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Sinauer Associates, Inc. W. H. Freeman and Company
Lecture Notebook to accompany
Copyright © 2012 Sinauer Associates, Inc. Cover photograph © Fred Bavendam/Minden Pictures.
This document may not be modified or distributed (either electronically or on paper) without the permission of the publisher, with the following exception: Individual users may enter their own notes into this document and may print it for their own personal use.
© 2012 Sinauer Associates, Inc.
Pathways that Harvest and Store Chemical Energy 6
2
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POL HillisSinauer AssociatesMorales Studio Figure 06.01 Date 07-05-10
Synthesis of ATP from ADP and Pi requires energy.
Hydrolysis of ATP to ADP and Pi releases energy.
EnergyEnergy
ADP
+ Pi
Endergonic reaction:(requires energy) • Active transport • Cell movements • Anabolism
Exergonic reaction:(releases energy) • Cell respiration • Catabolism
ATP
FIGURE 6.1 The Concept of Coupling Reactions (Page 101)
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 0602 Date 07-06-10
CH2O–O P
O
O–
PP O
O
O–
O
O
O–
H
H H
OH OH
NH2
HH
H
N
N
N
NC
C
C
CC
O
C C
Adenine
Ribose
Adenosine
(Adenosine monophosphate)AMP
(Adenosine diphosphate)ADP
(Adenosine triphosphate)
Phosphate groups
Hydrolysis of ATP to ADP breaks this bond, releasing energy.
ATP
FIGURE 6.2 ATP (Page 101)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 3
OAdenine—ribose –OP
O
O–
PP O
O
O–
O
O
O–
~ ~
OAdenine—ribose
O
O–
PP O HO
O
O–
O–P
O
O–
OH +~
ATP
ADP Pi
H2O+
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06 Intext 0601 Date 07-06-10
C HH
H
H
C C OHH
H
H
C C OH
H
C C OH
HO
C C O
O
C
Methane(CH4)
Methanol(CH3OH)
Formaldehyde(CH2O)
Formic acid
(HCOOH)
Carbon dioxide(CO2)
Most reduced stateHighest free energy
Most oxidized stateLowest free energy
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 0603 Date 07-06-10
A is oxidized,having lost electrons.
B is reduced,having gained electrons.
e–
e–e–
e–
e–
e–
Reducedcompound A(reducingagent)
Oxidizedcompound B(oxidizingagent)
Oxidizedcompound A
Reducedcompound B
A B
A B
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06 Intext 0602 Date 07-06-10
IN-TEXT ART (Page 102)
IN-TEXT ART (Page 102)
FIGURE 6.3 Oxidation, Reduction, and Energy (Page 102)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 4
NAD+AH BH
A BNADH
ReductionOxidation ReductionOxidation
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 0604 Date 07-26-10
One proton and two electrons are transferred to the ring structure of NAD+.
N
N
N
CH2
H HH H
OH OH
O
NH2
OP
N
CH2
H HH H
OH OH
O
H
OP
CONH2
+N
H
CONH2
O
O
O–
O–
O
HReductionNicotinamide
Reduced form ( )
Oxidation
Oxidized form ( NAD+ ) NADHH+ + 2e–(A)
(B)
Adenine
Ribose
FIGURE 6.4 NAD+/NADH Is an Electron Carrier in Redox Reactions (Page 103)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 5
POL HillisSinauer AssociatesMorales Studio Figure 06.05 Date 07-26-10
I think this is a mistake, making the ATP synthase an oval in (A). There is now no visual continuity between part (A) and part (B).
Cellular metabolism builds up H+ on one side of a membrane, creating an H+ gradient.
ATP synthase in the membrane uses the energy of the gradient to make ATP.
H+
H+
H+
H+
H+
H+
H+
H+ H+
H+
H+
H+
H+
H+
Pi+
Oxidation
Cellmembrane
(A)
(B)
ATPsynthase
Fo unit
H+
H+
H+
H+ H+
H+
Pi+
F1 unit
ATPADP
ATPADP
FIGURE 6.5 Chemiosmosis (Page 104)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 6
POL HillisSinauer AssociatesMorales Studio Figure 06.06 Date 07-05-10
HYPOTHESIS CONCLUSION
INVESTIGATION
Go to yourBioPortal.com for original citations, discussions, and relevant links for all INVESTIGATION figures.
In the absence of electron transport, an artificial H+ gradient is sufficient for ATP synthesis by organelles.
A H+ gradient can drive ATP synthesis by isolatedmitochondria or chloroplasts.
METHOD
FIGURE 6.6 An Experiment Demonstrates the Chemiosmotic Mechanism The chemiosmosis hypothesis was a bold departure from the conventional scientific thinking of the time. It required an
intact compartment separated by a membrane. Could a proton gradient drive the synthesis of ATP?
RESULTS
ANALYZE THE DATAIn another experiment, thylakoids were isolated at pH 7 and thenincubated with ADP, phosphate (Pi), and magnesium ions (Mg2+) at eitherpH 7 or pH 3.8. ATP formation was measured using luciferase, whichcatalyzes the formation of a luminescent (light-emitting) molecule if ATPis present. Here are the data from the paper:
A. Which reaction mixture is the control? Use the control data to correct the raw data for the other, experimental reaction mixtures and fill in the table.
B. Why did ATP production go down in the absence of Pi?C. What is the role of Mg2+ in ATP formation?
For more, go to Working with Data 6.1 at yourBioPortal.com.
Luciferase activity (light emission)
Reaction mixture Raw data Corrected data
Complete, pH 3.8 141 Complete, pH 7.0 12 Complete, pH 3.8 – Pi 12 " " – ADP 4 " " – Mg2+ 60 " " – chloroplasts 7
Organelles are isolated from cells and placed in amedium at pH 9. This results in a low H+ concentrationon both sides of the membrane.
The organelles are moved quickly to a neutral medium (pH 7).This raises the H+ concentration outside the organelleand creates a H+ gradient across themembrane. The outer membrane isfreely permeable to H+ but the innermembrane is not.
H+ movement into the organelle drives the synthesis of ATP in the absence of continuous electron transport.
Organelle
pH 9
pH 7
Outermembrane
Innermembrane
pH 9
pH 7
Pi+ADP
pH 7H+
H+ ATP
(Page 105)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 7
POL HillisSinauer AssociatesMorales Studio Figure 06.07 Date 09-13-10
ADP
In some form, all cells perform cellular respiration.
Green plants and some prokaryotic cells perform photosynthesis.
Catabolic pathways release energy, which is stored in the bonds of ATP and reduced coenzymes.
Photosynthesis is an anabolic pathway that uses energy released from ATP and reduced coenzymes.
Light energy is transformed into chemical energy in the first steps of photosynthesis.
All cells use energy released from catabolism to perform activities essential to life.
Oxidizedcoenzymes
Reducedcoenzymes
Cellularrespiration
Reducedcoenzymes
Photosynthesis
O2 CO2Carbohydrate
Lightenergy
AnabolismActive transport
ATP
ATP
FIGURE 6.7 ATP, Reduced Coenzymes, and Metabolism (Page 106)
POL HillisSinauer AssociatesMorales Studio Figure 06.07 Date 07-05-10
In cells, stepwise oxidation of glucose releases energy in small amounts that can be trapped by coenzymes.
If glucose is burned, the energy is released all at once as heat.
Free
ene
rgy
Small activation energy
Glucose + O2
(A) (B)
Glucose + O2
CO2 + H2O CO2 + H2O
Large activation energy provided by applied heat
FIGURE 6.8 Energy Metabolism Occurs in Small Steps (Page 106)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 8
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06.08 Date 09-13-10
CITRICACID
CYCLE
GLYCOLYSIS
ELECTRON TRANSPORT/ATP SYNTHESIS
Glucose
PYRUVATEOXIDATION
Pyruvate
Cytoplasm
Mitochondrial matrix
Inner mitochondrialmembrane
CO2 and H2O
FIGURE 6.9 Energy-Releasing Metabolic Pathways (Page 107)
POL HillisSinauer AssociatesMorales Studio Figure In text 06.03 Date 07-05-10
C
C O
OH
CH2O
H
H
P
Glyceraldehyde 3-phosphate
NAD+
NADH ATPPi
ADPC O
CH2O
O
C OHH
P
P
C O
CH2O
O–
C OHH
P
1,3-Bisphospho-glycerate
3-Phospho-glycerate
Glyceraldehyde 3-phosphate
dehydrogenase
Phospho-glycerate
kinase
IN-TEXT ART (Page 107)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 9
POL HillisSinauer AssociatesMorales Studio Figure 06.09 Date 09-13-10
Two of the first three steps are endergonic and require energy from ATP hydrolysis.
A six-carbon sugar is cleaved into two three-carbon sugars.
Later steps are exergonic and release energy, forming ATP and NADH.
HH HO
OH H
O
CH2OCH2O
OH
PP
C O
CH3
O–
C O
H
OH H
H OH
HO
H H
OH
CH2OH
O
C
C O
OH
CH2O
H
H
P
Fructose 1,6-bisphosphate
Two molecules of pyruvate
C O
CH3
O–
C O
One molecule of glucose
Two molecules of glyceraldehyde 3-phosphate
C
C O
OH
CH2O
H
H
P
NAD+
NADH
ATP
ATP
Pi+ADP
ATP
Pi+ADP
ATP
Pi+ADP
Step 1
Step 3
Step 2
Step 4
Step 6
Step 5
Step 7
Step 8
Pi+ADPStep 10
Step 9
NAD+
NADH
ATP
ATP
Pi+ADP
Pi+ADP
FIGURE 6.10 Glycolysis Converts Glucose into Pyruvate (Page 107)
POL HillisSinauer AssociatesMorales Studio Figure In text 06.04 Date 09-13-10
C O
CH3
O–
C O
H3
O
CoAC
C
Acetyl CoAPyruvate
NAD+
NADH CO2
Coenzyme A
IN-TEXT ART (Page 108)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 10
NAD+ NADH
Malate dehydrogenase
CH2
OC
COO–
COO–
Oxaloacetate
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06 Intext 0605 Date 07-06-10
CH2
C
COO–
COO–
HO
Malate
H
IN-TEXT ART (Page 108)
POL HillisSinauer AssociatesMorales Studio Figure 06.09 Date 09-13-10
H3
O
CoAC
C
The two-carbon acetyl group gets oxidized.
The four-carbon acceptor molecule is regenerated.
NADH is formed.
Two molecules of CO2 are released.
GTP is convertedto ATP.
FADH2 can be oxidized to FAD.
NAD+
NADH
+ PiGDP
NAD+
NADH
NAD+
NADH
CO2
CO2
Step 1
Step 2
Step 3CITRIC ACID CYCLE
Step 5
Step 7
Step 8
Step 4Step 6
Citrate Oxaloacetate
Acetyl CoA
6C4C
6C4C
5C
4C4C
4C
FADH2
FAD
GTP
FIGURE 6.11 The Citric Acid Cycle (Page 108)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 11
POL HillisSinauer AssociatesMorales Studio Figure 06.11 Date 09-13-10
Electron transport proteins pass electrons from NADH to O2, releasing energy that pumps H+ out of the mitochondrial matrix.
H+
H+
H+
H+
H+
H+
H+
H+
2
Inner mitochondrialmembrane
Mitochondrialmatrix
Cytoplasm
Outer mitochondrialmembrane
NADHNAD+
FADH2
H+ H+H+
H+H+
H+ H+H+
e– e–
e–
FAD
O2
H2O
ATPsynthase
Pi+ADP
Mitochondrion
H++
+ H+
e–
ATP
FIGURE 6.12 Electron Transport and ATP Synthesis in Mitochondria (Page 109)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 12
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 0612 Date 07-06-10
OC
COO–
CH3
CHO
CH3
CH2OH
CH3
GLYCOLYSIS
FERMENTATION
2 Pyruvate
2 NAD+
2 ATP 2
2
2 2+ Pi
2 NAD+
Glucose(C6H12O6)
2 Ethanol
2 CO2
2 Acetaldehyde
Pyruvate decarboxylase
Alcohol dehydrogenase
Summary of reactants and products:C6H12O6 + 2 ADP + 2 Pi 2 ethanol + 2 CO2 + 2 ATP
ADP
(A)
(B)
NADH
Lactate dehydrogenase
C
COO–
CH3
OHH
GLYCOLYSIS
FERMENTATION
2 Lactic acid(lactate)
2 Pyruvate
OC
COO–
CH3
2 NAD+
2 ATP 2
2
2 2+ Pi
2 NAD+
Glucose(C6H12O6 )
Summary of reactants and products:C6H12O6 + 2 ADP + 2 Pi 2 lactic acid + 2 ATP
ADP
NADH
NADH
NADH
FIGURE 6.13 Fermentation (Page 110)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 13
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 0613 Date 07-26-10
ELECTRON TRANSPORT/ATP SYNTHESIS
CITRICACID
CYCLE
GLYCOLYSIS
Pyruvate
PYRUVATEOXIDATION
Purines(nucleic acids)
Pyrimidines(nucleic acids)
Fatty acids
Lipids(trigly-
cerides)
Some amino acids
Polysaccharides(starch)
Glycerol
Glucose
Acetyl CoA
Some amino acids
Proteins
Some amino acids
FIGURE 6.14 Relationships among the Major Metabolic Pathways of the Cell (Page 112)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 14
POL HillisSinauer AssociatesMorales Studio Figure 06.14 Date 07-26-10
Sugars
Thylakoid
CALVINCYCLE
ELECTRON TRANSPORT
Lightreactions
Carbon-fixationreactions
Chlorophyll
Light(photon)
O2
NADPH NADP+++
Chloroplast
Pi
StromaThylakoid lumen
H+
H2O
ADP
Plant cellChloroplast
CO2
ATP
FIGURE 6.15 An Overview of Photosynthesis (Page 113)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 15
POL HillisSinauer AssociatesMorales Studio Figure 06.15 Date 07-05-10
Shorter wavelengths aremore energetic.
Longer wavelengths areless energetic.
The wavelength is the distance between two consecutive peaks of the wave.
X rays
Cosmic raysGamma rays
MicrowavesRadio waves
Visible light
1
10
102
103
104
105
106
Wavelength (nm)
700
400
600
500
Violet
Blue
Green
Yellow
Orange
Red
Ultraviolet (UV)
Infrared (IR)
FIGURE 6.16 The Electromagnetic Spectrum (Page 114)
Incr
easi
ng e
nerg
y
Photon
Excitedstate
Ground state
Absorptionof photon bymolecule
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06 Intext 0606 Date 07-06-10
IN-TEXT ART (Page 114)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 16
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06.16 Date 07-26-10
Blue and red wavelengths are absorbed by chlorophyll a and result in the highest rates of photosynthesis.
400 450 500 550Wavelength (nm)
600 650 700 750
Visible spectrum
Absorption spectrum of chlorophyll a
Action spectrum of photosynthesisby Anacharis
Anacharis
Abs
orba
nce/
activ
ity
FIGURE 6.17 Absorption and Action Spectra (Page 115)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 17
OO
H
CH
H3C
CH3
CH3
CH3
H2C
H3C
CH2
CH2
CO
HH
N N
N N
Mg2+
OCH3
CH
CH2
CH2
CH
HC CH
(CHO in chlorophyll b)
C
C
O
C
Light is absorbed by the complex ring structure of a chlorophyll molecule.
Hydrocarbon tails secure chlorophyll molecules to hydrophobic proteins inside the thylakoid membrane.
The reaction center is where chlorophyll gives up its excited electron.
Accessory chlorophylls absorb light and pass the energy to the reaction center.
Chloroplast
Thylakoid
Thylakoid lumen
Stroma
Thylakoidmembrane
Chlorophyllmolecules
Proteins
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06.17 Date 07-26-10
FIGURE 6.18 The Molecular Structure of Chlorophyll (Page 115)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 18
POL HillisSinauer AssociatesMorales Studio Figure 06.18 Date 07-05-10
The Chl in the reaction center of photosystem II absorbs light maximally at 680 nm, becoming Chl*. Water gets oxidized.
4321 H+ from H2O and electron transport through the electron transport system capture energy for the chemiosmotic synthesis of ATP.
The Chl in the reaction center ofphotosystem I absorbs lightmaximally at 700 nm, becomingChl*.
Photosystem I reduces an electron carrier, which is used to reduce NADP+ to NADPH.
e–
e–
e–
P700
+
Ene
rgy
of m
olec
ules
NADP+NADPH
+
H2O
O2
2
1/2P680
Photon
Photon
H+
H+
e–
e–
Electron transport
ADP + Pi
2
Photosystem I
2 e–
Photosystem II
Electroncarrier
ATP
FIGURE 6.19 Noncyclic Electron Transport Uses Two Photosystems (Page 116)
POL HillisSinauer AssociatesMorales Studio Figure 06.19 Date 07-05-10
The Chl* in the reaction center of photosystem I passes electrons to an electron carrier, leaving positively charged chlorophyll (Chl+).
4
3
1
The carriers of the electron transport system are in turn reduced.
2
Energy from electron flow is captured for chemiosmotic synthesis of ATP.
The last reduced electron carrier passes electrons to electron-deficient chlorophyll,completing the cycle andallowing the reactions to start again.
Ene
rgy
of m
olec
ules
Photosystem I
Electron transport
P700
e–
e–
e–
Photon
ADP + PiATP
Electroncarrier
FIGURE 6.20 Cyclic Electron Transport Traps Light Energy as ATP (Page 117)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 19
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06.20 Date 07-26-10
CO2 combines withits acceptor, RuBP,forming 3PG.
3PG is reduced to G3Pin a two-step reactionrequiring ATP and NADPH.
2
About one-sixth of the G3P moleculesare used to make sugars—the outputof the cycle.
43
1
The remaining five-sixths of the G3P molecules are processedin the series of reactions that produce RuMP.
RuMP is converted to RuBP in a reactionrequiring ATP. RuBP is ready to accept another CO2.
5
ELECTRONTRANSPORT
Thylakoid
Photon
CALVINCYCLE
Stroma
C PP C C
C PC CC PC C
PP C C C CC
C PC C
12 NADP+ 12+
12 NADPH
12 Pi
6
12
12
10 G3P
Other carbon compounds
6 RuMP
6 RuBP
Carbonfixation
Regenerationof RuBP
Reduction andsugar production
12 G3P
CALVIN CYCLE
ADP
CO2
START
Sugars
6
6
ADP
ATP
ATP
H+
12 3PG
2 G3P
FIGURE 6.21 The Calvin Cycle (Page 118)
© 2012 Sinauer Associates, Inc.
Chapter 6 | Pathways that Harvest and Store Chemical Energy 20
C
PC
C
C
C
C
H2O
C
OO–
HHO
PH2O
C OHH
PCH2O
PCH2O
C
C O
OHH
C OHH
OO–
+
C
C
C
C
C
C
C O2 +
The fate of the carbon atom in CO2 is followed in red.
The enzyme rubisco catalyzes the reaction of CO2 with RuBP.
The reaction intermediatesplits into two molecules of3-phosphoglycerate (3PG).
Carbondioxide
Rubisco
Ribulose 1,5-bisphosphate(RuBP)
Six-carbon skeletonof reaction intermediate
3-phosphoglycerate
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 0621 Date 07-06-10
FIGURE 6.22 RuBP Is the Carbon Dioxide Acceptor (Page 119)
C
C OHH
H
OH P
C O
H
Glyceraldehyde 3-phosphate (G3P)
Principles of LIFE HillisSinauer AssociatesMorales Studio Figure 06 Intext 0607 Date 07-06-10
IN-TEXT ART (Page 119)
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