Prescotts Microbiology, 9th Edition

11 Catabolism: Energy Release and

Conservation

CHAPTER OVERVIEW

This chapter presents an overview of energy release and conservation mechanisms

beginning with glucose degradation to pyruvate. Fermentation, aerobic respiration, and
anaerobic respiration are then examined. The consideration of chemoorganoheterotrophic
metabolism concludes with a discussion of the catabolism of lipids, proteins, and amino
acids. Chemolithotrophic metabolism follows and the chapter concludes with a discussion
of the trapping of energy by phototrophy.

LEARNING OUTCOMES

After reading this chapter you should be able to:

use the terms that describe a microbes carbon source, energy source, and electron
source
state the carbon, energy, and electron sources of photolithotrophs,
photoorganoheterotrophs, chemolithoautotrophs, chemolithoheterotrophs, and
chemoorganoheterotrophs
describe the products of the fueling reactions
discuss the metabolic flexibility of microorganisms
list the three types of chemoorganotrophic metabolisms
list the pathways of major importance to chemoorganotrophs and explain their
importance
propose an explanation that accounts for the existence of amphibolic pathways
describe in general terms what happens to a molecule of glucose during aerobic
respiration
list the end products made during aerobic respiration
identify the process that generates generate the most ATP during aerobic respiration
list the three major pathways that catabolize glucose to pyruvate
describe substrate-level phosphorylation
diagram the major changes made to glucose as it is catabolized by the Embden-
Meyerhof, Entner-Doudoroff, and pentose phosphate pathways that consume ATP,
produce ATP and NAD(P)H, generate precursor metabolites, or are redox reactions
calculate the yields of ATP and NAD(P)H by the Embden-Meyerhof, Entner-Doudoroff,
and pentose phosphate pathways
summarize the function of the Embden-Meyerhof, Entner-Doudoroff, and pentose-
phosphate pathways
draw a simple diagram that shows the connection between the Entner-Doudoroff
pathway and the Embden-Meyerhof pathway and the connection between the pentose
phosphate pathway and the Embden-Meyerhof pathway
create a table that shows which types of organisms use each of the glycolytic pathways
state the alternate names for the tricarboxylic acid (TCA) cycle
diagram the major changes made to pyruvate as it is catalyzed by the TCA cycle
identify those reactions of the TCA cycle that produce ATP (or GTP) and NAD(P)H,
generate precursor metabolites, or are redox reactions

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 Prescotts Microbiology, 9th Edition

summarize the function of the TCA cycle

diagram the connections between the various glycolytic pathways and the TCA cycle
locate the TCA cycle enzymes in bacterial, archaeal, and eukaryotic cells
compare and contrast the mitochondrial electron transport chain (ETC) and bacterial
ETCs
describe the chemiosmotic hypothesis
correlate the length of an ETC and the carriers in it with the strength of the proton
motive force (PMF) it generates
explain how ATP synthase uses PMF (proton motive force) to generate ATP
draw a simple diagram that shows the connections between the glycolytic pathways,
TCA cycle, ETC , and ATP synthesis
list uses for the PMF generated by bacterial cells in addition to ATP synthesis
calculate the maximum possible ATP yields when glucose is completely catabolized to
six molecules of CO2 during aerobic respiration
compare and contrast aerobic respiration and anaerobic respiration using glucose as a
carbon source
list examples of terminal electron acceptors used during anaerobic respiration
defend this statement: The use of nitrate (NO3-) as a terminal electron acceptor is
dissimilatory nitrate reduction.
predict the relative amount of energy released for each of the common terminal
acceptors used during anaerobic respiration, as compared to energy released during
aerobic respiration
list three examples of the importance of anaerobic respiration
compare and contrast aerobic respiration, anaerobic respiration, and fermentation of
glucose
list the pathways that may function during fermentation if glucose is the organisms
carbon and energy source
create a table that lists some of the common fermentation pathways and their
products, and gives examples of their importance
compare the use of ATP synthase during respiration and fermentation
discuss the role of ATP and UTP in the catabolism of monosaccharides other than
glucose
differentiate the catabolism of disaccharides and polysaccharides by hydrolysis from
their catabolism by phosphorolysis
discuss the fate of the fatty acid and glycerol components of triglycerides when
trigylcerides are catabolized
state the name of the enzymes responsible for hydrolyzing proteins into amino acids
distinguish deamination from transamination and explain how the two are related
draw a simple diagram that illustrates how the pathways used to catabolize reduced
organic molecules other than glucose connect to the glycolytic pathways and the TCA
cycle
describe in general terms the fueling reactions of chemolithotrophs
list the molecules commonly used as energy sources and electron donors by
chemolithotrophs
discuss the use of electron transport chains and oxidative phosphorylation by
chemolithotrophs
describe in general terms the fueling reactions of phototrophs
differentiate phototrophy from photosynthesis
describe the light and dark reactions that occur during photosynthesis
summarize the structure and function of the light-absorbing pigments used by oxygenic
and anoxygenic phototrophs
defend this statement: Oxidative phosphorylation and photophosphorylation by
chlorophyll-based phototrophs differ primarily in the energy source driving the
process.
distinguish cyclic photophosphorylation from noncyclic photophosphorylation

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 Prescotts Microbiology, 9th Edition

compare and contrast oxygenic photosynthesis, anoxygenic phototrophy, and

rhodopsin-bsaed phototrophy
list two examples of the importance of chlorophyll-based phototrophy

CHAPTER OUTLINE

I.Metabolic Diversity and Nutritional Types

A. Photoorganoheterotrophs
1. use organic matter as their electron and carbon source
2. common inhabitants of polluted lakes and streams
B. chemolithoheterotrophs
1. used reduced inorganic molecules for energy, derive carbon from organic
sources
2. contribute to biogeochemical cycles
II.Chemoorganotrophic Fueling Processes
A. Chemotrophic microorganisms vary in terms of their energy source (light, organic
molecules, inorganic molecules), and in terms of their electron acceptors
1. If the energy source is oxidized and degraded with the use of an exogenous
electron acceptor, the process is called respiration; in aerobic respiration the
final electron acceptor is oxygen, whereas in anaerobic respiration the final
electron acceptor is a molecule other than oxygen
2. If an organic energy source is oxidized and degraded without the use of an
exogenous electron acceptor, the process is called fermentation
B. For chemoorganoheterotrophic organisms, catabolism is often a three-stage
process during which nutrients are fed into common degradative pathways
including glycolysis and the tricarboxylic acid (TCA) cycle
1. Breakdown of polymers and other large molecules into their constituent parts
2. Initial degradation of the constituents parts
3. Completion of degradation accompanied by the generation of many ATP
molecules
C. Many of the catabolic pathways can also be used for synthesis (anabolic) reactions
and are termed amphibolic; reducing power is used to convert precursor
metabolites into macromolecules
III. Aerobic Respiration - completely catabolizes organic energy sources to carbon dioxide
using oxygen as the terminal electron acceptor; reducing power derives from the
glycolytic and TCA pathways
IV.From Glucose to Pyruvate
A. The Embden-Meyerhof Pathway
1. The most common pathway for glucose degradation (glycolysis), it is found in
all major groups of microorganisms
2. Functions in the presence or absence of oxygen and is divided into two parts:
a. In the 6-carbon stage, glucose is phosphorylated twice to yield fructose
1,6-bisphosphate; this requires the expenditure of two molecules of ATP
b. The 3-carbon stage cleaves fructose 1,6-bisphosphate into two 3-carbon
molecules, which are each oxidized to pyruvate; two molecules of ATP are
produced by substrate-level phosphorylation from each of the 3-carbon
molecules for a net yield of two molecules of ATP; two molecules of NADH
are also produced per glucose molecule
B. The Entner-Doudoroff pathway is an alternative glycolytic pathway used by some
microbes; the 6-carbon stage begins with only one phosphorylation event with
phosphogluconate as an intermediate with one pyruvate and one glyceraldehyde
3-phosphate produced; the 3-carbon stage is the same as the Embden-Meyerhof
pathway

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 Prescotts Microbiology, 9th Edition

C. Pentose Phosphate Pathway: A Major Producer of Reducing Power for Anabolic

Reactions
1. Known as the hexose monophosphate pathway; produces a variety of 3-, 4-, 5-,
6-, and 7-carbon sugar phosphates
2. Has several catabolic and anabolic functions (amphibolic)
a. Production of NADPH, which serves as a source of electrons for
biosynthetic processes
b. Production of 4- and 5-carbon skeletons that can be used for the synthesis
of amino acids, nucleic acids, and other macromolecules
c. Complete catabolism of hexoses and pentoses, yielding ATP and NADH
(made by converting NADPH to NADH)
V.Tricarboxylic Acid Cycle
A. Pyruvate can be oxidized to carbon dioxide by the tricarboxylic acid (TCA) cycle (or
Krebs cycle) after first being converted to acetyl-CoA; this preliminary reaction is
accompanied by the loss of one carbon atom as carbon dioxide and produces
NADH
B. Acetyl-CoA reacts with oxaloacetate (a 4-carbon molecule) to produce a 6-carbon
molecule (citric acid), which is subsequently oxidized to release two molecules of
carbon dioxide, regenerating the oxaloacetate; during this process, the following
occur:
1. ATP (as GTP) is produced by substrate-level phosphorylation
2. Three molecules of NADH and one molecule of FADH 2 are produced
C. Organisms that lack the complete TCA cycle usually have most of the TCA cycle
enzymes, because one of the TCA cycles major functions is to provide carbon
skeletons for use in biosynthesis
VI.Electron Transport and Oxidative Phosphorylation
A. Electron transport chains
1. The mitochondrial electron transport chain in eukaryotes uses a series of
electron carriers to transfer electrons from NADH and FADH 2 to O2
a. Electron carriers are located within the inner membrane of the
mitochondrion
b. During oxidative phosphorylation, three ATP molecules may be
synthesized when a pair of electrons passes from NADH to O 2; two ATP
molecules may be synthesized when electrons from FADH 2 pass to O2
2. Although they operate according to the same fundamental principles, bacterial
electron transport chains usually differ in structure: they may be branched, be
composed of different electron carriers, or may be shorter than mitochondrial
electron transport chains; bacterial electron transport chains are located in the
plasma membrane
B. Oxidative phosphorylation
1. The chemiosmotic hypothesis postulates that the energy released during
electron transport is used to establish a proton gradient that produces a proton
motive force (potential energy due to the difference in proton concentration
and charge on either side of the membrane), which can be used to drive ATP
synthesis, flagellar rotation, and transport of molecules across the membrane
2. ATP synthesis is catalyzed by the ATP synthase complex, which is thought to
behave like a small rotary motor where the energy released by the movement
of protons across the membrane, down the concentration gradient, is used to
make high-energy bonds in ATP
C. ATP yield during aerobic respiration
1. The net yield from the oxidation of a glucose molecule via glycolysis is 2 ATP
2. The number of ATP generated by aerobic respiration of a glucose molecule
depends on the precise nature of the electron transport system; mitochondrial
respiration typically yields 36 ATP (plus 2 from glycolysis)
VII.Anaerobic Respiration

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 Prescotts Microbiology, 9th Edition

A. Uses exogenous molecules other than oxygen as terminal electron acceptors; the
most commonly used alternative electron acceptors are nitrate, sulfate, and CO 2
B. Dissimilatory nitrate reduction occurs when nitrate is used as the terminal electron
acceptor; if the nitrate is reduced to nitrogen gas, the process is called
denitrification
C. Anaerobic respiration is not as efficient in ATP synthesis as aerobic respiration
because the alternative electron acceptors do not have as positive a reduction
potential as O2; despite this, anaerobic respiration is useful because it is more
efficient than fermentation
D. When several electron acceptors are present in the environment, microorganisms
will use these acceptors in succession starting with oxygen, then moving to nitrate,
manganese ion, ferric ion, sulfate, and finally carbon dioxide
VIII.Fermentation
A. Fermentation is a process in which an organism oxidizes the NADH produced by
one of the glycolytic pathways by using pyruvate or one of its derivatives as an
electron and hydrogen acceptor; thus the process involves the use of an
endogenous electron acceptor and regenerates NAD + to act as the oxidant in
glycolysis
B. Fermentation takes place in the absence of oxidative phosphorylation and ATP is
only generated through substrate-level phosphorylation
C. Many different types of fermentations are known
1. Alcoholic fermentations produce ethanol and CO 2
2. Lactic acid fermentations produce lactic acid (lactate)
a. Homolactic fermenters reduce almost all pyruvate to
lactate
b. Heterolactic fermenters form substantial amounts of products other than
lactate
3. Formic acid fermentation produces either mixed acids or
butanediol
D. Microorganisms can ferment substances other than sugars (e.g.,
amino acids); in the Strickland reaction, one amino acid is oxidized
while a second acts as the electron acceptor
IX.Catabolism of Organic Molecules other than Glucose
A. Carbohydrates
1. Most monosaccharides feed easily into the glycolytic pathway
2. Disaccharides are cleaved into monosaccharides either by hydrolysis or
phosphorolysis
3. Polysaccharides are cleaved into smaller molecules either by hydrolysis or
phosphorolysis; many however, are not easily degraded (e.g., cellulose, agar)
B. Reserve polymerswhen exogenous nutrients are absent, microorganisms
catabolize internal carbon and energy stores (e.g., glycogen, starch); this is
accomplished either by hydrolysis or phosphorolysis
X.Lipid Catabolism
A. Triglycerides are common energy sources; they are hydrolyzed to glycerol and fatty
acids
B. Fatty acids are catalyzed by the -oxidation pathway, which successively shortens
the chain by two carbons producing acetyl-CoA, NADH, and FADH 2; NADH and
FADH2 can be oxidized by an electron transport chain to produce ATP
XI.Protein and Amino Acid Catabolism
A. Proteins are degraded by proteases to their component amino acids
B. Amino acids are first deaminated (often by transamination) and then the remaining
carbon skeletons are converted to pyruvate, acetyl-CoA, or a TCA-cycle
intermediate
XII.Chemolithotrophy

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 Prescotts Microbiology, 9th Edition

A. A metabolic process that uses inorganic molecules as a source of energy; the

energy source is oxidized and the electrons are passed to an electron transport
chain; the terminal electron acceptor is usually O 2, but sulfate and nitrate also are
used; the most common electron donors (energy sources) are hydrogen, reduced
nitrogen compounds, reduced sulfur compounds, and ferrous iron (Fe 2+)
B. Chemolithotrophs are usually autotrophs; they use the Calvin cycle to fix carbon
dioxide; however, the oxidation of most inorganic molecules yields low levels of
ATP; therefore, in order to fuel carbon dioxide fixation, chemolithotrophs must
oxidize large amounts of inorganic material
C. Some inorganic energy sources (e.g., ammonia and nitrite) cannot donate
electrons directly to NAD+; chemolithotrophs that use such energy sources must
use their proton motive force to reverse electron flow in their electron transport
chain in order to generate the NADH needed for biosynthetic processes
XIII.Phototrophy
A. During photosynthesis, energy from light is trapped and used to produce ATP and
NADPH (light reactions), which are used to reduce carbon dioxide to carbohydrates
(dark reactions)
B. Light reactions in oxygenic photosynthesis
1. Oxygenic photosynthesis generates molecular oxygen when light energy is
converted to chemical energy; this process is found in plants, algae, and
cyanobacteria
2. Chlorophyll molecules and a variety of accessory pigments (carotenoids and
bilins) are used to form antennas; the antennas trap photons and transfer their
energy to reaction-center chlorophylls; these special chlorophylls are directly
involved in photosynthetic electron transport
3. Eukaryotes and cyanobacteria have two photosystems; in each, electrons from
the light-energized reaction-center chlorophylls are transferred to the
associated electron transport chain
a. Photosystem I can carry out cyclic photophosphorylation, producing ATP
b. Photosystems I and II, working together, can carry out noncyclic
photophosphorylation, producing ATP and NADPH; the electrons for
noncyclic photophosphorylation are obtained from water, which is oxidized
to O2 (oxygenic photosynthesis)
4. Photosynthetic electron transport takes place in membranes including the
thylakoid membranes of chloroplasts and cyanobacteria; ATP can be generated
through chemiosmosis
C. The light reaction in anoxygenic photosynthesis
1. Green and purple photosynthetic bacteria carry out anoxygenic photosynthesis
(they do not use water as a source of electrons, so do not produce O 2), and
they have modified photosynthetic pigments called bacteriochlorophylls
2. Many of the differences in the light reactions of the green and purple bacteria
are due to the fact that they only have a single photosystem
3. Green and purple bacteria are usually autotrophs that use NADH or NADPH for
carbon dioxide fixation; three methods for making NADH are known:
a. Reduction of NAD+ directly by hydrogen gas
b. Reverse electron flow
c. A simplified form of noncyclic electron flow
D. Rhodopsin-based phototrophy
1. Some archaea use light as a source of energy but instead of using chlorophyll,
these microbes use bacteriorhodopsin; analogous proteins in bacteria are
called proteorhodopsin
2. A retinal chromophore changes shape when excited by light and acts a proton
pump; this creates a proton gradient across a membrane that produces ATP
through chemiosmosis

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 Prescotts Microbiology, 9th Edition

CRITICAL THINKING

1. The authors make the statement, The use of a few common catabolic pathways, each
degrading many nutrients, greatly increases metabolic efficiency by avoiding the need
for a large number of less metabolically flexible pathways. Explain the significance of
this statement.

2. The overall yield of ATP in eukaryotes has a theoretical maximum of 38 ATP molecules
per molecule of glucose. However, usually only 36 ATP molecules are produced. Explain
this apparent discrepancy. Prokaryotes often have lower P/O ratios than eukaryotic
systems. Explain the significance of this relative to the aerobic yield of ATP.

3. Explain how isotopically labeled substates can be used to elucidate biochemical

pathways within a
particular organism.

CONCEPT MAPPING CHALLENGE

Construct a concept map that describes the metabolic processes used by

chemoorganotrophs to catabolize glucose. Use the concepts that follow, any other
concepts or terms you need, and your own linking words between each pair of concepts in
your map.

aerobic respiration anaerobic respiration fermentation glycolysis TCA cycle

ETC (electron transport chain) oxidative phosphorylation substrate-level phosphorylation
terminal electron acceptor proton motive force (PMF)

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