Studying of mechanism of ATP synthesis is a fascinating area. Because of why all organisms gain energy by using ATP. Electron Transport Chain is the primary mechanism of ATP synthesis in the biosphere & it is composed of reducing & organic chemicals such as cytochromes. Under this topic, we will study how biochemicals behave inside living cells and how organisms produce ATP through Electron Transport Chain. The chemistry of biochemicals is called as Biochemistry. And we are not going to study the in vitro chemistry of biochemicals. Instead we will study the “in vivo” chemistry of biochemicals which is physiology. As prokaryotes are the predecessors of all other organisms, other organisms and prokaryotes have many physiological activities in common. Therefore, understanding prokaryotic physiology help us to understand the physiology of other organisms as well.
For example, learning bacterial respiration help us to understand animal respiration as well. Understanding bacterial photophosphorylation help us to understand plant photophosphorylation as well.
We will study the methods of (Adenosine triphosphate) ATP synthesis used by all different organisms on earth. As the domain ‘Bacteria’ shows all the different methods of ATP synthesis, studying how bacteria produce ATP will give us an understanding of all the methods, seen in the entire biological world. ATP synthesis process is important because ATP is an important chemical needed by all organisms.
Why do organisms need ATP ?
There are thousands of different biochemical reactions taking place in living cells. Some of these reactions do not take place spontaneously, as they need an energy supply to take place (just like some invitro reactions need heat or some other source of energy). In living cells mainly ATP and some other chemicals provide energy for those reactions. As the number of reactions that need ATP are very high. A lot of ATP is required by a living cell. For example, a human sitting passively needs about 1.5kg of ATP per hour. As it is used in large amounts it has to be produced continuously. Every organism has a mechanism to produce ATP continuously as it is used continuously in large amounts. There has been no mechanism evolved during the evolution to store ATP. Instead there are mechanisms to produce it continuously.
Although the diversity of organisms is very wide, there is no such diversity in the methods of ATP production in the biosphere. In fact, there are only 2 main methods of ATP synthesis among living organisms. And these 2 methods also have fundamental similarities. (chemo trophy and photo trophy)
We will study these mechanisms in details. We will realize how efficient these mechanisms are. Another thing we will learn in this lecture series is how different organisms fulfill their carbon requirement. It is important to study this because C is one of the most required elements of organisms.
All organisms need carbon as one of the major elements in their composition. Some organisms have a unique ability to in cooperate CO2 gas with soluble cellular organic chemicals. This is a very crucial step in the carbon cycle.
All organic matter is decomposed releasing carbon as carbon dioxide to help the C cycle. There should a method to turn these CO2 into organic matter. The organisms who can fix CO2 are the organisms who carryout this crucial step in C cycle. They are called, “Carbon-autotrophs”.
Methods of ATP synthesis seen in the biosphere
Although the diversity of living organisms is very wide, their methods of ATP synthesis has no such diversity. In fact, there are only 2 main methods of ATP synthesis in the biosphere. Those are chemo trophy & photo trophy.
A close look at these 2 methods will show that these 2 methods also have many features in common. Both methods synthesize ATP using a membrane associated electron transport chain. The details of these 2 methods will be discussed later.
It should be noted here that some organisms do not use membrane associated process for ATP synthesis. They are Fermentative organisms. Fermentative chemotrophs have only some parts of the method used by respiratory chemotrophs.
What is the mechanism of ATP synthesis using a membrane?
A membrane which is able to synthesize ATP, have an electron transport chain within the membrane. It also must have ATP synthase enzyme embedded in the membrane.
Membrane associated ATP synthesis need also a method to give electrons into the transport chain and also a method to take C out at the end (terminal) of the electron transport chain. If there is no mechanism to take electrons out at the end there will be no flow of electrons, along electron transport chain.
The members of an electron transport chain are arranged in a way that it allows transport electrons from one end to the other end.
In previous diagram,
(a) can reduce (b)
(b) is reduced.
(b) has a potential to be reduced. It is the reduction potential of (b). It is the potential of (b) to become reduced. That can be called as the reduction potential of (b). It is the same parameter described as the redox potential. It can be measured in volts. A parameter that is measured in volts necessarily describe a relative value. Usually an energy difference so, reduction potential also describes the reduction ability in relative terms, relative to the reduction potential of the hydrogen electrode. Hydrogen electrode gives a situation where H+ can take electrons and become reduced (into H2) H+ can take electrons therefore it has a reduction potential. However, by convention the reduction potential of H+ is considered as 0 volt. The reduction potential of O2 when compared with H+, is +0.82 V. NAD+ also can be reduced but its reduction potential is less than that of H+. (It’s -0.32 V)
These values depend on the chemical nature of oxygen, H+ or NAD+. The reduction potential of a chemical does not depend only on the chemical nature of the chemical. It also depends on other factors such as the number of electrons involved, temperature, gas constant, Farad’s constant. It also depends on the concentrations of the reactors. H+ and electrons can form H2. Let us think about reduction potential of H+. If there are lot of H+ and electrons in a unit volume that H+ has a higher potential to become reduced. Why? Because there is a high possibility for H+, to hit against electrons & react. Therefore, in a situation where [H+] is very high, the reduction potential of H+ also becomes very high. Similarly, in situation where there is a very high H2 concentration in a unit volume, the potential for H+ to be reduced is low.
A Scientist known as Nernst recognized the impact of the above described factors on the reduction potential of a chemical. (Factors- gas constant(R), temperature (T), number of electrons(n), Faraday’s constant(F), chemical nature of the chemical and also the concentrations).
The following is the equation he gave to describe what he recognized,
E is the reduction potential of the reactant which react with electrons and going to be reduced. E0 is the reduction potential under standard conditions and it depends on its chemical nature. The equation shows that if the concentration of the reactants is very high. It has a higher potential to take electrons and to be reduced.
The composition and arrangement of electron transport chain
Electron transport chain (ETC) is composed of reducing (and oxidizable) organic chemicals such as cytochromes, Fe-S-proteins (Iron-Sulphur- protein, Flavoproteins and Quinones).
They can take electrons and give electron to the next. There’re 2 types of electron transport chain nature. Respiratory electron transport chain and photophosporylatory electron transport chain. Both have the same mechanism and they have only minor differences. The main difference is how electrons are given to them and how electrons are taken out from them (There must be a method to take electrons to an electron transport chain and also there may be a method to take electrons away from the Electron Transport Chain at its end terminal).
The member chemicals of the Electron Transport Chain are arranged (within the membrane) in the order of increasing reduction potential.
Each member has a slightly higher reduction potential than the previous member. That’s why electrons can move along the Electron Transport Chain in one direction. Cytochromes and Fe-S-proteins have metal centers. (Fe) These centers can take electrons. They’re reduced by taking electrons and are oxidized by giving electrons to the next member. Flavoproteins and quinones are also oxidizable, reducible organic molecules. But they don’t have metal centers.
So, how can they be oxidized/ reduced?
They take H to become reduced, they give H to become oxidized. (taking H or removing oxygen, reduce C atom). When C take H or remove O2, it’s reduced. Cytochromes and Fe-S-proteins give and take electrons. Therefore, they are known as electron carrier of the Electron Transport Chain. Flavoproteins and quinones give and take H for oxidation and reduction. Therefore, they are called H carriers of the Electron Transport Chain. The presence of these 2 types of Electron Transport Chain members help to achieve the arm of electron transport (ET).
What is the aim of Electron Transport?
The aim is synthesis of ATP. The transport of electron creates a condition which helps the ATP synthesis. In 1963, Mitchell(scientist) proposed the mechanism of ATP synthesis by ET. Later he won the Nobel for this finding. Transport of electrons help the translocation of protons from one side of the membrane, to the other side of the membrane.
1) From cytoplasm to periplasm in bacteria.
2) From mitochondrial matrix to the inter- membrane – space of mitochondria.
Oxidation = Complete loss of electrons / partially loss of electrons
There’re several mechanisms of proton translocation. Whatever the mechanism, the proton translocation creates a proton concentration difference across the membrane. It is possible for the creation of concentration difference because the lipid membrane is impermeable for charged H+ molecules (H+ cannot diffuse through the membrane along concentration gradient.). The concentration difference of protons gives potential energy difference across the membrane. The charge difference and pH difference together give this difference in potential energy (energy difference of E. coli – 0.2V). It is about 0.2V across the membrane of E. coli. This energy is known as the proton motive force(Δp) and it is the energy used for the synthesis of ATP.
ATP synthesis occurs with the help of membrane associated ATP synthase enzyme.
Membranes have ATP synthase enzyme embedded within. Part of the enzyme structure comes out from the membrane and that can be seen as white spots on the inner surface of inner mitochondrial membrane.
The 3D structure of the ATP synthase protein has a cavity in the part of the enzyme that comes out from the membrane. This cavity has binding sites for ADP and phosphate groups. Although H+ ions cannot diffuse through the membrane, they are pushed through the ATP synthase enzyme by the proton motive force.
The ATP synthase protein temporarily changes its 3D shape, due to H+ movement through it. When H+ goes through the enzyme, the cavity of the enzyme is opened and closed. When the cavity is closed, it physically forces ADP and PO43- molecules to come together forming ATP (Unless pushed together they will not form bonds because they repulse each other). This is the method of ATP synthesis in respiration (both anaerobic and aerobic) as well as in photophosphorylation.
Mechanism of proton translocation
Electron carrier and H carriers are located in the ETC one after the other. This alternating arrangement of H carriers and electron carriers help the translocation of protons. An electron carrier will take an electron and become reduced. The reduced electron carrier now has an electron to give to the next member of ETC. If the next member is a H carrier, it cannot take just an electron from the previous member. It needs a H. Therefore, it has to find a proton. A proton will be taken from the cytoplasm and the electron will be taken from the reduced electron carrier. That is how the H carrier finds a H to become reduced. Reduced H carrier has a H to give to next member of ETC. As it is an electron carrier, it doesn’t need the H, but only needs an electron. Therefore, it takes an electron from H and send the proton to outside of the membrane. This is how electron transport supports(causes) proton translocation.
There is another mechanism of proton translocation. That’s called “the loop mechanism”. In this mechanism, the carrier molecule moves within the membrane taking protons from one side & releasing them at the other side. We have understood that NADH (and similar reduced co-enzymes) are the compounds that supply electrons to the ETC (respiratory).
Michael T. Madigan, John M. Martinko, Kelly S. Bender, Daniel H. Buckley, D. A. S. (2015). BROCK BIOLOGY OF MICROORGANISMS (14th ed.). Pearson Education,Inc
Pasindu Chamikara – Microbiologist