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Sugars, concluded;
Electron Transport
and Oxidative
Phosphorylation
Andy Howard
Introductory Biochemistry
3 April 2008
3 April 2008
Electron Transport

This shows how we can really make
ATP from all those reducing
equivalents that we amassed during
glycolysis and the TCA cycle…
but first we have some unfinished
carbohydrate business to complete!
Sugars, concl’d; Electron Transport
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What we’ll discuss
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Remaining
carbohydrate issues
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Entner-Doudoroff
Pathway
Pentose Phosphate
Pathway
Glyoxylate Pathway
TCA cycle evolution
Sugars, concl’d; Electron Transport
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ETS and Oxidative
Phosphorylation
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Generalizations
about oxidationreduction reactions
Electron Transport:
Complexes I-IV
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Entner-Doudoroff Pathway
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Alternative catabolic pathway from glucose-6phosphate to smaller molecules
Found in some bacteria as alternative to normal
glycolytic pathway
Other bacteria that do have glycolytic pathway
possess these enzymes as a side-path
We’ve already discussed this: this is a review
Sugars, concl’d; Electron Transport
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Entner-Doudoroff reaction 1:
G6PDH
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Oxidizes glucose-6-phosphate to 6gluconolactone
We’ll meet this enzyme in the PPP
shortly
Sugars, concl’d; Electron Transport
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Entner-Doudoroff Pathway 2:
Gluconolactonase
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Dehydratase: Converts 6-Pgluconolactone to 6-P-gluconate
An example of a phosphorylated
sugar acid
Sugars, concl’d; Electron Transport
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Entner-Doudoroff Pathway 3:
6-P-gluconate dehydratase
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Converts 6-phosphogluconolactonate to
2-keto-3-deoxy-6-phosphogluconate with
release of water
First step differentiating this pathway
from the pentose phosphate pathway
Sugars, concl’d; Electron Transport
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Entner-Doudoroff Pathway 4:
KDPG Aldolase
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As usual, breaking C-C bonds is somewhat
special
Energetics fairly near isoergic, though
Cleaves KDPG to pyruvate and glyceraldehyde3-phosphate
Analogous to ordinary aldolase but secondary
product is more oxidized
Thus only one ATP produced per molecule of
glucose degraded here
Sugars, concl’d; Electron Transport
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KDPG aldolase
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EC 4.1.2.14
Class I aldolase
PDB 2C0A
71 kDa trimer
TIM barrel protein
E. coli
Strong similarities to other
aldolases, including fructose 1,6bisphosphate aldolase
Sugars, concl’d; Electron Transport
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Significance of this pathway
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Primary pathway for glucose degradation
in some organisms
Secondary pathway in some organisms
that do have standard glycolysis:
Provides degradative pathway for
gluconate and related compounds
Sugars, concl’d; Electron Transport
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Pentose Phosphate Pathway
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Pathway for converting 6-carbon sugar
phosphates to 5-C sugar phosphates
Provides ribose-5-phosphate
Provides reducing equivalents in the form
of NADPH that can be used in anabolic
reactions
Catabolic
Can be regarded as a cycle
Sugars, concl’d; Electron Transport
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Pentose Phosphate Pathway:
Oxidative Phase
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Begins with G6PDH and gluconolactonase,
just like Entner-Doudoroff pathway
Proceeds to ribulose-5-phosphate via a
second oxidative step
Remember that NADPH generally is used
in anabolism, and it has to come from
somewhere
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PPP
NADP+ + NADH  NADPH + NAD+
NAD kinase
Sugars, concl’d; Electron Transport
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Glucose-6-Phosphate
Dehydrogenase
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Catalyzes oxidation of G6-P to
6-phosphogluconolactone
Some isozymes will
oxidize other hexoses
Others are specific to
glucose
Sugars, concl’d; Electron Transport
PDB 1DPG
107 kDa dimer
Leuconostoc mesenteroidies
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Isozymes: G6PDH & H6PDH
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G6PDH is specific to glucose-6-P:
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Found almost exclusively in erythrocytes
Coded for on X chromosome
(1 copy/cell: Male has 1, female’s second is
inactive)
H6PDH: runs several hexose phosphates
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Found in many other tissues
Coded for on Chromosome 22
Sugars, concl’d; Electron Transport
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iClicker quiz
Why does it matter that the G6PDH gene
is located on the X chromosome?
(a) males don’t possess the gene
(b) females don’t possess the gene
(c) only one copy available per cell
(d) no DNA-repair mechanisms available
for X-Chromosome genes
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Sugars, concl’d; Electron Transport
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Medical issues with G6PDH
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Numerous identified mutations found
in human erythrocytes
All involve partial interference with
first reaction
Total absence of G6PDH is fatal
Survival of defective G6PDH genes:
individuals with these erythrocytes
have increased resistance to malaria
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Malaria: critical influence on
human evolution
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G6PDH
Sickle-cell anemia (Hb E6V)
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Similar natural history:
Heterozygotes for sickle-cell have
increased resistance to parasite
Behavior (post-WWII)
DDT, eradication of Anopheles
mosquitoes, thin eggshells in birds
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Gluconolactonase
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Converts gluoconolactone to 6phosphogluconate
Remember this is a hydratase, not an
oxidoreductase
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6-phosphogluconate
dehydrogenase
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Catalyzes oxidative
decarboxylation of 6phosphogluconate to ribulose5-phosphate
NADP is electron acceptor
Same superfamily of enzymes
as glycerol-3-P dehydrogenase
Sugars, concl’d; Electron Transport
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PDB 2PGD
106 kDa dimer
Sheep
3 April 2008
Non-oxidative phase
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Once we’ve made ribulose-5-phosphate,
we can go a couple of directions
Two transketolase reactions:
Kn + Am  An-2 + Km+2
One transaldolase:
Kn + Am  An-3 + Km+3
Sugars, concl’d; Electron Transport
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Non-oxidative steps
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Epimerases
,
isomerases,
transketolases,
transaldolases
Chart courtesy
Michael King,
Indiana State
Sugars, concl’d; Electron Transport
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Ribulose-5phosphate 3epimerase
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Converts RuBP to
xylulose-5-P
TIM-barrel protein
Co-regulated with
RuP isomerase
Sugars, concl’d; Electron Transport
PDB 2FLI
290 kDa dodecamer
Streptococcus pyrogenes
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RuP
Isomerase
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1.25Å structure available
from Midwest Structural
Genomics Project
Illustrates utility of highresolution structures
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PDB 1O8B
24 kDa monomer
E.coli
Finding hydrogens
Identifying secondary
conformations of sidechains
Sugars, concl’d; Electron Transport
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Transketolases
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Transfer 2-C fragment
from ketose to aldose
TPP-dependent enzyme
(characteristic of twocarbon transfers)
P. Asztalos et al (2007)
Biochemistry 46: 12037
Sugars, concl’d; Electron Transport
PDB 2R8O
147 kDa dimer
E.coli
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Transaldolases
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Transfer 3-carbon unit—
effectively moves a
dihydroxyacetone group
from ketose to aldose
Reaction:
sedoheptulose-7-phosphate +
glyceraldehyde-3-phosphate 
D-erythrose-4-phosphate +
D-fructose-6-phosphate
Schiff-base intermediate
Structurally related to TIMbarrel aldolases
Sugars, concl’d; Electron Transport
PDB 3CLM
39 kDa
monomer
Neisseria
gonorrhoeae
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Significance of the PPP
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Generates NADPH where it’s needed
Source of Ribose-5-phosphate
Several medical conditions associated
with deficiencies in these enzymes
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G6PDH problems already mentioned
Deficiencies in transaldolase lead to liver
problems (Verhoeven et al (2001) Am J
Hum Genet. 68: 1086)
Sugars, concl’d; Electron Transport
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Glyoxylate pathway
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Alternative fate for isocitrate
Absent in animals; fundamental in
bacteria, protists, fungi, plants
Especially prevalent in oily seed plants,
where seed oils are converted to
carbohydrates during germination
Sugars, concl’d; Electron Transport
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Glyoxylate pathway
reactions
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Isocitrate lyase:
isocitrate  glyoxylate + succinate
Malate synthase:
glyoxylate + acetyl CoA + H2O 
L-malate + CoASH + H+
This pathway skips two decarboxylations,
so it produces less NADH but doesn’t lose as
much carbon
Net reaction enables creation of
oxaloacetate that can go into
gluconeogenesis
Sugars, concl’d; Electron Transport
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TCA Cycle and Evolution
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The entire pathway didn’t evolve together
Some reactions much older than others
Some ran backward in early
implementations
Several enzymes adapted from amino
acid degradation
Youngest enzyme:
-ketoglutarate dehydrogenase
Sugars, concl’d; Electron Transport
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Aerobes and anaerobes
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Because of close coupling between TCA
cycle and oxidative phosphorylation, the
complete TCA cycle is an aerobic
phenomenon
Anaerobes do have most of these
enzymes, but the sequence of reactions
is different
Oxygen is actually toxic to many
anaerobes
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Overall role of electron transport
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Last 3 lectures: we discussed
carbohydrate metabolism and the Krebs
cycle, each of which produced some highenergy phosphate energy directly.
In both of those systems much of the
energy generated took the form of
reduced cofactors--NADH in both
systems, and FADH2 (or QH) in the Krebs
cycle.
Now we’ll see what happens to those!
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Reduced cofactors to ATP
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We will discuss how the energy latent
in these reduced cofactors can be
turned into energy in the form of highenergy phosphate bonds in nucleoside
triphosphates--the standard currency
of energy.
Sugars, concl’d; Electron Transport
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What the ETS does
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The electron transport system (ETS) is
responsible for these transformations.
Like the Krebs cycle or glycolysis, the
electron transport chain is a series of
chemical transformations facilitated by
proteins.
Sugars, concl’d; Electron Transport
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Roles of these systems
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Some of these proteins are enzymes in
the conventional sense
others are not--they're electron transport
proteins only:
so they can only be regarded as enzymes
if we allow that the entire ETS is a large,
multi-polypeptide transformation system-a multi-component enzyme
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The overall reactions
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NADH + H+ + (1/2)O2 + 2.5 ADP
+ 2.5 Pi  NAD + H2O + 2.5 ATP
ETS also catalyzes transformations of
the flavin coenzyme FAD:
FADH2 + (1/2)O2 + 1.5 ADP + 1.5 Pi 
FAD + H2O + 1.5 ATP
These are mediated through other
cofactors: Q, cytochromes, Fe-S
proteins, etc.
Proton translocation is crucial
Sugars, concl’d; Electron Transport
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Chemiosmotic theory:
What it says
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Protons are translocated from outside
of mitochondrial inner membrane into
its interior
That passage actually generates both
chemical and electrical energy.
This is because they are moving
down a concentration and electricalpotential gradient.
Sugars, concl’d; Electron Transport
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How it works
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This energy is used to drive the synthesis
of ATP from ADP and Pi within an
enzyme called ATP synthase, which is
(big surprise!) anchored on the inside of
the inner mitochondrial membrane.
The structure of two components of this
enzyme system were determined in 1999
by Andrew Leslie and others.
Sugars, concl’d; Electron Transport
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Oxidation state and energy
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We typically measure oxidation states in
volts.
We can relate the energy associated with
an oxidation-reduction reaction--the socalled change in redox potential--with the
change in the oxidation state of the
molecules involved in the reaction.
Sugars, concl’d; Electron Transport
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What is a volt?
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A volt is actually a measure of energy
per unit charge; in fact, a volt is one joule
per coulomb.
When we say that a double-A battery has
a voltage of 1.5 V, we mean that it can
(under optimal conditions) deliver 1.5
joules of energy
( = 0.359 cal, or 3.59*10-4 kcal) per
coulomb of charge.
Sugars, concl’d; Electron Transport
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Charge and energy
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One electron carries a charge of
1.602 * 10 -19 coulomb
If change in redox potential in a reaction is
0.32 V and all of that change is delivered to
a single electron:
then energy imparted to that electron is
eΔE =
(1.602 * 10-19 coulomb / e-) *
(0.32 J/coulomb)
= 0.513*10-19J / e- = 1.23* 10 -23 kcal / e-
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… in biochemical units …
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That doesn't sound like much, but if we
look at that on a per mole basis it's
(1.23 * 10-23 kcal/e-) *
6.022 * 1023 e -/mole
= 30.87 kJ/mol = 7.38 kcal/mol
which is a reasonable amount of
energy on the scale we're accustomed
to examining.
Sugars, concl’d; Electron Transport
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So what can we get?
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There is enough energy bound up in the
reduced state of NAD relative to the
oxidized state to drive the net creation of
2.5 molecules of ATP from ADP and
phosphate, as indicated in the equations
shown above.
Since there are NADH molecules
created in several steps in glycolysis and
the Krebs cycle, there numerous net ATP
molecules that arise from the overall
process.
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Results from Krebs cycle
3 NADH produce 7.5 ATP
 1 FADH2 produces 1.5 ATP
 1 substrate-level phosphorylation
 Total: 10 ATP per round, if we don’t
get interrupted!
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Sugars, concl’d; Electron Transport
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ETS: The big picture
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5 membrane-associated, multi-enzyme
complexes in mitochondrial inner
membrane
Complexes I-IV associated with electron
transport and proton translocation
Complex V uses proton gradient to
produces ATP from ADP and Pi
Sugars, concl’d; Electron Transport
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Complexes I-IV
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There are several multi-enzyme
complexes involved in converting the
reductive energy in NADH to its final
products.
# Name
I NADH-Ubiquinone oxidoreductase
II Succinate-ubiquinone oxidoreductase
III Ubiquinol-cytochrome c oxidoreductase
IV Cytochrome c oxidase
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Overview of Oxidative Steps
Chart courtesy
Michael King,
Indiana State
Sugars, concl’d; Electron Transport
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Complex I
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NADH:Ubiquinone oxidoreductase
Embedded in inner mitochondrial
membrane
Passes electrons from NADH to
ubiquinone
Sugars, concl’d; Electron Transport
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