Photosynthesis and Cellular Respiration Project PDF

Cell Respiration 1.​ Describe the structure of ATP and explain why its properties make it suitable for energy transfer within cells The structure of ATP consists of a nitrogenous base, adenine, the five carbon sugar ribose and three phosphate groups in a chain which are negatively charg...

Cell Respiration 1.​ Describe the structure of ATP and explain why its properties make it suitable for energy transfer within cells The structure of ATP consists of a nitrogenous base, adenine, the five carbon sugar ribose and three phosphate groups in a chain which are negatively charged, so ATP is classified as a nucleotide. ATP is often described as the energy currency of the cell as it is used for temporary storage of energy and for energy transfer between processes as well as different parts of the cell. During the process of hydrolysis, ATP is converted into ADP and a phosphate releases a small amount of energy, but this energy is enough for many processes within the cell and if any more energy is released it would be wasted by conversion to heat. 2.​ Outline three cellular processes that require ATP providing specific examples for each ATP can be used in the process of synthesizing macromolecules as synthesizing macromolecules is an anabolic process that involves the conversion of ATP to ADP. One or more ATP molecules is used every time a monomer is linked to the growing polymer and during synthesis of DNA when replication is occurring, RNA in transcription and proteins in translation all require energy from ATP. ATP can be used in active transport as pumping ions or other particles across a membrane against the concentration gradient requires energy from ATP. A pump protein changes between two confirmations, one that’s stable and one that’s less stable, during active transport and ATP is used to cause the change from the more stable conformation to the less stable conformation. The change back to the stable conformation happens without the use of energy. ATP can be required by cells for movement. An example would be muscle cells which can contract powerfully using large amounts of actin and myosin filaments and can exert force by sliding across each other with the use of ATP energy. 3.​ Explain the energy transformations that occur when ATP is hydrolyzed to ADP and when ADP is converted back to ATP ATP contains more chemical potential energy than ADP, so energy is released to convert ATP to ADP and a phosphate. Even though the amount of energy is relatively small, the energy is crucial to many processes within the cell. In some instances, the phosphate group can be attached to another molecule, such as a protein pump in a membrane or a substrate in a metabolic reaction and when the phosphate group detaches from a molecule it releases energy. This energy can create a change in the molecule such as a conformational change in membrane pump or a chemical change that converts a substrate into a product. Energy plays a key role in the conversion of ADP and a phosphate back to ATP and this energy can come from cell respiration, where energy is released by oxidizing carbohydrates, fats or proteins, photosynthesis, in which light energy is converted to chemical energy, and chemosynthesis, which is where energy is released by oxidizing inorganic substances such as sulfides. There is not an abundance of ATP within the cell and if ATP runs out, then all processes that require energy stop. This will cause irreparable damage to the cell and will lead to cell death. This is normally prevented by continual regeneration of ATP from ADP and a phosphate, however energy transfers during inconversions between ATP and ADP are 100% efficient, which causes some of the energy to become heat. 4.​ Compare and contrast the processes of cell respiration, and gas exchange, emphasizing their roles and energy production Cell respiration is a function of life that is performed by all living cells and is the process of breaking down organic molecules to produce ATP. In cell respiration,carbon compounds are oxidized to release energy, which is used to produce ATP. In many cells, cell respiration uses oxygen and produces carbon dioxide, therefore making it imperative for oxygen to enter cells through the plasma membrane, while simultaneously the carbon dioxide exits the cell. Together these movements are classified as a gas exchange, even though they do not involve direct one for one swapping of molecules. In contrast, both carbon dioxide and oxygen move across the membrane independently by simple diffusion. Gas exchange and cell respiration are different processes that are both dependent on each other. Without gas exchange, cell respiration would not be able to occur as there would be a lack of oxygen and an abundance of harmful carbon dioxide within the cell. And without cell respiration, gas exchange would be able to continue because the use of oxygen and production of carbon dioxide in respiration create the concentration gradients which cause the gases to diffuse. 5.​ Compare the processes of anaerobic and aerobic respiration in terms of substrates products, ATP yield and cellular location Cell respiration can be performed through a range of alternative metabolic pathways and some pathways are aerobic, meaning they use oxygen, while other pathways are anaerobic, meaning no oxygen is needed. In aerobic respiration, oxygen is used as an electron acceptor in oxidation reactions, carbohydrates such as glucose, lipids including fats and oils and amino acids after deanination can be used, and carbon dioxide and water are waste products. The yield of ATP in aerobic cell respiration is more than 30 ATP molecules per glucose. In anaerobic respiration, other substances act as oxygen acceptors in oxidation reactions, only carbohydrates can be used, and carbon dioxide plus either lactate or ethanol are the waste products, while water is not produced. The yield of ATP in anaerobic cell respiration is only 2 ATP molecules per glucose. 6.​ Design an experiment to measure the effect of temperature on the rate of cellular respiration in germinating seeds An respirometer measures any volume changes that are due to oxygen intake only since all carbon dioxide is absorbed by the base. The production of carbon dioxide usually adds to the volume of the air in the atmosphere while the oxygen intake reduces it. Since the base in the respirometer absorbs the carbon dioxide, it can now only measure the changes in volume that the oxygen intake causes. Respirometers are able to give accurate results as long as the variables, temperature and pressure, are controlled since temperature and pressure interact with each other and volume. An example of why making sure the variables are controlled is essential is that if air pressure outside the respirometer changes, the fluid in the capillary tube of some types of respirators will move without any oxygen uptake. 7.​ Explain the role of NAD in cellular, respiration, emphasizing its function in redox reactions Oxidation and reduction are chemical processes that always occur together and this happens because they involve transfer of electrons from one substance to another. Oxidation is the loss of electrons from a substance and reduction is the gain of electrons. Electron carriers are substances that can both accept and lose electrons and they are able to link oxidations and reductions in cells. The main electron carrier in respiration is NAD (nicotinamide adenine dinucleotide) The equation NAD + 2 electrons -> reduced NAD is the basis reaction of NAD. At first, NAD has one positive charge and exists as NAD+. However, substances are oxidized in respiration by removing two hydrogen ions and each hydrogen consists of an electron and a proton. NAD+ accepts two electrons and one proton from the hydrogen atoms and becomes NADH. NADH transports electrons to the electron transport chain. Then the other proton (H+) is released and creates NADH + H+. For simplicity, NAD in its reduced form is often shown as reduced NAD, rather than NADH + H+. Reactions involving NAD show that reduction can be achieved by accepting atoms of hydrogens, because they hold an electron. Therefore, oxidation can be accomplished by losing hydrogen atoms. 8.​ Describe the process of glycolysis, including phosphorylation, lysis, oxidation and ATP formation Glycolysis is the first part of aerobic respiration where glucose or another monosaccharide is the substrate, and it occurs in the cytoplasm and cells. In glycolysis glucose is converted to pyruvate by a chain of reactions each of which is catalyzed by different enzymes. The phosphorylation of glucose is stage one of Glycolysis. Phosphorylation is the addition of phosphate to a molecule and requires energy, but makes a molecule more unstable, and therefore is more likely to participate in subsequent reactions. In cells, many phosphorylations are carried out by transfers of phosphate from ATP. In the first stage of glycolysis, glucose is phosphorylated, and the reaction is usually shown in the way where phosphorylation of glucose is coupled to the conversion of ATP to ADP. In the first reaction, the phosphate is linked to the sixth carbon atom of the glucose molecule. In the next reaction glucose is converted to fructose creating a symmetrical molecule that can be split in half and then create a second phosphorylation. Stage two of glycolysis is lysis, and this is where the fructose bisphosphate is now split to form two molecules of triose phosphate. Stage 3 of glycolysis is oxidation where each of these triose phosphate is oxidized by removing a hydrogen atom. The hydrogen is accepted by NAD, which becomes reduced NAD and oxidation of sugar produces an organic acid. Stage four of glycolysis is ATP formation, where ATP is produced in the final reactions of glycolysis by transfer of phosphate groups to ADP. This occurs twice because bisphosphoglycerate has 2 phosphate groups. In these reactions the glycerate is converted to another organic acid pyruvate, and this is the end product of glycolysis. Two bisphosphoglycerate molecules are produced per glucose and each of them yield two ATP’s. Four ATP‘s are therefore produced per glucose in these final reactions of glycolysis. The overall outcome of ATP formation is that there’s a net yield of two ATP because two are used in the first stage of glycolysis and four are used in the final stage. 9.​ Explain how the conversion of pyruvate to lactate enables glycolysis to continue during anaerobic respiration Both ADP and NAD must be replenished for the process of glycolysis to continue in the cell. ADP will only run out if it has been converted to ATP, in which case there is no need to carry out glycolysis and NAD will run out unless it’s regenerated by oxidation of reduced NAD. There are several methods of regenerating NAD and in each case two hydrogen atoms (two protons and two electrons) are transferred to another molecule, which then oxidizes reduced NAD. In some human cells, and also some animals and bacterial cells hydrogen is transferred from reduced to pyruvate which is then reduced to lactate during anaerobic respiration. Two NAD molecules are used as each glucose is converted by glycolysis to pyruvate. Two pyruvates are produced and each of them can be used to convert a reduced in NAD back to NAD so all the NAD that was used in glycolysis is regenerated. For this reason cells should not run out of NAD as long, and as glucose is available and lactate concentration does not rise too high, anaerobic cell respiration should be able to be carried out in this way indefinitely. 10.​Discuss the use of anaerobic respiration in yeast for brewing and baking and outline the chemical pathways involved An aerobic stealth respiration by glycolysis converts pyruvate to ethanol and carbon dioxide is known as ethanol fermentation or alcoholic fermentation. This is used in both baking and brewing, and in both cases the organism that carries out the fermentation is yeast. Yeast is a unicellular fungus that occurs naturally in habitats where glucose or other sugars are available. Yeast is a facultative anaerobe meaning they can expire either aerobically or anaerobically. In the case of bread, in order to give bread a lighter texture yeast is often added to the dough to create bubbles of gas. If the dough is kept warm, the yeast will grow and expire and initially it will respire aerobically, but once all the oxygen in the dough has been used up, the yeast starts to expire and aerobically. Because the dough is very sticky, the carbon dioxide produced by anaerobic cell respiration cannot escape; instead it forms bubbles within the dough and these bubbles cause the dough to rise. While ethanol is also produced by anaerobic cell respiration, it evaporates during baking. 11.​Explain how pyruvate is converted into acetyl-CoA in the link reaction and its significance for aerobic respiration If oxygen is available, pyruvate can be oxidized to carbon dioxide and water and this gives a much higher yield of ATP than anaerobic cell respiration. Most of the reactions are part of the Krebs cycle, but an initial reaction is conversion of pyruvate from glycolysis into a two-carbon acetyl group. This conversion forms a link between glycolysis and the Krebs cycle, so it is referred to as the link reaction. In the link reaction, a complex of three enzymes are used to carry out processes. The first one is decarboxylation by removal of carbon dioxide in order to change three-carbon pyruvates into a two-carbon molecule. The next enzyme is oxidation by removal of two electrons. These electrons are accepted by NAD and therefore convert it into reduced NAD. The last enzyme is the binding of the acetyl group which was produced by the previous processes, to a complex carrier molecule called coenzyme A and the product is acetyl coenzyme A. 12.​Describe the key steps of the Krebs cycle, including the roles of oxidation, decarboxylation and substrate level phosphorylation Acetyl groups produced by the Link reaction are oxidized in a cycle of reactions that happen in the matrix of the mitochondria. This cycle is known as the Krebs cycle and acetyl groups are fed into the cycle by transfer from enzyme a to oxalate, therefore producing the organic acid citrate. Oxaloacetate has four carbon atoms and citrate has six and citrate is converted back into oxaloacetate by a series of enzyme catalyze reactions. The number of carbon atoms is decreased by two carboxylation reactions, in which carbon and oxygen are removed producing carbon dioxide. In aerobic cell respiration, all of the carbon in substrates such as sugar or fat is removed by decarboxylation in the Krebs cycle or the link reaction. Four reactions in the Krebs cycle are oxidation and release energy and much of the released energy is held by the electrons that are removed in the oxidation and these electrons are transferred either to NAD or FAD. Both of these molecules act as carriers of electrons, however they also accept protons meaning they are hydrogen carriers as well. When FAD or NAD accept a pair of electrons they become reduced. Reduced NAD and reduced FAD transfer electrons and the energy they are holding to the electron transport chain in the inner mitochondrial membrane. The net effects of one turn of the Krebs cycle are that one acetyl group is consumed, three NAD‘s are converted to reduced NAD and one FAD to reduce FAD, two molecules of carbon dioxide are released and one ADP is converted to ATP. 13.​Outline the role of the electron transport chain and cellular respiration, including the role of reduced NAD In the inner mitochondrial membrane there are groups of proteins that act as electron carriers by accepting and then passing on pairs of electrons. Together this sequence of carriers forms the electron transport chain, and the first carrier in the chain except a pair of electrons that were donated by NADH and this changes the carrier from an oxidized state to a reduced state and converts the reduced in NAD back to NAD. The carrier gains chemical energy by the transfer of electrons. The energy from the electron transport chain pumps protons across the membrane which creates a gradient. This gradient is used by ATP synthase to produce ATP in which cells use for energy. 14.​Explain how the flow of electrons along the electron transport chain generates a proton gradient The three main carriers in the electron transport chain each act as proton pumps, and they use energy release by the flow of electrons in the electron transport chain to protons across the inner mitochondrial membrane from the matrix to the membrane space between the inner and outer mitochondrial membranes. The first and second main electron carriers each pump four protons per pair of electrons, the third carrier pumps two. The electrochemical gradient is created when protons are pumped across the membrane during the electron transport chain, therefore building up a high concentration of protons in one area. 15.​Describe the process of chemiosmosis and its role in ATP synthesis in the mitochondrion ATP synthesis is a large and complex protein that phosphorylates ADP to produce ATP. This is an energy absorbing reaction so a source of energy is needed, and this energy is provided by the proton gradient created by the electron transport chain. This process used to couple with the proton gradient to synthesis of ATP called chemiosmosis. Chemiosmosis is the mechanism used by ATP synthesis to make ATP. The mechanism consists of a drum shaped part of ATP synthase, located in the membrane which consist of identical subunits each of which has a binding site for a proton. Next to this is another structure in the membrane which has 2 half channels for protons. One of these channels allows protons from the inter membrane space to embed to the subunit of the drum. The other half channel allows protons that were bound to a sub unit to exit the matrix. These 2 half channels are not aligned so for the protons to pass through the drum has to rotate. The energy released by movement of protons down their concentration gradient is transformed into kinetic energy and each proton is carried by the drum for almost a full rotation before it is released. The drum is connected to a stock that projects into a matrix and because of the tight connection rotation of the drum causes a stock to rotate at the same rate. The drum and the stock stock together are known as the rotor of ATP synthesis. In osmosis, a concentration gradient causes water to move across the membrane, but the energy released by this process is not utilized. In chemiosmosis, protons move down the concentration gradient from the high concentration into the intermembrane space to the lower concentration in the matrix. The energy release is used to link a phosphate group to ADP producing ATP. 16.​Explain the role of oxygen as the terminal electron acceptor and the electron transport chain ATP production by mitochondria can only continue when there is an electron flow and proton pumping, and this depends on reduced NAD supplying pairs of electrons to start the electron transport chain and for the electrons to be removed at the end of the chain. Each electron carrier in the ETC has a stronger affinity for electrons in the previous one so removal of electrons from the last electron carrier can only be done by a substance that has a very strong affinity for electrons. Most organisms use molecular oxygen for this purpose, and it is known as the terminal electron acceptor. The use of oxygen is the stage and aerobic cell respiration however, all of the previous stages apart from glycolysis depend on oxygen. Molecules of oxygen accept electrons from the final electron carrier and hydrogen ions from the matrix, therefore producing water. This also makes oxygen the final electron acceptor. 17.​Compare lipids and carbohydrates as respiratory substrates in terms of energy yield, and metabolic pathways There are many differences between lipids and carbohydrates as respiratory substrates. In carbohydrates, the first stage of respiration with sugar, such as glucose and fructose as a substrate is glycolysis. This generates some ATP and does not require oxygen therefore, anaerobic respiration is possible. Pyruvate can be converted to acetyl groups by the reaction and the acetyl groups can then be fed into the Krebs cycle. These stages can only happen if oxygen is available. As for lipids, the first stage of respiration with lipids, such as fat and oils is the breakdown of fatty acids to acetyl groups in the matrix of the mitochondrion. The acid groups are fed into the Krebs cycle and these stages only happen if oxygen is available so anaerobic respiration is not possible with lipids. For carbohydrates the energy yield program of carbohydrates is only 17 kJ per gram and this is about half that from lipid. Energy is released from a substrate by oxidizing carbon and hydrogen and in carbohydrates more than 50% of the mass is oxygen which does not yield energy. As for lipids, the energy yield program is 37 kJ per gram and this is nearly twice as much as that from carbohydrates. Nearly 90% of the mass of lipids is carbon and hydrogen from which there is a yield of energy in respiration. Photosynthesis 1.​ Describe the transformation of light energy to chemical energy during photosynthesis and its importance in ecosystems Light energy is absorbed by pigments that transform and transfer the energy to complex systems of molecules known as photosystems. There are collections of proteins found on thylakoid membranes of cyanobacteria, algae, and plants. They use the energy from light to reduce other molecules. Photosynthesis is an energy conversion, as light energy is converted into chemical energy in carbon compounds. The main groups of carbon compounds produced are carbohydrates, proteins, lipids, and nucleic acid. This transformation supplies most of the chemical energy needed for life processes in the ecosystem. In photos systems, ATP and NADPH are produced. 2.​ Outline how carbon dioxide is converted into glucose during photosynthesis, including the source of hydrogen Plants convert carbon dioxide and water into carbohydrates by photosynthesis. The equation that represents this process is: Carbon Dioxide + Water —> Glucose + Oxygen Hydrogen is needed for the reduction reaction that converts carbon dioxide into glucose. This hydrogen comes from photolysis, which is a reaction that splits molecules of water and this reaction only happens when light is available to provide energy. The formation of glucose can be linked to the Calvin cycle because the Calvin cycle is a process in plants where carbon dioxide is converted into glucose. This relates to glucose formation as it is similar to the plant's way of making sugar. 3.​ Explain the role of water in photosynthesis and identify the origin of oxygen as a byproduct Oxygen is a byproduct of photosynthesis and is usually a waste product. Oxygen is created when water molecules are split, and this process is known as photolysis. Prokaryotes were the first organisms to perform photosynthesis starting about 3500 million years ago. Millions of years ago algae and plants also began carrying out photosynthesis using chloroplast. Photolysis increases the concentration of oxygen inside the chloroplast and this causes oxygen to diffuse out of the chloroplast and then out of the leaf cells to air spaces inside the leaf. The oxygen then diffuses through the stomata to the air outside the leaf. The products of photolysis are oxygen, protons and electrons. 4.​ Design an experiment to separate and identify photosynthetic pigment using chromatography Chloroplast contains several types of chlorophyll, along with other pigments called accessory pigments. These pigments absorb different ranges of wavelength of light so they look different colors to us. Pigments can be separated by chromatography. Pigments are separated by solubility meaning that as a solvent travels along a leaf, more soluble pigments travel further while less soluble ones will stay behind. This differentiates the different chlorophyll pigments. The Rf value as a ratio is: The distance run moved by pigment divided by the distance run moved by solvent. 5.​ Explain the relationship between light wavelength, and the absorption of light by photosynthetic pigments The first stage in photosynthesis is the absorption of sunlight and this involves chemical substances called pigments. Pigments absorb light and so they appear different colors to us and the colors we see depend on the specific light wavelength that the pigment absorbs and transmits. A photon is a particle or unit of light and photons are discrete quantities of energy. The energy of a photon is related to its wavelength so the longer the wavelength the less energy the photon holds. Photons are absorbed by pigment molecules only if the energy they hold causes an electron in an atom of the pigment molecule to jump to a higher energy level, which is known as an excitation. A specific amount of energy is required for this to happen and this energy is only supplied by certain wavelengths of light. 6.​ Compare absorption spectra with action spectra, and discuss their significance in understanding photosynthesis An absorption spectrum is a graph that shows the percentage of light absorbed at each wavelength by a pigment or a group of pigments. On an absorption spectrum the Y axis is used for absorption of light, either with a percentage scale or with arbitrary units. The spectra for more than one pigment can be shown on the same graph. An action spectrum is a graph showing the rate of photosynthesis at each wavelength of light. On an action spectrum, the Y axis should be used for measure of the relative amount of photosynthesis. This is often given as a percentage of the maximum rate with a scale of 0 to 100%. When plotting, both action and absorption spectra, at the horizontal X axis should show wavelength of light in nanometers. The scale should extend from 400 nm (violet) to 700 nm (red). 7.​ Propose a hypothesis to investigate the effect of light intensity on the rate of photosynthesis and outline an experimental method Photosynthesis rates can be measured in leaf discs which are cut outs of young healthy leaves. If the disks are placed in a suitable environment and prevented from drying out, they will continue to photosynthesize for at least a few hours. The variable of light intensity plays a key role in the rate of photosynthesis as varying light intensities will greatly affect the rate of photosynthesis that occurs in the leaf discs. For this experiment, in order to test the hypothesis that light intensity does affect photosynthesis rates, there is a measurement of distance from the light source, proportional to the oxygen output of the leaf discs as they photosynthesize. 8.​ Discuss the use of carbon dioxide enrichment experiments to predict future rates of photosynthesis and plant growth The role of carbon dioxide in the Calvin cycle is to synthesize glucose and other carbohydrates in plants through the Calvin cycle. Carbon dioxide has the ability to limit rates of photosynthesis. Increasing carbon dioxide above current atmosphere levels of about 400 ppm has been found to increase rates of photosynthesis implant growth. It is common practice now to raise carbon dioxide levels in greenhouses above normal atmospheric temperatures on sunny days. The extra carbon dioxide can come from boilers that burn natural gas to produce heat or electricity for the greenhouse. One hypothesis is that higher atmospheric carbon dioxide concentrations will increase rates of photosynthesis and plant growth as they do greenhouses. This could happen with field crops tree, plantations, and natural income systems. If this increases plant biomass, it will help to moderate increases in atmospheric carbon dioxide. The goal of these experiments is to increase the carbon dioxide concentration while keeping the other factors unchanged, and these experiments cannot be done in laboratory or greenhouses as there are many factors that differ from those open conditions. Instead, they must be conducted in the free air so they are called free air carbon dioxide enrichment experiments (FACE). Some of the effects of free air carbon dioxide enrichment experiments could be climate research as it can help scientists understand the impact of carbon dioxide on climate change, can show how the increased carbon dioxide levels will affect plant growth and can help track pollution levels and assess the quality of air. 9.​ Describe the structure and function of photosystems in the thylakoid membrane Photosystems are pigment-protein complexes that are located in the thylakoid membrane of chloroplast. Each photosystem has a core complex connected to a light harvesting antenna complex. Pigment molecules with antenna complexes absorb light because it causes an electron in one atom of the pigment to become excited and jump to a higher energy level. A specific amount of energy is required for this to happen and this precise amount of energy is only supplied by a certain wavelength. The amount of energy decreases as the wavelength increases. The light energy that is absorbed by pigment can be readmitted as light when the electron drops back down to its original energy level; this is known as fluorescence. However, something different happens in the light harvesting complex. When the excited electron in a pigment molecule drops back down to its original level, the energy admitted is absorbed by an electron in the adjacent pigment molecule, causing it to become excited. This process is called excitation energy transfer, and it is repeated across the light harvesting complex. This way energy is transferred from pigment to pigment until it reaches the reaction century in the core complex. This process happens very fast and only takes a few femtoseconds. For this energy transfer to happen, the pigment molecules must be held in a precise array in terms of both distance between them and the relative orientations. Light energy that is absorbed by any of the pigments in the light harvesting complex is funneled into the core complex. Eventually, it reaches a special pair of chlorophyll molecules in the reaction center. These molecules are able to donate pairs of excited electrons to electron acceptors, and this completes the task of the photosystem. Light energy has been absorbed generating electrons in these electrons are admitted from the photo system, carrying the energy needed for later stages of photosynthesis. 10.​Explain the advantages of having a structured array of different pigment molecules in photosystems There are many advantages of the structural array of different types of pigment molecules in a photosystem. A photosystem combines over 100 pigment molecules which increases the number of photons absorbed per 2nd by two orders of magnitude which maximizes energy consumption. A photosystem combines different types of pigment in one array so a greater proportion of energy and sunlight can be used. Also accessory pigments that are present in photosystems are able to transfer energy. The pigment molecules in the structured array of the system are independent. Individually, they cannot perform any part of photosynthesis however, together they can harvest light energy very efficiently, allowing photosynthesis. Overall, the photosystems are able to maximize light absorption through their structural array. 11.​Outline the process of photolysis in photosystem II and its significance for photosynthesis Absorption of photons of light by photosystem II causes a special chlorophyll known as P680 in the reaction center to become oxidized by admitting excited electrons. P680 is a powerful reducing agent that is able to regain electrons from water and this happens in the Oxygen Evolving Complex (OEC) of photosystem II. The OEC contains a group of manganese, calcium and oxygen atoms and is in the core complex of the system next to the thylakoid space. The splitting of water is called photolysis because it only happens in the light when the P680 chlorophyll is oxidized. Photolysis occurs in photosystem II and happens in the OEC of the inner surface of the thylakoid membranes and the electrons are transferred to the reaction center to replace those admitted by the P680 chlorophyll. The protons are released into the thylakoid space contributing to a proton gradient across the thylakoid membrane. Oxygen molecules produced by photolysis are a waste product as they diffuse out from the thylakoids to the stroma of chloroplast. From there, they diffuse through the cytoplasm of the cell and eventually out of the organism. In plants with leaves, the oxygen diffuses out through the stomata.  12.​Describe how ATP is synthesized in the thylakoid membrane during photophosphorylation Excited electrons generated by photosystem II are passed to plastoquinone, an electron carrier in the thylakoid membrane. plastoquinone accepts two electrons and also two protons from the stroma becoming plastoquinol. The electron transport chain is a series of proteins in the inner mitochondrial membrane that transfers electrons from NADH to oxygen, therefore creating a proton gradient that helps produce ATP. This happens at binding sites in the reaction center of photosystems II. The plastoquinol will continue to move through the electron transport chains and will eventually reach photosystem I. The electrons will carry less energy than they did when admitted by the photosystem II. Energy from the electrons has been used to pump protons from the stroma to the thylakoid space, generating a proton gradient. Photolysis also contributes to this gradient by releasing photons inside the thylakoid space. The concentration gradient of protons across the thylakoid membrane is a store of potential energy. ATP and thylakoid membranes can generate ATP using the proton gradient. Protons travel across the membrane down the concentration gradient by passing through the enzyme ATP synthase. The energy released by the passage of protons is used to make ATP from ADP and inorganic phosphate. This method is very similar to the process that produces ATP that occurs inside the mitochondria and it’s given the same name of chemiosmosis. 13.​Explain the reduction of NADP in photosystem I and it’s important in light dependent reactions Photosystem I reduces in NADP+ to NADPH. Energy from photons of light is absorbed by pigment molecules in the photo system and passed to the reaction center then it reaches a special pair of chlorophyll molecules known as P700 that act as the primary electron donor. An electron and one of these chlorophyll molecules is excited and then admitted from the reaction center. It is passed via a short chain of electron carriers to the inside in a NADP reductase. This enzyme is positioned on the stoma side of the thylakoid membrane where it can receive electrons from photosystem I. When NADP reductase has received two excited electrons, it can convert a molecule of NADP in the stroma to reduced NADP. NADPH is used in the Calvin cycle for converting carbon dioxide into glucose. NADPH donates electrons and hydrogen ions to the carbon molecules formed during the cycle, which helps convert them into glucose and other carbohydrates. 14.​Discuss the roles of the thyroid membrane in the light dependent reactions of photosynthesis A thylakoid is a sac-like vesicle that performs the light dependent reactions of photosynthesis. In these reactions, light energy is absorbed and used to split water by photolysis, reduce in ADP and produce ATP by chemiosmosis. A thylakoid is a system because it contains interacting components that individually would not be able to carry out their functions. Thylakoids contain pigments and ATP synthase. Photosystem II absorbs light and uses the energy from it to excite electrons which are passed to the plastoquinone. Plastoquinone and the cytochrome complex use energy carried by excited electrons to pump protons from the stroma to the lumen of the thylakoid. Photosystem I absorbs light energy and uses energy from it to excite electrons, and these electrons are used to reduce NADP on the stoma side of the thylakoid membranes. 15.​Outline the process of carbon fixation by Rubisco, including the substrates and products Carbon dioxide is the carbon source for all organisms that carry out photosynthesis. The escape of carbon dioxide from photosynthesizing cells is prevented by carbon fixation. In the carbon fixation reaction, carbon dioxide is converted into a more complex carbon compound. This is arguably the most important chemical reaction in all living organisms. The product of the carbon fixation reaction is a three-carbon compound: glycerate-3-phosphate. Carbon dioxide does not react with a two carbon compound to produce glycerate-3-phosphate and it instead reacts with a five carbon compound called ribulose bisphosphate (Rubisco) and produces two molecules of glycerate-3-phosphate. 16.​Explain how glycerate-3-phosphate (GP) is converted into triose phosphate (TP) in the Calvin cycle RuBP is a five-carbon sugar derivative, and it is converted to glycerate-3-phosphate by the addition of carbon and oxygen, but not hydrogen. As a result, the amount of hydrogen relative to oxygen becomes less than two to one. Hydrogen has to be added to glycerate-3-phosphate by a reduction reaction to produce carbohydrates. This conversion involves both ATP and reduced NADP, produced by the light dependent reactions of photosynthesis. ATP provides the energy needed to perform the reduction and reduced NADP provides the electrons which are contained in hydrogen atoms. The product is a three-carbon sugar derivative called triose phosphate. This conversion happens in the stroma of the chloroplast and it is part of the light interdependent reactions of photosynthesis because light is not directly used. However, it can only continue for a short time and darkness as ATP and reduced NADP are required and they run out quickly. 17.​Describe the regeneration of RuBP in the Calvin cycle and it’s important for the continuation of photosynthesis The first carbohydrate produced by the light interdependent reactions of photosynthesis is triose phosphate. Two triose phosphate molecules can be combined to form hexose phosphate. Hexose phosphate molecules can be combined by condensation reaction to form starch, and when conditions in a leaf are suitable for photosynthesis, they rapidly accumulate in chloroplast. If all of the phosphate produced by photosynthesis was converted to hexose or starch the supplies of RuBP in the chloroplast would be used and this would cause carbon fixation to stop. Therefore, some triose phosphate has been used to regenerate RuBP and this process is a conversion of a three carbon sugar into a five carbon sugar through a series of reactions. For the Calvin cycle to continue as much RuBP must be produced as consumed. When RuBP and carbon dioxide are combined by rubisco only one of the six atoms is newly fixed and for this reason only one sixth of the triose phosphate molecules that are produced can be taken out of the Calvin cycle. Five sixths of the triose phosphate must be used to regenerate RuBP. Regeneration of RuBP requires the use of ATP and this is because the triose phosphate is converted into ribulose phosphate and this must be converted to RuBP.  18.​Discuss how the Calvin cycle provides precursors for the synthesis of other carbon compounds, such as amino acid and carbohydrates Six turns of the Calvin cycle are needed to produce one molecule of glucose and each turn of the cycle contributes one of the fixed carbon atoms in glucose. Glucose is usually converted to sucrose for transport from leaves to other parts to plant. At times, glucose is produced more quickly than it can be transported and at these times, it is converted to starch and stored temporarily inside chloroplast. At night when photosynthesis has stopped, the starch is broken down, and the carbohydrate is exported from the leaf. Glucose molecules are linked together in long chains to form starch which plants use to store energy. Glucose molecules are also linked together to form cellulose, which is a structural component in the cell walls of plants. 19.​Explain the interdependence of light dependent reactions, and light independent reactions of photosynthesis Light dependent reactions in the thylakoid membranes, or on the surface of them include photolysis, light absorption by generation of excited electrons, transport of electrons by carriers, ATP synthesis by chemiosmosis and the reduction of NADP. The products of these reactions are ATP, NADPH and oxygen. ATP and NADPH are used in the Calvin cycle to produce glucose, while oxygen is released as a byproduct. As for light interdependent reactions in the stroma, there is carbon fixation, synthesis of triose phosphate and other carbon compounds and regeneration of RuBP. As for the Calvin cycle, in low light intensity, the production of ATP and reduction NADP are restricted. Therefore, the conversion of glycerate-3- phosphate in the Calvin cycle is the rate limiting step. In high light intensity, carbon fixation is usually the rate limiting step as the use of reduced NADP is restricted, so supplies of NADP limit the light dependent reaction. Some photons of light absorbed by the photosystems are readmitted as fluorescence.