chemistry & Physics of Life

Laws of ThermodynamicsLaws of Thermodynamics

11stst Law LawThe total amount of energy in any process The total amount of energy in any process

stays constant OR energy in the universe stays constant OR energy in the universe stays constantstays constant

22ndnd Law LawAlthough the total energy in the universe Although the total energy in the universe

doesn’t change, less and less is available for doesn’t change, less and less is available for workwork

What is Work?What is Work?

Moving an object against a forceMoving an object against a force4 types4 types

Mechanical – moving against a forceMechanical – moving against a forceChemical – creating chemical bondsChemical – creating chemical bondsConcentration – changing concentration from Concentration – changing concentration from

one area to anotherone area to anotherElectrical – changing the separation of Electrical – changing the separation of

chargescharges

11stst Law of Law of ThermodynamicsThermodynamics

Energy can be Energy can be converted from converted from one form to one form to another but cannot another but cannot be created or be created or destroyeddestroyed

Universal Tendency – More DisorderUniversal Tendency – More Disorder

22ndnd Law of Thermodynamics – degree of disorder increases Law of Thermodynamics – degree of disorder increases Movement towards disorder is a spontaneous processMovement towards disorder is a spontaneous process Measure of disorder is entropy, Measure of disorder is entropy,

greater disorder = greater entropygreater disorder = greater entropy

Energy can be transformed Energy can be transformed from one form to anotherfrom one form to another

FREE ENERGY(available for work)

vs.HEAT

(not available for work)

Thermodynamics of CellsThermodynamics of Cells

Part of the energy that cells use is converted to heat Part of the energy that cells use is converted to heat and is released into the area around the celland is released into the area around the cell

While inside the cell becomes more ordered, the heat While inside the cell becomes more ordered, the heat put into the area around the cell causes more put into the area around the cell causes more disorder – disorder is greater outside the cell than the disorder – disorder is greater outside the cell than the order inside the cellorder inside the cell

CHEMICAL REACTIONS AND ENERGY TRANSFERS CHEMICAL REACTIONS AND ENERGY TRANSFERS ARE CONTROLLED IN LIVING SYSTEMSARE CONTROLLED IN LIVING SYSTEMS

Enzymes - mediate chemical reactions Enzymes - mediate chemical reactions Energy transfers are done in steps Energy transfers are done in steps

Example: There are two ways to get from the top of a very tall Example: There are two ways to get from the top of a very tall building to the bottom floor. Keep in mind that a person on the top building to the bottom floor. Keep in mind that a person on the top floor of a building has a lot of potential energy relative to the floor of a building has a lot of potential energy relative to the ground level.ground level.

Jump out the window! Jump out the window! Take the stairs and expend the potential energy a little at a time Take the stairs and expend the potential energy a little at a time

until you get to the bottom floor. until you get to the bottom floor. Both methods get you to the bottom floor but one method is Both methods get you to the bottom floor but one method is

destructive, while the other is not. These two situations are destructive, while the other is not. These two situations are analogous to uncontrolled vs. controlled energy transfers. analogous to uncontrolled vs. controlled energy transfers. Potential energy transferred gradually so more work is done than Potential energy transferred gradually so more work is done than heat.heat.

Hydrogen gas + oxygen + activation energy Hydrogen gas + oxygen + activation energy water and explosion water and explosion of heat, light and sound! (see of heat, light and sound! (see http://http://www.youtube.com/watch?vwww.youtube.com/watch?v=iwBYhJ2jHWw=iwBYhJ2jHWw))

Hydrogen is broken; electrons and protons released; electron Hydrogen is broken; electrons and protons released; electron transport system extracts some free energy from electrons in a transport system extracts some free energy from electrons in a stepwise manner (redox reactions) + heat; low energy electron stepwise manner (redox reactions) + heat; low energy electron combines with oxygen and hydrogen to produce water combines with oxygen and hydrogen to produce water process process is non-destructive to life & some energy used to do work!is non-destructive to life & some energy used to do work!

Regulation of energy-releasing (cellular Regulation of energy-releasing (cellular respiration) and energy-acquiring chemical respiration) and energy-acquiring chemical

reactions in biological systemsreactions in biological systems

•Chemically-mediated by enzymes and co-factors

•Occur in a step-wise manner

2H2 + O2 2H2O + energy

2H-H + O=O 2H2O + energy

+ +

Modes of Energy Transformation: Rapid & Modes of Energy Transformation: Rapid & UncontrolledUncontrolled

2H2H2 2 + O+ O22 2H 2H22O + energyO + energyRelease of energy can be uncontrolled Release of energy can be uncontrolled

and liberated mostly as heat! and liberated mostly as heat!

On May 6th, 1937 in Lakehurst, New Jersey. The German passenger Zeppelin Airship called the Hindenburg, was attempting a mooring when it exploded.

Modes of Energy Transformation: Released Modes of Energy Transformation: Released in controlled steps or stagesin controlled steps or stages

2H2H2 2 + O+ O22 2H 2H22O + energyO + energy Released in steps to salvage free energy and minimize Released in steps to salvage free energy and minimize

heat productionheat production

The electrons from the hydrogen bond go through a series of oxidation & reduction reactions. During each step some energy is harvested, while the remainder is released as heat.

Chemical ReactionsChemical Reactions

Occur in the cell under the control of Occur in the cell under the control of specialized proteins called enzymesspecialized proteins called enzymes

Each one accelerates or catalyzes Each one accelerates or catalyzes just one of the many reactions of the just one of the many reactions of the cellscells

EnzymesEnzymes

Metabolic pathways• series of enzyme-controlled reactions leading to formation of a product• each new substrate is the product of the previous reaction

Enzyme names commonly• reflect the substrate• have the suffix – ase• sucrase, lactase, protease, lipase

Tyrosinase and MelaninTyrosinase and Melanin

tyrosinasetyrosinase - A copper-containing - A copper-containing enzyme of plant and animal tissues enzyme of plant and animal tissues that catalyzes the production of that catalyzes the production of melanin melanin and other pigments from and other pigments from tyrosine by oxidation, as in the tyrosine by oxidation, as in the blackening of a peeled or sliced blackening of a peeled or sliced potato exposed to air.potato exposed to air.

Grey Squirrels:

Melanic and Albino Forms

Cofactors • make some enzymes active• ions or coenzymes

Coenzymes• organic molecules that act as cofactors• vitamins

Factors that alter enzymes• temperature and heat• radiation• electricity• chemicals• changes in pH

Factors that influence enzymatic activityFactors that influence enzymatic activity

Factors that influence enzymatic activityFactors that influence enzymatic activity

Competitive inhibitor - a substance that Competitive inhibitor - a substance that binds to the active site of the enzyme and binds to the active site of the enzyme and compete with the substrate for this place. compete with the substrate for this place. Non-competitive or allosteric inhibitor - a Non-competitive or allosteric inhibitor - a substance that binds to another part of substance that binds to another part of the the enzyme and cause an allosteric change in enzyme and cause an allosteric change in the the overall shape of the enzyme; this overall shape of the enzyme; this changes the changes the form of the active site so the form of the active site so the substrate can't bind substrate can't bind to it. to it. Allosteric Activators - essentially this is the Allosteric Activators - essentially this is the reverse of an allosteric inhibitor.reverse of an allosteric inhibitor.

Temperature Sensitive Tyrosinase – Temperature Sensitive Tyrosinase – Siamese Cats & Himalayan RabbitsSiamese Cats & Himalayan Rabbits

Cells Chemical Cells Chemical Pathways All Pathways All InterconnectInterconnect

Almost all plants are photosynthetic autotrophs, as Almost all plants are photosynthetic autotrophs, as are some bacteria and protistsare some bacteria and protists Autotrophs generate their own organic matter through Autotrophs generate their own organic matter through

photosynthesis or chemosynthesisphotosynthesis or chemosynthesis Sunlight energy is transformed into the energy stored in the form of Sunlight energy is transformed into the energy stored in the form of

chemical bondschemical bonds Chemical energy is transformed into the energy stored in the form of Chemical energy is transformed into the energy stored in the form of

chemical bondschemical bonds

(a) Mosses, ferns, andflowering plants

(b) Kelp

(c) Euglena (d) Cyanobacteria

PHOTOSYNTHESIS & CHEMOSYNTHESISPHOTOSYNTHESIS & CHEMOSYNTHESIS

Bacteria in Thermal Vents on the Sea FloorBacteria in Thermal Vents on the Sea Floor

Tubeworms and other animals living around thermal vents in the ocean depend on chemosynthetic bacteria for food.

THE SUN: MAIN SOURCE OF THE SUN: MAIN SOURCE OF ENERGY FOR LIFE ON EARTHENERGY FOR LIFE ON EARTH

Light Energy Harvested by Plants & Light Energy Harvested by Plants & Other Photosynthetic AutotrophsOther Photosynthetic Autotrophs

6 CO2 + 6 H2O + light energy → C6H12O6 + 6 O2

Sunlight – Ultimate Energy SourceSunlight – Ultimate Energy Source All organisms live on the organic molecules that are All organisms live on the organic molecules that are

made by photosynthetic organismsmade by photosynthetic organisms Photosynthesis traps the energy of the sun in the Photosynthesis traps the energy of the sun in the

chemical bonds of sugars which can be turned into chemical bonds of sugars which can be turned into nucleotides, amino acids and fatty acidsnucleotides, amino acids and fatty acids

2 steps2 steps Energy stored in ATP and NADPH, release OEnergy stored in ATP and NADPH, release O22 ATP and NADPH drive carbon fixation ATP and NADPH drive carbon fixation H H22O and COO and CO22 from from

air and make sugarsair and make sugars

Food Chain

THE FOOD WEBTHE FOOD WEB

MetabolismMetabolism 2 opposing pathways 2 opposing pathways

make up metabolismmake up metabolism Catabolism – process of Catabolism – process of

obtaining energy and obtaining energy and building blocks from building blocks from ‘food’ molecules‘food’ molecules

Anabolism – process of Anabolism – process of using energy and using energy and building blocks to create building blocks to create the macromolecules the macromolecules that make up the cellthat make up the cell

Energy Releasing Metabolic ReactionsEnergy Releasing Metabolic Reactions

Energy• ability to do work or change something• heat, light, sound, electricity, mechanical energy, chemical energy• changed from one form to another• involved in all metabolic reactions

Release of chemical energy• most metabolic processes depend on chemical energy• oxidation of glucose generates chemical energy• cellular respiration releases chemical energy from molecules and makes it available for cellular use

Oxidation of Organic MoleculesOxidation of Organic Molecules OxidationOxidation can be the process of adding O atoms can be the process of adding O atoms Cells can obtain energy from sugars by allowing the C and Cells can obtain energy from sugars by allowing the C and

H to combine with OH to combine with O22 to produce H to produce H22O and COO and CO22 in a in a process called process called respirationrespiration

Photosynthesis and respiration work togetherPhotosynthesis and respiration work together

Oxidation and ReductionOxidation and Reduction Oxidation can also be the process of electron Oxidation can also be the process of electron

transfer from one atom to another transfer from one atom to another OxidationOxidation is the removal of electrons is the removal of electrons ReductionReduction is the addition of the electrons is the addition of the electrons

Oxidation and reduction always occur Oxidation and reduction always occur simultaneouslysimultaneously

These reactions also occur in molecules with a These reactions also occur in molecules with a partial shift of electrons as in polar bondspartial shift of electrons as in polar bonds

Also with the addition of a HAlso with the addition of a H++ (hydrogenation (hydrogenation reaction) or the removal of a Hreaction) or the removal of a H++ (dehydrogenation (dehydrogenation reaction)reaction)

Reducing and Oxidizing AgentsReducing and Oxidizing Agents

e-

e-

e-

e-

A

A B

B

Reducing agent(electron donor)

Oxidizing agent(electron acceptor)

Oxidized Reduced

A is oxidized –loses electron

B is reduced –gains electron

Tip to Help RememberTip to Help Remember

LEO the lion goes GERose

lectrons

xidized

ain

lectrons

educed

Free EnergyFree Energy

Free Energy (G)Free Energy (G)

Energy that can be harvested to do Energy that can be harvested to do work or drive a chemical reaction work or drive a chemical reaction (remember the 4 types of work)(remember the 4 types of work)

Exergonic reactionsExergonic reactions – go from higher to – go from higher to lower energy level and are spontaneouslower energy level and are spontaneous

Endergonic reactionsEndergonic reactions – go from lower to – go from lower to higher energy levels and require an higher energy levels and require an input of energyinput of energy

ReactionsReactions

Barriers to Chemical ReactionsBarriers to Chemical Reactions Chemical reactions Chemical reactions

only proceed in the only proceed in the direction of the loss direction of the loss of free energyof free energy

Molecules in stable Molecules in stable states need to have states need to have an input of energy to an input of energy to cause them to go to cause them to go to a lower energy state a lower energy state – – activation energyactivation energy, , always positivealways positive

Activation EnergyActivation Energy

Activation EnergyActivation Energy

In chemistry, molecules that decrease In chemistry, molecules that decrease activation energy are activation energy are catalystcatalyst such as such as platinum and zinc platinum and zinc

In cells the activation energy is reduced In cells the activation energy is reduced by a special protein - by a special protein - enzymeenzyme

Enzymes link 1 or 2 molecules called Enzymes link 1 or 2 molecules called substratessubstrates and hold them in a way that and hold them in a way that greatly decreases the activation energy greatly decreases the activation energy – – transition statetransition state

Transition StatesTransition States

Energy GraphEnergy Graph

Enzymes as CatalystsEnzymes as Catalysts

Speed up reaction rates (x ~10Speed up reaction rates (x ~101414)) Selective – usually 1 enzyme for 1 reactionSelective – usually 1 enzyme for 1 reaction Have a unique shape that contains the Have a unique shape that contains the active siteactive site

and only a particular substrate can fitand only a particular substrate can fit site where reaction takes placesite where reaction takes place

Remain unchanged and can be used over and overRemain unchanged and can be used over and over

ReactionsReactions For reactions to occur, the enzyme and the For reactions to occur, the enzyme and the

substrate(s) need to be in contact with one substrate(s) need to be in contact with one anotheranother

Heat from other reactions keep the substrate Heat from other reactions keep the substrate moving through the cell by diffusion, can cover moving through the cell by diffusion, can cover great distancesgreat distances

Enzyme is large and relatively motionlessEnzyme is large and relatively motionless This arrangement allows for the substrate to This arrangement allows for the substrate to

finally collide with the active site, held there by finally collide with the active site, held there by multiple weak interactions until they dissociatemultiple weak interactions until they dissociate If too strong, then would not dissociateIf too strong, then would not dissociate If wrong substrate gets into the active site, no If wrong substrate gets into the active site, no

interactions will hold it there and it will leave quicklyinteractions will hold it there and it will leave quickly

Enzymatic Reactions are CoupledEnzymatic Reactions are Coupled

Even though enzymes are good catalysts, Even though enzymes are good catalysts, they are unable to perform reactions that they are unable to perform reactions that are thermodynamically unfavorableare thermodynamically unfavorable

Enzyme reactions are Enzyme reactions are coupledcoupled to harvest to harvest the energy and heat from a favorable the energy and heat from a favorable reaction to drive an unfavorable reactionreaction to drive an unfavorable reaction

Coupled ReactionsCoupled Reactions

G – Change G – Change in Free Energyin Free Energy

Value of G is only important Value of G is only important when the system undergoes a when the system undergoes a changechange

G is the measure of the G is the measure of the amount of disorder when a amount of disorder when a reaction takes placereaction takes place --G occur spontaneouslyG occur spontaneously ++G are unfavorableG are unfavorable

Need to link a -Need to link a -G reaction with G reaction with a +a +G so that the overall G so that the overall G is G is negativenegative

Coupled ReactionsCoupled Reactions

Concentration of ReactantsConcentration of Reactants

The amount of reactants in the reaction mix is The amount of reactants in the reaction mix is important for the important for the GG

In a reversible reaction, i.e., can go from A to B In a reversible reaction, i.e., can go from A to B and from B to A, when there is more A present, and from B to A, when there is more A present, the tendency will be to go from A to B rather the tendency will be to go from A to B rather than B to Athan B to A

G° or standard free-energy change – G° or standard free-energy change – depends on intrinsic characters of the reacting depends on intrinsic characters of the reacting moleculesmolecules

Equilibrium – forward and reverse reactions Equilibrium – forward and reverse reactions proceed at exactly equals rates so that no net proceed at exactly equals rates so that no net chemical change occurschemical change occurs

EquilibriumEquilibrium

Equilibrium Equilibrium constant (K) – constant (K) – number that number that characterizes the characterizes the equilibrium state equilibrium state for a reversible for a reversible chemical reaction; chemical reaction; given by the ratio given by the ratio of the forward and of the forward and reverse rate reverse rate constants of the constants of the reactionreaction

Enzymes and KEnzymes and K

Enzymes will lower the activation energy in Enzymes will lower the activation energy in the A to B direction to the same degree as in the A to B direction to the same degree as in the B to A directionthe B to A direction

The equilibrium constant and The equilibrium constant and G° remain G° remain unchangedunchanged

Sequential ReactionsSequential Reactions

Most of the Most of the G° G° values are values are known for the known for the reactions of the reactions of the cells and so we cells and so we can determine can determine overall overall G for a G for a pathway – add pathway – add up the up the G for G for each stepeach step

Activated CarriersActivated Carriers

Energy released by Energy released by catabolism is stored in catabolism is stored in the chemical bonds of the chemical bonds of carrier moleculescarrier molecules

The energy can be The energy can be moved around the cell moved around the cell to where it is neededto where it is needed

Carrier molecules in Carrier molecules in the cell are ATP, the cell are ATP, NADH and NADPHNADH and NADPH

Activated Carriers in MetabolismActivated Carriers in Metabolism

Activated Carrier

Group Carried in High-Energy Linkage

ATP phosphate

NADH, NADPH, FADH2 electrons and hydrogens

Acetyl CoA acetyl group

Carboxylated biotin carboxyl group

S-Adenosylmethionine

methyl group

Uridine diphosphate glucose

glucose

Coupled ReactionsCoupled Reactions

Enzyme catalyzed reactions capture the Enzyme catalyzed reactions capture the energy released from the oxidation of glucose energy released from the oxidation of glucose in a chemically useful form rather than as in a chemically useful form rather than as heatheat

ATPATP ATP – adenosine ATP – adenosine triphosphate – is the triphosphate – is the most important and most important and abundant activated abundant activated carrier in the cellcarrier in the cell

Synthesized by adding Synthesized by adding a phosphate group to a phosphate group to ADP (adenosine ADP (adenosine diphosphate) in an diphosphate) in an energy unfavorable energy unfavorable reactionreaction

ATP can release the ATP can release the energy when it is energy when it is needed by hydrolysisneeded by hydrolysis

Phosphate TransferPhosphate Transfer

Process of transferring Process of transferring a phosphate group to a phosphate group to another molecule is another molecule is the the phosphorylationphosphorylation reaction reaction

Enzyme that performs Enzyme that performs this reaction is a this reaction is a kinasekinase

ATP Functions inATP Functions inCondensation ReactionsCondensation Reactions

Transfer of a Carboxyl GroupTransfer of a Carboxyl Group

Synthesis of PolymersSynthesis of Polymers

Condensation reactions are unfavorable, require Condensation reactions are unfavorable, require energy inputenergy input

Hydrolysis reactions are favorable, can occur Hydrolysis reactions are favorable, can occur spontaneouslyspontaneously

PolysaccharidesPolysaccharides

ProteinsProteins

Nucleic Nucleic AcidsAcids

Nucleic Acid SynthesisNucleic Acid Synthesis

NADH and NADPHNADH and NADPH

NADH and NADPH are activated carriers NADH and NADPH are activated carriers that carry energy and Hthat carry energy and H++

NADNAD++ - nicotinamide adenine dinucleotide - nicotinamide adenine dinucleotideNADPNADP++ - nicotinamide adenine - nicotinamide adenine

dinucleotide phophatedinucleotide phophateBoth can pick up a HBoth can pick up a H++ and become and become

reduced, carries 2 ereduced, carries 2 e-- and H and H++

NADPHNADPH

The phosphate The phosphate group at the end of group at the end of the molecule causes the molecule causes the molecule to the molecule to have a different have a different shape and therefore shape and therefore can interact with can interact with different enzymes different enzymes than NADHthan NADH

Purpose of NADPH and NADHPurpose of NADPH and NADH

NADPH operates with enzymes that NADPH operates with enzymes that catalyze anabolic reactions – synthesis catalyze anabolic reactions – synthesis reactionsreactions

NADH usually works in catabolic reactions NADH usually works in catabolic reactions that generate ATP through the breakdown that generate ATP through the breakdown of food particlesof food particles