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ATP Synthase, Practice Problems and FAQs

ATP Synthase, Practice Problems and FAQs

You know that during the rainy season most of the dams will get filled and they are opened afterwards. People always visit dams to enjoy the beauty, especially when it is opened. You also might have visited some dams. But why are they opening the gates of dams? 



                                                                    GIF: Dam

The only goal in opening the dams is to maintain the required water level. Then only it can work properly without collapsing and creating floods. So what is the purpose behind the dams? One major purpose of the dam is to provide the water for irrigation purposes and the other is to generate electricity. They work on the principle of the conversion of the mechanical energy into the electrical energy. So when the water flows through the turbine, it rotates and as a result energy is released in the form of electricity. Just think about the world without electricity!! We really cannot live without it. Right? How we will see each other in the night without light. Every work at home also will be stopped.

Now think about the energy molecules present in a plant body. What are the major energy molecules present in a plant? ATP and NADPH are the major energy molecules of the plant. These molecules are formed as a result of the light reaction. Then they are used to produce the sugar during the dark reaction. But how are these molecules formed?

Just like the rotating turbine in the dam, plants also have a similar structure which is called the ATP synthase. This is a protein present on the thylakoid membrane of the chloroplast. This has the ability to spin and generate the ATP molecules. This is interesting. Right? But what helps in the spinning of this protein? How through spinning they produce ATP? So it is time to discuss more about the structure and function of ATP synthase and we will find out answers to all the above questions in this article. 

Table of contents:

  • ATP Synthase
  • Practice Problems
  • FAQs

ATP synthase

In addition to the photosystems and the cytochrome, the thylakoid membrane has another important protein, the ATP synthase. ATP synthase is an important enzyme which is seen in the mitochondrial membrane too. ATP synthase is an enzyme that catalyses the formation of ATP by the phosphorylation of ADP with inorganic phosphate, using a form of energy like the energy from a proton gradient.

ATP synthase as biocatalyst

Proteins that serve as catalysts are known as enzymes or biocatalysts. They can accelerate the chemical reactions without undergoing changes. The biochemicals which are acted upon by enzymes are known as substrates (S). The biochemicals that are formed after the completion of a reaction are called products (P). 

The substrate binds to the enzyme at its active site within a given cleft or pocket to convert it to a product. The structure formed after binding of the substrate and enzyme is called the enzyme-substrate complex (E-S complex). Finally an enzyme-product complex (E-P complex) is formed, once the substrate undergoes changes in the E-S complex. This E-P complex dissociates to form enzymes and products. 



                                                          Fig: Enzyme activity

For example, the ATP synthase interacts with ADP and Pi which are the substrates and ATP is formed. ATP is the product. ATP synthase enzyme is categorised as a ligase since it modifies ADP by forming a phosphodiester bond. This process is called phosphorylation, a biochemical procedure where phosphate is added to an organic molecule. This process is called photophosphorylation in the light reaction of photosynthesis as this process is dependent on light.



                                            Fig: Phosphorylation

Creation of proton gradient in the thylakoid lumen

Due to the transport of electrons through the complexes present in the thylakoid membrane in the chloroplast, there will be an influx of protons from the stroma to the lumen. It is mainly done by the plastoquinone molecules. As a result of photolysis of water, there will be generation of photons inside the lumen. Hence the concentration of protons inside the lumen increases and it results in the formation of a proton gradient in the thylakoid. This is the major factor that drives the ATP synthase. This proton gradient will make the protons travel from lumen to stroma through ATP synthase, which leads to the formation of ATP. During photosynthesis, this process takes place in the cyclic photophosphorylation process. 



                                              Fig: Cyclic photophosphorylation

To understand more about this, first we have to be familiar with the structure of ATP synthase. So now we will check out the structure of ATP synthase.

Structure of ATP synthase

ATP synthase is located in the inner mitochondrial membrane and thylakoid membrane. The enzyme can have two regions. They are FO and F1. FO will be on the membrane and the F1 projects towards the region where the ATP is needed. 

F

It is embedded in the thylakoid membrane. It forms a transmembrane channel that facilitates diffusion of H+ ions or protons across the membrane. It is a water insoluble protein. The ‘o’ in FO refers to its sensitivity to oligomycin, an antibiotic that blocks the flow of protons in ATP synthase. The FO is made up of a subunit with c-ring (probably eight copies), other subunits are a, b, d, F6, and the oligomycin sensitivity-conferring protein (OSCP). The peripheral stalk, which is located on one side of the complex, is made up of subunits b, d, F6, and OSCP. FO is connected to several other subunits that span the membrane, including e, f, g, and A6L. The FO side requires high concentration of protons as compared to the F1 side for the activation of ATP synthase enzymes.



                   Fig: FO 

F

They are large hydrophilic particles which can be observed through a transmission electron microscope. It extends out from the thylakoid membrane's outer surface. It faces the stroma. F1 is made up of nine subunits. It is composed of three copies of α and β subunits, and one copy of γ, δ and ε subunits. The central stalk of complex V in the electron transport chain is made up of the F1 subunits γ, δ and ε.

The γ subunit is slightly bent and it is surrounded by the α and β subunits. α and β subunits are hexameric and have 6 binding sites. Three binding sites are responsible for the synthesis of ATP and the other three are catalytically inactive. The β subunit is responsible for the synthesis of ATP from ADP. For this β subunit has to undergo some conformational changes and this is done with the help of the γ subunit. 



                    Fig: ATP synthase

Now the structure of ATP synthase is clear to you, right? So it will be easy to understand the mechanism by which the ATP synthase produces ATP. So next we will discuss the working mechanism of ATP synthase.

Working mechanism of ATP synthase

As we mentioned earlier there is a higher concentration of protons in the thylakoid lumen and a lower concentration of protons in the stroma. So, the protons should be able to diffuse from the lumen to the stroma. However, the thylakoid membrane is impermeable to H+ ions or protons. This is why the protons undergo facilitated diffusion instead. This is done through the ATP synthase enzyme. 

When the protons from the lumen diffuse through the ATP synthase, they cause the enzyme to churn and rotate. During this rotation, there is a conformational change in the F1. Adenosine diphosphate (ADP) molecules get hit with free phosphate molecules to form adenosine triphosphate (ATP). This happens with the help of the β subunit of the F1 particle. ATP is the energy currency of the cell and it is released into the stroma. This ATP will be used immediately in the biosynthetic reactions taking place at the stroma.



                             Fig: Working of ATP synthase

Mechanism of FO - F1 particle

The proton gradient creates a proton-motive force that comprises an electrical membrane potential and a pH differential. The energy which is released during the movement of protons causes rotation of two rotary motors. One is the ring of c subunits in FO, and along with this there will be rotation of subunits of F1, which are γ, δ and ε. It happens because γ, δ and ε are attached directly to the FO particle. Let’s see the mechanism in detail.

Protons pass through subunit a to the c-ring of the FO particle. The old proton in the C ring moves out into the stroma when a new proton joins the C ring. The C ring rotates as a result of the movement of protons. One molecule of ATP can be produced when three protons travel through FO.

The central asymmetric stalk, mostly made up of the gamma subunit, is closely connected to the c-ring; as a result, the gamma subunit rotates alongside the c-ring. This will cause the α3β3 of F1 to go through a series of conformational changes. 

The alternating alpha and beta subunits, three of each, are arranged around a spinning, asymmetrical gamma subunit in the F1 crystal structure. ATP is produced as a result of the conformational change in α3β3. This rotation of the gamma subunit which led to the conformational change in the α3β3 is called rotary catalysis. Paul Boyer proposed a theory for the ATP synthesis in the F1 binding subunit. So the ADP binds with Pi (inorganic phosphate) in the β subunit and the ATP is formed in the stroma of chloroplast which can be instantly used in the dark reaction.



                                                 Fig: Working of ATP synthase

Practice Problems

Q 1. Which of the following is not necessary for the chemiosmosis-based production of ATP?

a. Proton pump
b. NADPH
c. Proton gradient
d. ATP Synthase

Answer: Photophosphorylation is the term used for the light reaction of photosynthesis that produces ATP from ADP. Mitchell proposed the chemiosmotic theory to explain ATP production. In order to help with the generation of ATP, chemiosmosis entails the flow of ions along a concentration gradient across a biological membrane. Protons accumulate inside the lumen of thylakoids during the light-dependent processes of photosynthesis. When compared to the stroma of chloroplasts, the lumen of thylakoids contains a large quantity of protons, a proton gradient is created, and when this gradient breaks down, ATP is produced. The gradient is reduced as a result of protons being transported by ATP synthase over the membrane and into the stroma. An ATP synthase, a proton pump, a proton gradient, and a membrane are required for chemiosmosis to produce ATP. The assimilatory powers generated during the light reaction of photosynthesis include ATP and NADPH. Hence the correct option is b. 

Q 2. Which of the following statements are wrong about the ATP synthase?

I) ATP synthase is present in the thylakoid membrane and the mitochondrial membrane.
II) Proton gradient in the thylakoid is the major factor that drives the ATP synthase.
III) ATP synthase has two regions such as FO and F1.
IV) F1 will be on the membrane and the FO projects towards the region where the ATP is needed.

a. I
b. II
c. III
d. IV

Answer: In addition to the photosystems and the cytochrome, the thylakoid membrane has another important protein, the ATP synthase. ATP synthase is an important enzyme seen in the mitochondrial membrane. Proton gradient in the thylakoid is the major factor that drives the ATP synthase. This proton gradient will make the protons travel from lumen to stroma through ATP synthase, which leads to the formation of ATP. The enzyme can have two regions. They are FO and F1. FO will be on the membrane and the F1 projects towards the region where the ATP is needed. Hence the correct option is d. 

Q 3. Explain the structure of the FO particle?

Answer: FO is embedded in the thylakoid membrane. It forms a transmembrane channel that facilitates diffusion of H+ ions or protons across the membrane. It is a water insoluble protein. FO is made up of a subunit with c-ring (probably eight copies), other subunits are a, b, d, F6, and the oligomycin sensitivity-conferring protein (OSCP). The peripheral stalk, which is located on one side of the complex, is made up of subunits b, d, F6, and OSCP. F0 is connected to several other subunits that span the membrane, including e, f, g, and A6L.

Q 4. What is rotary catalysis in ATP synthesis?

Answer: The alternating alpha and beta subunits, three of each are arranged around a spinning, asymmetrical gamma subunit in the F1 crystal structure. ATP is produced as a result of the conformational change in α3β3. This rotation of the gamma subunit which led to the conformational change in the α3β3 is called rotary catalysis. 

FAQs

Q 1. Is ATP synthase similar in every organism?
Answer: No, not all organisms have an ATP synthase that is similar. The ATP synthase in bacteria is of the F type and is known as F ATPase. It has 8 distinct subunit types. One of the most extensively researched eukaryotic ATP synthases is seen in yeast, which has its five F1, eight FO, and seven associated proteins. The ATP synthase is organised extremely differently in eukaryotes from certain divergent lineages. Similar to other mitochondrial ATP synthases, Euglenozoa (flagellated protists) ATP synthase dimers have a boomerang-shaped F1 head, but the FO subcomplex contains a variety of distinct subunits. F-ATPases are typically absent in archaea. Instead, they use the A-ATPase or synthase which is a rotary machine that has structural similarities to the V-ATPase but primarily serves as an ATP synthase, to create ATP.

Q 2. Does ATP synthase rotate in a clockwise or counterclockwise direction?
Answer: Two large subunits, named FO and F1, make up the membrane-bound enzyme ATP synthase. When observing ATP synthesis ‘from the bottom’ (looking into the mitochondrial matrix from the intermembrane space), it turns clockwise. 

Q 3. Why is ATP synthase called a rotor stator molecular motor?
Answer: The ATP-driven F1 motor and the proton-driven FO motor, which rotate in opposition to one another, make up the ATP synthase complex. The rotating part of a machine is called the rotor. The non-moving and fixed counterpart in a machine is normally called a stator. On a molecular level, the processes by which rotation and catalysis are related in the active enzyme are now being revealed. Except for the gamma subunit, FO is stationary and F1 is always revolving. As a result, the name rotor stator motor is appropriate for ATP synthase.

Q 4. What does mitochondrial respiratory regulation entail?
Answer: Mitochondria's primary job, which is to produce ATP at a high rate in response to ADP, is encapsulated by mitochondrial respiratory regulation. A high respiratory control indicates that the mitochondria have a minimal proton leak, high substrate oxidation, and high ATP turnover rates.

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