BIOL 1400 Lec

Unit V: Microbial Metabolism

Arman M. Parayao, Ph D
Lecturer

Metabolic Diversity CHAPTER 2 • A Brief Journ

Energy Sources source of energy. This is

because competition with
sources is not an issue and
Chemicals Light bial habitats on Earth.
Two major forms of pho
one form, called oxygenic
if a microorganism has all the duced. Among microorgan
nutrients it needs and has acteristic of cyanobacteria
photosynthesis, occurs in t
transported them into its cell Chemotrophy Phototrophy
heliobacteria, and does not
anoxygenic phototrophs h
Organic Inorganic nism of ATP synthesis, a r
it must next conserve some of chemicals chemicals
synthesis evolved from th
(glucose, acetate, etc.) (H2, H2S, Fe2+, NH4+, etc.)
the energy released in energy- return to this topic in Chap
Chemoorganotrophs Chemolithotrophs Phototrophs
yielding reactions in order to Heterotrophs and Au
(glucose + O2 CO2 + H2O) (H2 + O2 H2O) (light)
grow. All cells require carbon in
either heterotrophs, which
carbon source, or autotro
ATP ATP ATP as their carbon source. C
Figure 2.18 Metabolic options for conserving energy. The organic heterotrophs. By contrast
and inorganic chemicals listed here are just a few of the chemicals used totrophs are autotrophs.
by one organism or another. Chemotrophic organisms oxidize organic or primary producers because
inorganic chemicals, which yields ATP. Phototrophic organisms use solar from CO2 for both their
energy to form ATP. ganotrophs. The latter eith
producers or live off produ
matter on Earth has been
Chemolithotrophs particular, the phototrophs
Many prokaryotes can tap the energy available from the oxida-
tion of inorganic compounds. This form of metabolism is called Habitats and Extreme
chemolithotrophy and was discovered by the Russian microbiolo- Microorganisms are presen
gist Winogradsky ( Section 1.9). Organisms that carry out port life. These include ha
chemolithotrophic reactions are called chemolithotrophs water, animals, and plants
(Figure 2.18). Chemolithotrophy occurs only in prokaryotes and made by humans. Indeed, s
is widely distributed among species of Bacteria and Archaea. natural sample is extremely
Several inorganic compounds can be oxidized; for example, H2, Some microbial habitats
H2S (hydrogen sulfide), NH3 (ammonia), and Fe21 (ferrous iron). survive, being too hot or to
 Metabolism
Cells coordinate many different
chemical reactions and
organize many different Heat Simple molecules such
released as glucose, amino acids,
m o l e c u l e s i n t o s p e c i fi c glycerol, and fatty acids
structures
ATP
Collectively, these reactions are Catabolic reactions Anabolic reactions
transfer energy from transfer energy from
called metabolism complex molecules ATP to complex
to ATP molecules
to refer to the sum of all chemical ADP+ P i
Metabolic
reactions within a living organism. reactions
Because chemicalare either
reactions
catabolic,
either release or require energy, metabolismwhich means
can be viewed energy
as an
Complex molecules such
energy-balancing act. Accordingly,
releasing,metabolism can be divided
or anabolic, which as starch, proteins, and Heat
into two classes of chemicalmeans
reactions: those requiring
energy that release energy lipids released

In living cells, the enzyme-regulated chemical reactions that Figure 5.1 The role of ATP in coupling anabolic and catabolic
catabolism breaks
the reactions. When complex molecules are split apart (catabolism), some
breakdown of complex organicmolecular
compounds structures
into simplerdown,
ones. of the energy is transferred to and trapped in ATP, and the rest is given
releasing energy reactions.
in the off as heat. When simple molecules are combined to form complex
process (reactions molecules (anabolism), ATP provides the energy for synthesis, and again
some energy is given off as heat.
which use water and in which chemical bonds are broken), and
anabolism uses energy to Q
build larger molecules from
smaller ones

Principles of bioenergetics

Energy is defined as the ability

to do work, and in
m i c r o b i o l o g y, e n e r g y
transformations are measured
in kilojoules (kJ), a unit of heat
energy

All chemical reactions in a cell

are accompanied by changes
in energy, energy being either
required or released as a https://qph.fs.quoracdn.net/main-qimg-ef07bffcfbc3998c0618a1566618f16f-c

reaction proceeds.
Basic bioenergetics

In microbiology we are interested in

free energy (abbreviated G), which
is the energy available to do work

Free energy released during a

reaction can be conserved by cells
in the form of ATP and a handful of
other energy-rich substances.

The change in free energy during a

reaction is expressed as △G 0’ ,
where the symbol△ is read as
“change in.” The “0” and “prime” in
△G0’ indicate that the free-energy
value is for standard conditions: pH
7 (approximate cytoplasmic https://qph.fs.quoracdn.net/main-qimg-ef07bffcfbc3998c0618a1566618f16f-c
conditions), 25°C, 1 atmosphere of
pressure, and all reactants and
products at molar concentrations.

Basic bioenergetics

If the △G0’ for this reaction is

negative in arithmetic sign, then the
reaction will proceed with the
release of free energy; such
reactions are said to be exergonic.

However, if △G0’ is positive, the

reaction requires energy in order to
proceed and such reactions are
endergonic.

Thus, exergonic reactions release

free energy whereas endergonic https://qph.fs.quoracdn.net/main-qimg-ef07bffcfbc3998c0618a1566618f16f-c

reactions require free energy.

 TAblE 3.3 Example of free-energy-change calculations
using Gf values or electrochemical potentials
For the reaction in which acetate is oxidized completely to CO2:a
CH3COO– + H+ + 2 O2 S 2 CO2 + 2 H2O
1. Calculation from Gf values:
¢G09 = [Gf (products) - Gf (reactants)]
= [Gf (2 CO2 + 2 H2O) - Gf (CH3 COO- + H+ + 2 O2)]
= -852 kJ/reaction
2. Calculation from the Nernst equation:b
¢G09 = -nF¢E09
= [-8(96.5)(1.1)]
= -849 kJ/reaction
a
The reaction is balanced and is an 8-electron oxidation (n = 8 in equation 2). Gf0 values were taken
from Table 3.2.
b
F is the Faraday constant (96.5 kj/V) and ¢E09 is calculated from the E09 values in Figure 3.10.

TAblE 3.2 Free energy of formation (Gf0, kJ/mol) for some common substancesa
Sugars Organic and fatty acids Amino acids and alcohols Gases and inorganic compounds
Fructose (-951.4) Acetate (-369.4) Alanine (-371.5) O2, N2, H2, S0, Fe0 (0)
Glucose (-917.2) Benzoate (-245.6) Aspartate (-700.4) CH4 (-50.8)
Lactose (-1515.2) Butyrate (-352.6) n-Butanol (-171.8) CO2 (-394.4); CO (-137.4)
Ribose (-369.4) Caproate (-335.9) Ethanol (-181.7) H2O (-237.2); H+ (-39.8); OH- (-198.7)
Sucrose (-757.3) Citrate (-1168.3) Glutamate (-699.6) N2O (+104.2); NO (+86.6)
Formate (-351.1) Glutamine (-529.7) NO2- (-37.2); NO3- (-111.3)
Fumarate (-604.2) Glycerol (-488.5) NH3 (-26.57); NH4+ (-79.4)
Glyoxylate (-468.6) Mannitol (-942.6) H2S (-27.87); HS- (+12.1)
Ketoglutarate (-797.5) Methanol (-175.4) SO42- (-744.6); S2O32- (-513.4)
Lactate (-517.8) n-Propanol (-175.8) Fe2+ (-78.8); Fe3+ (-4.6); FeS (-100.4)
Malate (-845.1)
Propionate (-361.1)
Pyruvate (-474.6)
Succinate (-690.2)
Valerate (-344.3)
a
Values for free energy of formation taken from Speight, J. 2005. Lange’s Handbook of Chemistry, 16th edition, and Thauer, R.K., K. Jungermann, and H. Decker. 1977. Energy conservation in anaerobic chemotrophic
bacteria. Bacteriol. Rev. 41: 100–180.
Catalysis and Enzymes
Free-energy calculations
reveal only whether
energy is released or
required in a given
Reaction: A + B C+D
reaction;
Activation
they say nothing about the energy—
no enzyme
rate of the reaction

Free energy
Substrates (A + B) Activation
If the rate of a reaction is energy with
enzyme
very slow, it may be of no ∆G0′= Gf0(C + D) –
Gf0(A + B)
value to a cell

For example, consider the

Products (C + D)
formation of water from
O2 and H2 (△G0’ = -237kJ) Progress of the reaction

Figure 3.7 activation energy and catalysis. Even chemical reactions that release
energy may not proceed spontaneously if not activated. Once the reactants are
activated, the reaction proceeds spontaneously. Catalysts such as enzymes lower the
required activation energy.

Catalysis and Enzymes

However, if O and H were
mixed in a sealed bottle, no
measurable amount of
water would form, even
after years. Reaction: A + B C+D

This is because the bonding Activation

of O2 and H2 to form H2O energy—
no enzyme
requires that these two
Free energy

gases become reactive. Substrates (A + B) Activation

energy with
enzyme
This requires that their ∆G0′= Gf0(C + D) –
bonds be broken and Gf0(A + B)
requires a small amount of
energy.
Products (C + D)
Th i s e n e r g y i s c a l l e d
activation energy Progress of the reaction

Figure 3.7 activation energy and catalysis. Even chemical reactions that release
energy may not proceed spontaneously if not activated. Once the reactants are
activated, the reaction proceeds spontaneously. Catalysts such as enzymes lower the
required activation energy.
 114 PART ONE Fundamentals of Microbiology

Reaction Activation Coenzyme

without enzyme energy
without
enzyme
+
Reaction Activation
with enzyme energy
with
enzyme Apoenzyme Cofactor
Reactant
A B (protein portion), (nonprotein portio
inactive activator
Initial energy level
Figure 5.3 Components of a holoenzym
both an apoenzyme (protein portion) and a
to become active. The cofactor can be a me
molecule, it is called a coenzyme (as shown
cofactor together make up the holoenzyme
Final energy level A B substrate is the reactant acted upon by the
Products Q How does the enzyme–substrate com
energy of the reaction?
Figure 5.2 Energy requirements of a chemical reaction. This graph
shows the progress of the reaction AB → A + B both without (blue line)
and with (red line) an enzyme. The presence of an enzyme lowers the dehydrogenase and oxidase enzymes
activation energy of the reaction (see arrows). Thus, more molecules of
names, such as lactate dehydrogenase
reactant AB are converted to products A and B because more molecules
of reactant AB possess the activation energy needed for the reaction. depending on the specific substrates on

Q Why does a chemical reaction require increased activation energy Enzyme Components
without an enzyme as a biological catalyst?
Although some enzymes consist entire
of both a protein portion, called an a
Enzymes are extremely efficient. Under optimum conditions, tein component, called a cofactor. Ion
they can catalyze reactions at rates 108 to 1010 times (up to or calcium are examples of cofactors. I
10 billion times) higher than those of comparable reactions molecule, it is called a coenzyme. Ap
without enzymes. The turnover number (maximum num- themselves; they must be activated b
ber of substrate molecules an enzyme molecule converts to apoenzyme and cofactor form a holo
enzyme (Figure 5.3). If the cofactor is
Catalysis and Enzymes
product each second) is generally between 1 and 10,000 and
will not function.
can be as high as 500,000. For example, the enzyme DNA
polymerase I, which participates in the synthesis of DNA, has Coenzymes may assist the enz
a turnover number of 15, whereas the enzyme lactate dehydro- removed from the substrate or by dona
genase, which removes hydrogen atoms from lactic acid, has a substrate. Some coenzymes act as electr
turnover number of 1000. trons from the substrate and donating
catalyst—aMany substance that Reaction: A + B C+D
enzymes exist in the cell in both active and inactive subsequent reactions. Many coenzyme
facilitates a reaction but is
forms. The rate at which enzymes switch between these two (Table 5.2). Two of the most important
not consumed by it Activation tabolism are nicotinamide adenine d
forms is determined by the cellular energy—
environment.
major catalysts in cells are no enzyme nicotinamide adenine dinucleotide p
Naming Enzymes compounds contain derivatives of the
Free energy

enzymes, which are Substrates (A + B) Activation

proteinsThe(or names
in a few cases, usually end in -ase. All enzymes can be
of enzymes energy with acid), and both function as electron
RNAs) grouped
that are into highly
six classes, according
enzyme is primarily involved in catabolic (e
∆G ′= to
0
Gf the
0 (C + type
D) – of chemical reac- +
specifictionforthey
thecatalyze
reactions G
(Table 5.1). Enzymes
f
0(A + B)
within each of the major NADP is primarily involved in a
they catalyze
classes are named according to the more specific types of reac- reactions. The flavin coenzymes, such
tions they assist. For example, the class called oxidoreductases is (FMN) and flavin adenine dinucleoti
involved with oxidation-reduction reactions (described Products (Cshortly).
+ D) tives of the B vitamin riboflavin and
Enzymes in the oxidoreductase class that remove hydrogen Another important coenzyme, coen
from a substrate are called dehydrogenases; Progress ofthose
the reaction
that add a derivative of pantothenic acid, anot
molecular oxygen (O2)3.7 called oxidases.
areactivation Ascatalysis.
you will zyme plays an important role in the sy
Figure energy and Evensee later,reactions
chemical that release
fatsareand in a series of oxidizing reacti
energy may not proceed spontaneously if not activated. Once the reactants
activated, the reaction proceeds spontaneously. Catalysts such as enzymes lower the
required activation energy.
 Catalysis and Enzymes
In an enzyme-catalyzed reaction:
114 PART ONE Fundamentals of Microbiology
the enzyme combines with
the reactant, called a
s u b s tReaction
r a t e , f o r m iActivation
without enzyme
ng an Coenzyme Substrate
energy
enzyme–substrate complex. without
enzyme
+
Th e n , a s t h e r e a c t i o n
Reaction Activation
with enzyme proceeds, the energy
product is
released andwiththe enzyme is
enzyme Apoenzyme Cofactor Holoenzyme
A B
Reactant returned to its original state, (protein portion), (nonprotein portion), (whole enzyme),
Initial energy level ready to catalyze a new inactive activator active

round of the reaction Figure 5.3 Components of a holoenzyme. Many enzymes require
both an apoenzyme (protein portion) and a cofactor (nonprotein portion)
the portion of the enzyme to to become active. The cofactor can be a metal ion, or if it is an organic
molecule, it is called a coenzyme (as shown here). The apoenzyme and
which substrate binds is the cofactor together make up the holoenzyme, or whole enzyme. The
Final energy level enzyme’s active site;
A B substrate is the reactant acted upon by the enzyme.
Products Q How does the enzyme–substrate complex lower the activation
the entire enzymatic reaction, energy of the reaction?
Figure 5.2 Energy requirements from substrate
of a chemical reaction.binding
This graph to
shows the progress of the reaction AB → A + B both without (blue line)
product release, may take
and with (red line) an enzyme. The presence of an enzyme lowers the dehydrogenase and oxidase enzymes have even more specific
activation energy of the reaction only a few
(see arrows). milliseconds.
Thus, more molecules of
names, such as lactate dehydrogenase and cytochrome oxidase,
reactant AB are converted to products A and B because more molecules
of reactant AB possess the activation energy needed for the reaction. depending on the specific substrates on which they act.

Q Why does a chemical reaction require increased activation energy Enzyme Components
without an enzyme as a biological catalyst?
Although some enzymes consist entirely of proteins, most consist
of both a protein portion, called an apoenzyme, and a nonpro-
Enzymes are extremely efficient. Under optimum conditions, tein component, called a cofactor. Ions of iron, zinc, magnesium,
they can catalyze reactions at rates 108 to 1010 times (up to or calcium are examples of cofactors. If the cofactor is an organic
10 billion times) higher than those of comparable reactions molecule, it is called a coenzyme. Apoenzymes are inactive by
without enzymes. The turnover number (maximum num- themselves; they must be activated by cofactors. Together, the
ber of substrate molecules an enzyme molecule converts to apoenzyme and cofactor form a holoenzyme, or whole, active
product each second) is generally between 1 and 10,000 and enzyme (Figure 5.3). If the cofactor is removed, the apoenzyme
can be as high as 500,000. For example, the enzyme DNA will not function.
polymerase I, which participates in the synthesis of DNA, has Coenzymes may assist the enzyme by accepting atoms
a turnover number of 15, whereas the enzyme lactate dehydro- removed from the substrate or by donating atoms required by the
genase, which removes hydrogen CH2OH atoms from lactic acid, has a
CH2OH substrate. Some coenzymes act as CH
Products electron
2OH carriers, removing
CH2OH elec-
O O Substrate O O
turnover number of 1000. H H H trons from the substrate and donating
H them to other
H molecules in
H O H OH H O
O subsequent reactions. Many Ocoenzymes OH H are derived from OH vitamins
Many enzymes existO in the OH cellH in both
β(1,4 active
OHandH inactive H
H ) H H OH H
forms. The rate at which enzymes switch between these two (Table 5.2). Two of the most important coenzymes in cellular me-
H R H R H R H R
forms is determined by1. the cellular
Substrate is
environment. tabolism are nicotinamide adenine dinucleotide (NAD!) and
Active site
bound to nicotinamide adenine dinucleotide phosphate (NADP!). Both
4. Products
O

enzyme O are released.

Naming Enzymes active site. 2. Enzyme–
substrate
compounds contain derivatives of the B vitamin niacin (nicotinic
The names of enzymes usually end in -ase. All enzymes can be
complex acid), and
O
both function3. Strain is
as electron
placed carriers. Whereas NAD+
forms.
grouped into six classes, according to the type of chemical reac- is primarily involved in catabolic
on bond. (energy-yielding) reactions,
tion they catalyze (Table 5.1). Enzymes within each of the major NADP+ is primarily involved in anabolic (energy-requiring)
classes are named according to the more specific types of reac- reactions. The flavin coenzymes, such as flavin mononucleotide
tions they assist. For example, the class called oxidoreductases is (FMN) and flavin adenine dinucleotide (FAD), contain deriva-
involved with oxidation-reduction reactions (described shortly). tives of the B vitamin riboflavin and are also electron carriers.
Enzymes in the oxidoreductase class that remove hydrogen Another important coenzyme, coenzyme A (CoA), contains
from a substrate are called dehydrogenases; those that add a derivative of pantothenic acid, another B vitamin. This coen-
molecular oxygen (O2) are called oxidases. As you will see later, zyme plays an important role in the synthesis and breakdown of
fats and in a series of oxidizing reactions called the Krebs cycle.
5. Enzyme is ready
to begin new
catalytic cycle.

Figure 3.8 The catalytic cycle of an enzyme. The enzyme depicted here, lysozyme, catalyzes the cleavage of
the b-1,4-glycosidic bond in the polysaccharide backbone of peptidoglycan. Following substrate binding in the
enzyme’s active site, strain is placed on the bond, and this favors breakage. Space-filling model of lysozyme courtesy
of Richard Feldmann.
 Catalysis and Enzymes
Many enzymes contain small
114 nonprotein
PART ONE Fundamentals of Microbiology molecules that
participate in catalysis but are not
themselves substrates.
Reaction Activation Coenzyme Substrate
These smallwithoutmolecules
enzyme can be
energy
without
divided into two classes based enzyme
on
the way they associate with the +
Reactionenzyme: Activation
with enzyme energy
prosthetic groupswith
that bind tightly
enzyme
Reactant Apoenzyme Cofactor Holoenzyme
A B to their enzymes, usually covalently (protein portion), (nonprotein portion), (whole enzyme),
Initial energy level and permanently inactive activator active

Figure 5.3 Components of a holoenzyme. Many enzymes require

By contrast, coenzymes, with a few both an apoenzyme (protein portion) and a cofactor (nonprotein portion)
exceptions, are loosely and often to become active. The cofactor can be a metal ion, or if it is an organic
transiently bound to enzymes; t molecule, it is called a coenzyme (as shown here). The apoenzyme and
cofactor together make up the holoenzyme, or whole enzyme. The
Final energy level A B substrate is the reactant acted upon by the enzyme.
hus, a single coenzyme molecule
Products
may associate with a number of Q How does the enzyme–substrate complex lower the activation
energy of the reaction?
different
Figure 5.2 Energy requirements of aenzymes.
chemical reaction. This graph
shows the progress of the reaction AB → A + B both without (blue line)
Most
and with (red line) an enzyme. coenzymes
The presence are derivatives
of an enzyme lowers the of dehydrogenase and oxidase enzymes have even more specific
activation energy of the reaction (see arrows). Thus, more molecules of
vitamins names, such as lactate dehydrogenase and cytochrome oxidase,
reactant AB are converted to products A and B because more molecules
of reactant AB possess the activation energy needed for the reaction. depending on the specific substrates on which they act.

Q Why does a chemical reaction require increased activation energy Enzyme Components
without an enzyme as a biological catalyst?
Although some enzymes consist entirely of proteins, most consist
of both a protein portion, called an apoenzyme, and a nonpro-
Enzymes are extremely efficient. Under optimum conditions, tein component, called a cofactor. Ions of iron, zinc, magnesium,
they can catalyze reactions at rates 108 to 1010 times (up to or calcium are examples of cofactors. If the cofactor is an organic
10 billion times) higher than those of comparable reactions molecule, it is called a coenzyme. Apoenzymes are inactive by
without enzymes. The turnover number (maximum num- themselves; they must be activated by cofactors. Together, the
ber of substrate molecules an enzyme molecule converts to apoenzyme and cofactor form a holoenzyme, or whole, active
product each second) is generally between 1 and 10,000 and enzyme (Figure 5.3). If the cofactor is removed, the apoenzyme
can be as high as 500,000. For example, the enzyme DNA will not function.
polymerase I, which participates in the synthesis of DNA, has Coenzymes may assist the enzyme by accepting atoms
a turnover number of 15, whereas the enzyme lactate dehydro- removed from the substrate or by donating atoms required by the
genase, which removes hydrogen atoms from lactic acid, has a substrate. Some coenzymes act as electron carriers, removing elec-
turnover number of 1000.
mentals of Microbiology trons from the substrate and donating them to other molecules in
Many enzymes exist in the cell in both active and inactive subsequent reactions. Many coenzymes are derived from vitamins
forms. The rate at which enzymes switch between these two (Table 5.2). Two of the most important coenzymes in cellular me-
forms is determined by the cellular environment.
zyme inhibitors. (a) An uninhibited Normal Binding of Substrate tabolism are nicotinamide
Action of Enzyme dinucleotide (NAD!) and
adenineInhibitors
ormal substrate. (b) A competitive nicotinamide adenine dinucleotide phosphate (NADP!). Both
Naming
type of noncompetitive inhibitor,Enzymes Substrate compounds
Competitivecontain derivatives Altered
of the B vitamin niacin (nicotinic
The names of enzymes usually end in -ase. All enzymes Active
can be
inhibitor
site acid), and both function as electron carriers. Whereas NAD+
active site
inhibition.
grouped into six classes, according to the type of chemical reac- is primarily involved in catabolic (energy-yielding) reactions,
ompetitive inhibitors operate
tion they in (Table 5.1). Enzymes within each of the major
catalyze NADP+ is primarily involved in anabolic (energy-requiring)
n to noncompetitive are named according to the more specific typesEnzyme
classesinhibitors? of reac- reactions. The flavin coenzymes, such as flavin mononucleotide
tions they assist. For example, the class called oxidoreductases is (FMN) and flavin adenine dinucleotide (FAD), contain deriva-
involved with oxidation-reduction reactions (described shortly). tives of the B vitamin riboflavin and are also electron carriers.
Enzymes in the oxidoreductase class that remove hydrogen Another important coenzyme,Non- coenzyme A (CoA), contains
a derivative of pantothenic acid, competitive
another B vitamin. Allosteric
This coen-
from a substrate are called dehydrogenases; those that add
molecular oxygen118(O2) PART ONE
are called Fundamentals
oxidases. of Microbiology
As you will see later,
inhibitor site
zyme plays an important role in the synthesis and breakdown of
(a) (b)and in a series of oxidizing(c)
fats reactions called the Krebs cycle.

Figure 5.7 Enzyme

makeinhibitors. (a)sulfanilamide
their folic acid, An uninhibited Normal
can kill bacteria butBinding
does not of Substrate
ay to control the growth of bacteriaenzyme
is to and its normal
control harm substrate.
human cells.(b) A competitive
Noncompetitive inhibitors do not compete with the sub- Substrate
inhibitor.
s. Certain poisons, such as cyanide, arsenic, (c) One type of noncompetitive inhibitor,
combine with enzymes and prevent causingthem strate
from inhibition.
allosteric for the enzyme’s active site; instead, they interact with Active site
s a result, the cells stop functioning and die. another part of the enzyme (Figure 5.7c ). In this process, called
nhibitors are classified as either competitive Q
How do allosteric (“other
or competitive space”)
inhibitors inhibition,
operate in the inhibitor binds to a site
comparison to noncompetitive inhibitors? binding site, called the
e inhibitors (Figure 5.7). Competitive inhibitors on the enzyme other than the substrate’s Enzyme
site of an enzyme and compete with the normal allosteric site. This binding causes the active site to change its
he active site. A competitive inhibitor can do this shape, making it nonfunctional. As a result, the enzyme’s activ-
ape and chemical structure are similar to those ity is reduced. This effect can be either reversible or irreversible,
substrate (Figure 5.7b). However, unlike the sub- depending on whether the active site can return to its original
shape. In some cases, allosteric interactions can activate an en-
 CHAPTER 5 Microbial Metabolism 119

Substrate and the bacteria stop synthesizing isoleucine. This condition is

maintained until the supply of isoleucine is depleted. This type
of feedback inhibition is also involved in regulating the cells’
Pathway production of other amino acids, as well as vitamins, purines,
Operates
and pyrimidines.

Ribozymes
Prior to 1982, it was believed that only protein molecules had en-
Pathway
zymatic activity. Researchers working on microbes discovered a
Shuts Down unique type of RNA called a ribozyme. Like protein enzymes,
ribozymes function as catalysts, have active sites that bind to sub-
Enzyme 1 strates, and are not used up in a chemical reaction. Ribozymes
specifically act on strands of RNA by removing sections and
splicing together the remaining pieces. In this respect, ribozymes
Allosteric Bound
site end-product are more restricted than protein enzymes in terms of the diversity
Intermediate A of substrates with which they interact.
CHECK YOUR UNDERSTANDING
Enzyme 2 ✓ What is a coenzyme? 5-3

Feedback Inhibition
✓ Why is enzyme specificity important? 5-4
✓ What happens to an enzyme below its optimal temperature?
Above its optimal temperature? 5-5
Intermediate B ✓ Why is feedback inhibition noncompetitive inhibition? 5-6
✓ What is a ribozyme? 5-7

Enzyme 3
Energy Production
LEARNING OBJECTIVES
End-product
5-8 Explain the term oxidation-reduction.
5-9 List and provide examples of three types of phosphorylation
reactions that generate ATP.
5-10 Explain the overall function of metabolic pathways.
Figure 5.8 Feedback inhibition.
Q Explain the differences between competitive inhibition and
Nutrient molecules, like all molecules, have energy associated
with the electrons that form bonds between their atoms. When
feedback inhibition.
it is spread throughout the molecule, this energy is difficult for
the cell to use. Various reactions in catabolic pathways, however,
normally be the substrate for the second enzyme in the path- concentrate the energy into the bonds of ATP, which serves as a
way, the second reaction stops immediately as well. Thus, even convenient energy carrier. ATP is generally referred to as hav-
though only the first enzyme in the pathway is inhibited, the ing “high-energy” bonds. Actually, a better term is probably un-
entire pathway shuts down, and no new end-product is formed. stable bonds. Although the amount of energy in these bonds is
By inhibiting the first enzyme in the pathway, the cell also keeps not exceptionally large, it can be released quickly and easily. In
metabolic intermediates from accumulating. As the cell uses up a sense, ATP is similar to a highly flammable liquid such as ker-
the existing end-product, the first enzyme’s allosteric site more osene. Although a large log might eventually burn to produce
often remains unbound, and the pathway resumes activity. more heat than a cup of kerosene, the kerosene is easier to ignite
The bacterium E. and provides heat more quickly and conveniently. In a similar
ofcoli
Oxidation-Reduction
120 Reactions
PART ONE Fundamentals can be used to demonstrate feed-
Microbiology
back inhibition in the synthesis of the amino acid isoleucine, way, the “high-energy” unstable bonds of ATP provide the cell
which is required for the cell’s growth. In this metabolic path- with readily available energy for anabolic reactions.
way, the amino acid threonine is enzymatically converted to Before discussing the catabolic pathways, we will consider two
isoleucine in five steps. If isoleucine isReduction
added to the growth general aspects of energyenergy
production:from nutrient
the concept molec
of oxidation-
medium for E. coli, it inhibits the first enzyme in the pathway, reduction and the mechanisms of ATP generation.
of which serve as energy so
e– highly reduced compounds
highly oxidized compounds.
dizes a molecule of glucose
A B A oxidized B reduced energy in the glucose molecu
ner and ultimately is trapped
Oxidation as an energy source for en
pounds such as glucose th
Figure 5.9 Oxidation-reduction. An electron is transferred from
are highly reduced compou
molecule A to molecule B. In the process, molecule A is oxidized, and
molecule B is reduced. of potential energy. Thus, g
organisms. Animation Oxid
TM

Q How do oxidation and reduction differ?

Oxidation is the removal of electrons (e−) from an atom or molecule, a reaction that
CHECK YOUR UNDERSTAN
often produces energy.
✓ Why is glucose such an impo
Oxidation-Reduction
Reduction Reactions
occurs when a molecule gains one or more electrons
Oxidation is the removal of electrons (e−) from an atom or mol- The Generation of AT
Oxidationecule, a reaction that often produces energy. Figure 5.9 shows an
and reduction reactions are always coupled; in other words, each time one
Much of the energy released
substanceexample
is oxidized, another isin simultaneously
of an oxidation which moleculereduced.
A loses anTheelectron
pairingtoof these
tions is trapped within the cel
is called oxidation-reduction
reactionsmolecule B. Molecule A has or a redox reaction
undergone oxidation (meaning that cally, an inorganic phosphate g
it has lost one or more electrons), whereas molecule B has under- input of energy to form ATP:
gone reduction (meaning that it has gained one or more elec-
trons).* Oxidation and reduction reactions are always coupled; ADP
in other words, each time one substance is oxidized, another is
simultaneously reduced. The pairing of these reactions is called Adenosine P ~ P

oxidation-reduction or a redox reaction.

Oxidation-Reduction Reactions
Half reaction
donating e– Electron Electron
donor acceptor
H2 2 e– + 2 H+
H2O H2 + –12 O2 H2O
–12 O
2 + 2 e– O 2–
Formation Net reaction
Half reaction of water
accepting e–

Figure 3.9 example of an oxidation–reduction reaction. Oxidations are the

removal of electrons from a substance, while reductions are the addition of electrons to
a substance.

In redox reactions of this type, we refer to the substance oxidized (in this
case, H2) as the electron donor, and the substance reduced (in this case,
O2) as the electron acceptor.

Many different electron donors exist in nature, including a wide variety of

organic and inorganic compounds

Many electron acceptors other than O2 exist as well, including many

nitrogen and sulfur compounds, such as NO3- and SO42-, and many
organic compounds

Energy-rich Compounds

The energy released from redox

reactions fuels energy-requiring cell
functions Compound G0′ kJ/mol

∆G0′ > 30kJ

But the free energy released in the –51.6
Phosphoenolpyruvate
coupled exergonic redox reaction must –52.0
1,3-Bisphosphoglycerate
first be trapped by the cell and
Acetyl phosphate –44.8
conserved
ATP –31.8
ADP –31.8
Energy conservation in cells is
accomplished through the formation of Acetyl-CoA –35.7
a set of compounds containing energy ∆G0′ < 30kJ
rich phosphate or sulfur bonds AMP –14.2
Glucose 6-phosphate –13.8
The biosynthesis of these compounds
functions as the free-energy trap, and
their hydrolysis releases this energy to
drive endergonic reactions
Energy-rich Compounds
NH2
CHO
N N
HCOH Anhydride bonds Ester bond
Ester bond
OHCH N N
O– O– O–
HCOH O
CH2 C COO– –
O P O P O P O CH2
HCOH O– O
Anhydride bond O O O
CH2 O P O– –
O P O–
O O OH OH

Glucose 6-phosphate Phosphoenolpyruvate Adenosine triphosphate (ATP)

Thioester
Anhydride bond
bond
O O O H CH3 O O–
H H
CH3 C~S (CH2)2 N C (CH2)2 N C C C CH2 O R H3C C O P O–
OH CH3 O

Acetyl Coenzyme A Acetyl phosphate

Acetyl-CoA

Figure 3.13 energy-rich bonds in compounds that conserve energy in microbial metabolism. Notice,
by referring to the table, the range in free energy of hydrolysis of the phosphate or sulfur bonds highlighted in the
compounds. The “R” group of acetyl-CoA is a 39-phospho ADP group.

Essentials of Catabolism
FOUNDATION FIGURE 5.11
An Overview of Respiration and Fermentation

respiration fermentation
Glycolysis produces
ATP and reduces NAD+ 1 Glycolysis
to NADH while oxidizing
glucose to pyruvic acid. Glucose
In respiration, the
pyruvic acid is converted
to the first reactant in NADH ATP
the Krebs cycle, acetyl
CoA.
Pyruvic acid

The Krebs cycle In fermentation, the

produces some ATP by pyruvic acid and the
2 electrons carried by
substrate-level phos-
phorylation, reduces the NADH from glycolysis
Pyruvic acid
electron carriers NAD+ Acetyl CoA (or derivative) NADH are incorporated into
and FAD, and gives off fermentation
CO2. Carriers from both end-products.
glycolysis and the Krebs
cycle donate electrons NADH
to the electron transport Krebs
chain.” FADH2 cycle brewer’s yeast
Formation of
fermentation
end-products

NADH &
FADH2
CO2
ATP
In the electron transport
chain, the energy of the
electrons is used to 3 Electrons KEYCONCEPTS
produce a great deal of To produce energy from
ATP by oxidative
glucose, microbes use two general processes:
phosphorylation.
ATP respiration and fermentation. Both usually start with
Electron
glycolysis but follow different subsequent pathways,
transport O2
depending on oxygen availability.
chain and A small version of this overview figure will be
chemiosmosis
included in other figures throughout the chapter to
H2O indicate the relationships of different reactions to the
overall processes of respiration and fermentation.

Because two molecules of ATP were needed to get glycolysis pentose phosphate pathway; another alternative is the Entner-
started and four molecules of ATP are generated by the process, Doudoroff pathway.
there is a net gain of two molecules of ATP for each molecule of
glucose that is oxidized. Animations Glycolysis: Overview, Steps
TM

The Pentose Phosphate Pathway

The pentose phosphate pathway (or hexose monophosphate
Alternatives to Glycolysis shunt) operates simultaneously with glycolysis and provides
Many bacteria have another pathway in addition to glycolysis a means for the breakdown of five-carbon sugars (pentoses)
for the oxidation of glucose. The most common alternative is the as well as glucose (see Figure A.3 in Appendix A for a more

123
acetyl-S-CoA 1 H2O 1 ADP 1 Pi S tats lack O2 or other electron acceptors that can substitute for O2
acetate2 1 HS-CoA 1 ATP 1 H1 in respiration (see Figure 4.22), and in such habitats, fermentation
the energy released in the hydrolysis of coenzyme A is conserved is the only option for energy conservation by chemoorganotrophs.
in the synthesis of ATP. Coenzyme A derivatives (acetyl-CoA is
just one of many) are especially important to the energetics of 4.8 Glycolysis
anaerobic microorganisms, in particular those whose energy In fermentation, ATP is produced by a mechanism called
metabolism depends on fermentation. We return to the impor- substrate-level phosphorylation. In this process, ATP is syn-
tance of coenzyme A derivatives many times in Chapter 14. thesized directly from energy-rich intermediates during steps in
the catabolism of the fermentable substrate (Figure 4.13a). This
Energy Storage Essentials of Catabolism
ATP is a dynamic molecule in the cell; it is continuously being
Intermediates
broken down to drive anabolic reactions and resynthesized at the Energy-rich
in chemoorganothrophs:
expense of catabolic reactions. For longer-term energy storage, Pi intermediates ATP
ADP
microorganisms produce insoluble polymers that can be catabo-
lized later for the production of ATP. A B B~P C ~P D
Fermentation is the form of
Examples of energy storage polymers in prokaryotes include (a) Substrate-level phosphorylation
glycogen, poly-β-hydroxybutyrate anaerobic catabolism in
and other polyhydroxyalka-
which
noates, and elemental sulfur, stored fromantheorganic
oxidationcompound
of H2S by + ++ + + + + + + + + + + + + + + + + +
Energized + – – – – – – – – – – – – – – – – –– +
sulfur chemolithotrophs. Theseispolymers
both anare electron
deposited donor
withinand membrane + –– – +
+ – – – +
the cell as large granules that can
anbe electron
seen with the light or elec-
acceptor, and + –
–
– +
–– – – – – – – – – – – – – – – –
tron microscope ( Section ATP
3.10).isInproduced
eukaryotic by microorga-
substrate- +
++ +
+
nisms, polyglucose in the form of starch and lipids in the form of ++ + + + + + + + + + + + + + + + +
level phosphorylation;
simple fats are the major reserve materials. In the absence of an ADP + Pi
external energy source, a cell can break down these polymers to ATP
make new cell material or to a n d rthe
supply e svery
p i r alow
t i oamount
n i s of the
energy, called maintenance energy,c a t a bneeded
o l i s mto imaintain
n w h i ccellh a + + + + ++ + + + +
integrity when it is in a nongrowing state. +
– – – – – – – – –
compound is oxidized with Less energized – +
membrane + – –
O2 (or an O2 substitute) as + – – – +
MiniQuiz – – – – – – –
the terminal electron + +
• How much energy is released per mole of ATP converted to + + + + + + + + +
a c cPer
ADP 1 Pi under standard conditions? e pmole
t oofr ,AMP con-
usually (b) Oxidative phosphorylation
verted to adenosine and Pi? a c c o m p a n i e d b y AT P
Figure 4.13 Energy conservation in fermentation and respiration.
production
• During periods of nutrient abundance, how can cells byprepare
oxidative
for
(a) In fermentation, substrate-level phosphorylation produces ATP. (b) In respi-
periods of nutrient starvation? phosphorylation ration, the cytoplasmic membrane, energized by the proton motive force, dis-
sipates energy to synthesize ATP from ADP 1 Pi by oxidative phosphorylation.

AP-2 APPENDIX A

H Figure A.2 Glycolysis (Embden-Meyerhof pathway). Each of the

ten steps of glycolysis is catalyzed by a specific enzyme, which is named
C O
under each step number. (See Figure 5.12, p. 124, for a simplified version of
H C OH glycolysis.)
HO C H

H C OH

H C OH

H C OH

H
Glucose (6C)
1 1 Glucose enters the cell and is phosphorylated by the enzyme hexokinase,

Hexokinase
which transfers a phosphate group from ATP to the number 6 carbon of the sugar.
ATP The product of the reaction is glucose 6-phosphate. The electrical charge of the
phosphate group traps the sugar in the cell because of the impermeability of the
ADP plasma membrane to ions. Phosphorylation of glucose also makes the molecule
more chemically reactive. Although glycolysis is supposed to produce ATP, in step
H 1 , ATP is actually consumed—an energy investment that will be repaid with
dividends later in glycolysis.
C O
Appendices

H C OH

HO C H

H C OH

H C OH

H C O P
H
Glucose
6-phosphate (6C)
2 2 Glucose 6-phosphate is rearranged to convert it to its isomer, fructose

Phosphoglucoisomerase
6-phosphate. Isomers have the same number and types of atoms but in different
structural arrangements.
H

H C OH

C O

HO C H

H C OH

H C OH

H C O P
H
Fructose H
6-phosphate (6C) H C O P

3 C O 3 In this step, still another molecule of ATP is invested in

ATP
Phosphofructokinase
glycolysis. An enzyme transfers a phosphate group from
HO C H
ADP
ATP to the sugar, producing fructose 1,6-diphosphate.
H
H Dihydroxyacetone
phosphate (3C) 4 This is the reaction from which glycolysis gets its
H C O P 4 name (“sugar splitting”). An enzyme cleaves fructose
1,6-diphosphate into two different three-carbon sugars:
C O Aldolase glyceraldehyde 3-phosphate and dihydroxyacetone
HO C H 5 phosphate. These two sugars are isomers.
Isomerase
H C OH
5 The enzyme isomerase interconverts the three-carbon
H C OH
sugars. The next enzyme in glycolysis uses only
H C O P H C O glyceraldehyde 3-phosphate as its substrate. This pulls
the equilibrium between the two three-carbon sugars in
H H C OH the direction of glyceraldehyde 3-phosphate, which is
Fructose removed as fast as it forms.
1,6-diphosphate (6C) H C O P
To
H step 6
Glyceraldehyde
3-phosphate (3C)

Glycolysis (Embden–Meyerhof–Parnas pathway)

 APPENDIX A AP3

6 2 NAD+ 6 An enzyme now catalyzes two sequential reactions while it holds

glyceraldehyde 3-phosphate in its active site. First, the sugar is oxidized at the
Triose phosphate 2 NADH + H+ number 1 carbon and NAD+ is reduced, resulting in the formation of NADH + H+.
dehydrogenase
Second, the enzyme couples this reaction to the creation of a high-energy
2 P i phosphate bond at the number 1 carbon of the oxidized substrate. The source of
O the phosphate is inorganic phosphate, which is always present in the cell. As
C O products, the enzyme releases NADH + H+ and 1,3-diphosphoglyceric acid.
P
Notice in the figure that the new phosphate bond is symbolized with a
H C OH high-energy bond (~), which indicates that the bond is at least as energetic as the
phosphate bonds of ATP.
H C O P
H
1,3-diphosphoglyceric
acid (3C)
(2 molecules)
2 ADP 7 At this step, glycolysis produces ATP. The phosphate group, with its
7
Phospho- 2 high-energy bond, is transferred from 1,3-diphosphoglyceric acid to ADP. For
ATP each glucose molecule that began glycolysis, step 7 produces two molecules of
glycerokinase
O ATP, because every product after the sugar-splitting step (step 4 ) is doubled. Of
course, two ATPs were invested to get sugar ready for splitting. The ATP ledger
C OH now stands at zero. By the end of step 7 , glucose has been converted to two
molecules of 3-phosphoglyceric acid.
H C OH

Appendices
H C O P
H
3-phosphoglyceric
acid (3C)
(2 molecules) 8 Next, an enzyme relocates the remaining phosphate group of
8
3-phosphoglyceric acid to form 2-phosphoglyceric acid. This prepares
Phospho- the substrate for the next reaction.
glyceromutase
Glycolysis (Embden–Meyerhof–Parnas pathway)

C OH

H C O P
H C OH
9 An enzyme forms a double bond in the substrate by extracting a water
H molecule from 2-phosphoglyceric acid to form phosphoenolpyruvic acid. This
2-phosphoglyceric
results in the electrons of the substrate being arranged in such a way that the
acid (3C)
remaining phosphate bond becomes very unstable.
100 UNIT 2 • Metabolism
9
and Growth (2 molecules)

H2O
Enolase 10 The last reaction of glycolysis produces another molecule of ATP by

O transferring the phosphate group from phosphoenolpyruvic acid to ADP. Because

this step occurs twice for each glucose molecule, the ATP ledger now shows a

is in contrast to oxidative phosphorylation, C O P

C OH
typical of respira- pathway. In Stage II, redox reactions occur, energy is conserved
net gain of two ATPs. Thus, the glycolysis of one molecule of glucose results in
two molecules of pyruvic acid, two molecules of NADH + H+, and two molecules
of ATP. Each molecule of pyruvic acid can now undergo respiration or
tion, in which ATP is produced at H C the expense of the proton fermentation. in the form of ATP, and two molecules of pyruvate are formed.
motive force (Figure 4.13b).Phosphoenolpyruvic H
acid (PEP) (3C)
The reactions
O of glycolysis are finished at this point. However,
The fermentable substrate in a fermentation (2 molecules)
is both
NAD the+ Helectron
NADH +CoA + COredoxC balance
2 CoA
has not yet been achieved. So, in Stage III, redox
donor and electron acceptor; not 10 all compounds can be fermented, reactions occur
To Krebsonce again and fermentation products are
2 ADP H C H

Pyruvate kinase 2 H cycle

Aerobic
but sugars, especially hexoses such as O
glucose, are excellentconditions
ATP
fer- formed
Acetyl CoA(Figure
(2C) 4.14).
(respiration)
mentable substrates. A common pathway C OH for the catabolism of CO2

glucose is glycolysis, which breaks down C O

glucose into pyruvate. Stage
+ I: Preparatory Reactions
O

100 is also
Glycolysis UNIT 2 • Metabolism
called and Growth
H C H
the Embden–Meyerhof–Parnas pathway In Stage
H C OH
H C OH I glucose is phosphorylated by ATP, yielding glucose
Anaerobic
H conditions H C OH

for its major discoverers. Whether Pyruvic acidglucose

(3C)
(2 molecules)
is fermented or
(fermentation)
6-phosphate;
H C H
OR
H the
C H latter is then isomerized to fructose 6-phosphate.

respired, it travels through this pathway.

is in contrast to oxidative phosphorylation, typical Here we focus on
of respira-
NADH + H NAD
the+ +
A second
pathway.
H
EthanolIn
phosphorylation
(2C)Stage
H
II, redox reactions
Lactic
leadsoccur,
to the production
energy of fructose
is conserved
reactions
100 of glycolysis
tion, in which
UNITATP2 •and
is the reactions
produced
Metabolism at
and the that followofunder
expense
Growth anoxic
the proton in1,6-bisphosphate.
theandform
CO (1C)
of acid
2
ATP,(3C)
Thetwo
and enzyme aldolase
molecules then splits
of pyruvate fructose 1,6-
are formed.
conditions.
motive force (Figure 4.13b). bisphosphate
The into twoare3-carbon
reactions of glycolysis finished at molecules, glyceraldehyde
this point. However,
The fermentable
Glycolysis substrateinto
can be divided in a fermentation
three stages,is each both the electron a
involving redox balance has
3-phosphate and notitsyet been achieved.
isomer, So, in Stagephosphate,
dihydroxyacetone III, redox which
is in contrast
donor to oxidative
and electron acceptor; phosphorylation,
not all compounds typical
can of respira-
be fermented, pathway.occur
reactions In Stageonce II, again
redox and
reactions occur, energy
fermentation is conserved
products are
series
100 of enzymatic
tion, in which
UNIT 2ATP•reactions.
is produced
Metabolism Stage andatIGrowth
comprises
the expense “preparatory”
of the proton can be form
in the convertedof ATP,into andglyceraldehyde
two molecules3-phosphate.
of pyruvate are To formed.
this point,
but
reactions;sugars,
these especially
are hexoses
not redox such as glucose, are
reactions and do not release energy excellent fer- formed
all of (Figure
the 4.14).
reactions, including the consumption of ATP, have pro-
motive
mentable force (Figure
substrates. 4.13b).
A common pathway for the catabolism of The reactions of glycolysis are finished at this point. However,
but instead lead to the production of a key intermediate of the ceeded withouthas redox
not reactions.
The fermentable substrate in a fermentation is both the electron
isglucose
in contrast is glycolysis,
to oxidative which breaks down glucose
phosphorylation, typical into of pyruvate.
respira- Stage I:InPreparatory
pathway. Stage II, redoxReactions
redox balance yet been achieved. So, in Stage III, redox
reactions occur, energy is conserved
donor
tion, inand
Glycolysis which electron
is also
ATP acceptor;
called
is produced not all
at compounds
the expense can
the Embden–Meyerhof–Parnas of thebe fermented,
pathway
proton reactions
Inthe
in Stage
form ofoccur
I glucose
ATP, is once
and twoagain
phosphorylated
moleculesand by fermentation
of ATP, are products
yielding
pyruvate glucose are
formed.
but
for
motive
Stage I
sugars,
its major especially
force (Figure 4.13b). hexoses
discoverers. such
Whether as glucose,
glucose is are excellent
fermented fer-
or formed (Figure 4.14).
The reactions of glycolysis areisomerized
6-phosphate; the latter is then finished at to this
fructose 6-phosphate.
point. However,
mentable
respired, itsubstrates.
The fermentable A common
travelssubstrate
through this
in pathway
pathway. for
Here wethefocus
catabolism
on the of redoxA second phosphorylation leads to the production
So, inDStagePofIII, fructose
P aOCH
fermentation is both the electron balance has not yet been achieved. OCH redox
HOCH
Stageoccur I: Preparatory again Reactions
2
glucose
donor
2
reactions ofglycolysis,
andiselectron ATP
glycolysis which
and
acceptor; notbreaks
the 2 down glucose into pyruvate.
reactions that follow
all compounds can beunder anoxic
fermented, 1,6-bisphosphate.
reactions ATP The enzyme
once aldolase
and then splitsproducts
fermentation fructose
C O are
1,6-
Glycolysis
conditions. O is also called the Embden–Meyerhof–Parnas O pathway O In Stage
bisphosphate I glucose
into two is phosphorylated
3-carbonO by
molecules, ATP, yielding
glyceraldehyde glucose
H but sugars, especially
H hexoses H such as glucose,
H are excellent P fer-
OCH2 formed H 2 (Figure
COH 4.14). P OCH2 H 2CO P
H COH 2 NAD+
for its major
H Glycolysis
mentable candiscoverers.
substrates. be A divided
common Whether
into A glucose
Hpathway
three stages,
for the iscatabolism
each fermented
involvingofa or B3-phosphate
6-phosphate; andtheits latter
isomer, is then Cisomerized tophosphate,
dihydroxyacetone fructose 2 6-phosphate.
which
series
respired,
OH
glucose of
isH enzymatic reactions.
it travels through
glycolysis, Stage
this
which breaks OH IH
pathway.
down comprises
Here we
glucose “preparatory”
into focus on the
pyruvate. H Stage
canAHbe I:
secondPreparatory
converted phosphorylation Reactions
into glyceraldehyde
H leadsHO 3-phosphate.
to the production To thisof point,
5 fructose
HO reactions
reactions;is OH
these are not redox reactions and OH
do follow
not release H
energy all Stage
of theOHreactions, including H enzyme
the consumptionOH then of
Glycolysis of glycolysis
also called1 and OH
the the reactions that
Embden–Meyerhof–Parnas 2under anoxic
pathway In 1,6-bisphosphate.
I glucose 3 is Thephosphorylated aldolase
by ATP, 4 ATP,
splitshave
yielding pro- 1,6-
fructose
glucose
but
for instead
Glycolysis
conditions.
its major lead to the
discoverers. production
(Embden–Meyerhof–Parnas
Whether of a key
glucose intermediate
is fermented of the
pathway)
or ceeded
6-phosphate; without
bisphosphate the redox
into
latter reactions.
is two
then 3-carbon
isomerized tomolecules, glyceraldehyde
fructose 6-phosphate.
HC O
H OH H OH OH OH HO H
Glycolysis can be divided into three stages, each involving a A second
respired,
Glucoseit travels through this pathway. Here we focus on the
3-phosphate and its isomer,
phosphorylation leadsdihydroxyacetone
to the production phosphate,
E of HCfructose
OH
which
series
Stage I ofofenzymatic
reactions glycolysis and reactions. Stage Ithat
the reactions comprises
follow under “preparatory”
anoxic can be converted
1,6-bisphosphate. Theinto glyceraldehyde
enzyme aldolase then 3-phosphate. To this
splits fructose 1,6-point,
6
Stage II H 2 CO P
reactions;
conditions.
HOCH2
these are not redox reactions and do not release energy bisphosphate all of the reactions,
into twoincluding 3-carbon the molecules,
consumption
D of2 ATP, have pro-
glyceraldehyde
P OCH
P OCH2
but instead
2Glycolysis
O– leadbe
can ATP
to divided
the production Oof
into 2three a key intermediate
– stages, each involvingofathe2 3-phosphate
O– ceeded withoutATPand itsredoxisomer, reactions.
dihydroxyacetone
2 O– phosphate,
C O 2 which
O O
series
OH Cof enzymatic H reactions. HStageOH CI comprisesH “preparatory”
P OCH2 OO can C Hbe 2COHconverted into P OCH glyceraldehyde
O
O C H2CO 3-phosphate.
P To this point,
H 10 9 8 2
7 H2COHO 2CNAD O +P
reactions; these are not redox reactionsAand do not release energy B all of the reactions, includingCthe consumption of ATP, have pro-
O C
Stage I
OH H P OOHC H P O CH
H H OH HO C H OH5
C H
but
HO instead leadOH to the production of a key OH intermediate of H the ceeded OHwithout redoxHreactions. OH
CH32 1 OH CH 2 HO CH2 3 P O CH2 4 D PP
OCH 2 2 F
OCH
HOCH P OCH2 2
Pyruvate ATP ATP
H O 2 ATP
OH H I OH
O OH H OH HO HG 2 ATPHC +O2CNADH
O
H I
Stage H H H P OCH2
H2COH O H2CO P P OCH2 + O
Glucose
H H E HC HOH 2COH 2 NAD
HOCH2 P OCH2 A B C D P OCH2 6
11 2 lactate H2CO P
StageOH
II H ATP OH H H H ATP H HO C O 5
StageHO O OH O OH H OH H OH
HIII 2 O– 2HPyruvate 1 H OH 2 O– H 2 P OCH2 2 OO– H2COH 3P OCH2 2 OO– H2CO P
12 13
4
2H2COH 2 NAD+
H H
HO C OH O
H AC OH O B
OH C OH O CC
HO CO H 7 O C HC
O P O
OH H 10 OH H 9 H H 8 2 ethanol
H + 2 HO 2
5
HO Glucose
O C OH OH P O C OH H P O C OH H OH C H OH OH EC H HC OH
1 2 3 4 6
Intermediates F 1, 3-Bisphosphoglycerate Enzymes 7 Phosphoglycerokinase
Stage II CH3 CH2 HO CH2 P O CH2 P OCHH22COF P
H
Pyruvate OH H OH OH OH HO H HC O
A Glucose 6-P – 2 ATP I –
G 3-P-Glycerate H –1 Hexokinase G –2 ATP 8 Phosphoglyceromutase
+ 2 NADH
2 O
Glucose 2 O 2 O 2 O E HC 2 OH
B Fructose 6-P 6
Stage IIO C 10
H 2-P-Glycerate
O C 9 O C 2 Isomerase 82 lactate O C 9 Enolase
7 H2CO O PC O P
11
C Stage
Fructose
O
2III O C
– 1, 6-P 2 Pyruvate I P O C
Phosphoenolpyruvate
2 O – P
2 O O – C 3 Phosphofructokinase 2 OOH– C H 10 OH
Pyruvate C H
kinase
12 13 2
O CCH3
D Dihydroxyacetone-P O C CH2 O HO C CH42 Aldolase PCO CH2 O C P P 2 F
OCH
Pyruvate 10 9 8 2 ethanol +O2 CO 2 G
7 11 Lactate dehydrogenase
O
2 ATP I H 2 ATP
O C
E Glyceraldehyde-3-P P O C P O C 5 Triosephosphate isomeraseOH C H OH C+ 2HNADH
Intermediates Enzymes
12 Pyruvate decarboxylase
7 Phosphoglycerokinase
F 1, 3-Bisphosphoglycerate
CH3 CH2 HO CH2 P O CH2 P OCH2 F
AEnergetics
PyruvateGlucose 6-P 1 6 Hexokinase11 2 lactate
Glyceraldehyde-3-P 13 Alcohol dehydrogenase
2 ATP G 3-P-Glycerate
I H G 2 8ATPPhosphoglyceromutase
+ 2 NADH
StageYeast
III 2 Pyruvate –239 kJ dehydrogenase
B Fructose 6-P Glucose 2 ethanol + 2 Isomerase
H 2-P-Glycerate 12 13 9 Enolase
2 CO2 2 lactate
C Fructose 1, 6-P 11
3 Phosphofructokinase 2 ethanol + 2 CO2 10 Pyruvate kinase
I Phosphoenolpyruvate
StageLactic
III 2 PyruvateGlucose
acid bacteria 2 lactate –196 kJ
D Dihydroxyacetone-P
Intermediates F 1, 3-Bisphosphoglycerate Aldolase 12 13
4 Enzymes 11 Lactate dehydrogenase
7 Phosphoglycerokinase
2 ethanol + 2 CO
E Glyceraldehyde-3-P
A Glucose 6-P G 3-P-Glycerate Hexokinase isomerase 2
5 1Triosephosphate 12 Pyruvate decarboxylase
8 Phosphoglyceromutase
Figure 4.14
IntermediatesEmbden–Meyerhof–Parnas
Energetics
pathway (glycolysis). The sequence
F 1, 3-Bisphosphoglycerate of reactions in the catab-
Enzymes
6 Glyceraldehyde-3-P 7
13 Phosphoglycerokinase
Alcohol dehydrogenase
olism ofBglucose
Fructose 6-P
to pyruvate and then on fermentation products. Pyruvate is the 2end
H to2-P-Glycerate Isomerase
product of glycolysis,
dehydrogenase
9 Enolase
A Glucose Yeast6-P Glucose 2 ethanol +
G 3-P-Glycerate –239 kJ 1 Hexokinase 8 Phosphoglyceromutase
and fermentation
C Fructose products
1, 6-P are made from I it. The blue table at the bottom left lists the
Phosphoenolpyruvate 3 energy yields from the
Phosphofructokinase 10 Pyruvate kinase
2 CO2
B Fructose
fermentation 6-P by yeast or lactic
of glucose acid bacteria.
H 2-P-Glycerate 2 Isomerase 9 Enolase
D Dihydroxyacetone-P 4 Aldolase 11 Lactate dehydrogenase
Lactic
C Fructose 1, 6-P acid bacteria Glucose 2 lactate – 196 kJ 3 Phosphofructokinase
I Phosphoenolpyruvate 10 Pyruvate kinase
E Glyceraldehyde-3-P 5 Triosephosphate isomerase 12 Pyruvate decarboxylase
D Dihydroxyacetone-P 4 Aldolase 11 Lactate dehydrogenase
FigureEnergetics
4.14 Embden–Meyerhof–Parnas pathway (glycolysis). The sequence of 6reactions Glyceraldehyde-3-P
in the catab- 13 Alcohol dehydrogenase
E Glyceraldehyde-3-P
olism of glucose –239Pyruvate 5 end
Triosephosphate
dehydrogenase isomerase 12 Pyruvate decarboxylase
Yeast to pyruvate andGlucose
then on to fermentation
2 ethanol +products. kJ is the product of glycolysis,
and fermentation
Energeticsproducts are made from it. The blue
2 CO 2
table at the bottom left lists 6the Glyceraldehyde-3-P
energy yields from the 13 Alcohol dehydrogenase
fermentation
Yeastof glucose by yeast or lactic acid bacteria. –239 kJ dehydrogenase
Glucose 2 ethanol +
Lactic acid bacteria Glucose 2 lactate –196 kJ
2 CO2
–196 kJ
Figure 4.14 Embden–Meyerhof–Parnas pathway (glycolysis). The sequence of reactions in the catab-
Lactic acid bacteria Glucose 2 lactate

olism of glucose to pyruvate and then on to fermentation products. Pyruvate is the end product of glycolysis,
Figure 4.14 Embden–Meyerhof–Parnas
and fermentation products are made from pathway (glycolysis).
it. The blue table at theThe sequence
bottom of reactions
left lists the energyin yields
the catab-
from the
olism of glucose
fermentation of to pyruvate
glucose by and then
yeast on to fermentation
or lactic acid bacteria.products. Pyruvate is the end product of glycolysis,
and fermentation products are made from it. The blue table at the bottom left lists the energy yields from the
fermentation of glucose by yeast or lactic acid bacteria.
 Fermentative Diversity
TAblE 3.4 Common fermentations and some of the organisms carrying them out
Type Reaction (substrate S products) Organisms
Alcoholic Hexosea S 2 ethanol + 2 CO2 Yeast, Zymomonas
Homolactic Hexose S 2 lactate- + 2 H+ Streptococcus, some Lactobacillus
Heterolactic Hexose S lactate- + ethanol + CO2 + H+ Leuconostoc, some Lactobacillus
Propionic acid 3 Lactate- S 2 propionate- + acetate- + CO2 + H2O Propionibacterium, Clostridium propionicum
Mixed acidb,c Hexose S ethanol + 2,3-butanediol + succinate2- + lactate-+ acetate- Enteric bacteria including Escherichia, Salmonella,
+ formate- + H2 + CO2 Shigella, Klebsiella, Enterobacter
Butyric acidc Hexose S butyrate- + 2 H2 + 2 CO2 + H+ Clostridium butyricum
Butanolc 2 Hexose S butanol + acetone + 5 CO2 + 4 H2 Clostridium acetobutylicum
Caproate/Butyrate 6 Ethanol + 3 acetate- S 3 butyrate- + caproate- + 2 H2 + 4 H2O + H+ Clostridium kluyveri
Acetogenic Fructose S 3 acetate- + 3 H+ Clostridium aceticum
a
Glucose is the starting substrate for glycolysis. However, many other C6 sugars (hexoses) can be fermented following their conversion to glucose. Except for Zymomonas, all organisms catabolize glucose by the
glycolytic pathway.
b
Not all organisms produce all products. In particular, butanediol production is limited to only certain enteric bacteria. The reaction is not balanced.
c
Other products include some acetate and a small amount of ethanol (butanol fermentation only).

Respiration and Electron Carriers CHAPTER 4 • Nutrition, Culture, and Metabolism of Microorganisms 103

O E0′(V)
+
C
Oxidation
CH3O C using
C CH3 O
2 as
CH3 the terminal +
CH3O C C (CH2 CH C CH2)nH
electron acceptor
C is called aerobic 4 H+
+
Com
ple
respiration; O oxidation
2H
using other –0.22 xI
–

Oxidized +
UNIT 2

e– FMN
–

acceptors under anoxic OH

conditions is + Fe/S
NAD+
C –0.32 V
called anaerobic respiration
CH3O C C CH3
NADH + H+
+
–

CH3O C C R
C 2 H+
+
r e s p i r a t i o n c o v e r s OHb oReduced th carbon Q
–

0.0 Complex II
Figure 4.18 Structure of oxidized
transformations and redoxand reduced reactions and
forms of coenzyme + Q
QH2 cycle FADH2 Succinate
Q, a quinone. The five-carbon unit in the side chain (an isoprenoid) –0.22 V
FAD
focuses on oftwo issues:
–
ENVIRONMENT

+ 2e
occurs in a number multiples, typically 6–10. Oxidized quinone requires Fumarate
2 e2 and 2 H1 (2 H) to become fully reduced (dashed red circles). Q Q
–

4 H+ e– e– 2 H+
– –

(1) how electrons are transferred +0.1 + cyt

flavoproteins, quinones accept 2 e2 1 2 H1 but transfer only bH CYTOPLASM
2 e to from the in organic compound to the
2 b L e–
the next carrier the chain; quinones typically participate Fe/S
– –

+ lex III
as linksterminal electron
between iron–sulfur acceptor
proteins and the firstand how
cytochromes Comp
in the electron transport chain. c1
this is coupled to energy
–

+
e– 4 H+ + 1
O2
–

2
MiniQuizconservation, and +0.36 cyt Com
p lex IV
a3 +0.82 V
cyt
• In what major way do quinones differ from other electron carriers c – H2O
a e
in the membrane? e– cyt
+
–

(2) the pathway by which organic

• Which electron carriers described in this section accept
–

2 e2 1 2 H1? Which accept electrons only?

carbon is oxidized into CO2. 2 H+
–

+0.39 +
+
4.10 The Proton Motive Force
The conservation of energy by oxidative phosphorylation is +
linked to an energized state of the membrane (Figure 4.13b). This E0′(V) +
energized state is established by electron transport reactions
between the electron carriers just discussed. To understand how Figure 4.19 Generation of the proton motive force during aerobic
respiration. The orientation of electron carriers in the membrane of
electron transport is linked to ATP synthesis, we must first
Paracoccus denitrificans, a model organism for studies of respiration. The
understand how the electron transport system is oriented in the 1 and – charges at the edges of the membrane represent H1 and OH2,
cytoplasmic membrane. Electron transport carriers are oriented respectively. E 09 values for the major carriers are shown. Note how when
in the membrane in such a way that, as electrons are transported, a hydrogen atom carrier (for example, FMN in Complex I) reduces an
protons are separated from electrons. Two electrons plus two electron-accepting carrier (for example, the Fe/S protein in Complex I),
protons enter the electron transport chain from NADH through protons are extruded to the outer surface of the membrane. Abbrevia-
NADH dehydrogenase to initiate the process. Carriers in the tions: FMN, flavin mononucleotide; FAD, flavin adenine dinucleotide; Q,
quinone; Fe/S, iron–sulfur–protein; cyt a, b, c, cytochromes (bL and bH,
electron transport chain are arranged in the membrane in order
low- and high-potential b-type cytochromes, respectively). At the quinone
of their increasingly positive reduction potential, with the final site, electrons are recycled during the “Q cycle.” This is because elec-
carrier in the chain donating the electrons plus protons to a ter- trons from QH2 can be split in the bc1 complex (Complex III) between the
minal electron acceptor such as O2 (Figure 4.19). Fe/S protein and the b-type cytochromes. Electrons that travel through
Citric Acid Cycle 106 UNIT 2 • Metabolism and Growth

Pyruvate– (three carbons)

NAD+ + CoA

The early biochemical steps in the NADH CO2 C2

respiration of glucose are the same Energetics Balance Sh
Acetyl-CoA C4
as those of glycolysis; all steps C5
(1) Glycolysis: Glucose + 2 NA
from glucose to pyruvate are the CoA C6
same.
Oxalacetate2– Citrate3– (a) Substrate-level phospho
NADH 2 ADP + Pi 2 ATP
However, whereas in fermentation (b) Oxidative phosphorylati
pyruvate is reduced and converted Aconitate3– 2 NADH 6 ATP
NAD+
into products that are excreted, in Malate2–
respiration pyruvate is oxidized to Isocitrate3–
(2) CAC: Pyruvate– + 4 NAD+ +
CO2. NAD(P)+
Fumarate2–
(a) Substrate-level phospho
FADH2 CO2
The pathway by which pyruvate is 1 GDP + Pi 1 GTP (=
completely oxidized to CO2 is FAD Succinate2–
-Ketoglutarate2– NAD(P)H (b) Oxidative phosphorylati
called the citric acid cycle (CAC) 4 NADH 12 ATP
1 FADH2 2 ATP
Succinyl-CoA CoA + NAD+

CoA (3) Sum: Glycolysis plus CAC

GTP GDP + Pi CO2 NADH

(a) (b)

Figure 4.21 The citric acid cycle. (a) The citric acid cycle (CAC) begins when the two-carbon com
acetyl-CoA condenses with the four-carbon compound oxalacetate to form the six-carbon compound
Through a series of oxidations and transformations, this six-carbon compound is ultimately converted
the four-carbon compound oxalacetate, which then begins another cycle with addition of the next mo
of acetyl-CoA. (b) The overall balance sheet of fuel (NADH/FADH2) for the electron transport chain an
generated in the citric acid cycle. NADH and FADH2 feed into electron transport chain Complexes I a
respectively (Figure 4.19).

Biosynthesis and the Citric Acid Cycle 4.12 Catabo

Besides playing a key role in catabolism, the citric acid cycle plays
Thus far in this c
another important role in the cell. The cycle generates several key
Glucose
chemoorganotrop
compounds, small amounts of which can be drawn off for biosyn-
sity, some of the a
thetic purposes
PEP Glycolysis when needed. Particularly important in this
electron donors,
regard are α-ketoglutarate and oxalacetate, which are precursors
flow. Figure 4.22
Pyruvate of several amino acids (Section 4.14), and succinyl-CoA, needed to
NAD+ + CoA generate energy o
CO2 form cytochromes, chlorophyll, and several other tetrapyrrole com-
tion. These includ
pounds
NADH (Figure 4.16). Oxalacetate is also important because it can
CO2 phototrophy.
be +converted
CO2 to phosphoenolpyruvate, a precursor of glucose. In
1. The citric acid cycle (CAC) begins
4. Oxaloacetate can be made Acetyl-CoA addition, acetatewhen
provides the starting material for fatty acid biosyn-
from C3 compounds by CoA
thesis (Section 4.15,
the two-carbon
acetyl-CoA
and condenses
see Figure
compound
with the The citric acid cycle thus
4.27).
Anaerobic Res
the addition of CO2.
four-carbon compound Under anoxic con
Citrateplays two major roles in to
oxaloacetate the cell:
form the bioenergetic and biosynthetic.
synthase can be used to su
Oxaloacetate the same six-carbon
MuchCitrate can be saidcompound
about citrate.
the glycolytic pathway, as certain
NADH processes are calle
intermediates from this pathway are drawn off for various biosyn-
Malate acceptors used in
NAD+ dehydrogenase theticAconitase
needs as well (Section 4.13).
reduced to nitri
Malate Aconitate 2. Through a series of Pseudomonas spe
C2 C5
MiniQuiz oxidations and
transformations, citrate Geobacter species
Aconitase
Fumarase • How many molecules of CO2 and pairs of converted
is ultimately electrons are released H2S, by Desulfov
C3 C6 back to the four-carbon
per pyruvate oxidized in the citric acid cycle?
compound oxaloacetate, methane, CH4, by
Fumarate C4 Redox Isocitrate
step • What two major roles do the citric whichacid cycle
then and glycolysis have
begins even certain orga
NAD(P)+ another cycle with
in common? addition of the next example Fe31, are
FADH2 Succinate Isocitrate
dehydrogenase dehydrogenase molecule of acetyl-CoA.
NAD(P)H
FAD CO2
Succinate c-Ketoglutarate
Succinyl-CoA c-Ketoglutarate
3. Two redox synthetase dehydrogenase
reactions occur CoA + NAD+
but no CO2 is Succinyl-CoA
released from NADH
CoA CO2
succinate to
oxaloacetate.
GTP GDP + Pi
or or
ATP ADP + Pi
 Electrons enter the CYTOPLASM Electrons exit the chain
chain from a primary by reducing the terminal
electron donor. Succinate Fumarate electron acceptor (O2).
–0.22 V
NAD+ NADH + H+
Complex II 1
4 H+ + 2 O2 H2O
–0.32 V
– FAD –
– – +0.82 V –
– 2 H+ 2 H+ – –
– – – –
– – – 2
FADH – – –
Complex I – – – – – Complex IV
cyt a3
FMN e – bH
Complex III
Q –
cyt e e–
e– Q-cycle reactions e–
Q Q bL
Fe/S 2e – cyt a
+ QH2 +
+ +
+ Fe/S c1 e– +
+ + e– cyt + +
4 H+ + c + 2 H+
+ + + + + +
+ + + + +
4 H+
When FMNH2 reduces an Fe/S Free energy released/2e–
protein (an electron-only
∆G0′ = –nF∆E 0 ′ = –2(96.5)(1.14) = –220 kJ
carrier), protons are extruded.
E0′(V) ENVIRONMENT E0′(V)
–0.22 +0.39
0.0 +0.26
+0.1

∆E0′ = 1.14V

Figure 3.22 generation of the proton motive sulfur protein; cyt a, b, c, cytochromes (bL and bH, low- to QH2, thus increasing the number of protons pumped
force during aerobic respiration. The orientation and high-potential b-type cytochromes, respectively). At at the Q-bc1 site. Electrons that travel to the Fe/S protein
of electron carriers in the cytoplasmic membrane of the quinone site, electrons are recycled from Q to bc1 proceed to reduce cytochrome c1, and from there
Paracoccus denitrificans. The + and - charges at the inner from reactions of the “Q cycle.” Electrons from QH2 can cytochrome c. Complex II, the succinate dehydrogenase
and outer membrane surfaces represent H+ and OH-, be split in the bc1 complex between the Fe/S protein and complex, bypasses Complex I and feeds electrons directly
respectively. Abbreviations: FMN, flavin mononucleotide; the b-type cytochromes. Electrons that travel through the into the quinone pool at a more positive E09 than NADH
FAD, flavin adenine dinucleotide; Q, quinone; Fe/S, iron– cytochromes reduce Q (in two, one-electron steps) back (see the redox tower in Figure 3.10).

CHAPTER 5 Microbial Metabolism 127

RESPIRATION FERMENTATION NADH KEY

NAD+
Glycolysis
Glucose
Reduction
NADH ATP FADH2
Pyruvic acid
FAD

Oxidation
Pyruvic acid Flow
Acetyl CoA (or derivative) NADH
FMN of e
lect
Fermentation ron
NADH
Krebs
Q s
NADH2 cycle Formation of
fermentation
end-products Cyt b
NADH
+
NADH ATP
CO2 Cyt c1
2
2 H+
Electrons
Cyt c

ATP
Cyt a
Electron
transport O2 Cyt a3
chain and
chemiosmosis
1
H2O
2 O2

Energy H2O

Figure 5.14 An electron transport chain (system). The inset indicates the relationship of the electron transport chain to
the overall process of respiration. In the mitochondrial electron transport chain shown, the electrons pass along the chain in a
gradual and stepwise fashion, so energy is released in manageable quantities. To learn where ATP is formed, see Figure 5.16.
Q What are the functions of the electron transport chain?

The CO2 produced in the Krebs cycle is ultimately liberated The cytochromes involved in electron transport chains include
into the atmosphere as a gaseous by-product of aerobic respira- cytochrome b (cyt b), cytochrome c1 (cyt c1), cytochrome c (cyt c),
tion. (Humans produce CO2 from the Krebs cycle in most cells cytochrome a (cyt a), and cytochrome a3 (cyt a3). The third class
of the body and discharge it through the lungs during exhala- is known as ubiquinones, or coenzyme Q, symbolized Q; these
tion.) The reduced coenzymes NADH and FADH2 are the most are small nonprotein carriers.
important products of the Krebs cycle because they contain The electron transport chains of bacteria are somewhat di-
most of the energy originally stored in glucose. During the next verse, in that the particular carriers used by a bacterium and the
phase of respiration, a series of reductions indirectly transfers order in which they function may differ from those of other bac-
the energy stored in those coenzymes to ATP. These reactions teria and from those of eukaryotic mitochondrial systems. Even
are collectively called the electron transport chain. Anima- a single bacterium may have several types of electron trans-
TM

tions Krebs Cycle: Overview, Steps port chains. However, keep in mind that all electron transport
chains achieve the same basic goal: to release energy as electrons
The Electron Transport Chain (System) An electron transport are transferred from higher-energy compounds to lower-energy
chain (system) consists of a sequence of carrier molecules that compounds. Much is known about the electron transport chain
 CHAPTER 4 • Nutrition, Culture, and Metabolism of Microorganisms 105

δ Figure 4.20 Structure and function of ATP

α δ synthase (ATPase) in Escherichia coli. (a)
β
Schematic. F1 consists of five different polypeptides
ADP + Pi α forming an α3β3γεδ complex, the stator. F1 is the
α catalytic complex responsible for the interconver-
α
β β F1 F1 sion of ADP 1 Pi and ATP. Fo, the rotor, is integrated
in the membrane and consists of three polypep-

UNIT 2
tides in an ab2c12 complex. As protons enter, the
ATP In In
dissipation of the proton motive force drives ATP
b2 b2 synthesis (3 H1/ATP). ATPase is reversible in that
γ γ
ATP hydrolysis can drive formation of a proton
ε
motive force. (b) Space-filling model. The color-

Siegfried Engelbrecht-Vandré
ε coding corresponds to the art in part a. Since pro-
ton translocation from outside the cell to inside the
cell leads to ATP synthesis by ATPase, it follows
c a that proton translocation from inside to outside in
a
the electron transport chain (Figure 4.19) repre-
sents work done on the system and a source of
Fo
Membrane Fo potential energy.
c12
Out Out

H+ H+ H+

(a) (b)

Reversibility of ATPase Respiration of Glucose

ATPase is reversible. The hydrolysis of ATP supplies torque for γε The early biochemical steps in the respiration of glucose are the
to rotate in the opposite direction from that in ATP synthesis, same as those of glycolysis; all steps from glucose to pyruvate
and this catalyzes the pumping of H1 from the inside to the out- (Figure 4.14) are the same. However, whereas in fermentation
side of the cell through Fo. The net result is generation instead of pyruvate is reduced and converted into products that are
dissipation of the proton motive force. Reversibility of the excreted, in respiration pyruvate is oxidized to CO2. The pathway
ATPase explains why strictly fermentative organisms that lack by which pyruvate is completely oxidized to CO2 is called the
electron transport chains and are unable to carry out oxidative citric acid cycle (CAC), summarized in Figure 4.21.
phosphorylation still contain ATPases. As we have said, many Pyruvate is first decarboxylated, leading to the production of
important reactions in the cell, such as motility and transport, CO2, NADH, and the energy-rich substance acetyl-CoA (Figure
require energy from the pmf rather than from ATP. Thus, 4.12). The acetyl group of acetyl-CoA then combines with the
ATPase in organisms incapable of respiration, such as the strictly four-carbon compound oxalacetate, forming the six-carbon com-
fermentative lactic acid bacteria, for example, functions unidirec- pound citric acid. A series of reactions follow, and two additional
tionally to generate the pmf necessary to drive these important CO2 molecules, three more NADH, and one FADH are formed.
cell functions. Ultimately, oxalacetate is regenerated to return as an acetyl
acceptor, thus completing the cycle (Figure 4.21).
130 PART ONE Fundamentals of Microbiology
MiniQuiz
• How do electron transport reactions generate the proton motive CO2 Release and Fuel for Electron Transport
force? The oxidation of pyruvate to CO2 requires the concerted activity
TABLE 5.3 ATP Yield during Prokaryotic Aerobic Respiration of OneofGlucose
• What is the ratio of H1 extruded per NADH oxidized through the
Molecule
the citric acid cycle and the electron transport chain. For each
pyruvate molecule oxidized through the citric acid cycle, three
Sourceelectron transport chain of Paracoccus shown in Figure 4.19? ATP Yield (Method)
At which sites in the chain is the proton motive force being CO2 molecules are released (Figure 4.21). Electrons released dur-
Glycolysis
established? ing the oxidation of intermediates in the citric acid cycle are
1. Oxidation
• What of glucoseintothe
structure pyruvic acid
cell converts the proton motive force to
Glycolysis transferred
2 ATP (substrate-level NAD1 to form NADH, or to FAD to form FADH2.
to phosphorylation)
ATP? How does it function? ATP This is where respiration and fermentation differ in aATP major way.
2. Production of 2 NADH 6 ATP (oxidative
Instead ofphosphorylation
being used in in
the reduction of pyruvate as in fermenta-
electron transport chain)
tion (Figure 4.14), in respiration, electrons
Electron from NADH and
transport chain
4.11 The Citric Acid Cycle
Preparatory Step FADH2 are fuel for the electron transportand
ing in thephosphorylation
reduction of in
chain, ultimately result-
chemiosmosis
an electron acceptor (O2) to H2O. This
1. Formation
Now thatof acetyl
we haveCoAa produces
grasp of how ATP is madeKrebs
in respiration,
cycle we 6 ATP (oxidative
2 NADH allows for
electron the complete
transport chain) oxidation of glucose to CO2 along with a
need to consider the important reactions in carbon metabolism much greater yield of energy. Whereas only 2 ATP are produced
Krebsassociated
Cycle with formation of ATP. Our focus here is on the citric per glucose fermented in alcoholic or lactic acid fermentations
acid cycle,
1. Oxidation also CoA
of succinyl called
to the Krebs cycle, a key pathway in 2 GTP (Figure
(equivalent of ATP;
4.14), substrate-level
a total of 38 ATPphosphorylation)
can be made by aerobically respir-
virtually
succinic acidall cells. ing the same glucose molecule to CO 1 H O (Figure 4.21b). 2 2
ATP
2. Production of 6 NADH 18 ATP (oxidative phosphorylation in electron transport chain)

3. Production of 2 FADH 4 ATP (oxidative phosphorylation in electron transport chain)

Total: 38 ATP

ENERGETICS BALANCE SHEET FOR AEROBIC RESPIRATION

are added to those generated by oxidation in glycolysis and the bacteria using nitrate and sulfate as final acceptors is essen-
Krebs cycle. In
(1) Glycolysis: aerobic
Glucose + 2 respiration
NAD+ among prokaryotes, a total tial for the nitrogen and sulfur+cycles
2 Pyruvate 2 ATP +that occur in nature.
2 NADH
of 38 molecules of ATP can be
(a) Substrate-level generated from
phosphorylation one+molecule
2 ADP Pi 2 ATPof The amount of ATP generated in anaerobic respiration var-
8 ATP to CAC to Complex I
glucose. Note that four of those ATPs come from substrate-level ies with the organism and the pathway. Because only part
(b) Oxidative phosphorylation 2 NADH 6 ATP
phosphorylation in glycolysis and the Krebs cycle. Table 5.3 pro- of the Krebs cycle operates under anaerobic conditions, and
vides a detailed accounting of the ATP yield during prokaryotic
(2) CAC: 2 Pyruvate + 8 NAD+ + 2 GDP + 2 FAD
because not all the carriers in the electron transport chain
6 CO2 + 8 NADH + 2 FADH2 + 2 GTP
aerobic respiration. participate in anaerobic respiration, the ATP yield (ATP) is never as
(a) Substrate-level phosphorylation 2 GDP + Pi 2 GTP
Aerobic respiration among eukaryotes produces (ADP) a total(ATP)
of high as in aerobic respiration. Accordingly,
to Complex I to Complexanaerobes
II tend
30 ATP (See Figure 3.22)
only 36 molecules of ATP. There are fewer ATPs than 24
inATP
pro- to grow more slowly than aerobes. Animations Electron
TM

(b) Oxidative phosphorylation 8 NADH

karyotes because some energy is lost when electrons 2 FADH2are shuttled
4 ATP Transport Chain: Overview, The Process, Factors Affecting ATP Yield
across the mitochondrial
(3) Glycolysis membranes that separate
plus CAC: Glucose 6 CO2 glycolysis
+ 6 H2O (in 38 ATP
CHECK YOUR UNDERSTANDING
the cytoplasm) from the electron transport chain. No such sepa-
ration exists in prokaryotes. We can now summarize the overall ✓ What are the principal products of the Krebs cycle? 5-13
reaction for aerobic respiration in prokaryotes as follows: ✓ How do carrier molecules function in the electron transport
chain? 5-14
C 6H12O 6 + 6 O 2 + 38 ADP + 38 P i smallest size, ✓ Compare the energy yield (ATP) of aerobic and anaerobic
for in text.
Glucose Oxygen 6 CO 2 + 6 H2O + 38 ATP respiration. 5-15
Carbon Water
dioxide
Fermentation
A summary of the various stages of aerobic respiration in pro- After glucose has been broken down into pyruvic acid, the
karyotes is presented in Figure 5.17. pyruvic acid can be completely broken down in respiration, as
previously described, or it can be converted to an organic product
Anaerobic Respiration in fermentation, whereupon NAD+ and NADP+ are regenerated
Catabolic Diversity CHAPTER 4 • Nutrition, Culture, and Metabolism of Microorganisms 107

Fermentation
Organic compound
Carbon flow Figure 4.22 Catabolic diversity.
CO2 (a) Chemoorganotrophs. (b) Chemolithotrophs.
Carbon flow in
respirations Electron transport/ ATP (c) Phototrophs. Chemoorganotrophs differ
Biosynthesis
generation of pmf NAD(P)H from chemolithotrophs in two important ways:
(1) The nature of the electron donor (organic
O2 Aerobic respiration versus inorganic compounds, respectively),
Electron S0 NO3– SO42– Organic e–
and (2) The nature of the source of cellular

UNIT 2
acceptors acceptors
carbon (organic compounds versus CO2
Anaerobic respiration respectively). However, note the importance of
Chemotrophs

(a) Chemoorganotrophy electron transport driving proton motive force

formation in all forms of respiration and in
photosynthesis.
H2, H2S, Fe2+, NH4+ CO2

Electron transport/ ATP

Biosynthesis
generation of pmf NAD(P)H

Electron S0 SO42– NO3– O2 Aerobic respiration

acceptors
Anaerobic respiration
(b) Chemolithotrophy

Light
Photoheterotrophy Photoautotrophy

Organic e– CO2
compound donor
Electron
Phototrophs

H2O
transport
H2S

Generation of pmf
and reducing power
Biosynthesis Biosynthesis

ATP NAD(P)H
(c) Phototrophy

minerals, such as metal oxides. These common minerals, widely exactly the same way as for chemoorganotrophs (Figure 4.19).
distributed in nature, allow for anaerobic respiration in a wide However, one important distinction between chemolithotrophs
variety of microbial habitats. and chemoorganotrophs, besides their electron donors, is their
Because of the positions of these alternative electron acceptors source of carbon for biosynthesis. Chemoorganotrophs use
on the redox tower (none has an E09 as positive as the O2/H2O organic compounds (glucose, acetate, and the like) as carbon
couple; Figure 4.9), less energy is released when they are reduced sources. By contrast, chemolithotrophs use carbon dioxide
instead of oxygen (recall that DG 09 is proportional to D E0 9 ; (CO2) as a carbon source and are therefore autotrophs (organ-
Section 4.6). Nevertheless, because O2 is often limiting or absent isms capable of biosynthesizing all cell material from CO2 as
in many microbial habitats, anaerobic respirations can be very the sole carbon source). We consider many examples of
important means of energy generation. As in aerobic respiration, chemolithotrophy in Chapter 13.
anaerobic respirations involve electron transport, generation of a
proton motive force, and the activity of ATPase. Phototrophy
Many microorganisms are phototrophs, using light as an energy
Chemolithotrophy source in the process of photosynthesis. The mechanisms by
Organisms able to use inorganic chemicals as electron donors are which light is used as an energy source are complex, but the end
called chemolithotrophs. Examples of relevant inorganic elec- result is the same as in respiration: generation of a proton motive
tron donors include H2S, hydrogen gas (H2), Fe21, and NH3. force that is used to drive ATP synthesis. Light-mediated ATP
synthesis is called photophosphorylation. Most phototrophs
Metabolic Diversity
Chemolithotrophic metabolism is typically aerobic and
begins with the oxidation of the inorganic electron donor use energy conserved in ATP for the assimilation of CO2 as the
(Figure 4.22). Electrons from the inorganic donor enter an elec- carbon source for biosynthesis; they are called photoautotrophs.
tron transport chain and a proton motive force is formed in However, some phototrophs use organic compounds as carbon
Phototrophy CHAPTER 2 • A Brief Jou

Energy Sources source of energy. This

because competition wit
phototrophy—the use of light sources is not an issue an
energy—is widespread in the Chemicals Light bial habitats on Earth.
microbial world. Two major forms of ph
one form, called oxygeni
duced. Among microorga
photosynthesis - the most acteristic of cyanobacteri
important biological process on photosynthesis, occurs in
Chemotrophy Phototrophy
Earth heliobacteria, and does no
anoxygenic phototrophs
Organic Inorganic nism of ATP synthesis, a
chemicals chemicals
the conversion of light energy to CHAPTER 2+ synthesis
44+, •etc.)Nutrition, Culture, and evolved from
Metabolism of
(glucose, acetate, etc.) (H2, H2S, Fe , NH
chemical energy return to this topic in Cha
Chemoorganotrophs Chemolithotrophs Phototrophs
Heterotrophs and A
O r g aFermentation
nisms that carry out (glucose + O2
Organic compound
CO2 + H2O) Carbon
(H2 + Oflow
2 H2O) (light)
Figure
All cells require 4.22in
carbon
p h o tCO
o s y2 n t h e s i s a r e c a l l e d either heterotrophs,
(a) Chemoorga whi
Carbon flow in
phototrophs. respirations Electron transport/ ATP carbon source,
(c) or autotr
Phototroph
ATP ATP ATP Biosynthesisas their carbon source.
generation of pmf NAD(P)H from chemolith
Figure 2.18 Metabolic options for conserving energy. The organic heterotrophs. By contra
Photosynthetic organisms are and inorganic chemicals listed here are just a few of the chemicals used totrophs (1)areThe nature
autotroph
also autotrophs, capable of0 by one O 2 Aerobic respiration versus inorgan
Electron – organism2– or Organic
another. Chemotrophic
e– organisms oxidize organic or primary producers becau
S NO SO
growing with COacceptors
2 as the sole
3
inorganic 4
chemicals, which yields ATP. Phototrophic organisms use solar
acceptors from COand 2 for(2) Thethe
both na
energy to form ATP.
carbon source. carbon
ganotrophs. (organ
The latter eit
Anaerobic respiration producers or live off prod
respectively). H
Chemotrophs

(a) Chemoorganotrophy matter on Earth has

electron been
transp
Chemolithotrophs particular, the phototroph
Many prokaryotes can tap the energy available from the oxida- formation in al
tion of inorganic compounds. This form of metabolism is called Habitats and Extrem
photosynthesi
H2chemolithotrophy
, H2S, Fe2+, NHand 4
+ was discovered by the Russian microbiolo-
CO2 Microorganisms are pres
gist Winogradsky ( Section 1.9). Organisms that carry out port life. These include
transport/ reactions are calledATP
chemolithotrophic
Electron chemolithotrophs water, animals, and plan
(Figure 2.18).ofChemolithotrophy occurs only in prokaryotes Biosynthesis
and
generation pmf NAD(P)H made by humans. Indeed
is widely distributed among species of Bacteria and Archaea. natural sample is extreme
Several inorganic compounds can be oxidized; for example, H2, Some microbial habita
21
Electron H S (hydrogen sulfide), NH3 (ammonia), and Fe (ferrous iron). survive, being too hot or t
S0 2SO42– NO3– O2 Aerobic respiration
acceptors Typically, a related group of chemolithotrophs specializes in the salty. Although such envi
oxidation of a related group of inorganic compounds, and thus
Phototrophy Anaerobic
we haverespiration
the “sulfur” bacteria, the “iron” bacteria, and so on.
life forms, they are often
nisms inhabiting such
(b) Chemolithotrophy The capacity to conserve energy from the oxidation of inor- extremophiles, a remark
ganic chemicals is a good metabolic strategy because competi- lectively define the physio
tion from chemoorganotrophs, organisms that require organic Extremophiles abound
Light
energy sources, is not an issue. In addition, many of the inorganic canic hot springs; on or i
Photoheterotrophy compounds oxidized by chemolithotrophs, Photoautotrophy
for example H2 and polar seas; in extremely s
H2S, are actually the waste –
products of chemoorganotrophs. having a pH as low as 0
Organic e
Thus, chemolithotrophs have evolved strategies CO2 for exploiting where hydrostatic pressu
compound resources that donor
chemoorganotrophs are unable to use, so it is
Electron Interestingly, these proka
Phototrophs

common for H O
species of these two physiological groups to live in
2
transport ular environmental extre
close association with one another. grow. That is why they ar
H2S
means “loving”). Table 2.1
Phototrophs ers” among extremophile
Generation of pmf
Phototrophic microorganisms contain pigments that allow
and reducing power each class and the types o
them to convert light energy into chemical energy, and thus revisit many of these org
Biosynthesis their cells appear colored (Figure 2.2). Unlike chemotrophic
Biosynthesis the special properties th
organisms, then, phototrophs do not require chemicals as a environments.

ATP NAD(P)H
(c) Phototrophy

Energy from light is used in the reduction of CO2 to organic compounds

minerals, such as metal oxides. These common minerals, widely
(photoautotrophy). exactly the same way as for chemo
distributed in nature, allow for anaerobic respiration in a wide However, one important distinction
variety
Some of microbial can
phototrophs habitats. and
also use organic carbon as their carbon source; this chemoorganotrophs,
lifestyle is besides th
called
Becausephotoheterotrophy.
of the positions of these alternative electron acceptors source of carbon for biosynthesis
on the redox tower (none has an E09 as positive as the O2/H2O organic compounds (glucose, aceta
couple; Figure 4.9), less energy is released when they are reduced sources. By contrast, chemolithot
0
instead of oxygen (recall that DG 9 is proportional to D E0 9 ; (CO2) as a carbon source and are th
Section 4.6). Nevertheless, because O2 is often limiting or absent isms capable of biosynthesizing all
in many microbial habitats, anaerobic respirations can be very the sole carbon source). We co
important means of energy generation. As in aerobic respiration, chemolithotrophy in Chapter 13.
anaerobic respirations involve electron transport, generation of a
proton motive force, and the activity of ATPase. Phototrophy
 H2, H2S, Fe , NH4 CO2

Electron transport/ ATP

Biosynthesis
generation of pmf NAD(P)H

Electron S0 SO42– NO3– O2 Aerobic respiration

acceptors
Phototrophy Anaerobic respiration
(b) Chemolithotrophy

Light
Photoheterotrophy Photoautotrophy

Organic e– CO2
compound donor
Electron
Phototrophs

H2O
transport
H2S

Generation of pmf
and reducing power
Biosynthesis Biosynthesis

ATP NAD(P)H
(c) Phototrophy

Photoautotrophy is comprised of two distinct sets of reactions that operate in parallel:

minerals, such as metal oxides. These common minerals, widely exactly the same way as for chemo
(1) light reactions that produce ATP and
distributed in nature, allow for anaerobic respiration in a wide However, one important distinction
variety of microbial habitats. and chemoorganotrophs, besides th
(2) light-independent dark reactions that reduce CO2 to cell material for autotrophic
Because of the positions of these alternative electron acceptors source of carbon for biosynthesis
growth
on the redox tower (none has an E09 as positive as the O2/H2O organic compounds (glucose, aceta
couple; Figure 4.9), less energy is released when they are reduced sources. By contrast, chemolithot
instead of oxygen (recall that DG 09 is proportional to D E0 9 ; (CO2) as a carbon source and are th
Section 4.6). Nevertheless, because O2 is often limiting or absent isms capable of biosynthesizing all
in many microbial habitats, anaerobic respirations can be very the sole carbon source). We co
important means of energy generation. As in aerobic respiration, chemolithotrophy in Chapter 13.
anaerobic respirations involve electron transport, generation of a
proton motive force, and the activity of ATPase. Phototrophy
Many microorganisms are phototrop
Chemolithotrophy source in the process of photosynt
Organisms able to use inorganic chemicals as electron donors are which light is used as an energy sour
called chemolithotrophs. Examples of relevant inorganic elec- result is the same as in respiration: ge
tron donors include H2S, hydrogen gas (H2), Fe21, and NH3. force that is used to drive ATP syn
Chemolithotrophic metabolism is typically
Prokaryotic phototrophs
aerobic and synthesis is called photophosphor
begins with the oxidation of the inorganic electron donor use energy conserved in ATP for the
Purple and green sulfur bacteria Cyanobacteria
(Figure 4.22). Electrons from the inorganic donor enter an elec- carbon source for biosynthesis; they
tron transport chain and a proton motive force is formedOxygenic
Anoxygenic in However, some phototrophs use org
Reducing power Carbon Energy Reducing power Carbon Energy
H2S ele CO2 H2O CO2
ctr ADP ele ADP
ons ctr
ons

electrons Light Light

S0

SO42– (CH2O)n ATP 1

–O (CH2O)n ATP
2 2

(a) (b)

Figure 14.1 Patterns of photosynthesis. Energy and reducing power synthesis in (a) anoxygenic and
(b) oxygenic phototrophs. Note that oxygenic phototrophs produce O2, while anoxygenic phototrophs do not.
Insets: Left, light photomicrographs of cells of a purple sulfur bacterium (Chromatium, cells 5 μm in diameter) and
a green sulfur bacterium (Chlorobium, cells 0.9 μm in diameter). Note the sulfur globules inside or outside the cells
produced from the oxidation of H2S. Right, interference-contrast photomicrograph of cells of a coccoid-shaped
cyanobacterium.
Chlorophyll and Bacteriochlorophyll

CH2 CH3
0.9
Chl a
CH H CH3 O C H H3C H 360 870
0.8 Bchl a
H
H3C C2H5 H3C 805
C2H5 0.7 430
N N N N 480 680
0.6

Absorbance
H Mg H H Mg H 475
N N 0.5 525
N N
H3C H3C
CH3 CH3 0.4 590
H H
H2C H H2C H 0.3
CH H O H O 0.2
2 CH2
COOCH3 COOCH3
Cyclopentanone Cyclopentanone 0.1
COOC20H39 ring COOC20H39 ring
Phytol Phytol 0
340 400 500 600 700 800 900
Chlorophyll a Bacteriochlorophyll a Wavelength (nm)
(a) (b)

Figure 14.2 structures and spectra of chlorophyll a and bacteriochlorophyll a. (a) The two molecules are
identical except for those portions contrasted in yellow and green. (b) Absorption spectrum (green curve) of cells of
the green alga Chlamydomonas. The peaks at 680 and 430 nm are due to chlorophyll a, and the peak at 480 nm is
due to carotenoids. Absorption spectrum (red curve) of cells of the phototrophic purple bacterium Rhodopseudomonas
palustris. Peaks at 870, 805, 590, and 360 nm are due to bacteriochlorophyll a, and peaks at 525 and 475 nm are
due to carotenoids.

Bacteriochlorophyll
Pigment/Absorption R R2 R3 R4 R5 R6 R7
1
maxima (in vivo)

Bchl a —C—CH3 —CH3 a —CH2—CH3 —C—O— CH3 P/Gg b —H R2

—CH3 R1
(purple bacteria)/ 3
805, 830–890 nm O O H3C 4 R3
N N
Bchl b —C—CH3 —CH3 c C—CH3 —CH3 —C—O— CH3 P —H R7 Mg
(purple bacteria)/ N N
835–850, 1020–1040 O H O
H3C R4
nm
HH
Bchl c H —C2H5 CH2
(green sulfur O
—C—CH3 —CH3 —C3H7d —C2H5 —H F —CH3 CH2 H R 5
bacteria)/745–755
nm OH —C4H9 —CH3 C O
O
Bchl cs H
R6
(green nonsulfur
—C—CH3 —CH3 —C2H5 —CH3 —H S —CH3
bacteria)/740 nm
OH

aNo double bond between C and

Bchl d H —C2H5 3
C4; additional H atoms are in
(green sulfur
—C—CH3 —CH3 —C3H7 —C2H5 —H F —H positions C3 and C4.
bacteria)/705–740
nm OH —C4H9 —CH3 bP, Phytyl ester (C H O—); F,
20 39
farnesyl ester (C15H25O—); Gg,
H —C2H5 geranylgeraniol ester (C10H17O—);
Bchl e
S, stearyl alcohol (C18H37O—).
(green sulfur
—C—CH3 —C—H —C3H7 —C2H5 —H F —CH3 cNo double bond between C and
bacteria)/719–726 3
nm OH O —C4H9 C4; an additional H atom is in
position C3 .
Bchl g H dBacteriochlorophylls c, d, and e

(heliobacteria)/ consist of isomeric mixtures with

—C CH2 —CH3 a —C2H5 —CH3 —C—O—CH3 F —H
670, 788 nm the different substituents on R3
O as shown.

Figure 14.3 structure of all known bacteriochlorophylls (bchl). The different substituents present in the positions R1
to R7 in the structure at the right are listed. Absorption properties can be determined by suspending intact cells of a phototroph
in a viscous liquid such as 60% sucrose (this reduces light scattering and smooths out spectra) and running absorption spectra
as shown in Figure 14.2b. In vivo absorption maxima are the physiologically relevant absorption peaks. The spectrum of
bacteriochlorophylls extracted from cells and dissolved in organic solvents is often quite different.
Reaction Centers and Antenna Pigments
LHΙΙ

LHΙΙ
LHΙ LHΙ
LHΙΙ LHΙ
LHΙ
LHΙ
LHΙ
LHΙ
LHΙ LHΙΙ Reaction
RC LHΙ
LHΙΙ LHΙ center
LHΙ LHΙΙ
LHΙ
LHΙ LHΙ LHΙ

Simon Scheuring
LHΙΙ
LHΙΙ

(a) (b)

Figure 14.4 arrangement of light-harvesting green, RC) where photosynthetic electron transport Phaeospirillum molischianum. This organism has two
chlorophylls/bacteriochlorophylls and reaction reactions begin. Pigment molecules are secured within types of light-harvesting complexes, LHI and LHII. LHII
centers within a photosynthetic membrane. (a) the membrane by specific pigment-binding proteins. complexes transfer energy to LHI complexes, and these
Light energy absorbed by light-harvesting (LH) molecules Compare this figure to Figure 14.12b. (b) Atomic force transfer energy to the reaction center (see Figure 14.11b).
(light green) is transferred to the reaction centers (dark micrograph of photocomplexes of the purple bacterium

A small number of these pigment molecules are present within photosynthetic reaction
centers, the complex macromolecular structures that participate directly in the
reactions that lead to energy conservation

Photosynthetic reaction centers are surrounded by larger numbers of light-harvesting

chlorophylls/bacteriochlorophylls. These so-called antenna pigments (also called light-
harvesting pigments) function to absorb light and funnel some of the energy to the
reaction center.

Sites of Photosynthesis

Vesicles
M.T. Madigan

(a)

Outer
membrane
Stroma Thylakoid Stacked thylakoids
Inner membrane membrane forming grana

Figure 14.5 The chloroplast. Details of chloroplast structure, showing how the
convolutions of the thylakoid membranes define an inner space called the stroma and
Steven J. Schmitt and M.T. Madigan

form membrane stacks called grana. Inset: Photomicrograph of cells of the green alga
Makinoella. Each of the four cells in a cluster contains several chloroplasts.
Lamellar
membranes

(b)

Figure 14.6 Membranes in anoxygenic phototrophs. (a) Chromatophores.

Section through a cell of the purple bacterium Rhodobacter showing vesicular
photosynthetic membranes. The vesicles are continuous with and arise by invagination of
the cytoplasmic membrane. A cell is about 1 μm wide. (b) Lamellar membranes in the
purple bacterium Ectothiorhodospira. A cell is about 1.5 μm wide. These membranes are
also continuous with and arise from invagination of the cytoplasmic membrane, but
instead of forming vesicles, they form membrane stacks.
 Sites of Photosynthesis

Niels-Ulrik Frigarrd
(a)

Bchl c, d, or e

Outer
membrane
Stroma Thylakoid Stacked thylakoids
Inner membrane membrane forming grana BP
In
Figure 14.5 The chloroplast. Details of chloroplast structure, showing how the
convolutions of the thylakoid membranes define an inner space called the stroma and
form membrane stacks called grana. Inset: Photomicrograph of cells of the green alga
Makinoella. Each of the four cells in a cluster contains several chloroplasts.

FMO

Out
RC
Membrane proteins
(b)

Figure 14.7 The chlorosome of green sulfur and green nonsulfur bacteria.
(a) Transmission electron micrograph of a cross section of a cell of the green sulfur
bacterium Chlorobaculum tepidum. Note the chlorosomes (arrows). (b) Model of
chlorosome structure. The chlorosome (green) lies appressed to the inside surface of the
cytoplasmic membrane. Antenna bacteriochlorophyll (Bchl) molecules are arranged in
tubelike arrays inside the chlorosome, and energy is transferred from these to reaction
center (RC) Bchl a in the cytoplasmic membrane through a protein called FMO. Base
plate (BP) proteins function as connectors between the chlorosome and the cytoplasmic
membrane.

Anoxygenic Photosynthesis

Light energy converts

weak donor into
–1.0 strong donor. Light Out (periplasm)
P870* 2 H+
Bchl
–0.75 H+
Excited P870 Bph c2 c2
(P870*) is a strong RC
–0.5 electron donor. QA P870
e– Q Q Q
E0′ QB P870* Quinone Fe-S
–0.25 LHΙΙ LHΙ e– Q pool Q
(V)
Q Bph Q Q Q –
e– e
pool QH2 bc1
0.0 In ground state, e–
P870 is a poor Q
electron donor. Cyt bc1
+0.25
Photosynthetic 2 H+ ATPase
Cyt c2
Cyclic electron flow membrane
+0.5 P870 generates proton ADP
motive force.
In (cytoplasm) ATP
+ Pi

Red or infrared light H+

(a) Electron flow in anoxygenic photosynthesis (b) Arrangement of protein complexes in the purple bacterium
reaction center

Figure 14.12 Electron flow in anoxygenic membrane; Cyt, cytochrome. (b) Arrangement of protein light-harvesting bacteriochlorophyll complexes; RC,
photosynthesis in a purple bacterium. (a) Schematic complexes in the purple bacterium reaction center reaction center; Bph, bacteriopheophytin; Q, quinone;
of electron flow in a purple bacterium. Bchl, leading to proton motive force (photophosphorylation) by FeS, iron–sulfur protein; bc1, cytochrome bc1 complex; c2,
bacteriochlorophyll; Bph, bacteriopheophytin; QA, QB, ATPase. Two protons are translocated for every electron cytochrome c2. For a description of ATPase function,
intermediate quinones; Q pool, quinone pool in that passes from the reaction center to Cyt bc1. LH, see Section 3.11.
 Anoxygenic Photosynthesis
Purple bacteria Green sulfur bacteria Heliobacteria
P798*
–1.25 P840*
Chl a–OH
–1.0 Chl a
P870*
Bchl FeS
–0.75
BPh FeS

–0.5
? Fd ? Fd
E0′ (V) NADH
–0.25
Cyt MQ
Q Cyt MQ bc1
0 Cyt
Reverse bc1
Cyt Cyt c553
electron
+0.25 bc1 P840 c553 P798
Cyt flow
c2
+0.5 P870
Light Light
Light

Figure 14.13 a comparison of electron flow in than that of NADH, is produced by light-driven reactions bacteriopheophytin; Q, quinone; MQ, menaquinone.
purple bacteria, green sulfur bacteria, and for reducing power needs. Cyclic electron flow in green P870 and P840 are reaction centers of purple and green
Heliobacteria. Reverse electron flow in purple bacteria sulfur bacteria and Heliobacteria would require electron bacteria, respectively, and consist of Bchl a. The reaction
is necessary to produce NADH because the primary transfer from the FeS-type photosystem to the center of Heliobacteria (P798) contains Bchl g, and the
acceptor (quinone, Q) is more positive in potential than menaquinone pool, but evidence for this mechanism is reaction center of Chloroflexus is of the purple bacterial
the NAD+/NADH couple. In green sulfur bacteria and limited, suggesting noncyclic electron flow in these type. Note that forms of chlorophyll a are present in the
Heliobacteria, ferredoxin (Fd), whose E0′ is more negative phototrophs. Bchl, bacteriochlorophyll; BPh, reaction centers of green bacteria and heliobacteria.

Oxygenic Photosynthesis
–1.25 P700*
P680* is an
extremely
good electron
donor. Chl a
–1.0
P680*

FeS
–0.75
Fd

–0.5 FNR
Ph Cyclic electron
flow generates NAD(P)H
proton motive
QA force.
–0.25
QB

PQ
E0′ pool
0.0
(V) Noncyclic
electron flow
generates Cyt b6f
proton motive
+0.25 force. PC

P700
Light
+0.5 Photosystem I

+0.75
H2O
2 e– P680 is an extremely
1
– O2 + 2 H+ poor electron donor
P680 2
+1.0 but an excellent
electron acceptor.
Light
Photosystem II
Figure 14.14 Electron flow in oxygenic photosynthesis, the “Z” scheme. Electrons flow through two
photosystems, PSI and PSII. Ph, pheophytin; PQ, plastoquinone; Chl, chlorophyll; Cyt, cytochrome; PC, plastocyanin;
FeS, nonheme iron–sulfur protein; Fd, ferredoxin; FNR, ferredoxin–NADP oxidoreductase; P680 and P700 are the
reaction center chlorophylls of PSII and PSI, respectively. Compare with Figure 14.12a.
 Oxygenic Photosynthesis

½ (NADP+ + H+) ½ NADPH

Light Stroma
H+ H+
–
e Light ADP + Pi 3 H+ ATP
e–
e– Fd
FNR
e–
QA QBe ¼PQH2 PQ FeS

Photosynthetic Chl a
Ph PQ pool e–
membrane
e–
P700
P680 e–
PQH2 FeS e–

Water-oxidizing Mn4Ca Fe PC Lumen

e– PC
complex H+
½ H2O ¼ O2 + H+ H+
3 H+
PSII Cyt b6f PSI ATP synthase

Figure 14.15 Electron transport in oxygenic when plastoquinone is oxidized by cytochrome b6f. light reactions are used in CO2 fixation by the Calvin cycle
photosynthesis. Photosystem II (PSII) is activated by Electrons are then transferred to plastocyanin (PC), which (see Section 14.5). Cyclic photophosphorylation occurs
photons, causing H2O to be oxidized on the Mn4Ca carries them to photosystem I (PSI). Upon activation by when FNR donates electrons to cytochrome b6f instead of
cluster of the water-oxidizing complex. Electrons are light, PSI reduces ferredoxin (Fd), with sequential to NADP+. During cyclic photophosphorylation, more ATP
transferred from PSII to the plastoquinone pool (PQ/ reduction of ferredoxin: NADP+ oxidoreductase (FNR), and less NADPH are produced than during noncyclic
PQH2). Protons are exchanged across the membrane and then NADP+. The ATP and NADPH produced by the photophosphorylation.

Calvin cycle 12 3-Phospho- 12 ATP

6 CO2 glycerate
(36 carbons) Energy input

RubisCO Carboxylation
12 1,3-Bisphospho-
6 Ribulose glycerate
1,5-bisphosphate (36 carbons)
(30 carbons) 12
NAD(P)H
Reducing
Regeneration of power input
CO2 acceptor and
6 energy input 12 Glyceraldehyde
ATP Phosphoribulokinase
3-phosphate
(36 carbons)
6 Ribulose
Removal of
5-phosphate
6 C for
(30 carbons)
Various sugar biosynthesis
rearrangements
Fructose
10 Glyceraldehyde 6-phosphate
3-phosphate (6 carbons)
(30 carbons)

To biosynthesis

Overall stoichiometry:
6 CO2 + 12 NADPH + 18 ATP C6H12O6(PO3H2)
+ 12 NADP+ + 18 ADP + 17 Pi

Figure 14.18 The Calvin cycle. Shown is the production of one hexose molecule
from CO2. For each six molecules of CO2 incorporated, one fructose 6-phosphate is
produced. In phototrophs, ATP comes from photophosphorylation and NAD(P)H from
light or reverse electron flow.
 CHAPTER 5 Microbial Metabolism 143

TABLE 5.6 Photosynthesis Compared in Selected Eukaryotes and Prokaryotes

Characteristic Eukaryotes Prokaryotes

Algae, Plants Cyanobacteria Green Bacteria Purple Bacteria

Substance That H atoms of H2O H atoms of H2O Sulfur, sulfur Sulfur, sulfur compounds,
Reduces CO2 compounds, H2 gas
H2 gas

Oxygen Production Oxygenic Oxygenic (and anoxygenic) Anoxygenic Anoxygenic

Type of Chlorophyll Chlorophyll a Chlorophyll a Bacteriochlorophyll a Bacteriochlorophyll a or b

Site of Photosynthesis Chloroplasts with Thylakoids Chlorosomes Chromatophores

thylakoids

Environment Aerobic Aerobic (and anaerobic) Anaerobic Anaerobic

The chlorophylls used by these photosynthetic bacteria are Chemoheterotrophs

called bacteriochlorophylls, and they absorb light at longer wave- When we discuss photoautotrophs, photoheterotrophs, and
lengths than that absorbed by chlorophyll a. Bacteriochlorophylls chemoautotrophs, it is easy to categorize the energy source and
of green sulfur bacteria are found in vesicles called chlorosomes carbon source because they occur as separate entities. However,
(or chlorobium vesicles) underlying and attached to the plasma in chemoheterotrophs, the distinction is not as clear because the
membrane. In the purple sulfur bacteria, the bacteriochloro- energy source and carbon source are usually the same organic
phylls are located in invaginations of the plasma membrane compound—glucose, for example. Chemoheterotrophs spe-
(chromatophores). cifically use the electrons from hydrogen atoms in organic com-
Table 5.6 summarizes several characteristics that distinguish pounds as their energy source.
eukaryotic photosynthesis from prokaryotic photosynthesis. Heterotrophs are further classified according to their
Animation Comparing Prokaryotes and Eukaryotes
TM

source of organic molecules. Saprophytes live on dead organic

matter, and parasites derive nutrients from a living host. Most
Photoheterotrophs bacteria, and all fungi, protozoa, and animals, are chemohet-
Photoheterotrophs use light as a source of energy but cannot con- erotrophs.
vert carbon dioxide to sugar; rather, they use as sources of carbon Bacteria and fungi can use a wide variety of organic
organic compounds, such as alcohols, fatty acids, other organic compounds for carbon and energy sources. This is why they can
acids, and carbohydrates. Photoheterotrophs are anoxygenic. The live in diverse environments. Understanding microbial diversity
green nonsulfur bacteria, such as Chloroflexus (klô-rō-flex ʹ us), is scientifically interesting and economically important. In some
and purple nonsulfur bacteria, such as Rhodopseudomonas situations microbial growth is undesirable, such as when rubber-
(rō-dō-sū-dō-mō ʹ nas), are photoheterotrophs (see also page 323). degrading bacteria destroy a gasket or shoe sole. However, these
same bacteria might be beneficial if they decomposed discarded CHAPTER
Chemoautotrophs rubber products, such as used tires. Rhodococcus erythropolis
Chemoautotrophs use the electrons from reduced inorganic (rō-dō-kok ʹ kus er-i-throp ʹ ō-lis) is widely distributed in soil
compounds as a source of energy, and they use CO2 as their and can cause disease in humans and other animals. However,
principal source of carbon. Energy sources
1 They fix CO2 in the Calvin-Benson this same species is able to replace sulfur atoms(feeders on others) require an organic ca
in petroleum
Cycle (see Figure 5.26). Inorganic sources of energy (electron with atoms of oxygen. A Texas company trophs
for these donors) is currently also referred to as lithotrophs (ro
areusing
organisms include hydrogen sulfide (H2S) for Beggiatoa (bej-jē- R. erythropolis to produce desulfurized oil. erotrophs are also referred to as organotrop
ä-tō ʹ ä); elemental sulfur (S) forPhotosynthetic pigmentsam-
Thiobacillus thiooxidans; Glucose, elemental
in conjunction
monia (NH3) for Nitrosomonas (nī-trō-sō-mō ʹ näs); with
nitrite ions
CHECK YOUR UNDERSTANDING
sulfur, ammonia, or If we combine the energy and carbon so
light gas (H2) for
(NO2!) for Nitrobacter (nī-trō-bak ʹ tėr); hydrogen ✓ Almosthydrogen
all medically following
important microbes belong
gas nutritional classifications for o
to which of the
four aforementioned groups? 5-23
Cupriavidus (kü ʹ prē-ä-vid-us); ferrous iron (Fe2+) for Thiobacil- totrophs, photoheterotrophs, chemoautotro
lus ferrooxidans; and carbon monoxide (CO) for Pseudomonas * * *
carboxydohydrogena (kär ʹ boks-i-dō-hi-drō-je-nä). The energy – We will next consider how cells use ATP pathways erotrophsfor the(Figure
syn- 5.28). Almost all of the m
e
derived from the oxidation of these inorganic compounds is microorganisms
thesis of organic compounds such as carbohydrates, lipids, pro- discussed in this book are
eventually stored in ATP, which is produced by oxidative phos- teins, andATP
nucleic acids. Typically, infectious organisms catabolize
phorylation.
from the host.
2 Electron carriers
Photoautotrophs
NAD+
NADP+ FAD Photoautotrophs use light as a source of
dioxide as their chief source of carbon. Th
e–
synthetic bacteria (green and purple bact
ATP teria), algae, and green plants. In the phot
of cyanobacteria, algae, and green plants,
3 Final electron acceptors of water are used to reduce carbon dioxid
given off. Because this photosynthetic pro
O2 NO3–, SO42– Organic
(aerobic (anaerobic compound is sometimes called oxygenic.
respiration) respiration) (fermentation) In addition to the cyanobacteria (see Fig
there are several other families of photosy
Figure 5.27 Requirements of ATP production. The production of Each is classified according to the way it
ATP requires 1 an2 energy
3 4 5source
6 7 (electron
8 9 10 donor), 1 2 the
3 4transfer
5 6 of7 8 9 10 bacteria cannot use H2O to reduce CO2 and
electrons to an electron carrier during an oxidation-reduction reaction, tosynthesis when oxygen is present (they mu
1and
2 3 the
4 5transfer
6 7 of 8 electrons
9 10 to a final electron acceptor.
environment). Consequently, their photosy
Q Are energy-generating reactions oxidations or reductions?

ALL ORGANISMS

Energy source

Chemical Light
end of Unit V