Photosynthesis Lecture Notes PDF

LECTURE Second LE Photosynthesis I. Just like cellular respiration, a metabolic reaction (chem reaction). a. Reactants: Carbon Dioxide and Waater b. Light: Necessitates light absorbing pigments (chl) c. Products: Atomic Oxygen and sugars (Glucose, etc.) i. Photosyn...

LECTURE Second LE Photosynthesis I. Just like cellular respiration, a metabolic reaction (chem reaction). a. Reactants: Carbon Dioxide and Waater b. Light: Necessitates light absorbing pigments (chl) c. Products: Atomic Oxygen and sugars (Glucose, etc.) i. Photosynthesis produces G3P glyceraldehyde-3-phosphate (trios sugar with 3C) II. This process is a big succeeding REDOX process d. Reduction (Carbon Dioxide -- gained electron via H addition) e. Oxidation (Water -- loss electron becoming atomic oxygen) III. Can also happen in algae, phytoplanktons, and bacteria. IV. Described as a process with 2 main components: f. Light Dependent Reaction ii. Happens in the thylakoid membranes where the chlorophyll and other components are embedded. iii. Light facilitates Photolysis of water. 1. Using the energy coming from the light, water molecules are cleaved into ½ O2 ((monoatomic Oxygen) and 2Hydrogen+ + 2e- a. The oxygen is released by plants during photosysnthesis iv. Second Function: Elevation of Light Energy 2. In the excited state of chlorophyll, the electron in it also gets excited. Necessitating to loos it or give it away. 3. Then after, to become stable again, they need to resuplement the lost electron from the photolysis/ v. Third: Production of ATP and NADH. 4. ATP goes to Calvin Cycle, which is a energy consuming reaction. b. From phosphorylation of ADP 5. NADH c. Reduction of NADP+ d. Serves as a strong reducing agent in the Calvin Cycle. i. Important for REDOX reaction to proceed. ii. Donor of electron. g. Calvin Cycle (Light Independent Reaction) vi. Happens in the Stroma (fluid environment that surrounds the thylakoid. V. Photosystems h. Complex of light capturing proteins and pigment (molecules) i. Embedded in the double layer thylakoid. j. Function: vii. To harvest light (due to the presesnce of pigments) k. Parts: viii. Light harvesting complex (ANTENNA Complex) 6. Main function is to harvest and collect light. 7. Primarily composed of pigments (with accessory pigments , carotenoids and xanthophylls) e. Accessory Pigments: Carotenoid and Xanthophyll. Chlorophyll B. f. Primary Pigment: Chlorophyll A (primary photosynthetic pigment) 8. Ensures the efficiency of light captures. 9. Forster resonance energy transfer (FRET) g. Light energy excites the electron too much making it unstable.. h. High excitation gets transferred to neighboring pigments till it reaches the reaction center. i. Highly dependent of distances and orientation. j. There should be a spectral overlap (similarity in the wavelength in light absorved. 10. The pigments found in antenna complex will have different energy level or states. k. Carotenoid (highest energy) l. xAnthophyll m. Chlorophyll B 11. These photosystems sacrifices a little bit of energy to ensure the end is the reaction center. n. There is a gradual decrease of energy via the thermodynamic laws. o. There is a funneling effect in the photosystems (specifically here). p. There is not a "random" arrangement of pigments in the antenna complex. q. Sacrificed energy results to 95-99% efficienctry. ix. Reaction Center (still has pigment) 12. Although not directly involved in the light transfer 13. Called it because the first REDOX reaction (atleast in the photosystem) happens here. r. Antenna complex pnly had energy transfer. 14. Structures: s. Contains a Dimer (of chlorophyll a) iii. Chlr a has the lowest energy level. iv. Ensuring the end point of energy transfer. t. Once there, the process of photoact or photoionization happens. v. Light energy excitation results to the release of electron. vi. The electron released becomes an electron carrier vii. Gets another electron from photolysis of water. u. Transfer of Electron follows viii. Photosystem II, to Plastoquinone, Cytochrome b6/f, plastocyanin, and photosystem I, lastly, perrodoxin. 1. No to direst PII to PI, due to compartmentalization of the thylakoid. 2. There is the distance between these photosystems that the excited electron cannot just travel to. 3. The passing of electron establishes the proton gradient. a. Plastoquinone during its acceptance of electron, releases hydrogen atoms in the thylakoid lumen. b. Trasnfer to Cb6f, also releases Hydrogen atom. c. At the last (Perredoxin), this uses up the Hydrogen atom in the chloroplast stroma. ix. ATP synthase produces ATP. 4. Works only when there is a steep proton gradient in the thylakoid lumen than the chloroplast stroma. d. Protons moves out the stroma. e. Passing through the synthase, gets phosphorylared (ADP to ATP) x. P680 and P700 are the name of the reaction centers at the PSII and PSI, respectively. 15. Congruent to the peak wavelength of light that they are able to absorb. Carbon Dioxide Assimilation - Plant absorbs carbon dioxide and incorporates it into organic compounds. I. Calvin Cycle (happening herer) a. Divided into 3 stages. b. Cyclical in nature. i. Taking some of the products to revgenerate RUBP to re assimilate Carbon Dioxide. II. Stages c. Carbon Fixation ii. RuBisCO -- Ribulose bisphosphate carboxylase 1. As a carboxylase, it incorporates the carbon of the carbon dioxide into other organic molecules. 2. (RuBP) Five carbon molecule. iii. Two phases: 3. Carboxylation of RuBP. a. Creation of unstable intermediate product 6carbon molecules.. 4. Hydrolysis b. Cleaving of the intermediate into 2 3carbon molecules. c. 3-PGA process. d. Reduction of 3-PGA iv. Phosphorylation 5. 6 ATP utilization to add another phosphate group. Via photsphoglucerate kinase (addition of phosphate). v. Reduction 6. Dehydrogenases uses 6 NADPH to create Trios phosphate (G3P and DHAP) d. Isomer of G3P. vi. 3mol of Carbon Dioxide results to 6 G3P 7. 1 is utilize another pathway. 8. 5 will be usd to regenerate RuBP. e. Regeneration of RuBP vii. Sugar Shuffle - Triose phosphate cleaves and reforms to several forms of sugars. 9. First 2 G3P is synthesized together to form 6carbon sugar (fru-1,6-bisphosphate) 10. Addition of another G3P to form 9carbon sugar intermediate, which is divided into xylulose-5-phosphate and erythrose-4-phosphate. 11. Xylulose can be utilized to regenerate RuBP due to 5 Carbon. e. Aldolase is responsible to the synthesizing of two sugars. 12. Addition of another g3p on erythrose, resulting to 7carbon molecule (Sedoheptulase) 13. Addition of the last g3p to the sedo, rsulting to a 10 carbon intermediate. 14. Cleaved by transketolase into Xylulose and Ribose. f. Isomerasion to form ribulose-bisphosphate. 15. Additiono f phosphate group from ATP, they are able to regenerate RuBP. f. Fate of the Triose phosphate (the 1 molecule that went to another pathway. viii. Sugars 16. Sucrose g. Important as the only translocatable form of sugar in plants. h. This are non-reducing, rather than other sugars which are reducing (a bit reactive in the event of transport through redox reaction). i. Syntehsis happens outside the chloroplast, in the cytosol and cytoplasm. j. 12 carbon sugar from fructose and glucose. k. Necessitates transport molecule 17. Starch l. Long chain of glucose units. m. Synthesized in the chloroplast (specifically in the stroma). n. ix. Sucrose and starch synthesis are competing processes. 18. Only one pool of g3p x. Pathway: 19. For starch synthesis, it happens in the stroma. 20. 2 g3p is combined to gether to form fruc-1 6 bisphosphate. 21. Reduction of one phosphate group. 22. Isomerization to form glucose 6 phosphate 23. Mutase trasnlocates the 6C phosphate to become 1C phosphate (location. 24. (Pyrophosphorylase) Reacts with ATP, taking Adenosine and a Phosphate group to form ADP-glucose. 25. Starch synthase joins ADP-glucose together to become starch. o. Forms: i. Amylose is a linear stach (addition of glucose unit to the 4^th^ carbon) 1. Necessitating starch synthase (alpha(1,4) link. ii. Amylopectin 2. Necessitating Q-enzyme (alpha 1,6) link, even with starch synthase. 3. Addition at the 6^th^ Carbon. 4. Branching structure is responsible for (pagkamalagkit of the rice) and making it need more water. xi. Sucrose Synthesis 26. Needing a transporter and another set of enzymes 27. Principal pathways p. Suc phos synthase q. Suc phos phosphatase 28. Pathways: r. Phosphate translocator enables phosphate and triose phosphate. s. Aldolase activity and phosphatase. t. Isomerizaation to for glucose 6 phosphate. u. Mutase activity. v. Rather than ATP, U(racil)TP is utilized. w. Results to UDP-glucose. x. Sucrose phosphate Synthase activity (joining together of the (UDP-glucose) to form sucrose phosphate. y. Enzyme sucrose phosphate phosphatase removes the remaining phosphate, ultimately creating sucrose. xii. Secondary Pathway: Features: 29. Alternative pathway 30. During times of very active growth or when undergoing abiotic stress. 31. Only sucrose synthase is present. z. The reaction it catalyzes is reversible. a. UDPglucose + fructose can be UDP + sucrose and vice versa. b. Commonly found in sinks in plants. iii. Where products of photosynthesis go. (roots, furits, and actively growing parts of plants). c. For starch synthesis, ADP is preferred. 32. Does not act with phosphoralated fructose. d. Need into dorm of UDP and ADP fructose. LCTURE NEXT: I. Additional info a. RUBISCO as carboxylase i. Fixation of Carbon from Carbon Dioxxide to RUBP b. RuBisCO as an oxygenase ii. Condensation of O2 with RuBP 1. Resulting to a 5 carbon molecule to create only 1 PGA 2. Results to the creation of phosphoglycerate. a. Goal of photorespiration II. Photorespiration c. There is a release of carbon dioxide. iii. Lowers the efficiency of photosynthesis d. Happens with very high temperateures and or high irradiance iv. Irradiance is the number of photons hitting a certain unit area (essentially higher intensity of light. v. RuBisCO oxygenase activity is heighten with the higher concentration of oxygen in the plant tissue. vi. The higher the temp, plants dessicate due to transpiration rate; 3. They close stomata, less water vapor outake but also less carbon dioxide intake. vii. Higher irradiance, increases photosynthesis rate, there is a faster depletion of carbon dioxide in the plant body. e. More common in tropical region. III. Pathways: f. Calvin Cycle AS OSYGENSAE. viii. 1 PGA and 1 phosphoglycerate per carbon dioxide molecule. 4. Needs to maximize the carbon atom (2C) to create mor PGA. ix. 1 G3P only is created; not enough to regenerate RuBP and other pathway. x. Peroxisome and mitochondria roles are necessitated. IV. C2 P g. Production of (2C) molecules such as the phosphoglycerate h. Pathway: xi. Chloroplast is necessary for Photorespiration. 5. Start is still the calvin Cycle. 6. Formation of 1 PGA and 2C PG 7. Phosphoglycolate to glycolate via phosphatase. xii. Glycolate transports to the Peroxisomes. 8. Glycolate is converted into glyoxylate via Redox b. Oxidized Glycolate i. Reduction of photosrespiration via the utilization of oxygen. ii. Taking two hydrogen to create water (with hydrogen peroxide as an intermediate). iii. Peroxidase and catalase degrades the hydrogen peroxide (reactive substance) into water and oxygen. Oxygen is reused 9. Aminotransferase catalyzes glycine. xiii. Trnsport of Glycine to mitochondrion to create serine. 10. Two glycine moleculesa are necessary to create a single serine (due to difference in the number of atom. c. Glycine has 2C and 1 N d. Serine is 3C 1N 11. Two glycine condenses into 4C atom molecule. Is utilized for serine structure and the 1 free is released as Carbon Dioxide. e. Problematic for photosynthesis as we are required to fix carbon dioxide. f. Increases the concentration of carbon dioxide in the plant body. g. Ultimately returning RuBisCo to its carboxylase. 12. The 2 Nitrogen, 1 is integrated to the serine and the other ass a free amino group (NH4+) 13. Total: h. Condensation of reaction of glycine to form serine i. Redox reaction due to NAD+ to NADH iv. Differing structure due to phorphate group but are both reducing agents. j. Oxydation of glycine k. Decarboxylation (removal of carbon atom in a molecule) l. Carboxylation into Carbon Dioxide. xiv. Back to the Top 14. Serine undergoes deamination (releasing the N group) m. Results to Hydroxypyruvate (negatively charged) 15. Undergoes redox reaction to become neutral; utilization of NADH to NAD+ (oxidized) n. Becoming Glycerate xv. Glycerate goes back to chloroplast 16. Glycerate (now 3 carbon atom) phosphorylation using ATP to become 3 phosphoglycerate. V. Signifiaccne of photorespiration i. Internal cellular recycling of Carbon dioxide (in the mitochondrion), Oxygen (in the peroxisome), and NH3 (for the formation of other amino acids -- can be used in the multiple varied processes) j. Glycolate production decreases levels of Oxygen. k. Physiological defends against high irradiance and thermal load excess xvi. Safety valve to dissipate excess energy (ATP NADH and NADPH) (heighten by increase photosynthetic activity). l. Contributes to cell amino pool (glycerine and serine) m. Response to niche diversification scheme xvii. Photorespiration happens in high temperature area. xviii. Enables the palnts to circumbent these conditions and ultimately enable them to occupy specific niche. n. Salvage or maximize 75% of carbon from glycolate for the Calvin Caycle xix. But it is not 100% efficient, some is loss xx. Less biomass than plants that doesn't undergo photorespiration. o. Not all plants do not photorespirate or do so just for a bit only. VI. Plants that do not phothoresppirate p. Carbon Dioxide concentration mechanism xxi. CO2 and HCO3 pumps 17. Pumping of carbon in the carbon dioxide to the chloroplast o. Common on aquatic organisms. 18. Pathway: p. Carbon dioxide is soluble in water, forming carbonic acid (H2CO3) v. Can be further broken down as bicarbonate atom and proton. 1. This is now negatively charged making it harder to diffuse through the membrane. 2. Hence, it needs to be transported through a pump; energy requiring (ACTIVE TRANSPORT). 3. Carbon dioxide can dissipate through the cell freely but relies on diffusion (so slower) which is why pumps are necessitated. q. carbonic anhydrase speeds up the conversion of carbon dioxide and carbonic acid. xxii. C4 pathway 19. Common in tropical and sub tropical regions 20. Do not serve to replace the calvin cycle as it is still involved. r. There is just additionalm ==m echanism to ensure the concentration 21. Hatch and Slack pathway. 22. SPACIAL SEPERATION s. Of the calvin cycle and the initial steps prior to it. 23. Mesophyll (ground tissue of the leaves) t. Where the initial fixation happens, passed to the bundle sheaths (ground tissue) that suroounds the vascular tissue. 24. Kranz anatomy u. Wreath -- german word. v. Mesophyl cells have a radial arrangement (surrounding the bundle sheats) 25. Bundle sheath is where calvin cycle happens. 26. Acknowledgement of HCO-3 as a substrate due to the incorporation of carbon dioxide within the plant. 27. C4 due to having a stable 4C 28. Pathway: w. Mesophyll cell, initial carbon fixation. (NOT RuBP) vi. Rather PEP or phosphoenolpyruvate (3C) vii. Addition of Carbon resulting to a 4 carbon organic acid (in the form of malate/malic acid or aspartate) via the PEPcarboxylase. x. Malate is transported to the bundle sheath cells which is why it is significant that they are close together (KRANZ ANATOMY). viii. Malate does not enter the Calvin Cycle. 4. It is the carbon (in the form of carbon dioxide) that enter the cycle. 5. The left 3C molecule is in the form of pyruvate. a. Will be going back to the mesophyll to to regenerate Phosphoenolpyruvate. 29. More specific type of plant undergoing C4 y. Enymes facilitating decarbocylation ix. NADP-malic x. NAD-malic xi. PEP carbocykinase xxiii. CAMP 30. More common on mas dry and hotter (dessert/arid plants) 31. Crassulacean Acid Metabolism 32. TEMPORAL z. Closed stomata in the day to prevent transpiration. a. Opened in the night to accept carbon dioxide. 33. More common in succulents too (crassulacean -- crassulacean). 34. Plant features of plants here: b. Contributes to prevent dessication. 35. Pathway; c. Enzymes and substrates utilized in C3 is utilized here. xii. Temporal difference d. During night time, the camp plants takes advantage of the low temp, open stomata, and take in carbon dioxide. e. In an aqueos environment (plant body) bicarbonate can happen. f. Bicarbocynate via PEP carboxylase to create 4C (oxaloacetate) g. Oxaloacetate via redox reaction by dehydrogenase to form Malate (malic acid -- in an aqueaos solution referring). xiii. STORED in the vaoucule in the night time. xiv. GOAL in night: To form 4C acid. h. During Day time: there is no additional formation of malic acid due to closed sotmata. i. Stored malic acid is transported to the chloroplast and decarboxylation happen. xv. Same with C3 j. Since stomata is closed, the CO2 concentration increases. xvi. RuBisCo as carboxylase agent to trigger Calvin Cycle. q. Factors affecting photosynthesis xxiv. Light indirectly activates RuBisCO C3 pathway) 36. The stroma becomes basic due to pump of protons in the thylakoid proton via cytochrome b6f. 37. That high pH breaks down the inhibitor of RuBisCO, increasing ATP, Magnesium ions (necessary for ATP binding -- phosphorylating) xxv. Activation of PEPcase in the C4 plants 38. Cascading redox reaction of ferredoxin and thrioredoxin to reduce the PEPcarboxylase to make it activated. xxvi. For CAMP plants. There is a diurnal regulation of the PEPcarboxylase in the presence of light. 39. Daytime, more acidic cytoplasm, inhibition of PEPcarbosylase. 40. Night time, more basic, activation of PEPcase xxvii. Phosphorylation 41. PEP has an amino acid terminal (add or taken away of phosphate group) k. Taken away makes the PEP inactive. l. Phosphorylation activates the PEPcase at night via kinase activity.