Catabolism:

Fermentation and Respiration

Catabolism: Fermentation and Respiration
• Major catabolic pathways that result in energy
conservation in chemoorganotrophs: fermentation and
respiration.
• Fermentation is a form of anaerobic catabolism in
which organic compounds both donate electrons and
accept electrons, and redox balance is achieved
without the need for external electron acceptors.
Catabolism: Fermentation and Respiration
Respiration is a form of aerobic or anaerobic
catabolism in which an organic or inorganic
electron donor is oxidized with O2 (in aerobic
respiration) or some other compound (in
anaerobic respiration) functioning as electron
acceptors.
Clycolysis and Fermentation
o The catabolism of glucose is the known as glycolysis.
o A series of reactions in which glucose is oxidized to
pyruvate.
o If glucose is respired, it is first catabolized through
glycolysis before pyruvate is further oxidized to CO2 in the
citric acid cycle.
o If the glucose is fermented, pyruvate is not oxidized
completely to CO2 but instead is used as an electron acceptor
to achieve redox balance in glycolysis.
Clycolysis and Fermentation
o In the series of reactions that are glycolysis, two are redox
reaction.
o During these reactions, free energy is released and conserved
by the simultaneous production of energy-rich compounds.
o ATP is made from these energy-rich compounds by
substrate-level phosphorylation, a process whereby the
energy-rich phosphate bond on the organic compound is
transferred directly to ADP to form ATP.
Clycolysis and Fermentation
The Three Stages of Glycolysis
 Glycolysis
can be divided into three stages, each consisting of one or
more enzymatic reactions.
 Stage I consists of “preparatory” reactions; these are not redox
reactions and do not release energy but instead form a key
intermediate of the pathway.
Clycolysis and Fermentation
The Three Stages of Glycolysis
In Stage II, redox reactions occur, energy is
conserved, and two molecules of pyruvate are
formed.
In Stage III, redox balance is achieved and
fermentation products are formed.
Clycolysis and Fermentation
To begin glycolysis, glucose is phosphorylated to
form glucose 6-phosphate.
The latter is then isomerized to fructose 6-
phosphate, and a second phosphorylation leads to
the production of fructose 1,6-bisphosphate.
These steps consume, rather than produce, ATP.
Clycolysis and Fermentation
o The enzyme aldolase then splits fructose 1,6-
bisphosphate into two 3-carbon molecules,
glyceraldehyde 3-phosphate and its isomer,
dihydroxyacetone phosphate, which is converted into
glyceraldehyde 3-phosphate.
o To this point, all of the reactions, including the
consumption of ATP, have proceeded without any
redox changes.
Clycolysis and Fermentation
o The first redox reaction of glycolysis occurs when
glyceraldehyde 3-phosphate is oxidized to 1,3-
bisphosphoglyceric acid.
o In this reaction (which occurs twice, once for each of the two
glyceraldehyde 3-phosphates), the enzyme glyceraldehyde-3-
phosphate dehydrogenase reduces NAD+ to NADH.
Clycolysis and Fermentation
o Each glyceraldehyde 3-phosphate molecule is
phosphorylated by the addition of inorganic phosphate.
o This reaction, in which inorganic phosphate is converted to
organic form, sets the stage for energy conservation, since
1,3-bisphosphoglyceric acid is an energy-rich compound.
Clycolysis and Fermentation
o ATP is then synthesized by substrate-level phosphorylation
when:
(1) each molecule of 1,3-bisphosphoglyceric acid is converted
to 3-phosphoglyceric acid.
(2) each molecule of phosphoenolpyruvate is converted to
pyruvate.
Clycolysis and Fermentation
o During the first two stages of glycolysis, two ATP molecules
are consumed and four ATP molecules are synthesized.
o The net energy yield in glycolysis is two molecules of ATP
per molecule of glucose fermented.
o The final stage of glycolysis achieves redox balance.
o During the formation of the two 1,3 bisphosphoglyceric acid
molecules, two NAD were reduced to NADH.
+
Clycolysis and Fermentation
o This NADH needs to be oxidized (returned to
NAD+) for the next round of glycolysis.
o In fermentation by yeast, pyruvate is reduced to
ethanol (ethyl alcohol) and carbon dioxide (CO2).
o By contrast, lactic acid bacteria reduce pyruvate
to lactate.
Fermentative Diversity
Glucose is needed for glycolysis, sugars other than
glucose must first be converted to glucose by
isomerase enzymes.
Polysaccharides such as cellulose and starch are also
fermentable by bacteria and produce sugars from them;
if the latter are not glucose, they must first be
converted to glucose before they enter glycolysis.
Fermentative Diversity
o Different types of fermentations are classified
by either the substrate fermented or the products
formed.
o All of the organisms(except for the bacterium
Zymomonas) use the glycolytic pathway to
catabolize glucose.
Fermentative Diversity
 In addition to the two (net) ATP produced in glycolysis,
some of the fermentations allow for additional ATP
synthesis by substrate-level phosphorylation.
 Fermentation product is a fatty acid formed from its
coenzyme-A precursor.
 CoA of fatty acids, such as acetyl-CoA, are energy-rich.
 The formation of a coenzyme-A during a fermentation
increases the yield of ATP.
Fermentative Diversity
 Some endospore-forming species of Clostridium
ferment amino acids while others ferment purines
and pyrimidines.
 Some fermentative anaerobes ferment aromatic
compounds.
Respiration: Citric Acid and Glyoxylate Cycles
o As an alternative to fermentation, glucose can be respired.
o During respiration, glucose is first catabolized through
glycolysis.
o But instead of reducing pyruvate to fermentation products
and discarding them, in respiration, pyruvate is fully
oxidized to CO2 through activities of the citric acid and
glyoxylate cycles, major pathways for respiring organic
compounds.
Respiration of Glucose
 The pathway by which pyruvate is oxidized to CO2 is called
the citric acid cycle (CAC).
 In the CAC, pyruvate is first decarboxylated, leading to the
production of CO2, NADH, and the energy-rich substance
acetyl-CoA.
 The acetyl group of acetyl-CoA then combines with the
four-carbon CAC intermediate oxaloacetate, forming the
six-carbon compound citric acid.
Respiration of Glucose
 A sequence of reactions follows, and two additional CO2
molecules, three more NADH, and one FADH2 are formed
per pyruvate oxidized.
 Oxaloacetate is regenerated as the next acetyl acceptor, thus
completing the cycle.
 For each 2 pyruvate oxidized through the citric acid cycle (2
pyruvate are produced from one glucose), 6 molecules of
CO2, 8 NADH, and 2 FADH2 are produced.
Respiration of Glucose
 FADH2 is a redox prosthetic group that can exist in either
an oxidized (FAD) or a reduced (FADH2) form.
 FADH2 must be reoxidized for the CAC to continue.
 Both NADH and FADH2 are oxidized in redox reactions
that occur in the electron transport chain, a series of
reactions that both consumes electrons (through the
reduction of O2) and produces ATP (through the proton
motive force).
Respiration of Glucose
 The combined activities of the CAC and electron transport chain
result in the complete oxidation of glucose to CO2 along with a
much greater yield of energy than is possible in fermentation.
 Whereas only 2 ATP are produced per glucose fermented in
alcoholic or lactic acid fermentations, a total of 38 ATP can be
made by aerobically respiring the same glucose molecule
toCO2.
 This is because in aerobic respiration, NADH oxidation yields 3
ATP and FADH2 oxidation yields 2 ATP
Biosynthesis and the Citric Acid Cycle
o The cycle is composed of several key organic compounds,
small amounts of which are drawn off during growth to
produce new cell material.
o a-ketoglutarate and oxaloacetate, which are precursors of
several amino acids and succinyl-CoA, needed to form
cytochromes and chlorophyll.
o Any shortage of oxaloacetate is corrected by the addition of
CO2 (carboxylation) to pyruvate or phosphoenolpyruvate.
Biosynthesis and the Citric Acid Cycle
o Oxaloacetate is also an important intermediate because it can
be converted to phosphoenolpyruvate (a precursor of glucose)
if necessary.
o In addition, acetate is important because it provides the raw
material for fatty acid biosynthesis.
o The CAC thus plays two major roles in the cell: glucose
respiration coupled to energy conservation and the
biosynthesis of key metabolites.
The Glyoxylate Cycle
o Two-carbon compounds such as acetate cannot be oxidized
by the citric acid cycle alone.
o This is because the citric acid cycle can continue only if
oxaloacetate is regenerated at each turn of the cycle.
The Glyoxylate Cycle
o If oxaloacetate is drawn off to biosynthesize glucose and
amino acid precursors, when cells are growing on non-glucose
substrates, the cycle would starve for what it needs to continue
functioning.
o Glyoxylate cycle (named because the C2 compound
glyoxylate is a key intermediate) becomes active and functions
to replenish oxaloacetate used for biosyntheses
The Glyoxylate Cycle
o The glyoxylate cycle is composed of several citric acid cycle
enzymatic reactions plus two additional enzymes: isocitrate
lyase, which cleaves isocitrate into succinate and glyoxylate,
and malate synthase, which converts glyoxylate and acetyl-
CoA to malate.
o The succinate formed can be used for biosynthesis while the
glyoxylate combines with acetyl-CoA (C2) to yield malate
(C4).
The Glyoxylate Cycle

o Three-carbon compounds such as pyruvate or compounds

that are converted to pyruvate (for example, lactate or
carbohydrates) also cannot be catabolized through the
citric acid cycle alone.
The Glyoxylate Cycle
o This is because any shortage of C4 CAC intermediates
is compensated by synthesizing oxaloacetate from
pyruvate or phosphoenolpyruvate.
o This occurs by carboxylation reactions catalyzed by the
enzymes pyruvate carboxylase or phosphoenolpyruvate
carboxylase, respectively.
Electron Transport
o Redox reactions occur in the membrane, protons are
separated from electrons across the membrane.
o Two electrons plus two protons enter the electron
transport chain when NADH is oxidized to NAD+
(through activity of the enzyme NADH dehydrogenase)
to begin the process of electron transport.
Electron Transport
o During electron transport, H+ ions are extruded to the
outer surface of the membrane.
o These protons originate from two sources:

(1) NADH
(2) The dissociation of H2O into H+ and OH- in the
cytoplasm.
o The extrusion of H+ to the environment results in the
accumulation of OH- on the inside of the cytoplasmic
membrane.
Electron Transport
o Despite their small size, neither H+ nor OH- can diffuse
through the membrane because they are charged and
highly polar.
o As a result of the separation of H+ and OH-, the inner
and outer surfaces of the membrane differ in charge, pH,
and electrochemical potential, this latter is called the
proton motive force (pmf) and energizes the membrane,
much like a battery
Electron Transport
o The energy of the pmf can also be tapped to support
other forms of work in the cell, such as nutrient
transport, flagellar rotation, and other energy-requiring
reactions.
Generation of the Proton Motive Force:
Complexes I and II
o The proton motive force forms from the activities of flavins,
quinones, the cytochrome bc1 complex, and the terminal
protein, cytochrome oxidase.
o Following the oxidation of NADH + H+ to form FMNH2, 4
H+ are released to the outer surface of the membrane when
FMNH2 donates 2 e- to non-heme iron (Fe/S) proteins that
form Complex I.
Generation of the Proton Motive Force:
Complexes I and II
o The term complex refers to the fact that several proteins are
present that function as a unit (in Escherichia coli, Complex
I contains 14 distinct proteins).
o Complex I is also called NADH: quinone oxidoreductase
because in which NADH is oxidized and quinone is
reduced.
Generation of the Proton Motive Force:
Complexes I and II
o Complex II bypasses Complex I and feeds electrons from
FADH2 directly to quinones.
o Complex II is also called the succinate dehydrogenase
complex because succinate (a product of the citric acid
cycle) as well as fatty acids donate electrons (through
FADH2) when they are oxidized.
Complexes III and IV: bc1 and a-Type Cytochromes

o Reduced ubiquinone (ubiquinol, QH2) passes electrons one

at a time to the cytochrome bc1 complex (Complex III).
o Complex III consists of several proteins that contain two b-
type hemes (bL and bH), one c-type heme (c1), and one
iron–sulfur cluster.
o The major function of the cytochrome bc1 complex is to
transfer e- from quinones to cytochrome c.
Complexes III and IV: bc1 and a-Type Cytochromes

o Complex IV functions as the terminal oxidase and reduces

O2 to H2O in the final step of the electron transport chain.

o ComplexIV also pumps protons to the outer surface of the

membrane.
Anaerobic Respiration
o Under anoxic conditions, electron acceptors other than O2
support respiration in a wide variety of Bacteria and Archaea
in the process called anaerobic respiration.
o Some of the electron acceptors used in anaerobic respiration
include nitrate (NO3-, reduced to nitrite, NO2-),ferric iron
(Fe3+, reduced to Fe2+), sulfate (SO42-, reduced to
hydrogen sulfide, H2S), carbon dioxide (CO2, reduced to
methane, CH4).
Chemolithotrophy and Phototrophy
o Organisms able to use inorganic chemicals as electron
donors are called chemolithotrophs.
o Examples of common inorganic electron donors include
H2S, H2, Fe2+, and NH4+.

o Chemolithotrophic metabolisms are typically aerobic and

begin with the oxidation of the inorganic electron donor and
the electrons entering an electron transport chain.
Chemolithotrophy and Phototrophy
o Chemoorganotrophs and chemolithotrophs differ
significantly in their source of cell carbon.
o Chemoorganotrophs are heterotrophs and thus use organic
compounds (glucose, acetate, and the like) as carbon
sources.
o By contrast, chemolithotrophs use carbon dioxide (CO2) as
a carbon source and are therefore autotrophs.