Carbon Metabolism and Photosynthesis

• Carbon metabolism in higher plants occurs via photosynthesis within chloroplast-containing mesophyll cells.
• Carbon dioxide enters leaves through stomata to undergo photosynthesis.
• Photosynthesis transforms light energy into chemical energy within a carbohydrate.
• Water is oxidized, releasing oxygen, while carbon dioxide is reduced to sugars during photosynthesis.

Light reactions

• Thylakoids are inner membrane sacs within the stroma and are stacked to form grana.
• Stroma refers to the fluid surrounding the thylakoids inside the chloroplast's double membrane.
• Grana lamellae are stacked membranes within a granum, while stroma lamellae are exposed membranes where stacking is absent.

Nature of Light

• Light can be considered both waves and photons, each with a quantum of energy.
• Visible light represents a small portion of the electromagnetic spectrum.
• Electromagnetic energy travels in waves characterised by wavelength, the distance between wave crests.
• Short wavelengths have high energy, whereas longer wavelengths have less energy

Photosynthetic Reactions

• Light reactions occur in the thylakoid membrane, where chlorophyll absorbs solar energy, energizes electrons, and converts solar energy into ATP and NADH via an electron transport chain.
• Dark reactions utilize ATP and NADH generated during light reactions to reduce carbon dioxide to a carbohydrate.

Pigments

• Pigments are any material that absorbs certain wavelengths.
• Plant pigments are built into the thylakoid membrane
• Chlorophyll transmits green wavelengths.
• Chlorophyll absorbs blue light to a higher energy state, than red light

Light absorption by chlorophyll

• Excited chlorophyll can re-emit a photon and return to ground state via fluorescence
• An excited chlorophyll can return to its ground state by converting excitation energy into heat.
• Chlorophyll facilitates energy transfer, where it transfers energy to another molecule which is referred to as resonance energy transfer.
• The photochemical reactions of photosynthesis are driven by the energy of the excited state.
• An absorption spectrum shows the wavelengths a pigment absorbs.
• Chlorophyll a absorbs blue and red light, reflecting green light.
• Action spectrum refers to the wavelengths effective for powering a photochemical process
• Absorption and action spectra match where the pigment used causes the response
• The rate of photosyntheses increases with the amount of light absorbed by pigments
• Red Drop Effect refers to how far-red light is insufficient to drive photosynthesis
• Enhancement Effect is where the photosynthetic rate is greater when both red and far-red lights are given together

Chlorophyll Structure

• Chlorophyll contains a magnesium-containing porphyrin-like ring structure crucial for electron transitions and redox reactions.

Accessory pigments

• Accessory pigments strongly absorb wavelengths that Chlorophyll a does not
• Antenna pigments, or light-harvesting complexes, are found in land plants
• Chlorophyll b absorbs mainly blue and orange light, reflects olive-green light.
• Carotenoids absorb in 400 to 500 nm range, providing photoreception, excessive light absorption and dissipation to prevent chlorophyll damage and interact with oxygen to convert to reactive toxic oxidative molecules
• Carotenoids help overcome the limitations of chlorophyll a absorbance, widening the photosynthesis action spectrum.
• Absorbed energy passes to chlorophyll a via resonance energy transfer, with notable efficiency.
• Xanthophylls are light harvesting and photoprotective, converting excess light energy that may lead to photoinhibition of photosynthesis.
• In high light, violaxanthin converts to zeaxanthin via antheraxanthin through violaxanthin de-epoxidase which is an enzyme.
• Zeaxanthin is unable to transfer its absorbed excitation energy to the PSII reaction center via chlorophyll b which results in it losing its absorbed energy as heat.
• In low light, violaxanthin acts as a light-harvesting pigment to transfer its absorbed excitation energy via chlorophyll b and chlorophyll a to the PSII reaction center
• Photosynthetic units contain photosystems I and II which are pigment-protein complexes.
• Photosystems are composed of antenna pigment complexes or light-harvesting complexes.
• Components include photochemical reaction centers in the thylakoid membrane.
• Excited chlorophyll molecules transfer energy to neighboring chlorophyll through resonance until it reaches the pair of chlorophyll a molecules in the reaction center
• The excited electron from chlorophyll a is donated to the primary electron acceptor.
• Photosystem I (PSI) possess low levels of chlorophyll b with a reaction center of P700.
• Photosystem I (PSI) has a pair of chlorophyll a absorbing far-red light >680nm.
• Photosystem 1 produces a strong reductant to reduce NADP+ and a weak oxidant.
• Photosystem II (PSII) possess almost equal amounts of chlorophyll b and a
• Photosystem II(PSII) reaction center is at P680
• Photosystem II has a pair of chlorophyll absorbing strongly red light of 680nm
• Photosystem II transfers electrons to the primary electron acceptor, resulting in a strong oxidant to oxidize water.
• Photosystem II produces a reductant that re-reduces the oxidant made by photosystem I
• The flow of electrons from H2O to NADP+ is referred to as the Z scheme.
• The reaction centers, antenna pigment-protein complexes, and electron transport enzymes are integral membrane proteins of the thylakoid membrane.
• Photosystem II is located predominantly in the stacked regions (grana lamellae) of the thylakoid membrane.
• Photosystem I and ATP synthase are found in the unstacked regions (stroma lamellae) protruding into the stroma
• Cytochrome b6f complexes are evenly distributed between the stroma and grana.
• With a 1.5:1 ration of photosystem I to II, the ratio may change depending on light conditions
• Energy transfer is efficient in antenna complexes when under optimal conditions.
• Electron transfer that occurs in the reaction center involves chemical changes in molecules.
• During water oxidation in the thylakoid lumen 4 electrons are removed from the two water molecules producing positive oxygen and generating four hydrogen ions :2H2O > O2 + 4H+ + 4 е-
• Excited P680 transfers an electron to pheophytin then oxidized P680+ is re-reduced by electrons from oxidation of water
• Two plastoquinones (QA & QB) receive electrons from phaeophytin.
• Reduced QB2- takes 2 protons from the stroma forming reduced plastohydroquinone whereafter cytochrome b6f receives electrons from reduced PQH2 and transfers electrons to plastocyanin, which reduces oxidized P700
• In plants, water is the ultimate electron donor and NADP+ is the ultimate electron acceptor.

Mechanism of electron and proton transfer

• Oxidized PQH2 near the luminal side of the complex transfers its two electrons to Rieske Fe-S protein and b-type cytochromes, expelling two protons to the lumen.
• Electrons from reduced Fe-S protein are transferred to cytochrome f (Cyt f) to plastocyanin which results in the production of more NADPH than ATP
• In the cyclic electron pathway A second QH2 is oxidized, with one electron going from FeSR to PC, finally to P700.
• Second electron flows via two b-type cytochromes, reducing semiquinone to plastohydroquinone, pumping two protons from stroma to the lumen
• With the cyclic pathway there are 4 protons transported across the membrane for every two electrons delivered to P700
• Electrons can be transferred from ferredoxin to the plastoquinone's instead of being used to make NADPH, producing more ATP.

ATP synthesis

• Thylakoid membrane impermeability results in H+ accumulation in lumen, leading to proton motive force or electrochemical potential gradient
• The Cytochrome b6f complex transports the two protons into the lumen and the proton flow is channeled through ATP synthase complex
• ATP synthetase phosphorylates ADP to ATP with CF0 forming a channel through which protons can pass

Carbon metabolism: Photosynthesis

• Melvin Calvin and his colleagues won the Nobel Prize (1961)
• Carboxylation of ribulose-1,5-bisphosphate (RuBP) is catalyzed by RuBP carboxylase (Rubisco), creating two molecules of 3-phosphoglycerate which is the first stable intermediate.
• Reduction of 3-PGA: 3-PGA kinase phosphorylates 3-PGA with ATP which then forms 1,3-biphosphoglycerate
• Regeneration of RuBP from G3P
• The C2 oxidative photosynthetic carbon cycle relies on the Calvin cycle as a RuBP supply.
• Balance between the two cycles is determined by rubisco’s kinetic properties, concentrations of CO2 and O2, and by temperature increase.
• Photorespiration and oxygenation increases are all relative to Photosynthesis and carboxylation with higher temperatures.
• Increase in kinetic properties of rubisco is caused by increase in oxygenation at high temperatures
• Glycine and serine are precursors of many biomolecules like chlorophyll, proteins, nucleotides.
• Glycolate protects C3 plants from photooxidation and photoinhibition
• C4 photosynthetic carbon fixation occurs in hot, dry environments.
• Crassulacean acid metabolism (CAM) occurs in desert, semi-arid regions.
• CO2 pumps occur at the plasma membrane and chloroplast envelope of cyanobacteria, algae, and aquatic plants.
• C4 plants include sugarcane, corn, bermuda-grass/tropical grasses, sedges, bougainvillea
• C4 is more efficient with photosynthesis than C3 plants at high temperature Kranz leaf anatomy: Leaf anatomy is two distinct chloroplast-containing cell C4 (Setaria viridis) types which include mesophyll and bundle sheath cells
• Mesophyll cells are no more than two or three cells from the nearest bundle sheath cell, with close vein spacing, extensive network connections that locate RuBP carboxylase only to bundle sheath cells
• CO2 enters and is converted in the chloroplast
• CO2 fixation by PEP is catalysed by PEP in mesophyll converting 4-C compound which then converts to C4 acid malate.
• Malate is decarboxylated to release CO2, which enters the C3 pathway and pyruvate transports back to mesophyll cell.
• Cacti, euphorbias, bromeliads, pineapple, vanilla, agave, orchids use crassulacean Acid Metabolism
• CO2 fixation in PEP is catalyzed by PEP carboxylase in the cytosol at night when stomata are open resulting in reduced acids
• Malate decarboxylation by NADP-malic enzyme in chloroplast during daytime happens when stomata are closed which result in CO2 refixation
• CAM has a high water effeciency rate
• Pyruvate-orthophosphate dikinase catalyzes reaction needed for regeneration of PEP in mesophyll cell
• High CO2 concentration with Rubisco in bundle sheath cells enhances carboxylation to reduce photorespiration
• High activity of PEP carboxylase allows C4 plants to reduce stomatal aperture, conserve water but still fix CO2.
• High PEP carboxylase has a high affinity for the substrate, HCO3-
• Atmospheric CO2 occurs and is reduced to malate and transferred into the mesophyll chloroplast by NADP-malate
• Both C4 and CAM: PEP carboxylase is inhibited by malate and activated by glucose-6-phosphate.
• CAM PEP carboxylase: Phosphorylation of a serine residue by carboxylase-kinase diminishes in malate inhibition. Glucose-6-phosphate enhances the action and glucose allows night activity. Dephosphorylation of serine is done by the enzyme.
• Starch and sucrose originate from triose phosphate generated by the Calvin cycle
• Chloroplast and cytosol have processes that occur for conversion of triose phosphates

Sucrose synthesis

• Chloroplast triose phosphate is exported to the cytosol via the phosphate (Pi) translocator in exchange for cytosolic orthophosphate (Pi) when cytosolic Pi concentration is high.
• When cytosolic Pi concentration is low, the triose phosphate is retained within the chloroplast via synthesis of starch
• Photosynthetically Active Radiation is a measurement that measures quantity, duration, and quality as light is used by the intact leaf.
• Leaves optimize light absorption through arrangement of thickness and perpendicular light with leaves.

Adaptations of leaves for light

• Patches of sunlight that pass through small gaps to provide for growth when the sun is weak
• Epidermal light focusing increases light reaching the chloroplast of plants allowing them to grow in the forest understory.
• Leaf adaptations minimize heating and other problems associated with too much light
• Shade leaves: more total chlorophyll per reaction center, higher ratio of chlorophyll b to chlorophyll a, lower rubisco and thinner than sun leaves.
• Sun leaves: more rubisco, larger pool of xanthophyll cycle components, thicker and longer palisade cells than the shade leaves.
• Light Compensation Point defines the rate at which photosynthetic assimilation exactly balances CO2 via mitrochondrial respiration
• Light Saturation point defines when that carbon fixation has reached its max point
• With Shade adepted plants due to less Rubisco, less resperation and the ability to survive long bouts of time without light
• Faster CO2 fixation from C4 then C3 under increasing light intensity
• Xanthophyll cycles can only take place in sun and shaded environments nonphotochemicaly
• Isoprene is the most common volatile hydrocarbon released into the atmosphere from plants, synthesising it in the chloroplast
• Types of Photoinhibition include both Dynamic and Chronic. Dynamic photoinhibition occurs during excess light and Chronic takes an extensive period
• The rate at which temperature effects the process depends on what the plant has adapted to
• Photosynthesis is limited by rubisco activity where a response occurs
• Both CAM and C4 plants can conserve more water under water stress
• At low and intermediates CO2 concentrations Photosynthesis is limited by the use if Rubisco
• All C3 plants are limited over a broad range of CO2

Carbon metabolism: respiration and lipid metabolism

• This entails lipids to sugars (gluconeogenesis) , aerobic repsiration, and carbohydrate translocation within a plant
• Aerobic respiration refers to how molecules are subsequent oxidized in a controlled process during sugar splitting
• Sucrose becomes the sugar to split through glycolysis in plants
• All life uses similar methods though pentose pathways exists for special needs
• The presence and lack of oxygen dictates what is generated here
• The presence and lack of carbohydrates dictates some of the processes like glucogenisis
• Both plant hormones and sugar levels must be ideal here as they are tightly controlled
• Phloem translocates products of photosynthesis from mature leaves to areas of and storage. It also redistributes various nutrients
• Pholem translocation comes in many forms that is both affected by living and abiotic factors