Chemical Reactions in Cells

Chemical Reactions in CellsChemical Reactions in Cells

Energetics, Enzymes and Energetics, Enzymes and Metabolic ReactionsMetabolic Reactions

EnergyEnergy• Energy is the capacity for work or Energy is the capacity for work or

change.change.

• Kinetic Energy = energy of movementKinetic Energy = energy of movement

• Potential Energy = stored energy Potential Energy = stored energy

• 11stst Law of Thermodynamics Law of Thermodynamics– Energy can be transferred and Energy can be transferred and

transformed from one form to another but transformed from one form to another but it cannot be created or destroyed.it cannot be created or destroyed.

EnergyEnergy• 22ndnd Law of Thermodynamics Law of Thermodynamics– Energy transfer or transformation Energy transfer or transformation

increases the entropy of the universeincreases the entropy of the universe– Increase in entropy = randomnessIncrease in entropy = randomness– Energy conversions result in a loss of Energy conversions result in a loss of

useful energyuseful energy

usable usable usable

usable

Free Energy = Energy Useful for ChangeFree Energy = Energy Useful for Change

GGreactionreaction = G = Gproductsproducts – G – Greactantsreactants

•Spontaneity of a reaction depends on free Spontaneity of a reaction depends on free

energy changeenergy change GG

•If is positive, free energy is consumed If is positive, free energy is consumed GG

•If is negative, free energy is released If is negative, free energy is released and the reaction is spontaneousand the reaction is spontaneous

GG

Free Energy = Energy Useful for ChangeFree Energy = Energy Useful for Change

•Free Energy change depends on changes inFree Energy change depends on changes in

–total energy (enthalpy)total energy (enthalpy)

–entropy (unusable energy, disorder)entropy (unusable energy, disorder)

HHSS

•In living systems, entropy changes have In living systems, entropy changes have substantial influence substantial influence

–when is positive, and the term is large, when is positive, and the term is large, a negative value predicts a spontaneous a negative value predicts a spontaneous reactionreaction

SSTTGG

SS

GG HH SSTT== ––

Chemical ReactionsChemical Reactions

• Involve the breaking and formation of Involve the breaking and formation of chemical bondschemical bonds

– Reactants are converted to products. Reactants are converted to products.

– Two types of reactions based on Two types of reactions based on energy use:energy use:

• Exergonic– free energy releasedExergonic– free energy released

• Endergonic – free energy consumedEndergonic – free energy consumed

Exergonic Reactions

EnergyEnergycontentcontent

ofofmoleculesmolecules

highhigh

lowlow

Burning glucose (sugar):Burning glucose (sugar):an exergonic reactionan exergonic reaction

Progress of reactionProgress of reaction

Activation energy neededActivation energy neededto ignite glucoseto ignite glucose

Activation energy neededActivation energy neededto ignite glucoseto ignite glucose

Glucose + OGlucose + O22Glucose + OGlucose + O22

Energy released byEnergy released byburning glucoseburning glucose

Energy released byEnergy released byburning glucoseburning glucose

C OC O22 + H + H22OOC OC O22 + H + H22OO

Reactants changed to Reactants changed to transition-state speciestransition-state speciesReactants changed to Reactants changed to transition-state speciestransition-state species

GG

Endergonic Reactions



highhigh

lowlow

Photosynthesis:Photosynthesis:an endergonic reactionan endergonic reaction

Progress of reactionProgress of reaction

GlucoseGlucoseGlucoseGlucose

Net energyNet energycaptured bycaptured bysynthesizingsynthesizing

glucoseglucose

COCO22 + H + H22OOCOCO22 + H + H22OO

ActivationActivationenergy fromenergy from

light capturedlight capturedby photosynthesisby photosynthesis

GG

Applying Your KnowledgeApplying Your Knowledge

1.1. Endergonic ReactionEndergonic Reaction

2.2. Exergonic ReactionExergonic Reaction

A. Which type of reaction would be spontaneous?A. Which type of reaction would be spontaneous?

B. For which type of reaction will the products B. For which type of reaction will the products have a higher energy than the reactants?have a higher energy than the reactants?

C. Which type of reaction releases energy?C. Which type of reaction releases energy?

D. Which type of reaction would have a positive D. Which type of reaction would have a positive value for G?value for G?

ATP Provides Energy for Cellular Reactions

+ Pi + free energy

kcal/mol . G3 7

+ H2O

Short-Term Energy StorageShort-Term Energy Storage

• Chemical Energy is stored in the bonds Chemical Energy is stored in the bonds of ATPof ATP– ATP = adenosine triphosphateATP = adenosine triphosphate– ADP = adenosine diphosphateADP = adenosine diphosphate– to store energyto store energy

• ADP + Phosphate + EnergyADP + Phosphate + Energy ATP ATP

– to release energyto release energy• ATP ATP ADP + Phosphate + Energy ADP + Phosphate + Energy

Coupled ReactionsCoupled Reactions Pairing of an Exergonic reaction, often Pairing of an Exergonic reaction, often

involving ATP, with an Endergonic reaction involving ATP, with an Endergonic reaction

Note that overall free energy change is negativeNote that overall free energy change is negative

Metabolic ReactionsMetabolic Reactions

• AnabolicAnabolic– link simple molecules to produce complex link simple molecules to produce complex

molecules molecules (eg. dehydration synthesis of starch) (eg. dehydration synthesis of starch)

– require energyrequire energy

• CatabolicCatabolic– break down complex molecules to release break down complex molecules to release

simple ones simple ones (eg. hydrolysis of starch(eg. hydrolysis of starch sugars) sugars)

– release energy stored in chemical bondsrelease energy stored in chemical bonds

Metabolic PathwaysMetabolic Pathways

AA BB CC DDDD EEEE

FFFF GGGG

Enzyme 1Enzyme 1 Enzyme 2Enzyme 2 Enzyme 3Enzyme 3 Enzyme 4Enzyme 4

Enzyme 5Enzyme 5 Enzyme 6Enzyme 6

InitialInitialReactantsReactants

IntermediatesIntermediates FinalFinalProductsProducts

Pathway 1Pathway 1Pathway 1Pathway 1

Pathway 2Pathway 2Pathway 2Pathway 2

Enzymes Assist in Biological ReactionsEnzymes Assist in Biological Reactions

Enzymes are biological catalysts.Enzymes are biological catalysts.

biological: composed of protein or, rarely, biological: composed of protein or, rarely, RNARNA

catalyst: speeds up a reaction without catalyst: speeds up a reaction without being changed by the reactionbeing changed by the reaction

Properties of EnzymesProperties of Enzymes

• Enzymes speed up biological reactions Enzymes speed up biological reactions by lowering the activation energy for the by lowering the activation energy for the reaction. reaction. – Enzymes provide a surface where the Enzymes provide a surface where the

catalysis takes placecatalysis takes place– The reaction reaches equilibrium more The reaction reaches equilibrium more

rapidly rapidly

–– The value of and the ratio of The value of and the ratio of reactants and products at equilibrium is reactants and products at equilibrium is the same as for an uncatalyzed reaction the same as for an uncatalyzed reaction

GG



highhigh

lowlowProgress of reactionProgress of reaction

ActivationActivationenergy withoutenergy without

catalystcatalyst

ActivationActivationenergy withenergy with

catalystcatalyst

Activation Energy: Controls Rate of ReactionActivation Energy: Controls Rate of Reaction

Amount of energy required for

reaction to occurtransition state

GG


• Enzymes are SPECIFIC for the Enzymes are SPECIFIC for the reactants (substrates) in the reactions reactants (substrates) in the reactions that they catalyze. that they catalyze.

• Only substrates that fit the active site of Only substrates that fit the active site of the enzyme can bind and complete the the enzyme can bind and complete the reactionreaction– active site: region on enzyme where active site: region on enzyme where

substrates bindsubstrates bind

Enzyme-Substrate InteractionsEnzyme-Substrate Interactions

SubstrateSubstrateSubstrateSubstrateSubstrateSubstrateSubstrateSubstrate

EnzymeEnzymeEnzymeEnzyme

ActiveActiveSiteSite

ActiveActiveSiteSite

11 Substrates Substrates enter active enter active sitesite

11 Substrates Substrates enter active enter active sitesite

induced fit

22 Shape change Shape change promotes reactionpromotes reaction

22 Shape change Shape change promotes reactionpromotes reaction

33 Product released;Product released;enzyme ready againenzyme ready again

33 Product released;Product released;enzyme ready againenzyme ready again

Chemical Events at Active SitesChemical Events at Active Sites

• Enzymes hold substrates in the proper Enzymes hold substrates in the proper orientation for the reaction to take placeorientation for the reaction to take place


• Enzymes induce strain in the substrate to Enzymes induce strain in the substrate to produce a transition state favorable to produce a transition state favorable to reactionreaction

• Active site provides a microenvironment Active site provides a microenvironment that favors the chemical reactionthat favors the chemical reaction


• Active site directly participates in the Active site directly participates in the reaction reaction – covalent bonding can occur between covalent bonding can occur between

enzyme and substrateenzyme and substrate– R groups of the enzyme’s amino acids can R groups of the enzyme’s amino acids can

temporarily add chemical groups to the temporarily add chemical groups to the substratessubstrates

Molecules that Assist EnzymesMolecules that Assist Enzymes

• Cofactors: Cofactors: inorganic ions that bind to inorganic ions that bind to enzymes, eg. zincenzymes, eg. zinc

• Coenzymes: Coenzymes: small organic factors that small organic factors that temporarily bind to enzymes, eg. biotin, NAD, temporarily bind to enzymes, eg. biotin, NAD, ATPATP

• Prosthetic groups: Prosthetic groups: non-protein factors that non-protein factors that are permanently bound an enzyme, eg. hemeare permanently bound an enzyme, eg. heme

Factors Influencing Reaction RateFactors Influencing Reaction Rate

• Substrate ConcentrationSubstrate Concentration

Rate is proportional to substrate

concentration

Rate is more rapid

Rate no longer increases since the active sites of all enzymes are saturated with substrate


• Competitive Inhibitors: Bind at the active Competitive Inhibitors: Bind at the active site, compete for binding with substratesite, compete for binding with substrate– Irreversible: form covalent bond with amino Irreversible: form covalent bond with amino

acids in the active siteacids in the active site

DIPF


• Competitive Inhibitors: Bind at the active Competitive Inhibitors: Bind at the active site, compete for binding with substratesite, compete for binding with substrate– Reversible: molecule similar to substrate Reversible: molecule similar to substrate

occupies active site but does not undergo occupies active site but does not undergo reactionreaction


• Non-Competitive Inhibitors: Bind to a Non-Competitive Inhibitors: Bind to a different site, cause a conformational different site, cause a conformational change in the enzyme that alters the change in the enzyme that alters the active site active site – Reversible Reversible


• Allosteric Regulation Allosteric Regulation – Conversion between Conversion between

active and inactive forms active and inactive forms of an enzyme due to of an enzyme due to binding of regulatory binding of regulatory molecules at an allosteric molecules at an allosteric sitesite• Activators stabilize the Activators stabilize the

active formactive form

• Allosteric inhibitors Allosteric inhibitors stabilize the inactive stabilize the inactive formform


• Allosteric Regulation Allosteric Regulation – Cooperativity: a substrate causing Cooperativity: a substrate causing

induced fit in one enzyme subunit can induced fit in one enzyme subunit can cause a change to the active form in all cause a change to the active form in all the other subunitsthe other subunits

Enz. 5Enz. 5Enz. 5Enz. 5DDDD

Enz. 4Enz. 4Enz. 4Enz. 4CCCC

Enz. 3Enz. 3Enz. 3Enz. 3BBBB

Enzyme Regulation: Feedback InhibitionEnzyme Regulation: Feedback Inhibition

Enz. 2Enz. 2Enz. 2Enz. 2AAAA

Feedback InhibitionFeedback InhibitionIsoleucine allosterically Isoleucine allosterically

inhibits enzyme 1inhibits enzyme 1

Enz. 1Enz. 1Enz. 1Enz. 1

CHCH33CHCH33

CCCC

CCCC

COOHCOOHCOOHCOOH

OHOHOHOH

NHNH33NHNH33HHHH

HHHHCHCH22

CHCH22

CCCC

CCCC

COOHCOOHCOOHCOOH

CHCH33CHCH33

NHNH33NHNH33HHHH

HHHH

CHCH33CHCH33

ThreonineThreonine(substrate)(substrate)ThreonineThreonine(substrate)(substrate) IsoleucineIsoleucine

(end product)(end product)IsoleucineIsoleucine

(end product)(end product)

Feedback Inhibition: The product of a pathway inhibits an initial step in the pathway to decrease its own production

Commitment step


• Three dimensional structure of an Three dimensional structure of an enzyme preserves its ACTIVE SITEenzyme preserves its ACTIVE SITE

• Conditions that can affect three Conditions that can affect three dimensional structure include: heat, pH dimensional structure include: heat, pH (acid/base balance) and other chemicals (acid/base balance) and other chemicals (salt, charged ions) (salt, charged ions)

Effects of Temperature and pH on Effects of Temperature and pH on Enzymatic ActivityEnzymatic Activity

fewer collisions fewer collisions between enzyme between enzyme and substrateand substrate

enzyme unfoldsenzyme unfolds(denatures)(denatures)

enzyme unfoldsenzyme unfolds(denatures)(denatures)

Applying Your KnowledgeApplying Your Knowledge

A.A. Where can an inhibitor bind to stabilize the Where can an inhibitor bind to stabilize the inactive form of an enzyme?inactive form of an enzyme?

B.B. Where do the substrates bind? Where do the substrates bind? C.C. Enzymes Enzymes (raise or lower)(raise or lower) the the (1, 2, 3, 4 or 5)(1, 2, 3, 4 or 5) of a of a

reaction. reaction. D.D. What is the model for a shape change What is the model for a shape change

caused by substrate binding to the enzyme?caused by substrate binding to the enzyme?

1.1. Active SiteActive Site2.2. Activation Energy Activation Energy 3.3. Allosteric SiteAllosteric Site4.4. Commitment stepCommitment step5.5. Induced fit Induced fit

Documents

Chemical Reactions in Cells