BOTANY ASSIGNMENT

Absorption spectrum is the electromagnetic spectrum, broken by a specific pattern of dark lines or bands, observed when radiation traverses a particular absorbing medium. The absorption pattern is unique and can be used to identify the material. Action Spectrum is the efficiency with which electromagnetic radiation produces a photochemical reaction plotted as a function of the wavelength of the radiation. Anabolic reactions are chemical reactions in which simpler substances are combined to form more complex molecules. Anabolic reactions usually require energy. Anoxygenic photosynthesis is the phototrophic process where light energy is captured and converted to ATP, without the production of oxygen. ATP synthetase is an enzyme complex that catalyses the formation of ATP from ADP and inorganic phosphate. It occurs in the inner mitochondrial membrane and is responsible for oxidative phosphorylation during respiration. It is also found in the thylakoid membranes of chloroplasts, where it generates ATP in the light-dependent reactions of photosynthesis. Hence, ATP synthetase is of fundamental importance to the vast majority of living organisms. Bacteriochlorophylls are photosynthetic pigments that occur in various phototrophic bacteria. Groups that contain bacteriochlorophyll conduct photosynthesis, but do not produce oxygen. They use wavelengths of light not absorbed by plants or Cyanobacteria. C3 cycle is a series of biochemical redox reactions that take place in the stroma of chloroplasts in photosynthetic organisms. It is also known as the dark reactions. C4 metabolism is a processin which the CO2 is first incorporated into a 4-carbon compound. Stomata are open during the day. Uses PEP Carboxylase for the enzyme involved in the uptake of CO2. This enzyme allows CO2 to be taken into the plant very quickly, and then it "delivers" the CO2 directly to RUBISCO for photosynthesis. Photosynthesis takes place in inner cells (requires special anatomy called Kranz Anatomy). Chemiosmotic phosphorylation is a process in which a proton gradient across a mitochondrial membrane and ATP synthesis pump metabolites across a membrane and phosphorylation means the metabolic process of introducing a phosphate group into an organic molecule. Chlorophyll is the molecule that absorbs sunlight and uses its energy to synthesise carbohydrates from CO2 and water. It is a green pigment found in cyanobacteria and the chloroplasts of algae and plants.

Crassulacean acid metabolism, also known as CAM photosynthesis, is a carbon fixation pathway that evolved in some plants as an adaptation to arid conditions. In a plant using full CAM, the stomata in the leaves remain shut during the day to reduce evapotranspiration, but open at night to collect carbon dioxide (CO2). The CO2 is stored as the four-carbon acid malate, and then used during photosynthesis during the day.

Cyclic electron transport is a light-driven flow of electrons through a photosynthetic reaction centre with the electrons returning to the reaction centre via an electron transport pathway. Cyclic electron transport will normally generate an electrochemical potential (typically pH) gradient across a membrane but does not result in the net production of reductant. The pH gradient generated may drive the production of adenosine triphosphate (ATP) (cyclic photophosphorylation) or may regulate photosynthesis. Cytochromes are, in general, membrane-bound hemoproteins that contain heme groups and carry out electron transport. Any of a class of iron-containing proteins important in cell respiration as catalysts of oxidationreduction reactions.

Electron Transport Chain is a process used in both respiration and photosynthesis that produces energy (ATP) through oxidative phosphorylation. It begins with an electron-carrying molecule transferring its electrons to an enzyme embedded in a membrane. Through a series of redox reactions, electrons move from one enzyme to another. At each stop, a small amount of energy is released - this is used to make ATP. There is high potential energy in the first steps, but as electrons progress through the chain, free energy is incorporated into ATP as usable chemical energy. Entropy is the measure of the amount of energy in a physical system not available to do work. As a physical system becomes more disordered, and its energy becomes more evenly distributed, that energy becomes less able to do work. Gluconeogenesis is a metabolic pathway that results in the generation of glucose from noncarbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids.

Greenhouse effect is a process by which thermal radiation from a planetary surface is absorbed by atmospheric greenhouse gases, and is re-radiated in all directions. Since part of this re-radiation is back towards the surface and the lower atmosphere, it results in an elevation of the average surface temperature above what it would be in the absence of the gases.

Heterotrophs is an organism that cannot synthesize its own food and is dependent on complex organic substances for nutrition.

Light compensation point is the amount of light intensity on the light curve where the rate of photosynthesis exactly matches the rate of respiration. At this point, the uptake of CO2 through photosynthetic pathways is exactly matched to the respiratory release of carbon dioxide, and the uptake of O2 by respiration is exactly matched to the photosynthetic release of oxygen.

Light-dependent reactions or photosynthesis, is the first stage of photosynthesis, the process by which plants capture and store energy fromsunlight. In this process, light energy is converted into chemical energy, in the form of the energy-carrying molecules ATP and NADPH. In the light-independent reactions, the formed NADPH and ATP drive the reduction of CO2 to more useful organic compounds, such as glucose.

Noncyclic electron transport is the process smooth electron flow from water to NADPH.

Oxidation state is an indicator of the degree of oxidation of an atom in a chemical compound.

Oxidative phosphorylation is a metabolic pathway that uses energy released by the oxidation of nutrients to produce adenosine triphosphate.

Oxidized compound is oxidized when an element in that compound loses electrons. This makes the entire compound more positive due to the decrease in negative charge that electrons hold.

Oxygenic photosynthesis use of light energy to synthesise ATP and NADPH by noncyclic photophosphorylation with the production of oxygen from water.

Ozone is a triatomic molecule, consisting of three oxygen atoms. It is an allotrope of oxygen that is much less stable than the diatomic allotrope, breaking down with a half life of about half an hour in the lower atmosphere, to normal dioxygen. Ozone is formed from dioxygen by the action of ultraviolet light and also atmospheric electrical discharges, and is present in low concentrations throughout the Earth's atmosphere.

3 phosphoglyceraldehyde is a chemical compound that occurs as an intermediate in several central metabolic pathways of all organisms. It is a phosphate ester of the 3-carbon sugar glyceraldehyde and has chemical formula C3H7O6P. Photoautotrophs is an organism, typically a plant, obtaining energy from sunlight as its source of energy to convert inorganic materials into organic materials for use in cellular functions such as biosynthesis and respiration.

A photon is an elementary particle, the quantum of light and all other forms of electromagnetic radiation, and the force carrier for the electromagnetic force, even when static via virtual photons.

The production of ATP using the energy of sunlight is called photophosphorylation. In photophosphorylation, light energy is used to create a high-energy electron donor and a lower-energy electron acceptor.

Photorespiration is a process in plant metabolism by which RuBP (a sugar) has oxygen added to it by the enzyme instead of carbon dioxide during normal photosynthesis. This is the beginning step of the CalvinBenson cycle. This process reduces efficiency of photosynthesis in C3 plants.

Photosystem I is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin.

Photosystem II is the first protein complex in the Light-dependent reactions. It is located in the thylakoid membrane of plants, algae, and cyanobacteria. The enzyme captures photons of light to energize electrons that are then transferred through a variety of coenzymes and cofactors to reduce plastoquinone to plastoquinol.

Pigment is a material that changes the color of reflected or transmitted light as the result of wavelengthselective absorption. This physical process differs from fluorescence, phosphorescence, and other forms of luminescence, in which a material emits light.

Plastocyanin is an important copper-containing protein involved in electron-transfer. The protein is monomeric, with a molecular weight around 10,500 Daltons, and 99 amino acids in most vascular plants. It was the first blue copper proteins to be characterised by X-ray crystallography.

Plastoquinone is a quinone molecule involved in the electron transport chain in the light-dependent reactions of photosynthesis. Plastoquinone is reduced forming plastoquinol. It transports the protons to the lumen of thylakoid discs, while the electrons continue through the electron transport chain into the cytochrome b6f protein complex.

Quality of Sunlight refers to the colors of wavelengths it contains.

Quantum is a discrete unit of electromagnetic energy or of a roentgen. A quantity becomes quantized when its magnitude is restricted to a discrete set of values as opposed to a continuous set of values.

Reaction center is a structure that contains a pair of special molecules of chlorophyll a whose properties differ from all other molecules of cholorophyll a in the unit.

Reduced compound is the element or compound in a reduction-oxidation reaction that donates an electron to another species; however, since the reducer loses an electron we say it is "oxidized". This means that there must be an "oxidizer"; because if any chemical is an electron donor (reducer), another must be an electron recipient (oxidizer). Thus reducers are "oxidized" and oxidizers are "reduced".

Reducing power is the ability to force electrons onto compounds. They take in the most highly-oxidized froms of carbon and hydrogen and then convert them to carbohydrates, fats and other compounds that are very reduced.

Carboxylase is an enzyme that catalyzes a carboxylation or decarboxylation reaction.

RUBISCO is an enzyme involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is converted by plants to energy-richmolecules such as glucose.

Stroma is the matrix of the chloroplast which is a thick fluid in between grana where various enzymes,molecules and ions are found, and where the dark reaction (or carbohydrate formation reactions) of photosynthesis occurs.

Stroma reactions is where conversion of carbon dioxide to carbohydrate occurs.

Substrate-level phosphorylation is a type of metabolism that results in the formation and creation of adenosine triphosphate (ATP) or guanosine triphosphate (GTP) by the direct transfer and donation of a phosphoryl (PO3) group to adenosine diphosphate (ADP) orguanosine diphosphate (GDP) from a phosphorylated reactive intermediate.

Thylakoid lumen is a saclike membrane that contains the chlorophyll in cyanobacteria and in the chloroplasts of plant cells and green algae. In chloroplasts, thylakoids are arranged in stacks called grana.

Z-scheme describes the oxidation/reduction changes during the light reactions of photosynthesis. In the Zscheme, electrons are removed from water and then donated to the lower oxidized form of P680. REVIEW QUESTIONS: 1. Entropy Living organisms are highly ordered thus, their entropy decrease. After death, decay is the process by which an organism's molecules become more disordered and scattered thus their entropy increases. 2. Photoautotrophs include all green plants, all cyanobacteria, and few bacteria capable of photosynthesis. Heterotrophs include all animals, all completely parasitic plants, all fungi, and nonphotosynthetic prokaryotes. Photoautotrophs gather energy directly from the light and use it to assimilate small inorganic molecules into their own tissues. Young seedlings are white and can be heterotrophic while germinating underground. Seedling can become photoautotrophic only after they emerge into sunlight.

3. Because each molecule is recycled and reused repeatedly, thousands of times per second. ATP is converted to ADP and phosphate by metabolic reactions. Each molecule is an energy carrier, shuttling between reactions that release energy and those that consume it. 4. Three methods of phosphorylation: photophosphorylation, substrate-level phosphorylation, and oxidative phosphorylation. 5. Reduction reaction is the one that reduces the positive chatge of an atom. Every oxidation occurs simultaneously with a reduction simply because we need two half-reactions to form a whole reaction. 6. Oxygen has an oxidation state of -2 while hydrogen has +1. CO2 O -2 CH2O O -2 Malic acid 5xO 5 x -2 = -10 O -2 H +1 6xH 6 x +1 = -6 C +4 H +1 4xC 4 x +1= +4 C 0

7. NADP+ and NADP+ are oxidizing agents while NADH and NADPH are reducing agents. 8. Water molecules is the ultimate source of electron in photosynthesis. These molecules are excellent because they diffuse into the plants automatically from soil, air, or water; it is safe to absorb large quantities of carbon dioxide and water to store high concentrations of hydrates. It is necessary for raw materials to be cheap; that is, the plant must be able to obtain them without expending much energy. 9. An absorption spectrum is a graph that shows which wavelengths are most strongly absorbed by a pigment, whereas an action spectrum shows which wavelengths are most effective at powering a photochemical process. 10. It does not use high energy quanta because it has too much energy. If it did it would knock electrons completely away from the pigment, disrupting bonding orbitals and causing the molecules to break apart. It does not also make use of long-wavelength radiatios because, it has so little energy per quantum that they cannot appreciably boost an electrons energy. 11. The most common accessory pigments in land plants are chlorophyll b and carotenoids. Only infra-red lights penetrate deeply into water. 12. Electron carriers that transport electrons from photosystem 2 to 1: Plastocyanin, cytochrome b6f, plastoquinone, quinone, phaeophytin. Plastocyanin contains copper. 13. In this oxidized state, bonding orbitals could easily rearrange causing the molecule to break down and be destroyed.

14. Reaction that breaks down water and produce oxygen and protons are located on the lumen side of the thylakoid membrane, in the granum areas. This membrane is not permeable to protons; therefore as light reactions run, the thylakoid interior accumulates protons, and their concentration increases. The mechanism of ATP generation in chloroplasts is similar to that in mitochondria and takes the required energy from the proton motive force (PMF). However, chloroplasts rely more on the chemical potential of the PMF to generate the potential energy required for ATP synthesis. .

15. Yes. The function of the reaction center chlorophyll is to use the energy absorbed by and transferred to it from the other chlorophyll pigments in the photosystems to undergo a charge separation, a specific redox reaction in which the chlorophyll donates an electron into a series of molecular intermediates called an electron transport chain. Yes. These channels are complex sets of enzymes that can synthesize ATP from ADP and phosphate. 16. Ribulose -1,5- biphosphate is the acceptor molecule that reacts with a molecule of carbon dioxide. This reaction is catalyzed by the enzyme called RuBP carboxylase producing 2 molecules of3phosphoglyceraldehyde. 17. RuBP carboxylase is by no means ideal. Its active site recognizes and binds to carbon dioxide only poorly and it has low substrate specificity, frequently putting oxygen rathen than carbon dioxide onto RuBP. The amino acid sequences of RuBP carboxylase from all plants are virtually identical. Apparently, all mutations that cause any change in structure, however slight, disturb the active sites and are selectively disadvantageous. 18. Short-term storage: ATP and NADPH can be used witiln the cell and last only briefly. intermediate-term storage: the simple sugar glucose and the disaccharide sucrose arte stable enough to be moved from cell to cell, either in the vascular tissue of a plant or in a blood stream. Long-term storage: Starch is a large, high-molecular -weight polymer of glucose, too large to be transported. it lasts for years, and does not cause the cells to absorb water. 19. Quality of light refers to the colors of wavelengths it contains. At noon, plants in deserts, grasslands and the canopy receive sunlight vertically through the atmosphere, more blue light is transmitted and even though the blueness of the sky suggests that all reds, gressn and yellows have been blocked, enough of all these wavelengths penetrate to Earth's surface to allow efficient photosynthesis. However, herbs and shrubs that grow near soil level in a forest are understory plants and the light that they receive has already passed through the leaves of canopy, so the dim light by these plants are depleted in these critical wavelengths. Similarly, algae that grow near the surface of lakes or oceans receive complete light, but water absorbs red and violet. Algae at deep regions receive mostly green and blue light and must have special Accessory pigments capable of absorbing these wavelengths efficiently. 20. Plants growing near the equator receive intense light because the sun is always mre or less directly overhead at noon, whereas plants near the poles receive very little light. Plants growing in the shadow of mountains or in deep canyons receive much less light than plants that grow on slopes that face the sun. 21. No RuBP carboxylase will not be functioning. Because when light is bright and the low concentration of carbon dioxide is rate limiting there is so much light that as quickly as ADP and NADP+ come to the thylakoids, they are reprocessed immediately into ATP and NADPH. NADP would be in the reduced form.

22. In the brightest envirinments, the air is so clear that the sunlight is frequently too intense during summer months: deserts, mountains, valleys, plains etc. A common method is the production of a thick layer of dead trichomes, plant hairs. a heavy coating of wax can also reflect light, and cutin in goot at absorbing the more harmful short wavelengths. 23. Carbon dioxide diffusesinto leaf faster if its concentration in air is higher or if its concentration inside leaf protoplasm is lower. Plants can do nothing about the CO2 level in the external air, and many also have poor control over the protoplasmic concentration. Carbon dioxide diffusion into the leaf is slow, whereas water loss may be high. This is more important for a plant in a desert. 24. PEP carboxylase is contained in the mesophyll cells while RuBP carboxylase is located exclusively in the bundle sheath of chloroplasts. 25. Stomata are open at night when it is cool. It reduces transpiration, and usually air is calmer at night; therefore water molecules near stomata are not blown away immediately and may diffuse back into the plant. It is effective for conserving water, but the lack of light energy creates a problem for photosynthesis. 26. Crasslucean acid metabolism is not particularly efficient; the total amount of CO2 is so small that it may be used entirely in C3 metabolism. They are not stable enough and each cell has too little. No the acidity of our blood must be efficient. 27. Crasslucean acid metabolism is selectively advantageous in a hot, very dry climate where survival rather than rapid growth is more important. In these habitats, unaided C3 metabolism is so wasteful of water that C3 plants cannot survive. In the most arid regions, C4 plants barely get by, growing in slightly less stressful microhabitats. 28. Global Warming is the increase of Earth's average surface temperature due to effect of greenhouse gases, such as carbon dioxide emissions from burning fossil fuels or from deforestation, which trap heat that would otherwise escape from Earth. With less carbon dioxide, more heat would be lost and erath would be frozen like Mars. With more, more heat would be trapped and our world be as hot as Venus, at 800oC with lakes of molten lead.

29. The Kyoto protocol is a treaty designed to reduce production of greenhouse gases. Signed by 166 countries except United States. Coal and oil are burned by the US that produces CO2. China and India with combined populations of almost 2 billion people, are modernizing so rapidly that soon they will be producing more carbon dioxide that the United States is.