Introductory Microbiology
Chap. 5 Outlines Microbial Metabolism
I.
II.
III.
IV.
V.
VI.
VII.
VIII.
IX.
X.
XI.
Catabolic and Anabolic Reactions
Enzymes
Energy Production
Carbohydrate Metabolism
Lipid and Protein Catabolism
Biochemical Tests and Bacterial Identification (Lab, not on lecture exam)
Photosynthesis
A Summary of Energy Production Mechanisms
Metabolic Diversity among Organisms
Metabolic Pathways of Energy Use
The Integration of Metabolism
Introduction
What basic things do living organisms have to acquire in order to live?
What determines what molecules or energy sources a specific species needs or is able to use?
All living cells’ energy ‘currency’:
Term: Phosphorylation
Note: Cells use only two kinds of energy: 1) light energy: trapped and used by plants, algae, and some bacteria for
photosynthesis and 2) chemical energy: the energy held in the bonds of various chemicals. Cells do not use thermal
or electrical energy because they don't have thermal or electrical converters. Thermal potential (that is, temperature)
affects the rate of chemical reactions, but does not provide any energy. What about the electrical signals of nervous
impulses? The cells use energy in the form of ATP to generate electric potentials in the membrane of nerve cells and
fibers. Those electrical signals are not ‘used’ by the cell to perform other work.
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Most metabolic processes are ‘similar’ in all cells, but not all. Microbes can do
things we cannot do! Crazy things, like eat petroleum or radioactive materials and
things that are waste products to us. On the other hand, there are microbes that
cannot live in our environment, such as those that are killed by oxygen.
I. Catabolic and Anabolic Reactions
LO/CYU 5-1
A.
METABOLISM :


Two categories of Chemical Processes: Catabolic and Anabolic Reactions
Metabolic ‘Pathways’
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B. Molecules and Energy- intertwined….
LO/CYU 5-2
Role of ATP
Fig. 2.18 on p. 49
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II. Enzymes: How they function and what can affect them
Enzymes increase the rate of chemical reactions by decreasing the activation energy required for
that specific reaction.
LO/CYU 5-4
A. Collision Theory




The collision theory states that chemical reactions occur when atoms, ions, and molecules
collide
Activation energy is the amount of energy needed for them to collide ‘hard’ enough to
disrupt electronic configurations and produce a chemical reaction
Reaction rate is the frequency of collisions with enough energy to bring about a reaction.
Reaction rate can be increased by enzymes or by increasing temperature or pressure
B. Enzymes and Chemical Reactions
Catalysts
Substrate(s)
Product(s)
Decrease activation energy
C. Enzyme Specificity and Efficiency
Specificity
The turnover number is generally 1 to 10,000 molecules per second
D. Naming Enzymes
See Table 5.1 p. 116 Enzyme Classification Based on Type of Chemical Reaction Catalyzed
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E. Enzyme Components
Fig. 5.3 p. 116
LO/CYU 5-3
Apoenzyme (protein portion)
Cofactor (nonprotein portion)
Holoenzyme
LO/CYU 5-4
F. The Mechanism of Enzymatic Action: The sequence of events in enzyme action on the
reactant(s), the enzyme’s substrate(s).
Lock and Key Model
Fig. 5.4 p. 118
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G. Factors Influencing Enzyme Activity
Fig. 5.7 p. 120
End of Chap. ‘Study Questions’ Review #2 a-c & Critical Thinking #2
LO/CYU 5-5
See ARA Assignment #2
III. Energy Production
LO/CYU 5-8
A. Introduction
1.
Energy is found in the
in nutrient molecules.
that form bonds between the atoms
2. Why is ATP a good energy carrier?
B. Oxidation-Reduction Reactions
Fig. 5.9 p. 122
End of Chapter ‘Study Questions’ Multiple Choice #1
Provide
energy for
ATP
generation
Removal and Gain of
6
1. Oxidation
2. Reduction
3. Redox
4. Dehydrogenation
5. NAD+
Fig. 5.10 p. 123
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C. The Generation of ATP: Phosphorylation of ADP to ATP
LO/CYU 5-9
When does ‘ADP + P
Text p. 122
ATP’ actually occur?
1. Substrate-level phosphorylation
3 ways
ATP is
formed
2. Oxidative phosphorylation
3. Photophosphorylation
End of Chapter ‘Study Questions’ Review #5
8
Substrate-level phosphorylation

A chemical reaction where a phosphate group is transferred from a molecule to ADP.
This requires a specific enzyme that can transfer this phosphate from this specific
molecule (the enzyme’s substrate) to ADP.

ATP is produced this way during
 FERMENTATION
 Glycolysis (or alternative pathways)
 Krebs cycle
Oxidative phosphorylation

Energy is released from transfer of electrons (oxidation) from one compound to another
(reduction). This energy is used to generate ATP in the electron transport chain.

An electron transport chain (ETC) couples a chemical reaction between an electron donor
(such as NADH) and an electron acceptor (such as a cytochrome molecule) to the transfer
of H+ ions across a membrane (this transfer of H+ ions is called chemiosmosis). This
occurs during a set of biochemical reactions.

This occurs during respiration.
Photophosphorylation

Light causes chlorophyll to give up electrons. The electrons go through a process similar
to what happens during respiration (an electron transport chain and chemiosmosis occur).
This process releases energy that is used to bond a phosphate to ADP producing ATP.

The ATP produced is used to produce food molecules (sugars-glucose).
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C. Metabolic Pathways of Energy Production
LO/CYU 5-10
In the cell, there are many series of enzymatically catalyzed chemical reactions
that store energy and release energy from organic molecules- carbohydrates, proteins, and
lipids. Catabolic reactions with these molecules release energy for ATP production and
anabolic reactions use the energy in those ATPs primarily to synthesize large forms of
these molecules.
Why do cells use metabolic pathways to release energy?
IV. Carbohydrate Metabolism
(CATABOLIC METABOLISM)
LO/CYU 5-11
A. Glycolysis



Biochemical pathway (10 reactions) in which ONE molecule of GLUCOSE is
OXIDIZED to form 2 molecules of PYRUVIC ACID.
NAD (nicotinamide adenine dinucleotide, an important electron carrier) is reduced
ATP is required in the first stage of glycolysis and formed in the later stage of glycolysis
Fig. 5.11 Foundation Figure: An Overview of Respiration and Fermentation
Fig. 5.12 Outline of the reactions of glycolysis (Slides 1 & 2)
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B. Alternatives to Glycolysis
Text discussion p. 125, 127
1. Pentose Phosphate Pathway: Breaks down 5-C sugars and glucose. Other
needed molecules are produced as intermediates,but it only nets 1 ATP.
2. Entner-Doudoroff Pathway: Breaks down glucose w/ some different enzymes.
NEXT: Either Cellular Respiration or Fermentation
C. Cellular Respiration (Fermentation later)
Define respiration: p. 127
1. Aerobic Cellular Respiration
a. After glycolysis is the Preparatory
Step before the Krebs Cycle
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c. Krebs cycle
LO/CYU 5-13
Fig. 5.13 p. 128
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d. Electron transport chain/ Chemiosmosis/ADP Phosphorylation
Electron transport chain: A series of electron carriers are oxidized
(lose/donate electrons) & other electron carriers are reduced (gained
electrons) as electrons are passed from one electron carrier to another.
NADH and FADH2 will donate their electrons to electron carriers located
in the prokaryotic plasma membrane. Eukaryotes- this occurs in the
mitochondria.
Oxygen is the final electron acceptor in aerobic respiration.
Before continuing, turn the page and draw the electron transport chain. Then come back!
Info:

Some electron carriers pick up one electron, others pick up more than one electron.
 Some electron carriers carry hydrogen atoms (1e-, 1p+); others ONLY CARRY
ELECTRONS (THE PROTON IS SEPARATED FROM THE ELECTRON IN THE H
ATOMS).

In the electron transport system, FADH2 donates its electrons after NADH.

There also is anaerobic respiration where the final electron acceptor is NOT oxygen. Less
common & doesn’t produce as much ATP.
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Electron Transport Chain
14
Chemiosmosis
Fig. 5.15 p. 130, Fig. 5.16 p. 131
LO/CYU 5-14
1) Occurs simultaneously with the electron transport chain (they are coupled) to transfer the
energy to form ATP from ADP and phosphate (ADP phosphorylation).
2) At certain points along the electron transport chain, the hydrogen atom is ‘split’; the electron
and the proton are separated.
Remember, some electron carriers carry hydrogen atoms (1e- & 1p+), others only carry e-. So
what happens to the protons in the H atoms when an electron carrier only picks up the e-?
3) The protons are pumped out of the cell (through the plasma membrane) & the electron is then
passed to other electron carriers.
4) This creates a situation where there are more protons on the external side of the plasma
membrane than are on the internal side of the plasma membrane; in other words, a gradient is
formed.
5) This gradient creates a force.
6) Chemiosmosis is the process of creating a proton gradient (by movement of protons across
the plasma membrane) and the subsequent movement of the protons back into the cell through
specific channels through the enzyme ATP synthase.
ATP Generation: ADP Phosphorylation
1) Bonding of a phosphate group to ADP to form ATP.
2) The energy required to bond the phosphate to ADP (and that is then stored in the resulting
bond) is provided by the movement of protons back into the cell during chemiosmosis.
3) When the protons rush back into the cell (due to the gradient), energy is released. This may
cause a CONFORMATIONAL (shape) change in the enzyme ATP synthase.
ATP synthase that then catalyzes the reaction:
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Fig. 5.16 p. 131
ETC and Chemiosmotic Generation of ATP
How many ATPs are generated from aerobic respiration through Substrate-Level
Phosphorylation only?
How many ATPs are generated from aerobic respiration through Substrate-Level and Oxidative
Phosphorylation?
SLIDE Comparing Eukaryotes and Prokaryotes: Where in the cell do these processes occur?
Overview Fig. 5.17 Summary of aerobic respiration p. 133
Overall Summary Reaction of Aerobic Respiration:
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Anaerobic Respiration.
LO/CYU 5-15
Slide
What takes the place of oxygen?
EXAMPLES:
a. Sulfate. In marine sediments this leads to large amounts of sulfate reduction - Sulfate
SO42- is converted (reduced) to hydrogen sulfide H2S - which some may be familiar with
as the rotten egg smell and black material that can be found just a few centimeters below
sediment surfaces.
b. Nitrate NO3-. which is converted (reduced) to nitrite NO21-, nitrous oxide N2O, or
nitrogen gas N2 in the process.
c. Metal ions. For example: Fe+2, Mn+2
d. Carbonate, CO32-. is converted (reduced) to methane, CH4. This is called
methanogenesis Very little energy is obtained from methanogenesis and vast amounts of
substrate need to be turned over to make a ‘living’.
The amount of energy generated varies depending on the electron acceptor (2-36 ATPs).
What are the organisms that undergo anaerobic respiration?
Primarily live in

conditions.
Aerobic respiration: The final electron acceptor in the electron transport chain is
molecular oxygen (O2).
VS.

Anaerobic respiration: The final electron acceptor in the electron transport chain is not
O2 (But it is generally an inorganic molecule). Yields less energy than aerobic respiration
because only part of the Krebs cycles operates under anaerobic conditions.
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D. Fermentation
LO/CYU 5-16

FERMENTATION Scientific definition:
 Releases energy from oxidation of organic molecules
 Does not use oxygen
 Does not use the Krebs cycle or ETC
 Uses an organic molecule (pyruvic acid) as the final electron acceptor to form
‘end-products’ (acids and alcohols)
 2 ATPs netted
Fig. 5.18 b p. 134
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Two Primary Categories of Fermentation
Fig. 5.19 p. 136
Examples of Types & Importance of Fermentation
Table 5.4 p. 137
Table 5.4 p. 137
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See Table 5.5 Aerobic Respiration, Anaerobic Respiration, and Fermentation
Compared p. 137
Fig. 5.11 p. 125 Foundation Figure An Overview of Respiration and
Fermentation
End of Chapter ‘Study Questions’
Review #4 a and b
Multiple Choice #7-10
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V. Lipid and Protein Catabolism
LO/CYU 5-17
Summary of the interrelationships of carbohydrate, lipid and protein catabolism
Fig. 5.21 p. 138
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VI. Biochemical Tests and Bacterial Identification: Directly relates to your ‘Unknown’
laboratory exercises/ Not on lecture exam
VII. Photosynthesis
p. 140-1
CYU 5-19, 5-20, 5-21
http://www.solarnavigator.net/photosynthesis.htm
 Conversion of light energy into chemical energy (ATP) which is used to
synthesize nutrients (glucose)
 Overall Summary Reaction?
 Compare and Contrast: Oxidative Phosphorylation and
Photophosphorylation.
 Oxygenic versus Anoxygenic
Oxygenic
6 CO2 + 12 H2O + Light energy 
C6H12O6 + 6 H2O + 6 O2
Anoxygenic
6 CO2 + 12 H2S + Light energy 
C6H12O6 + 6 H2O + 12 S
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VIII. A Summary of Energy Production Mechanisms
p. 141
LO/CYU 5-22
See Requirements for ATP (energy sources, electron carriers, final electron acceptors)
Fig. 5.27 p. 143
End of Chapter ‘Study Questions; Multiple Choice #3
IX. Metabolic Diversity among Organisms p. 142
LO/CYU 5-23
Four Categories (Nutritional Patterns): Where do you get your energy and where do you get your
Carbon for the organic molecules you need?
Nutritional Type
Energy Source
Carbon Source
Example
Photoautotroph
Light
CO2
Oxygenic: Cya
Anoxygenic: G
Photoheterotroph
Light
Organic compounds
Green, purple
Chemoautotroph
Chemical
CO2
Iron-oxidizing
Chemoheterotroph
Chemical
Organic compounds
Fermentative
Animals, proto
(See Fig. 5.28 p. 143)
End of Chapter ‘Study Questions’ Review #7
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X. Metabolic Pathways of Energy Use
p. 146
LO/CYU 5-24
Now you have ATP and Carbon (and some other basic stuff), what are you going to do with it?
Describe the major types of anabolism and their relationship to catabolism.
A. Polysaccharide Biosynthesis
B. Lipid Biosynthesis
C. Amino acid and Protein Biosynthesis
D. Purine and Pyrimidine Nitrogen base Biosynthesis
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XI. The Integration of Metabolism p. 147
LO/CYU 5-25
Amphibolic pathways: Metabolic pathways that have both catabolic and anabolic functions
Same figure on Slides 8 & 9. Fig. 5.33 p. 149
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Metabolism The Big Picture
End of Chapter ‘Study Questions’ Review #1h
Same figure on Slide 10
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