Introduction: biosynthesis

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Introduction biosynthesis
. The combined processes whereby the major
constituents of the bacterial cell are
synthesized is called biosynthesis. In the last
lecture we covered the production of ATP and
NAD(P)H from light and an electron donor. These
are required in autotrphic CO2 fixation (plants
and bacteria) which is the ultimate sustainer of
all food chains. Do not forget the nitrogen,
sulphur, phosphate, iron and trace elements.
Carbon dioxide is the primary substrate
supporting life and is incorporated into cells by
different mechanisms. In this lecture we will
look at, some carbon fixation mechanisms and the
assimilation of nitrogen and sulphur.
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Overview of the reactions of cellular synthesis
and biodegradation
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Biosynthesis
Heterotrophic bacteria Chemoorganotrophic
bacteria can utilize a wide range of carbon
compounds (sugars from polysaccharides, amino
acids from proteins, nucleotides from DNA and RNA
etc.) as energy sources. All of these bacteria
use the same compounds or derivatives thereoff as
carbon sources. Then they are called
Heterotrophic bacteria. The basic principles are
often illustrated by using glucose as an
example. The major pathways for the degradation
of carbohydrates and the tricarboxylic acid cycle
are used as a source of precursor molecules for
the biosynthesis of cell material.
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Embden-Meyerhof (EM) pathway, or glycolysis
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Entner-Doudoroff (ED) pathway
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Krebs cycle, or tricarboxylic acid (TCA) cycle
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Hexose monophosphate shunt (HMS), or pentose
phosphate pathway
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Feeling adventurous ?

• Go to Encyclopedia of Escherichia coli Genes and
  Metabolism at http//biocyc.org/ for full
  details of all known pathways in Escherichia coli
  and some other bacteria.

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superpathway of leucine, valine, and isoleucine
biosynthesis
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The glyoxylate cycle
The glyoxylate cycle is a special case for
organisms growing on a C2 carbon compound
(Example Eschericia coli growing on acetate) and
new enzymes are required to incorporate this
substrate.
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Glyoxylate cycle
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Biosynthesis
Autotrophic bacteria Autotrophic bacteria use
carbon dioxide as their sole source of
carbon. Most of the chemolithotrophic and
photosynthetic bacteria are autotrophic. The
mathanogenic archaea are also autotrophic. The
Calvin cycle for CO2 fixation is the most
widespread pathway of CO2 fixation, but it is
only found in aerobic or aerotolerant
bacteria. Some bacteria specializing in the
metabolism of C1 compounds (methane, methanol,
methylamine) have special pathways. Several
different pathways for CO2 fixation are found in
the strict anaerobic bacteria (Green sulphur
bacteria) and archaea (methanogens).
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Calvin cycle
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Biosynthesis
Autotrophic bacteria Autotrophic bacteria use
carbon dioxide as their sole source of
carbon. Most of the chemolithotrophic and
photosynthetic bacteria are autotrophic. The
mathanogenic archaea are also autotrophic. The
Calvin cycle for CO2 fixation is the most
widespread pathway of CO2 fixation, but it is
only found in aerobic or aerotolerant
bacteria. Some bacteria specializing in the
metabolism of C1 compounds (methane, methanol,
methylamine) have special pathways. Several
different pathways for CO2 fixation are found in
the strict anaerobic bacteria (Green sulphur
bacteria) and archaea (methanogens).
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Pathways of carbon assimilation in methane-using
organisms
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Pathways of carbon assimilation in methane-using
organisms
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Biosynthesis
Autotrophic bacteria Autotrophic bacteria use
carbon dioxide as their sole source of
carbon. Most of the chemolithotrophic and
photosynthetic bacteria are autotrophic. The
mathanogenic archaea are also autotrophic. The
Calvin cycle for CO2 fixation is the most
widespread pathway of CO2 fixation, but it is
only found in aerobic or aerotolerant
bacteria. Some bacteria specializing in the
metabolism of C1 compounds (methane, methanol,
methylamine) have special pathways. Several
different pathways for CO2 fixation are found in
the strict anaerobic bacteria (Green sulphur
bacteria) and archaea (methanogens).
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The reductive citric acid pathway, present in
green sulfur and a few other bacteria
Present in green sulfur bacteria (Chlorobium
limicola), thermophilic hydrogen-oxidizing
bacteria (Hydrogenobacter thermophilus), and some
of the sulfate-reducing bacteria (Desulfobacter
hydrogenophilus).
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Pathway of CO2 fixation in acetogenic bacteria
This pathway is present in homoacetogenic
bacteria (Clostridium thermoaceticum), most of
the sulfate-reducing bacteria (Desulfobacterium
autotrophicum), and selected methanogenic archaea
(Methanosarcina barkeri). THF, tetrahydrofolic
acid CorE, vitamin B12 corrinoid enzyme.
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Carbon fixation in Chloroflexus.
Chloroflexus is considered to have a very old
pathway for the fixation of CO2. There are very
few atrains of this bacteria and the
hydroxypropionate pathway is very unusual in so
much that it is not found in any other species of
bacteria or archaea.
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The hydroxypropionate pathway, present in
Chloroflexus.
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Assimilation of ammonia
Nitrogen is a major constituent of biological
molecules Some bacteria and archaea can fix
atmospheric nitrogen, dinitrogen N2 and the
product is ammonia. This process will be
described later in the course when we meet these
organisms. Many bacteria and archaea can reduce
nitrate to ammonia (assimilative nitrate
reduction) for biosynthetic purposes. This is not
to be confused with dissimilative nitrate
reduction in which nitrate is used a a terminal
electron acceptor in energy metabolism. Inorganic
nitrogen in the form of ammonia is converted to
organic nitrogen in glutamate and glutamine.
These amino acids are then the major donors of
organic nitrogen most biosynthetic reactions.
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Assimilation of ammonia
Together, the glutamate dehydrogenase and
glutamine synthetase reactions result in the
assimilation of two ammonia molecules (shown as
the ammonium ion, NH4).
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Transamination reactionThe glutamate-dependent
transamination of an a-keto acid is a fundamental
reaction of amino acid synthesis.
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Assimilation of sulphur
Sulphur is a major constituent of biological
molecules Many bacteria and archaea can reduce
sulphate to hydrogen sulphide (assimilative
sulphate reduction) for biosynthetic purposes.
This is not to be confused with dissimilative
sulphate reduction in which sulphate is used a a
terminal electron acceptor in energy metabolism
by the Sulphate reducing bacteria. Inorganic
sulphur, in the form of hydrogen sulphide, is
used directly in most biosynthetic reactions.
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Sulphur assimilation
Sulfate is assimilated through the production of
sulfide (S2-), which is then used in the
synthesis of organic sulfur-containing compounds.
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Origin of the nine atoms in the purine ring
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Origin of the six atoms in the pyrimidine ring
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Biosynthesis of a fatty acid I
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Biosynthesis of a fatty acid
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Biosynthesis of phospholipids
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Biosynthesis of phospholipids
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Synthesis of cell structures from glucose
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