SBI4U1 Metabolism Class Notes PDF

SBI4U1 Metabolism Photosynthesis Photosynthesis transforms light energy into chemical energy of high-energy compounds (molecules that store and release significant amounts of energy during biochemical reactions, an example is ATP, which provides the energy needed for cellular activities when hydro...

SBI4U1 Metabolism Photosynthesis Photosynthesis transforms light energy into chemical energy of high-energy compounds (molecules that store and release significant amounts of energy during biochemical reactions, an example is ATP, which provides the energy needed for cellular activities when hydrolysis takes place and their phosphate bonds are broken ). Photosynthesis helps plants produce structural and metabolic substances crucial to their survival. Within photosynthesis, there are 2 sets of reactions: light-dependent ( uses light energy to make ATP and NADPH), and light-independent ( also known as the Calvin cycle; uses ATP and NADPH to make a high-energy organic molecule). These 2 reactions are interconnected and work together to convert light energy into chemical energy stored in glucose. The Calvin cycle cannot take place until the light-dependent reaction creates ATP and NADPH (energy carriers) to drive the synthesis of glucose. The equation for this process is 6CO2 + 6H2O + energy —> C6H12O6 + 6O2 Plant Structure Water enters the plant through roots and is transported to leaves through the veins (transpiration: capillary action (water sticks to the walls of the plant’s xylem and each other allowing water to move upwards against gravity), root pressure (when the water enters through the roots it creates a pressure that pulls the water up), transpirational pull ( as water moves up and evaporates through the stomata, it creates a negative pressure that pulls more water up from the roots)). CO2 enters the plant through the stomata underneath the leaves and diffuses into the chloroplast with water. 1 Chloroplast Inside the chloroplast, there are many interconnected disks of thylakoids and these disks are stacked together to form grana. Embedded in the thylakoid are photosynthetic pigments. The aqueous fluid that surrounds the grama is the stroma. Within the stroma are the enzymes that catalyze the conversion of CO2 and H2O into carbohydrates. The light-dependent reactions take place on the membrane of the thylakoid, and the Calvin cycle takes place in the stroma. Light Dependent Reactions Photons are packets of light energy absorbed by chlorophyll molecules within the thylakoid membranes. Photons carry 2 specific amounts of energy. Longer wavelength photons have smaller amounts of energy, shorter wavelengths have larger amounts of energy. Pigments absorb certain wavelengths of visual light while reflecting others. Chlorophyll pigments are located on the thylakoid membrane. Chlorophyll does not absorb green light but absorbs red and blue light instead. There 2 types of chlorophyll a and b. Chlorophyll a is the primary pigment involved in photosynthesis, it absorbs light most efficiently in the blue, violet and red parts of the electromagnetic spectrum. CH3 (methyl) is in chlorophyll a. Chlorophyll b is an accessory pigment. It helps capture light and passes it to chlorophyll a. This absorbs light in the blue and red-orange parts of the spectrum. CHO (aldehyde) is in chlorophyll b. Chlorophyll a and b are both in the porphyrin ring. Its tail and the hydrocarbon tail in the phospholipid membrane create London dispersion forces when they interact. Another photosynthetic pigment is beta- carotene which is a member of carotenoid, it's the orange colour found in carports and autumn leaves. They absorb blue and green light so they appear red, orange, and yellow in colour. It can also be converted into vitamin A which is then converted into retinal, a visual pigment in the eyes. Light Dependent Reactions The first step of photosynthesis is photoexcitation when the energy from light photons is absorbed by electrons in the bonds on chlorophyll a, this all takes place in photosystem II. The antenna complex is the surrounding pigments that gather the light energy and 2 transfer the light energy to the reaction centers. When the reaction center receives the energy, an electron becomes excited and has the energy to be passed to an electron-accepting molecule. The electron acceptor is now reduced and at a higher energy level. When excited the electrons jump up (gain energy) and down (lose energy, the energy jumps to the next pigment and the process repeats. Plants and algae have photosystems I and II. Photosystems are one of two (there's photosystem I and II) proteins-based complexes composed of clusters of pigments that absorb light energy on the thylakoid membrane. Chlorophyll molecules associated with different proteins in a photosystem can absorb light energy of various wavelengths. Chlorophyll does this by passing the energy to a unique pair of ‘chlorophyll a’ molecules within the group of proteins. The special ‘chlorophyll a’ with proteins is called the reaction center (a special pair of chlorophyll surrounded by proteins, it's special because it's able to donate electrons). A special pair of chlorophyll is found at the core of the reaction center. There are a large number of additional proteins to bind the chlorophyll molecules. The reaction center of photosystem I is P700 (wavelength of light it absorbs), for photosystem II it's called P680. Photosynthesis starts when a photon strikes photosystem II. P680 absorbs a photon and excites an electron. The excited electron turns P680 into P680+ which pulls electrons from the water found in the lumen. The water splits and 4 electrons are removed one at a time. P680+ accepts the electrons and passes them on to another pheophytin (electron carrier). The P680+ absorbs another photon, becomes reduced and passes on another electron. This process repeats 4 times to form an oxygen molecule. The equation for this process is 2H2O —> 4H2 + O2. From Pheophytin, the electrons are transferred along an electron transport system by electron carriers PQ (plastoquinol). During each transfer, a small amount of energy is produced. The released energy is used by a protein complex b6-f complex (also known as the cytostome complex) to pump hydrogen ions from the stoma into the thylakoid space to generate a concentration gradient. This is known as photophosphorylation. Electrons pass through the b6-f complex to the PC (plastocyanin) and then to photosystem I. Photosystem I also absorbs light energy but lost electrons for P700 are replaced by electrons from photosystem II. Electrons received by photosystem I are used by the enzyme NADP reductase (also known as ferredoxin) to reduce NADP+ to NADPH. NADPH is used to drive light-independent reactions. Back to photophosphorylation. The H+ pumped from the stroma to the lumen cannot escape the membrane except through ATP synthase. As the protons in the lumen build up, as well as 3 the water splitting that took place near photosystem II, the concentration gradient is formed. Also during this process, ADP becomes ATP. By this point, the ATP and NADPH are created so that they can help with the light-independent reactions. There are also 2 types of photophosphorylation. In cyclic photophosphorylation, it starts from P700 to ferredoxin then back to PQ. This process only produces ATP and only occurs where NADPH is not needed. The non-cyclic photophosphorylation is the normal one. Light Independent Reactions Light-independent reactions are also known as the Calvin cycle. Phase 1 of the Calvin cycle is fixing the CO2. This starts when 3 molecules of CO2 (inorganic) combine with RuBP ( ribulose-1,5-bisphosphate) with the help of Rubisco. This forms an unstable intermediate compound that splits into 6 molecules of PGA (3-phosphoglycerate). Phase 2 starts when PGA is activated by ATP which turns into ADP. The phosphate groups that separate combine with PGA to form 6 molecules of 1,3- bisphosphate. The 1,3- bisphosphate activates with NADPH which turns into NADP+ which forms 6 molecules of G3P (glyceraldehyde 3- phosphate). One molecule of G3P leaves the cycle while the other 5 continue. The one molecule that leaves requires another, which means 6 cycles in total to form glucose. Phase 3 starts when the reduced G3P is used to make more RUBP. This happens when ATP breaks and reforms the G3P’s chemical bonds into 5 RUBPs. Then this cycle just continues. When hydrogen is added to the G3P through H2O, it goes from inorganic to organic with the addition of the hydrogen, because in organic molecules the carbon always has to be bonded to hydrogen. C4 Plants In C4 plants CO2 is fixed by an addition to a three-carbon compound called PEP in the mesophyll cell by an enzyme called PEP carboxylase. PEP carboxylase is more efficient than rubisco when there is a low amount of CO2. The enzyme produces a 4-carbon compound called oxaloacetate which is then converted into malate and then transported to the budle-sheath cells where the Clavin cycle takes place. This cycle decreases the overall rate of photophosphorylation but maximizes CO2 levels. Examples of C4 plants are corn and sugar grass. 4 CAM Plants CAM plants go through the same pathway except that the whole process happens in the same cell, the palisade cell. CO2 is separated by the time of day. Malate is stored in the vacuole during the night. When there is enough ATP and NADH the malate exits the vacuole and is decarboxylated to free the CO2 which then enters the Calvin cycle. Examples of CAM plants are pineapple and cacti. Cellular Respiration There are 4 stages of cellular respiration. Glycolysis The word glycolysis means splitting glucose into smaller molecules, and it's a 10-step reaction that occurs in the cytosol. Its main function is to split glucose into 2 molecules of pyruvate, and it yields 2NADH and 2ATP. This process starts when glucose enters the cell and phosphorylation makes it more chemically reactive. 2 phosphate groups are then transferred to an isomerized version of fructose-1,6- bisphosphate and from there ATP phosphorylation(when ATP become ADP)takes place. The end result of that is fructose- 1,6- biphosphate. These early steps are also called the energy investment phase because this is where ATP is becoming ADP, so energy is being invested. The steps after this are the energy return steps, and they start with the splitting of Fructose-1,6- bisphosphate. It gets split into DHAP (dihydroacetatephospate) and G3P (glycogen 3 phosphate, also part of the Calvin cycle). DHAP eventually also becomes G3P. Both molecules of G3P become oxidized using NAD+, which becomes NADH. In this process, energy gets released and this energy is used to attach phosphate to sugars, making 1,3-bisphosphoglycerate. Then the phosphate groups are transferred to ADP making ATP, and this is done through substrate-level 5 phosphorylation. In the end, there are 2 products, 2 molecules of pyruvate and 2 molecules of ATP, there's also 2 molecules of NADH. Pyruvate Oxidation This process takes place in the cytosol. The 2 pyruvate molecules are transported through the 2 mitochondrial membranes by a protein channel into the matrix. There it met with multiple enzymes and the pyruvate is changed in 3 ways: 1. CO2 gets removed. 2. The remaining 2 carbon fragment is oxidized, while NAD+ is reduced to NADH 3. coenzyme -A is attached to the remaining acetyl group forming acetyl-CoA From here the acetyl-CoA can choose to go through the Krebs cycle if energy is immediately needed. If not, it can become a lipid and be stored for the long term. Krebs cycle This process takes place within the matrix. Acetyl-CoA enters the cycle and combines with oxaloacetate to make citrate when NAD+ undergoes reduction and forms NADH. Throughout the cycle, citrate loses CO2 2 times (discarded as waste), reduces NAD+ 3 times, forms ATP 1 time, forms FADH2 from FAD 1 time, and has H2O added once. Throughout the cycle it changes from citrate to isocitrate to alpha-ketoglutarate to succinyl- CoA to succinate to fumarate back to oxalate, and the cycle repeats. Everything in this cycle has to be multiplied by 2 because 2 pyruvate molecules entered this cycle. Electron Transport Chain & Chemiosmosis This occurs across the inner membrane, the more cristae (folds), the more this chain repeats, and the more ATP is generated. The NADH and FADH from the Krebs cycle and the NADH from glycolysis, become NADH after entering the matrix, the energy from the 2 energy carriers push out H+ from within the matrix when the electron passes through the electron receptors. The corresponding positive charge that occurs when the concentration of the H+ ions increases within the inner membrane space forms electric energy that is 6 connected by chemical energy to power the ATP synthase. Through the ATP synthase, ADP and a phosphate group make ATP, this process is called oxidative phosphorylation. Anaerobic Respiration Aerobic respiration(with oxygen) is more efficient in terms of energy production while anaerobic respiration allows organisms to generate energy quickly when oxygen is not available. There are 2 types of aerobic respiration to focus on. Lactic Acid Fermentaion After glycolysis occurs, the 2 pyruvate molecules receive hydrogen molecules from NADH reoxidizing it back to NAD+ to be reused in the next cycle of glycolysis. The pyruvate is mutated into lactate. In mussels, lactate must be reoxidized to protect the mussels from acidity which increases due to the amount of hydrogen ions. Once oxygen is restored it goes from the cell into the bloodstream, turns back into pyruvate and is oxidized or converted into glycogen and stored in the muscle. Ethanol Fermentation After glycolysis occurs, the 2 pyruvate molecules lose a carbon molecule creating acetaldehyde. The lost carbon combines wth oxygen to create CO2. Acetaldehyde receives hydrogen from NADH resulting in the production of ethanol. This is applicable to yeast and bacteria. In Class Lab Muscle fatigue is a result of multiple factors. 1. ATP depletion; during intense exercise muscles use ATO rapidly for contraction. Both aerobic and anaerobic cellular respiration are used to replenish the ATP but prolonged and intense consumption of ATP exceeds the rate of ATP production. 2. Anaerobic respiration and lactic acid; when oxygen supply is inefficent for aerobic respiration, muscles switch to anaerobic respiration. In animals when anaerobic respiration takes place, lactic acid is a by product, and the accululation of lactic acid 7  lowers the pH in muscles leading to a burning sensation as well as contributing to muscle fatigue. 3. Glycogen depletion; musicals store glycogen as a source of glucose for energy, during proloned excersie stores can become depleted reducing the availibilty of gluces for ATP production. 8