1 an introduction to metabolism chapter 8. energy & matter universe is composed of 2 things...
TRANSCRIPT
Energy & MatterEnergy & Matter
Universe is composed of 2 things ……Universe is composed of 2 things ……
EnergyEnergy Ability to do workAbility to do work
o Force on an object that causes it to moveForce on an object that causes it to move
MatterMatter Anything that has mass and occupies Anything that has mass and occupies
spacespace Atoms/elementsAtoms/elements
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MetabolismMetabolismtransforming matter and transforming matter and
energyenergy
Metabolism -- totality of an organism’s Metabolism -- totality of an organism’s chemical reactionschemical reactions Arises from interactions between molecules Arises from interactions between molecules
within the cellwithin the cell
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Organization of the Organization of the Chemistry of Life into Chemistry of Life into Metabolic PathwaysMetabolic Pathways
A metabolic pathway begins with a A metabolic pathway begins with a specific molecule and ends with a specific molecule and ends with a productproduct
Each step is catalyzed by a specific Each step is catalyzed by a specific enzymeenzyme
Enzyme 1
A BReaction 1
Enzyme 2
CReaction 2
Enzyme 3
DReaction 3
ProductStartingmolecule
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Catabolic pathways -- release energy Catabolic pathways -- release energy break down complex molecules into simpler break down complex molecules into simpler
compoundscompounds
Anabolic pathways -- consume energy Anabolic pathways -- consume energy build complex molecules from simpler onesbuild complex molecules from simpler ones
Bioenergetics -- study of how organisms Bioenergetics -- study of how organisms manage their energy resourcesmanage their energy resources
Kinds of PathwaysKinds of Pathways
Chemical ReactionsChemical Reactions
FunctionalityFunctionality CatabolicCatabolic AnabolicAnabolic
Energy RequirementsEnergy Requirements EndergonicEndergonic ExergonicExergonic
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Chemical ReactionsChemical Reactions
Reactions can be categorized as Reactions can be categorized as exergonicexergonic or or endergonicendergonic based based on energy gain or losson energy gain or loss
Chemical reactions require initial Chemical reactions require initial energy input (energy input (activation energyactivation energy))
Molecules need to be moving with Molecules need to be moving with sufficient collision speedsufficient collision speed
The electrons of an atom repel other The electrons of an atom repel other atoms and inhibit bond formationatoms and inhibit bond formation
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EnergyEnergy
The ability to do The ability to do workwork Work -- Work -- force on an object that causes force on an object that causes
it to moveit to move What’s moving?What’s moving?
Two kinds of energyTwo kinds of energy KineticKinetic Potential – can be Potential – can be positionalpositional
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The two fundamental typesThe two fundamental types Kinetic -- Kinetic -- energy of movementenergy of movement
o Heat (thermal energy) -- random Heat (thermal energy) -- random movement of atoms or moleculesmovement of atoms or molecules
Potential -- Potential -- stored energy (can be stored energy (can be because of location!)because of location!)
o Chemical energy -- available for release Chemical energy -- available for release in a chemical reactionin a chemical reaction
What Is Energy?What Is Energy?
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Overview: The Energy of Overview: The Energy of LifeLife
Living cell -- miniature chemical Living cell -- miniature chemical factory factory
Energy transformed and storedEnergy transformed and storedEnergy observed in many formsEnergy observed in many forms
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The Laws of Energy The Laws of Energy TransformationTransformation
Thermodynamics -- study of energy Thermodynamics -- study of energy transformationstransformations Describe availability & usefulness of energyDescribe availability & usefulness of energy
Closed system -- isolated from its Closed system -- isolated from its surroundingssurroundings
Open system -- energy and matter can Open system -- energy and matter can be transferred between the system and be transferred between the system and its surroundingsits surroundings
An open hydroelectric system
G < 0
G = 0
A closed hydroelectric system
G < 0
Closed and open hydroelectric systems can serve as analogiesClosed and open hydroelectric systems can serve as analogies
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Laws of ThermodynamicsLaws of ThermodynamicsFirst -- First -- In any process, the total energy In any process, the total energy
of the universe remains constant.of the universe remains constant. Principle of conservation of energyPrinciple of conservation of energy Energy can be transferred and Energy can be transferred and
transformedtransformed Energy Energy cannotcannot be created or destroyed be created or destroyed
Second -- The entropy of an isolated Second -- The entropy of an isolated system not in equilibrium will tend to system not in equilibrium will tend to increase over time, approaching a increase over time, approaching a maximum value at equilibrium. maximum value at equilibrium. During every energy transfer or During every energy transfer or
transformation, energy is transformation, energy is ““lostlost”” (the amount of (the amount of useable energy decreases; disorder increases)useable energy decreases; disorder increases)
EntropyEntropyEntropy – randomnessEntropy – randomness
Energy conversions increase entropy in Energy conversions increase entropy in the universethe universe
Spontaneous processes increase Spontaneous processes increase entropyentropy Explosions; car rustingExplosions; car rusting
Non-spontaneous process – energy Non-spontaneous process – energy inputinput Rocks rolling uphillRocks rolling uphill
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EnthalpyEnthalpyEnthalpy (H) – total potential energy of Enthalpy (H) – total potential energy of
systemsystem Total energy = Usable Energy + Unusable EnergyTotal energy = Usable Energy + Unusable Energy
Entropy (S) – randomness or disorder Entropy (S) – randomness or disorder (unusable energy)(unusable energy)
Free Energy (G) – energy available to do workFree Energy (G) – energy available to do work ΔΔG -- change in free energyG -- change in free energy ΔΔG = G = ΔΔGGfinalfinal – – ΔΔGGinitialinitial
A negative A negative ΔΔG – spontaneousG – spontaneous
Note – as entropy increases, free energy Note – as entropy increases, free energy decreasesdecreases
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Exergonic ReactionsExergonic Reactions Exergonic reactionsExergonic reactions release release
energyenergy Reactants contain more energy than Reactants contain more energy than
productsproducts
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Exergonic ReactionsExergonic Reactions Exergonic reactionsExergonic reactions release release
energyenergy Reactants contain more energy than Reactants contain more energy than
productsproducts
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Endergonic ReactionsEndergonic ReactionsEndergonic reactions require an input Endergonic reactions require an input
of energyof energy Products contain more energy than Products contain more energy than
reactantsreactants
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Endergonic ReactionsEndergonic ReactionsEndergonic reactions require an input Endergonic reactions require an input
of energyof energy Products contain more energy than Products contain more energy than
reactantsreactants
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Coupled ReactionsCoupled Reactions
Exergonic reactions drive Exergonic reactions drive endergonic reactionsendergonic reactions The product of an energy-yielding The product of an energy-yielding
reaction fuels an energy-requiring reaction fuels an energy-requiring reaction in a reaction in a coupled reactioncoupled reaction
The parts of coupled reactions often The parts of coupled reactions often occur at different places within the occur at different places within the cellcell
Energy-carrier moleculesEnergy-carrier molecules transfer transfer the energy within cellsthe energy within cells
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ATP powers cellular work ATP powers cellular work by coupling exergonic by coupling exergonic
reactions to endergonic reactions to endergonic reactionsreactions
Cells do work:Cells do work: MechanicalMechanical TransportTransport ChemicalChemical
Cells manage energy resources by Cells manage energy resources by energy coupling: the use of an exergonic energy coupling: the use of an exergonic process to drive an endergonic oneprocess to drive an endergonic one
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The Structure and The Structure and Hydrolysis of ATPHydrolysis of ATP
ATP (adenosine triphosphate) -- cell’s ATP (adenosine triphosphate) -- cell’s energy shuttleenergy shuttle
ATP provides energy for cellular ATP provides energy for cellular functionsfunctions
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Hydrolysis of ATPHydrolysis of ATP High energy phosphate bonds -- broken by High energy phosphate bonds -- broken by
hydrolysishydrolysis Energy release -- chemical change to a state of Energy release -- chemical change to a state of
lower free energy, not from the phosphate lower free energy, not from the phosphate bonds themselvesbonds themselves
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Energy from ATP hydrolysis can be used Energy from ATP hydrolysis can be used to drive an endergonic reactionto drive an endergonic reaction
Overall, the coupled reactions are Overall, the coupled reactions are exergonicexergonic
NH2
Glu
Pi
Pi
Pi
Pi
Glu NH3
P
P
P
ATPADP
Motor proteinMechanical work: ATP phosphorylates motor proteins
Protein moved
Membraneprotein
Solute
Transport work: ATP phosphorylates transport proteins
Solute transported
Chemical work: ATP phosphorylates key reactants
Reactants: Glutamic acidand ammonia
Product (glutamine)made
+ +
+
PhosphorylationPhosphorylation
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The Regeneration of ATPThe Regeneration of ATP
ATP -- renewable resource ATP -- renewable resource regenerated by addition of a phosphate regenerated by addition of a phosphate
group to ADPgroup to ADPThe energy comes from catabolic The energy comes from catabolic
reactions in the cellreactions in the cellThe potential energy stored in ATP The potential energy stored in ATP
drives most cellular workdrives most cellular work
LE 8-12LE 8-12
Pi
ADP
Energy for cellular work(endergonic, energy-consuming processes)
Energy from catabolism(exergonic, energy-yielding processes)
ATP
+
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Exergonic ReactionsExergonic Reactions Exergonic reactionsExergonic reactions release release
energyenergy Spontaneous?Spontaneous?
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The Activation Energy The Activation Energy BarrierBarrier
Chemical reactions -- bond breaking and Chemical reactions -- bond breaking and bond formingbond forming
The initial energy -- free energy of The initial energy -- free energy of activation, or activation energy (Eactivation, or activation energy (EAA) )
EEAA often supplied in the form of heat often supplied in the form of heat from the surroundingsfrom the surroundings
LE 8-14LE 8-14
Transition state
C D
A B
EA
Products
C D
A B
G < O
Progress of the reaction
Reactants
C D
A B
Fre
e e
nerg
y
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How Enzymes Catalyze How Enzymes Catalyze ReactionsReactions
Lowering Energy of Activation (ELowering Energy of Activation (EAA)) Enzymes do not affect the change in Enzymes do not affect the change in
free-energyfree-energy hasten reactions that would occur eventuallyhasten reactions that would occur eventually
Biological catalystsBiological catalysts Specific for the molecules they catalyzeSpecific for the molecules they catalyze Activity often enhanced or suppressed by Activity often enhanced or suppressed by
their reactants or productstheir reactants or products
LE 8-15LE 8-15
Course ofreactionwithoutenzyme
EA
without enzyme
G is unaffectedby enzyme
Progress of the reaction
Fre
e e
nerg
y
EA withenzymeis lower
Course ofreactionwith enzyme
Reactants
Products
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CatalystsCatalysts Catalyst -- chemical agent that speeds up Catalyst -- chemical agent that speeds up
a reaction without being consumed by a reaction without being consumed by the reactionthe reaction
Enzyme -- catalytic proteinEnzyme -- catalytic protein Example: Hydrolysis of sucrose by Example: Hydrolysis of sucrose by
sucrasesucrase
SucroseC12H22O11
GlucoseC6H12O6
FructoseC6H12O6
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Enzymes are a type of protein that acts as a Enzymes are a type of protein that acts as a catalyst, speeding up chemical reactionscatalyst, speeding up chemical reactions
EnzymesEnzymes
Substrate(sucrose)
Enzyme(sucrose)
Fructose
Glucose
Enzymes can Enzymes can perform their perform their functions functions repeatedly, repeatedly, functioning as functioning as workhorses workhorses that carry out that carry out the processes the processes of lifeof life
LE 8-17LE 8-17
Enzyme-substratecomplex
Substrates
Enzyme
Products
Substrates enter active site; enzymechanges shape so its active siteembraces the substrates (induced fit).
Substrates held inactive site by weakinteractions, such ashydrogen bonds andionic bonds.
Active site (and R groups ofits amino acids) can lower EA
and speed up a reaction by• acting as a template for substrate orientation,• stressing the substrates and stabilizing the transition state,• providing a favorable microenvironment,• participating directly in the catalytic reaction.
Substrates areconverted intoproducts.
Products arereleased.
Activesite is
availablefor two new
substratemolecules.
LE 8-18LE 8-18An enzyme’s An enzyme’s activity can activity can be affected be affected by:by: General General
environmental environmental factorsfactors
o temperaturetemperatureo pHpH
Chemicals that Chemicals that specifically specifically influence the influence the enzymeenzyme
Optimal temperature fortypical human enzyme
Optimal temperature forenzyme of thermophilic (heat-tolerant bacteria)
Temperature (°C)
Optimal temperature for two enzymes
0 20 40 60 80 100
Rate
of
reacti
on
Optimal pH for pepsin(stomach enzyme)
Optimal pHfor trypsin(intestinalenzyme)
pH
Optimal pH for two enzymes
0
Rate
of
reacti
on
1 2 3 4 5 6 7 8 9 10
LE 8-19LE 8-19 Competitive -- Competitive --
bind to the active bind to the active site of an enzymesite of an enzyme
Noncompetitive -- Noncompetitive -- bind to another bind to another part of an enzymepart of an enzyme changes shape changes shape makes active site makes active site
less effectiveless effective
Substrate
Active site
Enzyme
Competitiveinhibitor
Normal binding
Competitive inhibition
Noncompetitive inhibitor
Noncompetitive inhibition
A substrate canbind normally to the
active site of anenzyme.
A competitiveinhibitor mimics the
substrate, competingfor the active site.
A noncompetitiveinhibitor binds to the
enzyme away from theactive site, altering the
conformation of theenzyme so that its
active site no longerfunctions.
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Regulation of enzyme Regulation of enzyme activity helps control activity helps control
metabolismmetabolism
Chemical chaos -- if cell’s metabolic Chemical chaos -- if cell’s metabolic pathways were pathways were notnot tightly regulated tightly regulated
Cells switch genes on or off that Cells switch genes on or off that encode specific enzymesencode specific enzymes
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Allosteric Regulation of Allosteric Regulation of EnzymesEnzymes
Enzymes -- active and inactive Enzymes -- active and inactive formsforms The binding of activator -- stabilizes The binding of activator -- stabilizes
the active formthe active form The binding of an inhibitor -- stabilizes The binding of an inhibitor -- stabilizes
the inactive formthe inactive form
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LE 8-20aLE 8-20aAllosteric enzymewith four subunits
Regulatorysite (oneof four)
Active form
Activator
Stabilized active form
Active site(one of four)
Allosteric activatorstabilizes active form.
Non-functionalactive site
Inactive formInhibitor
Stabilized inactive form
Allosteric inhibitorstabilizes inactive form.
Oscillation
Allosteric activators and inhibitors
function function affected by affected by binding of a binding of a regulatory regulatory molecule at molecule at anotheranother site site
Allosteric Allosteric regulationregulation
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Allosteric RegulationAllosteric RegulationCooperativity -- can amplify enzyme activityCooperativity -- can amplify enzyme activity
Substrate
Binding of one substrate molecule toactive site of one subunit locks allsubunits in active conformation.
Cooperativity another type of allosteric activation
Stabilized active formInactive form
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Feedback Feedback InhibitionInhibition
End product of a End product of a metabolic metabolic pathway shuts pathway shuts down the down the pathwaypathway
Intermediate A
Isoleucineused up bycell
Feedbackinhibition Active site of
enzyme 1 can’tbindtheoninepathway off
Isoleucinebinds toallostericsite
Intermediate B
Intermediate C
Intermediate D
End product(isoleucine)