lecture notebook to accompany principles of life€¦ · formaldehyde (ch. 2. o) formic acid...

Sinauer Associates, Inc. W. H. Freeman and Company

Lecture Notebook to accompany

Copyright © 2012 Sinauer Associates, Inc. Cover photograph © Fred Bavendam/Minden Pictures.

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© 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)

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How do metabolic pathways happen? -complex chemical pathways occur in intermediate reactions. - catalysis of an enzyme. - metabolic pathways similar in all organisms: bacteria to plants. -in eukaryotes, metabolic pathways are compartmentalized in organelles. -each pathway is controlled by key enzymes that can be inhibited or activated. Remember chemical energy available to do work is free energy (G)

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>>>needed>>>

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In cells, energy is coupled: exergonic reaction energy is used in an endergonic reaction.

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The product molecules (ADP) in this reaction have less free energy than the reactant (ATP) so the change is negative

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ATP+ H20>>>ADP + Pi + free energy

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The free energy of the P--O bond between phosphate groups is much higher than the energy of the O-H bond that forms hydrolysis

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Phosphate groups are negatively charged and repel each other.


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


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


IN-TEXT ART (Page 102)


FIGURE 6.3 Oxidation, Reduction, and Energy (Page 102)

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Free-energy of the P-O is denoted by the wavy chemical lines. The free-energy is much higher than the energy of the O-H bonds.

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Another way of transferring energy in chemical reactions is to transfer electrons. A reaction in which one substance transfers one or more electrons to another substance is called an oxidation-reduction, or redox reaction. "OIL RIG"- oxidation is loss, reduction is gain "LEO GER"- loses an electron; oxidized gains electron; reduced

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Oxidation and reduction always occur together: as one chemical is oxidized, the electrons it loses are transferred to another chemical reducing it. Transfers of hydrogen atoms involve transfers of electrons (H=H+ + e-).. So when a molecule loses an H atom it becomes oxidized



NAD+AH BH

A BNADH

ReductionOxidation ReductionOxidation


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)




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)

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ADP and Phosphate bind at the active site making ATP.

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Chemiosmosis is when a cell can generate a proton (hydrogen ion) gradient across a membrane. The proton gradient can be moved to an area of lower concentration by a membrane embedded channel for H ion diffusion. The channel turns and releases energy used to make ATP from ADP. If the proton gradient is destroyed and oxygen is still delivered, ATP cannot be made but the oxidation of NADH still happens and energy is produced in the form of heat. Example: newborn infants have this capability. Heat is produced for the infants that make up for the lack of body hair to prevent heat loss.




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)




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)


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)

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Cellular respiration and photosynthesis are related by use of energy transferring substrates, ATP and reduced enzymes.

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Net goal of these two pathways is to take light energy and convert it into chemical energy to fuel the process of life.

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NAD+ NADH



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


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Glycolysis- the 6 carbon monosaccharide glucose is converted into two-three carbon molecules of pyruvate

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Pyruvate oxidation- 2 3-carbon molecules of pyruvate are oxidized to 2 two-carbon molecules of acetyl CoA and two molecules of CO2.

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Citric acid cycle- (Kreb's cycle) two 2-carbon molecules of acetyl CoA are oxidized to four molecules of CO2.

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Glycolysis is the breaking of a sugar molecule.

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(with Oxygen)

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3 Big ole steps to cellular respiration! Remember take in Oxygen and glucose (food) and give off Carbon dioxide and water! 1. Glycolysis 2. Citric acid cycle (or Krebs back in my day 3. Electron transport chain




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


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Final products of glycolysis 2 molecules of pyruvate 2 molecules of ATP 2 molecules of NADH

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Focus on the energy investment; ATP to trap and destabilize glucose, then energy return through SLP (substrate level phosphorylation) It is an enzyme facilitated transfer of a phosphate group to ADP

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You do not have memorize the steps of glycolysis.



NAD+ NADH

Malate dehydrogenase

CH2

OC

COO–

COO–

Oxaloacetate


CH2

C

COO–

COO–

HO

Malate

H

IN-TEXT ART (8)


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)

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This happens inside of the mitochondria.

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Carbon dioxide is released

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Hey!! The acetyl CoA comes from glycoysis. It is produced to kick off the citrate.......hence the citric acid cycle.

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NADH is moving electrons and.......

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moving more electrons

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Yay! More Carbon dioxide for photosynthesis

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How this is converted does not matter! Just know it is important for more energy production. Just remember when this is over we have about 32 molecules of ATP. Yipee! Breathe in....Breathe out!




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)

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What the heck is this??? You ask?? This is the electron transport chain with in the mitochonidria. Last step of cellular respiration.

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More ATP is produced along with the release of water.....another product of the citric acid cycle ....also called cellular respiration. We also have oxidative phosphorylation happening here. Do you see it? News Flash!!! Total ATP molecule production can vary. Up to 38 ATP molecules can be produced but some can be lost through leaky membranes. An average of 29-36 ATP molecules can be produced during cellular respiration.

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Proton gradient

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motor




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)

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No oxygen present......well glycolysis can still produce a little bit of ATP, not as much as aerobic.

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Beer, wine.... the stuff you are not old enough to drink!!

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Cramps!!!




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)

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Other substances produced during cellular respiration.

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Quiz tomorrow!!!!




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)




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






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)



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


FIGURE 6.18 The Molecular Structure of Chlorophyll (Page 115)




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)


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)




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)



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


FIGURE 6.22 RuBP Is the Carbon Dioxide Acceptor (Page 119)

C

C OHH

H

OH P

C O

H

Glyceraldehyde 3-phosphate (G3P)






FIGURE 6.23 Products of Glucose Metabolism (Page 120)

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