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METABOLISM OF ORGANIC AND
INORGANIC MATTERGunjan Mehta
Deptt. of Biotechnology,
Virani Science College, Rajkot
Metabolism of Organic matter 1. Fermentation 2. Respiration
1. Fermentation: “Special kind of redox reaction in which both electron donors and acceptors are organic in nature”. Internally generated organic compounds such as
pyruvic acid can serve as electron acceptor when external electron acceptor is absent.
Reduced compounds produced during such reactions are secreted in extracellular.
Fermentation yields less amount of ATP molecules than respiration, as in fermentation reaction organic compounds can’t be fully oxidized to CO2 & H2O.
Fermentation
In Fermentation, the organic compounds are simply rearranged into a form containing less energy than the organic substrate.
Fermentation generate few ATPs per molecule of substrate than respiration, hence more substrate molecules should be metabolize during it.
ATP synthesis during fermentation is substrate level phosphorylation and remains largely restricted to amount formed during glycolysis.
Chemiosmotic synthesis and oxidative phosphorylation of ATP don’t occur in fermentation.
Fermentation
Respiration
“Biochemical process in which organic compound serve as electron donor while external compound serve as terminal electron acceptor”. R
esp
irati
on Aerobic
Anaerobic
Aerobic Respiration When O2 serve as terminal electron
acceptor.
Anaerobic respiration
Instead of O2 other inorganic compound serve as terminal electron acceptor.
Anaerobic Metabolism
Terminal Electron acceptor
Product Example
Anaerobic respiration
Fe3+, S Fe2+,
H2SDenitrifiers,
Sulfur reducers etc
Denitrification
NO3-, NO2
- NO2, N2O, N2
Paracoccus denitrifucans
Sulfate reduction
SO42- H2S Desulfovibrio
desulfuricans
Methanogenesis
CO2 CH4 Methanococccus spp
Aerobic Vs Anaerobic respiration Aerobic respiration is very imp process in
bioremediation as various organic compounds will be fully oxidized and converted to inorganic minerals. In bacteria this procedure involves enzymes capable of adding O2.
1. Monooxygenase- one O2 molecule 2. Dioxygenase- two O2 molecule Anaerobic respiration: Carried out by
obligatory anaerobes and facultative anaerobes. O2 will be given preference.
Fermentation vs Respiration
Respiration is more efficient than fermentation because of following reasons…
1. The difference in reducing potential between the primary electron donor and terminal electron acceptor is high.
2. In respiration complete oxidation of organic matter will occur compared to fermentation where incomplete oxidation will occur.
Metabolism of Inorganic matter
1. Nitrate reduction 2. Sulfate reduction 3. Lithotrophy: a) Hydrogen bacteria b)
Sulfur bacteria
Mainly followed during anaerobic respiration by Nitrate reducing bacteria, Sulfate reducing bacteria and many other lithotrophic bacteria.
These metabolic pathways are the most integral parts of Biogeochemical cycles.
Nitrate reduction/ Denitrification Nitrate reduction takes place through both assimilatory
and dissimilatory cellular functions. Assimilatory denitrification: nitrate is reduced to
ammonia, which then serves as a nitrogen source for cell synthesis. Thus, nitrogen is removed from the liquid stream by incorporating it into cytoplasmic material.
Dissimilatory denitrification: nitrate serves as the electron acceptor in energy metabolism and is converted to various gaseous end products but principally molecular nitrogen, N2, which is then stripped from the liquid stream.
A relatively small fraction of the nitrogen is removed through assimilation. Dissimilatory denitrification is, therfore, the primary means by which nitrogen removal is achieved.
Nitrate reduction
A carbon source is also essential as electron donor for denitrification to take place..
Denitrification releases nitrogen which escapes as an inert gas to the atmosphere while oxygen released stays dissolved in the liquid and thus reduces the oxygen input needed into the system. Each molecule of nitrogen needs 4 molecules of oxygen during nitrification but releases back 2.5 molecules in denitrification. Thus, theoretically, 62.5% of the oxygen used is released back in denitrification.
Assimilatory denitrification
Nitrate is reduced to ammonia, which then serves as a nitrogen source for cell synthesis. Thus, nitrogen is removed from the liquid stream by incorporating it into cytoplasmic material.
Assimilatory denitrification
Assimilatory denitrification
Since oxidation state of nitrogen in nitrate is +5 and in ammonia it is -3. Total 8 e- must be transferred to nitrate in order to reduce it to ammonia.
Dissimilatory denitrification In dissimilatory denitrification, nitrate serves
as the electron acceptor in energy metabolism and is converted to various gaseous end products but principally molecular nitrogen, N2, which is then stripped from the liquid stream.
Dissimilatory denitrification is the primary means by which nitrogen removal is achieved.
Dissimilatory denitrification
Dissimilatory denitrification Nitrogenous oxides, principally NO3-, NO2- are
used as terminal electron acceptor in the absence of O2 and reduced molecular nitrogen N2 during microbial metabolism.
Enzymes for denitrification procedure are oxygen sensitive and works under anaerobic condition.
All denitrifying organisms are facultative anaerobes such as Pseudomonas and Alcaligens.
Achromobacter, Vibrio, Flavobacterium
Sulfate reduction
SO42-( most oxidized form of S) can be used as terminal
electron acceptor by a specialized group of microbes which are known as Sulfur reducing bacteria….
SO42- first reduced to sulfite(SO3
- ) and then to sulfide(H2S) or S2- and then incorporated into Cysteine.
The oxidation level of S in SO42- is (+6) and in sulfide it
is (-2), so total 8 electrons are required to reduce SO42-
to S2-. Gram +ve: Desulfotomaculum Gram –ve: Desulfovibrio Archaebacteria: Archaeglobus
Assimilatory sulfate reduction
Adenosine-PO2-PO2-PO3+ SO42-
-PPi ATP sulfurylase Adenosine- PO3 –SO3
Adenosine phosphosulfate (APS)/ AMP-SO2
APS phosphorylase Phosphoadenosine phosphosulfate/ SO3- -
AMP- SO2
-AMP-3’-P PAPS reductase SO3
-2
Assimilatory sulfate reduction
SO3-2
3NADPH3NADP Sulfite reductase H2S +O- acetyl serine
-acetate acetyl serine sulfhydrilase L- Cysteine
Assimilatory sulfate reduction
Assimilatory sulfate reduction
There is sound thermodynamic reason behind the formation of APS, which is AMP derivative of sulfate.
The reduction potential of sulfate can be increased by attaching AMP, which makes it a better electron acceptor than free sulfate.
Formation of PAPS: The reductant is sulfhydryl protein called thioridoxin, which accepts e- from NADPH.
3 ATP molecules are used: a. 2 ATP for PAPS b. 1 ATP for AMP formation
Dissimilatory sulfate reduction
Dissimilation of sulfate is very rare as it yields less amount of energy than any alternative e- donor as nitrate or oxygen.
Since energy influences growth and metabolism of these SRBs, it shows slow growth.
Comparative pathways
Lithotrophy
The study of metabolism of organism using reduced inorganic material is called lithotrophy.
CO2- Lithoautotrophs(Most of) H2, NH3, H2S, NO2, Fe+2, CO-
Lithotrophs(Some) Consist of one of the major class of
autolithotrophs and very important for it.
Classification of lithotrophs
1. Hydrogen bacteria:
Sulfur oxidizing bacteria:
e- donor
e-accept
or
Final Product
Example
H2 O2 H2O Alkaligens eutrophus
e- donor
e-accepto
r
Final Product
Example
H2S, S2-, S2O3
O2 SO42- Thiobacillus
thioxidans, Baggiatoa
Classification of lithotrophs
3. Iron oxidizing bacteria
4. Nitrogen oxidizing bacteriaa. Ammonia oxidizing:
e- donor
e-accepto
r
Final Product
Example
Fe+3 O2 SO42- Thiobacillus
thioxidans,
e- donor
e-accepto
r
Final Product
Example
NH4+ O2 N2O, NO-, NO2, NO3-
Nitrosomonas eutropy
Classification of lithotrophs
3. Iron oxidizing bacteria
4. Nitrogen oxidizing bacteriaa. Ammonia oxidizing:
e- donor
e-accepto
r
Final Product
Example
Fe+3 O2 SO42- Thiobacillus
thioxidans,
e- donor
e-accepto
r
Final Product
Example
NH4+ O2 N2O, NO-, NO2, NO3-
Nitrosomonas eutropy
Classification of lithotrophs
b. Nitrite oxidizing:
5. Methanogens
e- donor
e-accepto
r
Final Product
Example
NO2- O2 NO3- Nitrobacter
winograsky e-
donore-
acceptor
Final Product
Example
H2 CO2, Acetate
, Methyl
CH4 Methanococcus spp
Classification of lithotrophs
6. Methylotrophse-
donore-
acceptor
Final Product
Example
CH4 CO2 Organic compoun
d
Methylococcus
Hydrogen bacteria
Facultative lithotrophs Also known as hydrogen oxidizing bacteria
capable of utilizing H2 as source of energy. Majority of these bacteria are aerobic
capable of utilizing O2 as terminal e- acceptor.
However they are not purely dependent on H2 as energy source but are capable of utilizing other organic sources. That’s why it is facultative lithotrophs.
CO2+ 2H2[CH2O]n+H2O Hydrogen is oxidized by membrane bound
hydrogenase.
Sulfur oxidizing bacteria
It includes….1. Photosynthetic sulfur oxidizers: Green sulfur
bacteria & purple sulfur bacteria2. Non- Photosynthetic sulfur oxidizers: colourless
sulfur bacteria such as Baggiatoa, Thiothrix Almost all are gram –ve e- donors for SOBs: H2S, S2-, S2O3
Comprises physiologically diverse group of bacteria:1. Obligatory autotrophs(CO2- sole C source)
2. Facultative heterotrophs(Mixotrophic) Eg: Baggiatoa
Sulfur oxidizing bacteria
On the basis of pH requirement:1. Neutrophile: pH= 7.02. Acidophile: pH= 1- 5 (Thiobacillus thioxidans)
S2-/ H2S
[S]- linear polysulfate Sulfur oxidase/ sulfite oxidase
SO32- APS
APS
SO42-
Sulfur oxidizing bacteria
Few sulfur oxidizing bacteria are archaebacteria such as Sulfolobus.
Lives on sulfur rich spring- hot spring in temperature range upto 90º C and pH=1.
H2S+2CO2 SO42- + 2H+
S+ H2O+O2 SO42-+ 2H+
S2O3+ H2O+2O2 SO42- + 2H+