Prescott’s 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:
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use the terms that describe a microbe’s 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 EmbdenMeyerhof 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
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
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Prescott’s Microbiology, 9th Edition
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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 CO 2
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 organism’s 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
compare and contrast oxygenic photosynthesis, anoxygenic phototrophy, and rhodopsin-bsaed phototrophy
list two examples of the importance of chlorophyll-based phototrophy
CHAPTER OUTLINE
I.
II.
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
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
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Prescott’s Microbiology, 9th Edition
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 EmbdenMeyerhof pathway
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 FADH2 are produced
C. Organisms that lack the complete TCA cycle usually have most of the TCA cycle enzymes, because one
of the TCA cycle’s 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 FADH2 to O2
a. Electron carriers are located within the inner membrane of the mitochondrion
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Prescott’s Microbiology, 9th Edition
b.
During oxidative phosphorylation, three ATP molecules may be synthesized when a pair of
electrons passes from NADH to O2; two ATP molecules may be synthesized when electrons
from FADH2 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
A. Uses exogenous molecules other than oxygen as terminal electron acceptors; the most commonly used
alternative electron acceptors are nitrate, sulfate, and CO2
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 CO2
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 polymers—when exogenous nutrients are absent, microorganisms catabolize internal carbon and
energy stores (e.g., glycogen, starch); this is accomplished either by hydrolysis or phosphorolysis
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manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
X.
Lipid Catabolism
A. Triglycerides are common energy sources; they are hydrolyzed to glycerol and fatty acids
B. Fatty acids are catalyzed by the β-oxidation pathway, which successively shortens the chain by two
carbons producing acetyl-CoA, NADH, and FADH2; 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
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 O2), 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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Prescott’s 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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manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.