Photosynthesis I: Preliminary PDF

Photosynthesis I: Preliminary Photosynthesis transforms the sun's energy into chemical energy in the form of high energy compounds. the process of photosynthesis can be summarized by the following equation: 6CO2 (g) + 6H2O (l) + energy => C6H12O6 (s) + 6O2 (g) Carbon dioxide and wa...

Photosynthesis I: Preliminary Photosynthesis transforms the sun's energy into chemical energy in the form of high energy compounds. the process of photosynthesis can be summarized by the following equation: 6CO2 (g) + 6H2O (l) + energy => C6H12O6 (s) + 6O2 (g) Carbon dioxide and water, with the energy of the sun, or used to produce glucose and oxygen. This equation represents an overall process, which is composed of over 100 individual reactions that are divided into two sets. The first set, the light-dependent reactions, involve light energy being trapped and used to generate two high energy compounds: adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). In the light-independent reactions, the energy of ATP and reducing power of NADPH are used to make a high energy organic molecule. In leaves, carbon dioxide enters through openings called stomata: water enters plants through the roots and is transported to the leaves through the veins. The CO2 and water diffuse into the cells and then enter the chloroplasts, where photosynthesis takes place. A membrane system within the chloroplastic forms interconnected discs called thylakoids that stack to form grana and are connected by lamellae. The grana within the chloroplasts are surrounded by a fluid called stroma, which contains enzymes that catalyze the conversion of the carbon dioxide and water into carbohydrates. When light is absorbed, it is absorbed in the form of “packets” of energy called photons; each wavelength of light is associated with photons of one distinct amount of energy. The wavelength of the photon, and thus the color of light, that an atom or molecule absorbs is determined by the energy level in that atom or molecule. An atom or molecule can absorb photons only if they have an amount of energy that is exactly equal to the difference between the two energy levels. A compound that absorbs a certain wavelength of light is called a pigment. A photosynthetic pigment traps light energy and passes it onto other compounds. Pigments embedded in the thylakoids absorb light energy, initiating the light-dependent reaction. The main type of photosynthetic pigment in plants is chlorophyll, of which there are two types: chlorophyll-a and chlorophyll-b. The reason that leaves appear green is that a chlorophyll solution absorbs red and blue light, while reflecting or transmitting green light. Another pigment, beta-carotene, part of a very large group of pigments called carotenoids, are also present in leaves. They absorb blue and green light, and reflect yellow, orange, and red. The colored leaves in Autumn are due to the presence of these pigments. Chlorophyll molecules act as clusters of chlorophyll and other pigment molecules, which are embedded in the thylakoid membranes. The core group of chlorophyll molecules and proteins is called a photosystem. When a pigment molecule absorbs a photon, the molecule passes the energy to a pair of chlorophyll-a molecules associated with a specific group of proteins. This is called the reaction centre; the antenna complex includes all surrounding pigment molecules that gather the light energy. When a reaction center receives energy from the antenna complex, an electron in the reaction center becomes “excited”. The electron is raised to a higher energy level, and is passed to an electron acceptor molecule Chloroplasts of plants and algae have two photosystems called Photosystem I and Photosystem II. Photosystems I and II are also called P700 and P680 respectively, for the wavelength of light (in nanometres) the photosystems absorb. They were named for the order discovered, not the order in which they appear in the process - Photosystem II comes first, followed by Photosystem I. Photosynthesis II: The Light-Dependent Reactions The light-dependent reactions of photosynthesis occur in the thylakoid membrane and proceed like so: Step 1: When the P680 molecule absorbs light energy and expels an electron, it becomes positively charged, and can pull electrons from stable water molecules. A water-splitting complex holds two water molecules in place as an enzyme strips for electrons one at a time. P680 plus accepts them and processes them one at a time to an electron carrier. This process repeats a total of four times to form one oxygen molecule from the leftover oxygen from the water, which is released into the atmosphere. The hydrogen ions remain in the thylakoid space. Step 2: The energized electrons are transferred along a series of electron carrying molecules. These molecules are collectively known as an electron transport system. With each transfer of electrons across the system, a small amount of energy is released. The release energy is used by a protein complex called the b6f complex to pump hydrogen ions from the stroma into the thylakoid space across the thylakoid membrane. This pumping of electrons generates a hydrogen ion concentration gradient across the thylakoid membrane. Step 3: Simultaneously, light energy is absorbed by P700. The excited electrons are passed to a high energy electron acceptor, and the lost electrons are replaced by the electrons from the end of the electron transport change from P680. Step 4: The electrons being passed on from P700 are used by the enzyme NADP reductase to reduce NADP to form NADPH. the reducing power of NADPH will be used in the light independent reactions. The electron transport chain utilizes many electron carriers in a series of redox reactions to transfer electrons across the chain to form NADPH at the end. The electron transport chain looks like this: PSII (P680) -> plastoquinone (PQ) -> b6f (cytochrome b6f complex) -> plastocyanin (PC) -> PSI (P700) -> ferredoxin (FD) -> FNR (ferredoxin reductase) (NADP reductase) The movement of hydrogen ions is linked to ATP synthesis by chemiosmosis. The process is called photophosphorylation, since the ultimate energy source is light photons. The hydrogen ions that are pumped from the stroma to the thylakoid space by the b6f complex of the electron transport chain cannot diffuse back across the membrane. The ATP synthase molecule embedded in the thylakoid membrane provides the only pathway for the hydrogen ions to move down the concentration gradient As the hydrogen ions move across the gradient, the energy of the gradient is used to generate ATP molecules The production of ATP by the passing of electrons through the above chain is considered non-cyclic photophosphorylation, as the flow of electrons is unidirectional - straight from PSII to NADP reductase to form NADPH. The passage of one electron pair through the system generates one NADPH and slightly more than one ATP, which is an insufficient ratio for the light independent reactions, which require three ATP molecules and two NADPH. The chloroplasts are able to produce more ATP through cyclic photophosphorylation. When the path is cyclical, excited electrons leave PSI and are passed to an electron acceptor; instead of being used to reduce NADP+, they are passed back to the b6f complex and back to PSI. The same electron is used to generate the proton gradient in the same manner as non-cyclic phosphorylation, an ATP synthase by chemiosmosis also occurs. NADPH and oxygen are not produced by cyclic photophosphorylation. The relative activities of these two pathways vary depending on the relative amounts of ATP and NADPH required by the light independent reactions in the stroma. Photosynthesis III: The Light-Independent Reactions and Alternate Photosynthetic Pathways The key step in the synthesis of carbohydrates in plants is conversion of carbon dioxide to organic compounds, and a process called CO2 assimilation. This assimilation of carbon dioxide occurs by a cyclical pathway that continually regenerates its intermediates. The Calvin cycle, named in honor of its discover Melvin Calvin, converts inorganic carbon in the form of CO2, into organic carbon in the form of the three carbon molecule glyceraldehyde-3-phosphate (G3P), which is used as a starting substrate in other metabolic pathways. The Calvin cycle can be divided into three phases. The first is called carbon dioxide fixation, when the carbon atom in CO2 bonds to a pre-existing molecule in the stroma called ribulose-1,5-bisphosphate (RuBP). The resulting six-carbon compound is unstable and immediately breaks down into two identical three-carbon compounds called 3-phosphoglycerate (PGA). Because these compounds are the first stable compounds of this process, plants that use this method for photosynthesis are called C3 plants; the process is called C3 photosynthesis. CO2 + RuBP => unstable C6 => 2 PGA The reaction is catalyzed by the enzyme ribulose bisphosphate carboxylase (rubisco). The second is called reduction, in which the newly formed three carbon compounds are in a low energy state. To convert them into a high energy state, they are activated by ATP to form 1,3-diphosphoglycerate (DGAL), and then reduced by NADPH, producing two G3P molecules. Some of these compounds leave the cycle to be used for making glucose and other carbohydrates, some remain within the cycle and move on. The third phase is called regenerating RuBP, in which most of the G3P molecules are used to make more RuBP. Energy from ATP is used to break and reform the bonds to make the RuBP from G3P, so the cycle can continue. The Calvin cycle must be completed six times to make one glucose molecule. Of 12 G3P molecules produced by six cycles, 10 are used to regenerate RuBP, and two are used to make one glucose molecule. The net equation for the Calvin cycle is as follows: 6CO2 + 18 ATP + 12 NADPH + water => 2G3P + 16 Pi +18 ADP + 12 NADP+ Rubisco is important to carbon fixation but holds a critical flaw: it can use oxygen as a substrate instead of carbon dioxide. When oxygen binds to RuBP instead of CO2 in photorespiration, the products are two carbon compounds and one PGA. Photorespiration reduces the efficiency of photosynthesis significantly - under normal conditions of temperature of 25° C, C3 plants lose 20% of their energy used to fix one CO2 molecule. In nature, photosynthetic efficiency ranges from 0.1% to 3%. Some plants that are native to hotter, drier climates have developed mechanisms for mitigating photorespiration. C4 plants have a structure that separates the initial uptake of carbon dioxide from the Calvin cycle into different types of cells. In the outer layer of mesophyll cells, CO2 is fixed by addition to a three-carbon compound called phosphoenolpyruvate (PEP) to produce oxaloacetate, giving these plants the name C4. The oxaloacetate is converted to the four-carbon compound malate and transported into the bundle sheath cells where it is carboxylated. The products, a three-carbon compound called pyruvate, are transported back to the mesophyll cells and converted into PEP. The bundle-sheath cells are impermeable to carbon dioxide - CO2 is concentrated in the bundle-sheath cells where the Calvin cycle takes place, making C4 photosynthesis much more efficient. Crassulacean acid metabolism (CAM) plants use a pathway identical to C4 plants, but the reactions take place in the same cell. CO2 fixation is separated from the Calvin cycle by time of day instead of by different cell types. To prevent water loss, CAM plants keep their stomata closed during the day, and carbon fixation happens at night while the stomata is open. The reactions proceed until malate forms, at which point it is stored in a large vacuole until daytime. When the light dependent reactions have produced enough ATP and NADPH, it exits the vacuole and is decarboxylated, freeing the CO2 which is fixed by rubisco and enters the Calvin cycle. Cellular Respiration I: Glycolysis and Pyruvate Oxidation Cellular respiration includes the catabolic pathways that break down energy rich compounds to produce ATP. Aerobic respiration refers to the pathways that require oxygen. The overall reaction is this: C6H12O6 (s) + 6O2 (g) => 6CO2 (g) + 6H2O(l) + energy This process consists of four stages; the primary objective is to make ATP. This happens via substrate level phosphorylation, where a phosphate group is removed from some substrate molecule and combined with ADP to form ATP. A maximum of 38 molecules of ATP are formed by the breakdown of one molecule of glucose. In glycolysis, glucose is split into smaller molecules. This process occurs in the cytoplasm and is anaerobic. There are 10 steps: I. ATP is used to phosphorylate glucose into glucose-6-phosphate, catalyzed by hexokinase.  II. Glucose-6-phosphate is rearranged to form fructose-6-phosphate, catalyzed by phosphoglucose isomerase. III. Fructose-6-phosphate is phosphorylated by ATP to form fructose-1,6-bisphosphate, catalyzed by phosphofructokinase IV. Fructose-1,6-bisphosphate is unstable and splits into two different three carbon compounds: dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P), catalyzed by aldolase V. DHAP is converted into G3P by means of another reaction catalyzed by isomerase. VI. The two G3P molecules are oxidized by NAD+ to form two NADH molecules, then phosphorylated to form two 1,3-bisphosphoglycerate (BPG) molecules; this is catalyzed by glyceraldehyde-3-phosphate dehydrogenase. VII. By substrate level phosphorylation, a phosphate is removed from the two substrate molecules by ADP to form 2 ATP leaving two 3-phosphoglycerate (3PG) molecules - this is catalyzed by phosphoglycerate kinase. VIII. The 3PG molecules are rearranged to form two 2-phosphoglycerate (2PG) molecules, catalyzed by phosphoglyceromutase. IX. A water molecule is removed to form two phosphoenolpyruvate (PEP) molecules; this is catalyzed by enolase. X. ADP is phosphorylated into ATP, leaving two pyruvate molecules; this is catalyzed by pyruvate kinase. In summary: the first five steps convert glucose into G3P; the second five convert the G3P into pyruvate. The net reaction of glycolysis can be written as: glucose + 2NAD+ + 2ADP + 2Pi => 2 pyruvate + 2H2O + 2NADH + 2ATP The process consumes two molecules of ATP and produces four molecules of ATP, making for a net production of two ATP. What follows is an intermediate step to prepare the products of glycolysis for the next stage. The pyruvate is transported from the cytosol into the mitochondrial matrix, where it reacts to convert it into a 2 carbon molecule. The reaction takes place in five steps and is catalyzed by pyruvate dehydrogenase. A carboxyl group is removed from pyruvate, forming CO2 (decarboxylation) The remainder, an acetyl group, is oxidized by NAD+, forming NADH. For every cycle of glycolysis, two pyruvates reduce two NAD+ molecules to form two NADH. It is then associated with a carrier molecule called coenzyme-A (CoA) to form acetyl-CoA. For each glucose molecule that enters glycolysis, two pyruvate molecules are oxidized to form acetyl-CoA, an intermediate to the next major metabolic pathway. This process is commonly called pyruvate oxidation or pyruvate decarboxylation. Cellular Respiration II: The Krebs Cycle and Oxidative Phosphorylation The Krebs cycle, also known as the citric acid cycle or tricarboxylic cycle, is a cyclic pathway occurring in the mitochondrial matrix. Each molecule of acetyl-CoA carries two carbons from the molecule of glucose that originally entered glycolysis. These two carbons will be oxidized and released as carbon dioxide. For each glucose molecule that enters glycolysis, two molecules of acetyl-CoA enter the Krebs cycle. There are eight (nine) steps: I. Acetyl-CoA reacts with a four-carbon molecule called oxaloacetate to form citrate, a six-carbon molecule - this is catalyzed by citrate synthase.  II. Citrate is isomerized to isocitrate, by the removal and subsequent addition of a water molecule. This two-step (hence nine steps total) process is catalyzed by aconitase. III. Isocitrate is oxidized by NAD+ to form NADH, releasing a carbon in the form of carbon dioxide. This leaves behind a five-carbon molecule called ɑ-ketoglutarate. This is catalyzed by isocitrate dehydrogenase. IV. ɑ-ketoglutarate is oxidized by NAD+ to form NADH, releasing a carbon in the form of carbon dioxide. This leaves behind a four-carbon molecule that picks up coenzyme A to become succinyl-CoA. This is catalyzed by ɑ-ketoglutarate dehydrogenase. V. The CoA in succinyl-CoA is replaced by a phosphate via substrate level phosphorylation by guanosine diphosphate (GDP) to form guanosine triphosphate (GTP). The phosphate is then transferred from GTP to ADP to become ATP. The product of this step is called succinate and is catalyzed by succinyl-CoA synthetase. VI. Succinate is oxidized by FAD+ to form FADH2, leaving behind a four-carbon molecule called fumarate. This is catalyzed by succinate dehydrogenase. VII. Water is added to fumarate to form malate, catalyzed by fumarase. VIII. Malate is oxidized by NAD+ to form NADH, making the starting compound, oxaloacetate, and catalyzed by malate dehydrogenase. This is what makes the process cyclic. Per acetyl-CoA molecule that enters the Krebs cycle, two molecules of CO2, three molecules of NADH, one molecule of FADH2, and one molecule of ATP are produced. Since two pyruvate molecules are oxidized for every cycle of glycolysis, the numbers must be doubled to tally per glucose molecule. This would total to four molecules of CO2, 6 molecules of NADH, two molecules of FADH2, and two molecules of ATP. The majority of ATP produced from aerobic respiration comes from the process called oxidative phosphorylation. Much of the energy still resides in the reduced electron carriers, and ADH and FADH2. The two parts of this process occur in the inner mitochondrial membrane. The electron transport chain (ETC) is a series of electron carriers and proteins embedded in the inner membrane of the mitochondrion. There are four complexes labelled I-IV. Each of these complexes use energy released from the passing of the electrons to pump hydrogen ions out of the matrix into the intermembrane space creating a hydrogen ion gradient across the membrane. I. NADH dehydrogenase accepts electrons from NAD+ and pumps protons across the mitochondrial membrane. these electrons are transported to ubiquinone (coenzyme Q) (CoQ) II. Succinate dehydrogenase accepts electrons from FADH2. and thus is irrelevant in the process of ATP synthesis. Sometimes this complex is skipped entirely and the FADH2 pathway starts right at complex III. The electrons are transported to coenzyme Q. III. The bc1 complex oxidizes coenzyme Q and pumps protons across the mitochondrial membrane. These electrons are transported to cytochrome C (Cyt C) IV. The cytochrome oxidase complex oxidizes cytosome C and pumps protons across the mitochondrial membrane. These electrons are transferred to molecular oxygen, combining electrons, protons and oxygen and catalyzing the formation of water. The corresponding positive charge that occurs when the concentration of hydrogen ions increases within the inner membrane space relative to the matrix forms electrical energy that is connected to chemical energy by ATP synthase. As electrons are moving through ATP synthase down their gradient, the energy is used to phosphorylate ADP into ATP. This process is called chemiosmosis. Cellular Respiration III: Net Yield and Anaerobic Respiration Several factors must be accounted for in order to tell you the maximum number of ATP molecules produced. In the electron transport chain, for every two electrons that pass through each hydrogen pump, one ATP molecule is produced. Thus, when two electrons from NADH pass through three complexes, three ATP are produced; when two electrons from FADH2 pass through two complexes, two ATP are produced. The two NAD+ reduced by glycolysis yield two NADH molecules that are unable to pass through the impermeable mitochondrial membrane. The electrons must be carried into the mitochondrion by one of two shuttle mechanisms. In one case, they are delivered to an FAD molecule, producing two atp; in a second case, they're delivered to an NAD+ molecule, producing three ATP. To tally the maximum number of ATP produced from one glucose molecule: 2 ATP are synthesized directly from glycolysis, as well as 2 NADH Depending on which shuttle pathway the NAD+ molecules take, they can either form four or six ATP; these are the indirect contributions by glycolysis. The main product of glycolysis are two pyruvate molecules which enter the Krebs cycle as acetyl-CoA; pyruvate oxidation produces 2 NADH, yielding 6 ATP Going through the Krebs cycle twice for each pyruvate molecule directly yields two ATP, as well as 6 NADH and two FADH2 The 6 NADH produce 18 ATP, and the 2 FADH form 4 ATP; these are the indirect contributions of the Krebs cycle. This tallies to either 36 or 38 total ATP produced by one molecule of glucose. In prokaryotes, since they do not have to expend two ATP to transport the nadh from glycolysis across the mitochondrial membrane, and consistently produce 38. This figure is theoretical, and experimental tallies are much lower. There are many reasons for this. Some protons leak through the inner mitochondrial membrane without passing through an ATP synthase complex. Some of the energy from the hydrogen gradient into the mitochondria is used to transport pyruvate from glycolysis and the cytoplasm to the mitochondria. Some energy is used to transport ATP out of the mitochondria for use and the cytoplasm. Experimental values are closer to 30 to 32 ATP molecules produced per molecule of glucose. Anaerobic respiration is carried out by organisms and environments where oxygen is not as readily available. An inorganic molecule other than oxygen, such as sulfate, nitrate, or carbon dioxide, is used as the final electron acceptor during the chemiosmotic synthesis of ATP. Many single celled organisms, such as yeast, use solely glycolysis for energy, and multicellular organisms use it as the first stage of aerobic respiration. During exercise, for example, oxygen cannot be supplied fast enough to usable cells to keep up with demand, so they rely on glycolysis for energy. The NADH that is being reduced cannot be reoxidized fast enough and must find another pathway, or glycolysis will cease. Different organisms have different ways to reoxidize the reduced NADH, typically by reducing an organic molecule. This is called fermentation. It is much less efficient, only producing the amount of ATP generated during glycolysis, but it is still common. There are two common types: Lactate fermentation is when the pyruvate from glycolysis reacts with NADH to reoxidize it back to NAD+ to be reused in the next cycle of glycolysis. The pyruvate is converted into lactic acid or lactate. In muscles, the lactate must be reoxidized in order to protect the tissues from the acidity which increases through the accumulation of hydrogen  ions. Once oxygen is restored, the lactate is transported out of the cells into the bloodstream, converted back into pyruvate and oxidized, or converted into glycogen and stored in the muscle. Ethanol fermentation is carried out by yeast as well as some bacteria, it which pyruvate is converted to acetaldehyde and carbon dioxide, which is then used to reoxidize NADH back into NAD+ to be used in the next cycle of glycolysis. This leaves ethanol as a product. The byproducts of ethanol fermentation in yeast have been put to use practically, such as the carbon dioxide product in manufacturing baked goods, as well as the ethanol product in alcoholic beverages as well as gasoline.