Metabolism Lectures
Outline:
 Part I: Fermentations
 Part II: Respiration
 Part III: Metabolic Diversity
Learning objectives are:
 Learn about anaerobic respiratory metabolisms.
 How can an inorganic compound be use as an energy source.
low Eo’
electron flow
hi Eo’
Respiration Review
2H+
Electron Tower
H+
H+
3H+
per
Q
cyto
2NADH
2NAD+
2H+
H+
O2
4H+
2 H2O
H+
ATP
ADP
Anaerobic Respiration
 Anaerobic metabolism is of clinical importance:
– Deep tissue infections can lead to abscess formation,
foul-smelling pus, and tissue destruction
 Uses inorganic and organic molecules other than
oxygen as terminal electron acceptors
–
 Extensive list of electron acceptors
– oxyanions, metals, metal oxides, organic acids, inorganic
 Energy and carbon sources are diverse
–
Metabolic Classification Based on
Oxygen Concentrations
 Points of reference:
– Atmospheric oxygen is ~21% (v/v) (or 2.1 x 105 parts per
million)
– Low solubility in water: up to 14 parts per million (T and P
dependent)
 Remember metabolic classifications:
–
–
–
–
Strict aerobe (non-fermentative, respires oxygen)
Strict anaerobe (sensitive to oxygen)
Facultative anaerobe: (fermentative and/or respiration)
Microaerophilic (or microaerophile)
 40:1 anaerobes to facultative anaerobes in human
feces
Diversity of electron acceptors for
respiration
 Organic compounds:
– Eg. fumarate, dimethylsulfoxide (DMSO), Trimethylamine-Noxide (TMAO)
 Inorganic compounds:
– Eg. NO3-, NO2-, SO42-, S0, SeO42-, AsO43-
 Metals:
– Eg. Fe3+, Mn4+, Cr6+
 Minerals/solids:
– Eg. Fe(OH)3, MnO2
 Gasses:
– Eg. NO, N2O, CO2
Why is there so much
diversity?
How can prokaryotes
accomplish this?
Answer:
Electron acceptor “modules”
Electron donor modules
Cyt b, Fe/S, FAD
fumarate
Fumarate reductase
Dehydrogenase:
Lactate
Succinate
Formate
NADH
Glycerophosphate
Hydrogenase
Cyt b, Fe/S, Mo
MQ
UQ
DMSO
DMSO reductase
Cyt b, Fe/S, Mo
TMAO
TMAO reductase
Cyt b, Fe/S, Mo
Nitrate reductase
NO3-
Modularity of electron transport chains
what do most of these have in common?
Example 1.
Nitrate reduction
Figure 24.19 Nitrogen cycle
78% N2
Nitrate reducing bacteria
 Contribute to denitrification (removal of ?)
 Beneficial process for sewage treatment plants
Nitrogenous waste good food for algae
 Dissimilatory nitrate reduction widespread in microbes
– Used for making energy via oxidative phosphorylation
 Nitrate is a strong oxidant similar to oxygen
 Some microbes can take Nitrate all the way to Nitrogen
gas:
–
Pseudomonas stutzeri
– E0’ +0.74 V compared to +0.82 for 1/2O2/H2O
– How many electrons are used from NO3- to N2?
Dissimulative NO3- reduction
Denitrification by Pseudomonas stutzeri
Denitrification by Pseudomonas stutzeri

Four terminal reductases
–
–
–
–

Nap: Nitrate reductase (Mo-containing enzyme)
Nir: Nitrite reductase
Nor: Nitric oxide reductase
N2or: Nitrous oxide reductase
All can function independently but they operate in unison
Dissimilatory nitrate reduction: Biochemistry
 Electron donor: lactate, formate, H2, others
– Uses special dehydrogenases for these.
 Enzymes are membrane-bound
 Periplasmic nitrate reductases (NapA) contains
a molybdenum cofactor
 Coupled to the generation of PMF
 ATP synthesized by oxidative phosphorylation
Nitrate vs. oxygen vs. denitrification respiration
oxygen
nitrite
denitrification
How much energy
is made by
reducing nitrate to
nitrite with NADH?
What’s reduce and oxidized?
example
Nitrate
(NO3-)
?NAD+
?e-
Nitrite
(NO2-)
?ATP
Determining oxidation state of N and # of electrons:
Nitrate= N(x) + 3O2-  x + 3(-2) = -1  x=
Nitrite= N(x) + 2O2-  x + 2(-2) = -1
 x=
We only need to oxidize ______ NADH for this:
NADH + H+
NAD+ + 2H+ + 2e-
Find ∆Eo’ of nitrate/nitrite and NAD+/NADH Use Nernst Eq to find ∆Go’
?NADH
Example 2.
Arsenate reduction
Eo’+0.139 V
Arsenate  arsenite
Arsenic respiring bacteria and human health



Arsenic is mainly a
groundwater pollutant
Affects ~140 million people
among ~70 countries
Arsenate (As[V]):
–
–

Arsenite (As[III]): H3AsO3
–
–
–


Like phosphate: H2AsO4Affects ATP synthesis
More toxic than As(V)
Binds proteins
Causes DNA damage
Microbes respire arsenate and
make arsenite
Medical Geology problem
http://phys4.harvard.edu/~wilson
Respiring AsO43-
2As(V)
Shewanella sp.
strain ANA-3
Lactate
Dividing cell
2As(III)
As2S3
Respiring O2
Acetate
+
CO2
Isolation of strain
Example 3. Iron
FeIII-oxide
Iron oxide
reducing
bacteria
2Fe(III)
2Fe(II)
OM
c-heme

Examples:
–

Geobacter, Shewanella,
Rhodoferrax
Q
How do they do it?
QH2
NADH2
NAD+
CM
Chemolithotrophy and Oxidation of Inorganic
Molecules
A. A pathway used by a small number of microorganisms
called chemolithotrophs
B. Produces a significant but low yield of ATP
C. The electron acceptor is commonly O2, some others
include sulfate and nitrate
D. The most common electron donors are hydrogen,
reduced nitrogen compounds, reduced sulfur
compounds, and ferrous iron (Fe2+)
Geological, biological, and anthropogenic sources of reduced inorganic
compounds supporting chemolithotrophs
Typical habitats
of chemolithotrohs:
Near the interface of
oxic/anoxic conditions
Energy yields from various inorganic
electron donors:
Oxidation of sulfur-compounds

E.g.: Sulfur oxidizing Thiobacillii
–
Thiobacillus thiooxidans Thiobacillus ferrooxidans
Reactions

ΖGϋΥkJ/mol
H2S + 2 O 2 >>> SO 42- + 2H+
-798.2
HS- + 1/2O 2 + H+ >>> S0 + H 2O
-209
S0 + H 2O + 1.5 O 2 >>> SO 42- + 2H+
-587
S2O32- + H 2O + 2O 2 >>> 2 SO 42- + 2H+
-818
Produces sulfuric acid (H2SO4)
–
–
Acidification of soil
Dissolution of minerals, e.g. CaCO3
Lecture Summary
 Anaerobic respiration
–
–
–
–
–
–
Alternative terminal electron acceptors are used
ATP generated by oxidative phosphorylation
Often not as energetically favorable as oxygen respiration
Anaerobic electron transport chains are branched
Ecologically and medically significant
In some cases toxic metals are used as electron acceptors
 Chemolithotrophy
– Energy sources are reduced inorganic compounds
– Chemolithotrophs often live near redox gradients where there is
a mixture of reduced and oxidized chemicals.