Autotrophic Metabolism

Metabolism is a biological process necessary for sustaining life.

The Three Main Purposes of the Chemical Reactions in Metabolism are: 

• The conversion of food to energy for running the cellular processes, 

• Converting food/fuel to building blocks for proteins, lipids, nucleic acids and some other carbohydrates, and 

• The removal of metabolic wastes. 

Metabolism can also sometimes mean all the chemical reactions that take place within a living organism. It includes digestion, and transport of substances into and between different cells which are known as intermediary metabolism or intermediate metabolism. Of different types of metabolic processes, autotrophic metabolism is a type of metabolism. Autotrophic metabolism is the process in which the organism carries out its own metabolic activity. 

Autotrophic Metabolism in Bacteria

Many of the cellular components are made up of carbon. The carbon is obtained from carbon dioxide for autotrophic bacteria. Autotrophism can only be carried out by a cell if it is capable of carrying out photosynthesis or aerobic respiratory mechanisms. Both these mechanisms are the only mechanisms which can provide enough energy for carbon fixation.  It majorly involves three pathways: Calvin cycle - reductive pentose phosphate, reductive tricarboxylic acid, and acetyl CoA pathway. 

The Calvin cycle which was explained by Melvin Calvin is one of the most widely distributed metabolic pathways. It operates in plants, algae, photosynthetic bacteria and most of the aerobic lithoautotrophic bacteria. The main step in the cycle is the reaction between ribose 1,5-bisphosphate with carbon dioxide. It results in two molecules of 3-phosphoglycerate which is a precursor to glucose. But the main concern about this cycle is that it is an energy-expensive cycle. This is because the synthesis of one molecule of glyceraldehyde-3-phosphate requires consumption of nine molecules of ATP and oxidation of six molecules of the electron donor NADPH (reduced form of nicotinamide adenine dinucleotide phosphate).  

The aerobic non photosynthetic lithoautotroph bacteria are the ones that use carbon dioxide as their carbon source and also produce energy from inorganic compounds. These inorganic compounds are electron donors with oxygen molecules as their electron acceptor. There are diverse types of these bacteria and are normally known by their electron donor that they use. An example of this is Nitrosomonas europaea. They oxidise ammonia to nitrate. On the other hand, Nitrobacter winogradskyi which oxides nitrite to nitrate. The bacterial species, Thiobacillus oxidizes thiosulfate and sulphur to sulphate and the bacteria A. ferrooxidans, oxidizes the ferrous ions to the ferric form. Because of these different oxidising abilities allows the bacteria, A. ferrooxidans, to tolerate high concentrations of many different ions of iron, copper, cobalt, nickel and zinc. All the types of bacteria that bind the lithoautotrophs are unable to use organic compounds to a significant amount. Oligotropha carboxidovorans is another bacterial species which oxidizes carbon monoxide to carbon dioxide. Similarly, just like the bacterial species Oligotropha carboxidovorans, Alcaligenes eutrophus, oxidises hydrogen gas. Some other bacterias as well do the oxidation although not to the degree as seen in Oligotropha carboxidovorans.

The energy obtained from metabolism is available from the oxidation of the electron donors. It is basically in the same way as used by the respiring heterotrophs, which transfer the electrons from an organic molecule to oxygen. A proton gradient is created across the cell membrane when the electrons pass along the electron transport chain. This gradient in turn is used to generate the ATP or energy molecules. The other reactions in the lithoautotrophs are the ones that are used for the removal of the electrons from the inorganic donor and used for carbon dioxide fixation.

Role of Photosynthesis in Metabolism

Autotrophy is defined as the ability of an organism to use inorganic carbon in the form of carbon dioxide as a single source of carbon for the production of organic compounds which are absolutely essential for building the cellular components. Hence, it is also sometimes known as carbon-autotrophy. This also differentiates these organisms from the organisms using molecular nitrogen as the single source of nitrogen. These organisms are known as nitrogen autotrophs. But in generality, autotrophy is normally used to refer to carbon autotrophy. This property of carbon autotrophy is present in plants, algae, and the phototrophic bacteria which also includes the cyanobacteria. 

Apart from the organisms that carry out the photosynthesis there are many different groups of non-photosynthetic bacteria. These bacteria are able to grow using carbon dioxide as the single and sole source of carbon by the ability for oxidizing the inorganic compounds. Such organisms are known as chemoautotrophic or chemolithotrophic. At the end of the aerobic respiratory process, along with the release of energy of respiratory substances, carbon dioxide is also released. This carbon dioxide is poor in energy content. This energy poor compound is in turn used to create organic molecules with high energy content in autotrophic metabolism. 

Therefore, converting carbon dioxide to organic compounds requires a lot of energy from an outside source. In the case of photosynthesis the best source is the radiation energy. Similarly, in the case of chemolithotrophy the best source is the oxidation energy of inorganic compounds. In both cases, the molecule that drives the conversion of carbon dioxide to organic compounds is ATP. Hence, both the cases require generation of ATP molecules. This ATP is produced with the help of the photosynthetic pigment. This process is known as photophosphorylation. Similarly, in chemoautotrophy the oxidation energy of inorganic compounds produces ATP through the respiratory chain through oxidative phosphorylation.

Autotrophic metabolism is a sum of two sets of reactions. In one of the sets the ATP and the reducing force are produced and in the other set these molecules are used and reduced from carbon dioxide to organic compounds. The first set of reactions are different in phototrophic and non-phototrophic autotrophs but the second set is the same for both the types of organisms. Most of the autotrophs carry out the reactions for reduction of CO2 through a cyclic pathway. It is known as reductive pentose phosphate pathway and more commonly known as Calvin-Benson cycle. The reduction of CO2 to produce organic compounds is commonly known as CO2 fixation. 

Hence, it can be seen that there are similarities between the phototrophic and non-phototrophic autotrophic metabolism. Most of the phototrophic organisms are known to carry out some sort of photosynthesis. But the non-green autotrophs are known to carry out an allied process known as chemosynthesis.

In the photosynthesis reaction, the first step is the absorption of the photons by a series of light harvesting pigments. One of the more commonly known pigments of these types are chlorophylls which you know very well. The pigments are present in a pigment-protein complex. Hence, they are known as antenna-complexes, because they are able to collect the light of different wavelengths. An example of this is the absorption of light of different wavelengths. They absorb the light of longer wavelengths which goes into the infrared regions by some of the bacteriochlorophylls. 

So, in the same manner, carotenoids are pigments which absorb light of shorter wavelengths. They generally absorb wavelengths in the yellow region of the spectrum. The light energy which is absorbed by the available antenna system, is then passed forward or transmitted to a special centre. This special centre is a photo reactive centre which is known as the reaction centre located in the photosynthetic lamellae along with the pigment protein complex. These lamellae are parts of the chloroplasts in the eukaryotic organisms. While in the prokaryotic organisms they are the intracellular membrane system that is produced by the invagination of the cytoplasmic membrane known as chromatophores. In the reaction centre pigment complex when excitation occurs, the energy is transferred from the antenna pigments and it then releases energy-rich electrons. These electrons are then further accepted by the primary electron acceptor which is ferredoxin. The electrons from the ferredoxin are then transferred to the secondary electron acceptors.

Hence, the reaction centre becomes positively charged due to the loss of electrons. With proper position of the secondary electron acceptors led to the electron transport in one direction which is across the membrane. The proton transport is then in the opposite direction with the consequent generation of an electric field because of charge separation. The separation of the charge is used for the generation of the ATP by a mechanism known as chemiosmotic mechanism. 

There are two types of electron flow that result in the generation of ATP through photosynthesis. They are: cyclic and non-cyclic. In the cyclic type of electron flow, the electrons start from being ejected by the reaction centre. They pass through a series of electron acceptors from higher energy level then slowly to lower energy level. Thus, it forms a closed circuit. The electrons that are lost from the circular flow are utilized for the phosphorylation of ADP to ATP. Hence, the only product of the cyclic electron flow is ATP. In this case, no NADH2 is produced. On the other hand in the noncyclic pathway, the electrons that are released by the reaction centre pigment complex are accepted by ferredoxin. On acceptance of ferredoxin they are used for the reduction of NAD/NADP. Thus, it becomes necessary to take the electrons from the exogenous source so that the reaction centre can be reoxidised. On reoxidation it reaches the ground state and becomes ready for the next release of electrons. For both the green plants and cyanobacteria, water behaves as the electron donor. This happens as water is photolysed by chlorophyll producing H+ and (OH)-.

The protons are known for the reduction of NADP. The electrons of (OH)- are passed on to positively charged reaction centres through the cytochromes. Also, along with this, molecular oxygen (O2) is produced. In green plants, photosynthesis happens in the form of two light reactions. They are Photosystem I and Photosystem II. The pigment complexes of these two systems are known as P700 and P680 respectively.

For an oxygenic bacteria the photosynthesis reaction is somewhat different. One of the major differences for the bacterial photosynthesis and plant photosynthesis is that there is only one photosystem in the bacterial one which is Photosystem I. And as Photosystem II is involved in oxygen evolution through photolysis of water it is absent in bacteria. Hence, in the bacterial non-cyclic electron transport chain, the exogenous electron donor will be H2, H2S, SO, S2O32- or other organic compounds.

Other Different Modes of Autotrophic Metabolism

Chemoautotrophy or also known as chemolithotrophy is another mode of autotrophic metabolism. It is very specialised and limited to only some groups of non-photosynthetic autotrophic bacteria. Some of the given bacteria are able to grow both chemoorganotrophic ally and chemoautotrophic ally. Some of the examples of these types of facultative autotrophs are Alcaligenes eutrophus and Nitrococcus oceanus. Other chemoautotrophic bacteria are bound in nature as they are not capable of using their organic compounds as a carbon source. The species belonging to the genera Nitrosomonas and Thiobacillus are some of the examples of this type. But the point to note is that some species of Thiobacillus are facultative. 

As per the oxidisable inorganic substrate, the chemoautotrophic bacteria can be further classified into nitrifying bacteria, sulfur oxidising bacteria, hydrogen oxidizing bacteria, iron oxidising bacteria and carbon monoxide bacteria. Almost all of them are strictly dependent on oxygen. But not the facultative ones as they can grow in the absence of free oxygen. This is because they depend on using the nitrate as an option for the electron acceptor which is known as nitrate respiration. Examples include Paracoccus dentrifican and Thiobacillus dentrificans.