(Please check out my video about this topic :))
Photosystems:
Photosystems are light harvesting complexes which directly convert energy from the photons of light to excited electrons. They are embedded in the thylakoid membranes and they consist of a reaction center (where chlorophyll a is present) and many antenna pigments that funnel light energy to the reaction center. There are two photosystems: Photosystem II (P680) and Photosystem I (P700). The two photosystems cooperate, and photosystem II is where the whole series light dependent reactions starts.
What happens when the electrons in the reaction center get excited?
One possibility: Noncyclic photophosphorylation
We have to keep in mind that photosystem II and photosystem I cooperate. However, here I'm going to describe the process starting from photosystem II. So first the light energy is captured by photosystem II, and the antenna pigments in photosystem II pass it on to the reaction center containing chlorophyll a. Next, two electrons in the reaction center get excited by the light energy and thus they move to a higher energy level. They are captured by primary electron acceptor. But: two electrons have just been lost from the reaction center, and they need to be replaced somehow. The solution to this is photolysis. Photolysis means essentially splitting of a water molecule to two protons, two electrons and one oxygen atom. Two oxygen atoms combine to form the diatomic oxygen molecule, and the two electrons will are now replaced by the electrons from water.
After the electrons have been accepted by an electron acceptor, they move through an electron transport chain, which consists of plastoquinone (Pq), a cytochrome complex and plastocyanin (Pc). Keep in mind that as the electrons are transferred from one electron carrier to the next (in other words: as one electron carrier is oxidized and the other gets reduced), protons from the chloroplast stroma move through the thylakoid membrane into the thylakoid space called lumen. These protons are going to be essential in ATP synthesis. The ATP synthase is also embedded in the thylakoid membrane, and the protons that have migrated to the lumen are goig to flow through the ATP synthase, providing energy for the phosphorlyation of ADP into ATP ( the reaction is ADP + Pi -> ATP). This is just like in the electron transport chain in animal cells.
Now, at the end of the first electron transport chain, these excited electrons form photosystem II will replace the excited electrons from photosystem I. What happens in photosystem I is very similar to the scenario in photosystem II. The electrons in the reaction center get excited by the photons of light, but this time, they are replaced by electrons from photosystem II, the same ones that have moved down this first electron transport chain.
The excited electrons from photosystem I also move down an electron transport chain. The difference here, though, is that at the end of this electron transport chain, NADPH is made. What happens is that NADP+ is reduced to NADPH because it accepts two protons and these two electrons that have travelled down this electron transport chain.
Another possibility: Cyclic flow
When there is a shortage of ATP, but not NADPH, more ATP can be produced using the cyclic flow mechanism. The essence of the cyclic flow is recycling of electrons. This takes place when the two excited electrons in photosysthem I are are accepted by primary electron acceptor, but then they travel back to the cytochrome complex in the electron transport chain which they have already passed through (the first electron transport chain). This causes an increase in proton gradient in the thylakoid lumen, which increases the rate of the phosphorylation of ADP into ATP.
(Please check out my video about this topic :))
Photosynthesis is important for all of us. It is the mechanism the plants utilize to convert light energy from a light source (like our sun) to chemical bond energy and fix the that enters the plant into organic compounds (glucose). This is what makes the plant alive, so that either humans can eat it and get the nutrients they need, or animals can eat the plant to obtain essential nutrients and later humans can eat the animal and get the nutrients from the animal. This is why photosynthesis is essential for life on Earth. But how do plants do it?
The process of photosynthesis takes place in the chloroplast, which is an organelle in the plant
cell. Photosynthesis is a series of different reactions, which are subdivided into light dependent and light independent reactions. The chloroplast is enclosed by a double membrane, and it contains grana, which
consist of layers of thylakoid membranes where the light dependent
reactions occur, and stroma, where the light independent reactions
occur. In order to convert this light energy into chemical bond energy that plants can use, we need some substances that can absorb this light energy first and foremost, and these substances are called pigments.
The chloroplast looks like this:
Pigments absorbing light energy:
Light energy is captured by the pigments in the plants. There are different kinds of pigments, all depending on what wavelenghts of visible light they absorb. In plants we have chlorophylls (absorb wavelengths of light in red, blue and violet range) and cartenoids (absorb wavelengths of light in blue, green and violet range).
There are two types of chlorophyll: chlorophyll a and b. Chlorophyll b and cartenoids are called antenna pigments because they absorb the light energy from the sunrays striking them and transfer photons of light to chlorophyll a, which is directly involved in the transfer of electrons which happens in light independent reactions. The picture below shows what wavelengths different pigments absorb:
Light dependent reactions: Light energy is directly used to make ATP and NADPH
The energy from the sun that is transferred to chlorophyll a by antenna pigments is used to excite electrons in chlorophyll a-molecules to make these electrons available to be caught by primary electron acceptor and then transported through the electron transport chain.The flow of electrons in the electron transport chain provides energy to reduce ADP and NADP+ to ATP and NADPH. Double bonds in chlorophyll a molecules are important because they are source of the excited electrons. The picture below shows the structure of chlorophyll a:
Light independent reactions, or the Calvin cycle: ATP and NADPH from light dependent reactions are used to fix carbon in carbondioxide to glucose.
This is a cycle where carbondioxide is fixed to form a 3-carbon sugar, phosphoglyceraldehyde (also called PGAL or G3P), after 3 runs of the cycle, so the cycle needs to run three times to produce one molecule of glucose. The Calvin cycle occurs only in light, even though it does not directly use light energy. Instead, it uses ATP and NADPH from the light reactions and oxidizes them back to ADP and NADP+.
The electron transport chain (ETC) takes place in the inner mitochondrial membrane. During this process, the electrons donated by the electron carriers (such as NADH) pass through a chain of protein complexes embedded in the inner mitochondrial membrane. These electron carrieres were reduced during processes occuring before the ETC, for instance glycolysis and citric acid cycle.
(the ETC takes place in the inner membrane)
The movement of electrons initiates pumping of protons to the intermembrane space. This way, a proton gradient is created, and thus, the protons from the intermembrane space will flow back to the matrix through the ATP synthase, which is embedded in the inner mitochondrial membrane. When protons flow through the ATP synthase, ATP is made.
The image above gives us a pretty detailed picture of the process. Let's now examine it:
As you can see, there are four protein complexes embedded in the inner mitochondrial membrane. The ATP synthase, which you can see on the right side of the image, isn't considered a part of the ETC. Let's look what happens in each complex:
(PLEASE LOOK AT THE PICTURE ABOVE FOR REFERENCE. I ALSO INVITE YOU TO WATCH MY VIDEO ABOUT THIS TOPIC HERE)
Complex I: The NADH donates its two electrons to complex I. These electrons are first accepted by FMN, and then flow to the iron-sulfur center, which is also an electron acceptor. Next, these two electrons are transferred to a mobile protein called ubiquinone (or coenzyme Q). Coenzyme Q then moves through the phospolipid bilayer and donates these two electrons to complex III (yes, to complex III, not to complex II). This leads to pumping of four protons (4 H+) to the intermembrane space.
But let's hold on for a second and see what happens in complex II:
Complex II: This is where succinate comes in and reduces FAD to form FADH2. This way, it donates two electrons. These two electrons are going to be transferred to the iron-sulfur center and later to ubiquinone.
Complex III: The ubiquinone reduces the cytochrome b by giving away the two electrons. Then, cytochrome b is oxidized and the electrons travel to the iron-sulfur center. From there, they are passed to the cytochrome c1. Next, the cytochrome c1 captures these two electrons. Since cytochrome c1 can move from complex III to complex IV, it moves and thus carries these electrons to complex IV. When electrons are transferred from complex III to cytochrome c, four protons are also pumped from the matrix to the intermembrane space.
Complex IV: First of all, after cytochrome c has arrived, it gives the two electrons that it carries. These electrons are given to reduce cytochrome a. Then, they are passed to cytochrome a3, and later, to oxygen, the final electron acceptor. When oxygen accepts electrons (and two protons from the matrix), water is formed. When the electrons are transferred in complex IV, only two protons are pumped into the intermembrane space.
ATP synthesis:
(the awesome picture below, which I found online, for educational purposes only, illustrates the process)
The movement of electrons provided energy for pumping protons to the intermembrane space. Next, these protons are going to flow through the ATP synthase back to the matrix. As they flow through ATP synthase, they initiate movement of the top part of the ATP synthase (the one with C10 subunits). This again makes the gamma subunit spin. Since the lowest part of the ATP synthase doesn't move, the spinning of gamma subunits causes conformational changes in the beta subunits. These beta subunits are the subunits that synthesize ATP out of ADP and Pi, which are already present in the matrix.
(PLEASE CHECK OUT THE VIDEO ABOUT THIS TOPIC :))
The citric acid cycle is the process that occurs during cellular respiration after the cell has successfully completed glycolysis and after the pyruvate has gone through the pyruvate dehydrogenase complex, where the end product was the Acetyl-CoA. This molecule is now going to be oxidized to CO2, by the series of reactions in the citric acid cycle. During the citric acid cycle, the cell makes some ATP, GTP and some electron carriers: NADH and FADH2. These electron carriers are later going to be utilized in the electron transport chain, to make more energy. The citric acid cycle takes place in the mitochondrial matrix.
The steps of the citric acid cycle:
1. Oxaloacetate is joined together with Acetyl-CoA, forming citrate. One water molecule is consumed, and the CoA is kicked off. The enzyme that is used here to catalyze the reaction is called citrate synthase.
2. Citrate is isomerized to form isocitrate. The enzyme that catalyzes this reaction is called aconitase.
3. Isocitrate is oxidized to form alpha-ketoglutarate. During this reaction, an NAD+ is reduced to form NADH, and carbondioxide is also released. The enzyme that plays the crucial role here is the isocitrate dehydrogenase
4. Thanks to the alphaketoglutarate dehydrogenase, the alpha-ketoglutarate becomes succinyl CoA. An NAD+ gets reduced and forms NADH, the CoA is joined to the molecule and CO2 is released.
5. Succinyl-CoA is now converted to succinate. The CoA is kicked off, and one GDP gets reduced to form GTP. An ADP comes in and takes the phosphate group from the GTP, so that it can become ATP. The enzyme that catalyzes this reaction is called succinyl-CoA synthetase. It has this name because the reaction is reversable.
6. The succinate is oxidized into fumarate. Two of the hydrogen atoms in the succinate are kicked off and picked up by the FAD. This way, the FAD is reduced to form FADH2, which is later going to be utilized in the electron transport chain. The enzyme that removes these hydrogens from th succinate is called succinate dehydrogenase.
7. Fumarase reduces fumarate to form malate. The way it does that is that it joins one water molecule to the fumarate.
8. Lastly, malate dehydrogenase removes hydrogens from the malate. Thus, malate is converted back to oxaloacetate, the molecule we started with. The hydrogens are picked up by the electron carriers.
Pyruvate dehydrogenase complex is a mechanism that occurs between glycolysis and the citric acid cycle. This is because pyruvate cannot enter the citric acid cycle right after glycolysis. The purpose of pyruvate dehydrogenase complex is to modify (or convert) pyruvate, the end product of glycolysis, to the acetyl CoA, which enters the citric acid cycle.
The enzymes involved are:
- E1: Pyruvate dehydrogenase (the TPP, or thiamine pyrophosphate is attached to it)
- E 2: Dihydrolipoyl transacetylase (the lipoic acid is attached to it)
- E 3: Dihydrolipoyl dehydrogenase (the FAD is attached to it)
Let's now look at what happens in details (please, look at the picture below while you read):
E1:
First of all, pyruvate comes in and interacts with TPP, which is attached to E1 (pyruvate dehydrogenase). TPP has a ring that interacts directly with pyruvate. As a result, a CO2 is released, and the rest of the pyruvate (the hydroxyethyl group) is attached to the TPP, forming hydroxyethyl TPP.
E2:
Next, the hydroxyethyl group is transferred to the disulfide bond in the lipoic acid. Remember, the lipoic acid is attached to the second enzyme (E2) of the pyruvate dehydrogenase complex, the dihydrolipoyl transacetylase. That leads to the reduction of one of the sulfurs, because it gains hydrogen (this hydrogen comes from the hydroxyethyl group). The hydroxyethyl group without one of this hydrogens, which was given off to this sulfur is now forming acetyl group. An acetyl group attached to a sulfur forms a thioester bond, which is a high energy bond. The CoA-SH comes in and takes the acetyl group from this sulfur on the lipoic acid. CoA-SH also gives of its hydrogen to the sulfur, so now, we have made the acetyl CoA.
(Both of the sulfurs that before formed the disulfide bond are now reduced, because each of them has a hydrogen)
E3:
Furthermore, the lipoic acid cannot react with the hydroxyethyl TPP, because it doesn't have the disulfide bond. The FAD, which is attached to the third enzyme, dihydrolipoyl dehydrogenase, picks up these hydrogens, regegenerating the disulfide bond. As a result, FADH2 is formed. However, it cannot flow right to the ETC (electron transport chain), because it is attached to the dihydrolipoyl dehydrogenase. The NAD+ then comes in and becomes reduced to NADH + H+.
In addition:
The TPP is regenerated when hydroxyethyl group is removed from hydroxyethyl TPP.
The lipoic acid is regenerated when the disulfide bond is regenerated.
The FAD is regenerated when NAD+ comes in and picks up the hydrogen (a hydrogen ion is also released as a result of that) from FADH2.
This is going to be much easier to understand if you watch my video about this :).
Please, check out my video about enzymes :)
What are enzymes?
Enzymes refer to proteins that catalyze chemical reactions in our body. They are also called catalytic proteins. Enzymes speed up (or catalyze) chemical reactions by lowering the energy of activation (EA), which is the amount of energy needed to start a reaction. Enzymes exhibit tertiary structure.
How do enzymes work?
An enzyme binds to a substrate, forming enzyme-substrate complex. Thus, enzymes bind to the substrates when they are ''in action'', or when they catalyze a reaction. When an enzyme binds to a substrate, the shape of the enzymes alters as the substrate enters the active site, which is the place on the enzyme where the substrate can bind. Enzymes are substrate specific, which means that for instance enzyme A binds only to the substrate A etc.
However, enzymes often require assistance from substances called coenzymes and cofactors. These are substances that help enzymes in reaction catalysis, but cannot catalyze a reaction on their own. Coenzymes are organic substances, while cofactors are inorganic.
Competitive and noncompetitive (allosteric) inhibition
The enzymatic activity is highly controlled and regulated. This can be done in a number of ways. For instance, genes that code for a specific enzymes can be switched on and off. The enzymes that have already been produced are regulated by competitive and noncompetitive inhibition.
Competitive inhibition means that the substrate and a substrate-like substance (an inhibitor) ''competete'' for the active site of the enzyme. If the inhibitor binds to the enzyme, the enzyme won't work.
Noncompetitive inhibition, also known as allosteric inhibition, means that the inhibitor binds to another site of the enzyme (not to the active site). That causes the whole enzyme to undergo a change in its conformation, and the active site is changed. Thus, it's impossible for the substrate to bind to the enzyme.
PLEASE WATCH THIS VIDEO THAT I'VE MADE ABOUT GLYCOLYSIS :)
Step 1:
A phosphate is attached to the glucose molecule. The phosphate comes from ATP, which becomes ADP after donating the phosphate. The enzyme that facilitates this reaction is called hexokinase. When the first step is finished, we have
glucose-6-phosphate.
Step 2:
An isomer of glucose-6-phosphate is created by the enzyme phosphoglucose isomerase. The isomer created is called fructose-6-phosphate.
Step 3:
The enzyme called phosphofructokinase attaches a phosphate from ATP to fructose-6-phosphate. The phosphate is attached on the first carbon of
fructose-6-phosphate, so the product that is formed is fructose1,6-bisphosphate. Of course, ATP donated a phosphate, so it left off as ADP.
Steps 4 and 5:
In the fourth step, the enzyme aldolase splits fructose 1,6-bisphosphate to two three-carbon molecules, which are isomers of each other. These are dihydroxyacetone phosphate and glyceraldehyde 3-phosphate.
In step 5, the enzyme triphosphate isomerase converts dihydroxyacetone phosphate into glyceraldehyde 3-phosphate.
(Remember, since we have now 2 three-carbon molecules, so there is double amount of each product from now. For instance, if one ATP is produced from one three-carbon molecule, there are two ATP molecules produced in total.)
Step 6:
Glyceraldehyde 3-phosphate is converted to 1,3-bisphosphoglycerate. The enzyme that catalyzes this reaction is called glyceraldehyde phosphate dehydrogenase. Hydogen ion is released, and NAD + Pi come in. Pi is donated to the glyceraldehyde 3-phosphate, and it is attached to the 1st carbon. NAD picks up the hydrogen ions. What we get is 1,3-bisphosphoglycerate.
Step 7:
The phosphate is removed from 1,3-bisphosphoglycerate, and 3-bisphosphoglycerate is formed. The phosphate that has been removed is attached to the ADP that comes in, so it becomes ATP. The enzyme that catalyzes this reaction is phosphoglycerate kinase.
Step 8:
The enzyme phosphoglyceromutase removes the phosphate from the third carbon of the 3-phosphoglycerate, and attaches it on the 2nd carbon. Thus, 3-phosphoglycerate becomes 2-phosphoglycerate.
Step 9:
2-phosphoglycerate is converted to phosphoenolpyruvate by enolase. During this reaction, water is released.
Step 10:
Phosphoenolpyruvate (PEP) looses its phosphate. This phosphate is donated to ADP, so it becomes ATP. The enzyme that catalyzes this reaction is called pyruvate kinase. The end product of glycolysis is pyruvate, which is used later in cellular respiration.
