ch.8 an introduction to metabolism flow of energy through life life is built on chemical reactions...
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Ch.8An
Introduction to Metabolism
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Flow of energy through lifeFlow of energy through life
• Life is built on chemical reactions– transforming energy from one form to another
organic molecules ATP & organic molecules
organic molecules ATP & organic molecules
sun
solar energy ATP & organic molecules
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Metabolism
– Is the totality of an organism’s chemical reactions
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Organization of the Chemistry of Life into Organization of the Chemistry of Life into Metabolic PathwaysMetabolic Pathways
A metabolic pathway begins with a specific molecule and ends with a product
Each step is catalyzed by a specific enzyme
Startingmolecule
Product
Enzyme 1 Enzyme 2 Enzyme 3
B CA D
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MetabolismMetabolism• Chemical reactions of life
– forming bonds between molecules• dehydration synthesis
• synthesis
• anabolic reactions
– breaking bonds between molecules• hydrolysis
• digestion
• catabolic reactions
That’s why they’re calledanabolic steroids!
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ThermodynamicsThermodynamics• Energy (E)~ capacity to do work; Kinetic energy~ energy of motion;
Potential energy~ stored energy
• Thermodynamics~ study of E transformations
• 1st Law: conservation of energy; E transferred/transformed, not created/destroyed
• 2nd Law: transformations increase entropy (disorder, randomness)
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Free energyFree energy
• Free energy: portion of system’s E that can perform work (at a constant T)
• Exergonic reaction: net release of free E to surroundings
• Endergonic reaction: absorbs free E from surroundings
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Change in free energy, ∆G
• The change in free energy, ∆G during a biological process– Is related directly to the enthalpy
change (∆H) and the change in entropy (∆S)
∆G = ∆H – T∆S
T = temp in Kelvin (K)
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Chemical reactions & energyChemical reactions & energy• Some chemical reactions release energy
– exergonic– ∆G < 0– spontaneous– digesting polymers– hydrolysis = catabolism
digesting molecules= LESS organization=lower energy state
Figure 8.6
Reactants
ProductsEnergy
Progress of the reaction
Amount ofenergyreleased (∆G <0)
Fre
e e
ne
rgy
(a) Exergonic reaction: energy released
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Chemical reactions & energyChemical reactions & energy• Some chemical reactions require input of energy
– endergonic– ∆G > 0– non-spontaneous– building polymers – dehydration synthesis = anabolism
building molecules= MORE organization=higher energy state
Figure 8.6
Energy
Products
Amount ofenergyreleased (∆G>0)
Reactants
Progress of the reaction
Fre
e e
ne
rgy
(b) Endergonic reaction: energy required
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The energy needs of lifeThe energy needs of life• Organisms are endergonic systems
– What do we need energy for?• synthesis
– building biomolecules
• reproduction• movement• active transport• temperature regulation
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Where do we get the energy from?Where do we get the energy from?• Work of life is done by energy coupling
– use exergonic (catabolic) reactions to fuel endergonic (anabolic) reactions
+ + energy
+ energy+
digestion
synthesis
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ATP
Living economyLiving economy• Fueling the body’s economy
– eat high energy organic molecules • food = carbohydrates, lipids, proteins, nucleic acids
– break them down• digest = catabolism
– capture released energy in a form the cell can use
• Need an energy currency– a way to pass energy around
– need a short term energy storage molecule
Whoa! Hot stuff!
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ATPATP
high energy bondsHow efficient!Build once,use many ways
• Adenosine TriPhosphate– modified nucleotide
• nucleotide = adenine + ribose + Pi AMP
• AMP + Pi ADP• ADP + Pi ATP
– adding phosphates is endergonic
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How does ATP store energy?How does ATP store energy?
PO–
O–
O
–O PO–
O–
O
–O PO–
O–
O
–OPO–
O–
O
–O PO–
O–
O
–OPO–
O–
O
–O PO–
O–
O
–O PO–
O–
O
–O
• Each negative PO4 more difficult to add– a lot of stored energy in each bond
• most energy stored in 3rd Pi
• 3rd Pi is hardest group to keep bonded to molecule
• Bonding of negative Pi groups is unstable– spring-loaded– Pi groups “pop” off easily & release energy
Instability of its P bonds makes ATP an excellent energy donor
I thinkhe’s a bitunstable…don’t you?
AMPAMPADPATP
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How does ATP transfer energy? How does ATP transfer energy?
PO–
O–
O
–O PO–
O–
O
–O PO–
O–
O
–O7.3energy+P
O–
O–
O
–O
• ATP ADP– releases energy
• ∆G = -7.3 kcal/mole
• Fuel other reactions• Phosphorylation
– released Pi can transfer to other molecules• destabilizing the other molecules
– enzyme that phosphorylates = “kinase”
ADPATP
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It’snever thatsimple!
An example of Phosphorylation…An example of Phosphorylation…
• Building polymers from monomers– need to destabilize the monomers
– phosphorylate!
C
H
OH
H
HOC C
H
O
H
C+ H2O++4.2 kcal/mol
C
H
OHC
H
P+ ATP + ADP
H
HOC+ C
H
O
H
CC
H
P+ Pi
“kinase” enzyme
-7.3 kcal/mol
-3.1 kcal/mol
enzyme
H
OHC
H
HOC
synthesis
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Can’t store ATP good energy donor,
not good energy storagetoo reactivetransfers Pi too easilyonly short term energy storage
carbohydrates & fats are long term energy storage
ATP / ADP cycleATP / ADP cycle
A working muscle recycles over 10 million ATPs per second
Whoa!Pass methe glucose(and O2)!
ATP
ADP Pi+
7.3 kcal/mole
cellularrespiration
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Another example of Phosphorylation…Another example of Phosphorylation…
• The first steps of cellular respiration– beginning the breakdown of glucose to make ATP
glucoseC-C-C-C-C-C
fructose-1,6bPP-C-C-C-C-C-C-P
DHAPP-C-C-C
G3PC-C-C-P
hexokinase
phosphofructokinase
Thosephosphatessure make ituncomfortablearound here!
C
H
P
C
P
CATP2
ADP2
activationenergy
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Too much activation energy for lifeToo much activation energy for life
• Activation energy– amount of energy needed to destabilize the
bonds of a molecule– moves the reaction over an “energy hill”
glucose
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Reducing Activation energyReducing Activation energy• Catalysts
– reducing the amount of energy to start a reaction
Pheeew…that takes a lotless energy!
reactant
product
uncatalyzed reaction
catalyzed reaction
NEW activation energy
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CatalystsCatalysts• So what’s a cell got to do to reduce
activation energy?– get help! … chemical help… ENZYMES
G
Call in the ENZYMES!
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Substrate Specificity of Enzymes
• The substrate– Is the reactant an enzyme acts on
• The enzyme– Binds to its substrate, forming an
enzyme-substrate complex
• The active site– Is the region on the enzyme
where the substrate binds
Figure 8.16
Substrate
Active site
Enzyme
(a)
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Naming conventionsNaming conventions• Enzymes named for reaction they catalyze
– sucrase breaks down sucrose
– proteases break down proteins
– lipases break down lipids
– DNA polymerase builds DNA• adds nucleotides
to DNA strand
– pepsin breaks down proteins (polypeptides)
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Factors Affecting Enzyme FunctionFactors Affecting Enzyme Function• Enzyme concentration
• Substrate concentration
• Temperature
• pH
• Salinity
• Activators
• Inhibitors
catalase
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Factors affecting enzyme function Factors affecting enzyme function • Enzyme concentration
– as enzyme = reaction rate• more enzymes = more frequently collide with substrate
– reaction rate levels off• substrate becomes limiting factor• not all enzyme molecules can find substrate
enzyme concentration
reac
tion
rat
e
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Factors affecting enzyme function Factors affecting enzyme function
substrate concentration
reac
tion
rat
e
• Substrate concentration – as substrate = reaction rate
• more substrate = more frequently collide with enzyme
– reaction rate levels off• all enzymes have active site engaged• enzyme is saturated• maximum rate of reaction
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Factors affecting enzyme functionFactors affecting enzyme function• Temperature
– Optimum T° • greatest number of molecular collisions• human enzymes = 35°- 40°C
– body temp = 37°C
– Heat: increase beyond optimum T°• increased energy level of molecules disrupts bonds in
enzyme & between enzyme & substrate– H, ionic = weak bonds
• denaturation = lose 3D shape (3° structure)– Cold: decrease T°
• molecules move slower • decrease collisions between enzyme & substrate
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Enzymes and temperatureEnzymes and temperature• Different enzymes function in different
organisms in different environments
37°Ctemperature
reac
tion
rat
e
70°C
human enzymehot springbacteria enzyme
(158°F)
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Factors affecting enzyme functionFactors affecting enzyme function• pH
– changes in pH• adds or remove H+
• disrupts bonds, disrupts 3D shape – disrupts attractions between charged amino acids – affect 2° & 3° structure– denatures protein
– optimal pH?• most human enzymes = pH 6-8
– depends on localized conditions– pepsin (stomach) = pH 2-3– trypsin (small intestines) = pH 8
720 1 3 4 5 6 8 9 10 11
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Factors affecting enzyme functionFactors affecting enzyme function• Salt concentration
– changes in salinity• adds or removes cations (+) & anions (–)
• disrupts bonds, disrupts 3D shape – disrupts attractions between charged amino acids
– affect 2° & 3° structure
– denatures protein
– enzymes intolerant of extreme salinity• Dead Sea is called dead for a reason!
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Enzyme cofactors
• Cofactors– Are non-protein enzyme helpers e.g.
zinc, iron, copper atoms
• Coenzymes– Are organic cofactors e.g. vitamins
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coenzymes in group transfer
reactions
coenzyme abbreviation entity transfered
nicotine adenine
dinucelotide
NAD - partly composed of
niacin
electron (hydrogen atom)
nicotine adenine
dinucelotide phosphate
NADP -Partly composed of
niacin
electron (hydrogen atom)
flavine adenine
dinucelotide
FAD - Partly composed of
riboflavin (vit. B2)
electron (hydrogen atom)
coenzyme A CoA Acyl groups
coenzymeQ CoQ electrons
(hydrogen atom)
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Enzyme Regulation
• Regulation of enzyme activity helps control metabolism
• A cell’s metabolic pathways– Must be tightly regulated
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Enzyme Inhibitors• Competitive
inhibitors– Bind to the active
site of an enzyme, competing with the substrate
Figure 8.19 (b) Competitive inhibition
A competitiveinhibitor mimics the
substrate, competingfor the active site.
Competitiveinhibitor
A substrate canbind normally to the
active site of anenzyme.
Substrate
Active site
Enzyme
(a) Normal binding
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Enzyme Inhibitors
• Noncompetitive inhibitors– Bind to another part of an enzyme,
changing the function
Figure 8.19
A noncompetitiveinhibitor binds to the
enzyme away fromthe active site, altering
the conformation ofthe enzyme so that its
active site no longerfunctions.
Noncompetitive inhibitor
(c) Noncompetitive inhibition
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Allosteric regulationAllosteric regulation• Conformational changes by regulatory
molecules – inhibitors
• keeps enzyme in inactive form
– activators • keeps enzyme in active form
Conformational changes Allosteric regulation
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Feedback inhibition
– The end product of a metabolic pathway shuts down the pathway
Active siteavailable
Isoleucineused up bycell
Feedbackinhibition
Isoleucine binds to allosteric site
Active site of enzyme 1 no longer binds threonine;pathway is switched off
Initial substrate(threonine)
Threoninein active site
Enzyme 1(threoninedeaminase)
Intermediate A
Intermediate B
Intermediate C
Intermediate D
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
End product(isoleucine)
Figure 8.21
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Cooperativity Cooperativity • Substrate acts as an activator
– substrate causes conformational change in enzyme
• induced fit
– favors binding of substrate at 2nd site
– makes enzyme more active & effective
• hemoglobin
Hemoglobin 4 polypeptide chains can bind 4 O2; 1st O2 binds now easier for other 3
O2 to bind