Introduction: biosynthesis

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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.

Overview of the reactions of cellular synthesis and biodegradation

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.

Embden-Meyerhof

(EM) pathway, or glycolysis

Entner-Doudoroff (ED) pathway

Krebs cycle, or tricarboxylic acid (TCA) cycle

Hexose monophosphate shunt (HMS), or pentose phosphate pathway

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.

superpathway of leucine, valine, and isoleucine

biosynthesis

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.

Glyoxylate cycle

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).

Calvin cycle

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).

Pathways of carbon assimilation in methane-using organisms

Pathways of carbon assimilation in methane-using organisms

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).

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).

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; [Cor]E, vitamin B12 corrinoid enzyme.

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.

The hydroxypropionate pathway, present in Chloroflexus.

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.

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

+).

Transamination reactionThe glutamate-dependent transamination of an α-keto acid is a fundamental

reaction of amino acid synthesis.

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.

Sulphur assimilation

Sulfate is assimilated through the production of sulfide (S2

-), which is then used in the synthesis of organic sulfur-containing compounds.

Origin of the nine atoms in the purine ring

Origin of the six atoms in the pyrimidine ring

Biosynthesis of a fatty acid I

Biosynthesis of a fatty acid

Biosynthesis of phospholipids

Biosynthesis of phospholipids

Synthesis of cell structures from glucose