Botany Lec

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Classification of PlantsPlants are classified in several different ways, and the further away from the garden we get, the more the name indicates a plant's relationship to other plants, and tells us about its place in the plant world rather than in the garden. Usually, only the Family, Genus and species are of concern to the gardener, but we sometimes include subspecies, variety or cultivar to identify a particular plant. Starting from the top, the highest category, plants have traditionally be


<p>Classification of PlantsPlants are classified in several different ways, and the further away from the garden we get, the more the name indicates a plant's relationship to other plants, and tells us about its place in the plant world rather than in the garden. Usually, only the Family, Genus and species are of concern to the gardener, but we sometimes include subspecies, variety or cultivar to identify a particular plant. Starting from the top, the highest category, plants have traditionally been classified as follows. Each group has the characteristics of the level above it, but has some distinguishing features. The further down the scale you go, the more minor the differences become, until you end up with a classification which applies to only one plant. CLASS Angiospermae (Angiosperms) Gymnospermae (Gymnosperms) SUBCLASS Dicotyledonae (Dicotyledons, Dicots) Monocotyledonae (Monocotyledons, Monocots) Plants which produce flowers Plants which don't produce flowers Plants with two seed leaves Plants with one seed leaf</p> <p>SUPERORDER A group of related Plant Families, classified in the order in which they are thought to have developed their differences from a common ancestor. There are six Superorders in the Dicotyledonae (Magnoliidae, Hamamelidae, Caryophyllidae, Dilleniidae, Rosidae, Asteridae), and four Superorders in the Monocotyledonae (Alismatidae, Commelinidae, Arecidae, Liliidae) The names of the Superorders end in -idae ORDER Each Superorder is further divided into several Orders. The names of the Orders end in -ales FAMILY Each Order is divided into Families. These are plants with many botanical features in common, and is the highest classification normally used. At this level, the similarity between plants is often easily recognisable by the layman. Modern botanical classification assigns a type plant to each Family, which has the particular characteristics which separate this group of plants from others, and names the Family after this plant. The number of Plant Families varies according to the botanist whose classification you follow. Some botanists recognise only 150 or so families, preferring to classify other similar plants as sub-families, while others recognise nearly 500 plant families. A widely-accepted system is that devised by Cronquist in 1968, which is only slightly revised today. Links to the various methods of classification are on this website. The names of the Families end in -aceae SUBFAMILY The Family may be further divided into a number of sub-families, which group together plants within the Family that have some significant botanical differences.</p> <p>The names of the Subfamilies end in -oideae TRIBE A further division of plants within a Family, based on smaller botanical differences, but still usually comprising many different plants. The names of the Tribes end in -eae SUBTRIBE A further division, based on even smaller botanical differences, often only recognisable to botanists. The names of the Subtribes end in -inae GENUS This is the part of the plant name that is most familiar, the normal name that you give a plant Papaver (Poppy), Aquilegia (Columbine), and so on. The plants in a Genus are often easily recognisable as belonging to the same group. The name of the Genus should be written with a capital letter. SPECIES This is the level that defines an individual plant. Often, the name will describe some aspect of the plant - the colour of the flowers, size or shape of the leaves, or it may be named after the place where it was found. Together, the Genus and species name refer to only one plant, and they are used to identify that particular plant. Sometimes, the species is further divided into sub-species that contain plants not quite so distinct that they are classified as Varieties. The name of the species should be written after the Genus name, in small letters, with no capital letter. VARIETY A Variety is a plant that is only slightly different from the species plant, but the differences are not so insignificant as the differences in a form. The Latin is varietas, which is usually abbreviated to var. The name follows the Genus and species name, with var. before the individual variety name. FORM A form is a plant within a species that has minor botanical differences, such as the colour of flower or shape of the leaves. The name follows the Genus and species name, with form (or f.) before the individual variety name. CULTIVAR A Cultivar is a cultivated variety, a particular plant that has arisen either naturally or through deliberate hybridisation, and can be reproduced (vegetatively or by seed) to produce more of the same plant. The name follows the Genus and species name. It is written in the language of the person who described it, and should not be translated. It is either written in single quotation marks or has cv. written in front of the name.</p> <p>Example of ClassificationThe full botanical classification of a particular Lesser Spearwort with narrow leaves is Category Scientific Name Common Name</p> <p>CLASS SUBCLASS</p> <p>Angiospermae Dicotyledonae</p> <p>Angiosperms Dicotyledons Magnolia Superorder Buttercup Order Buttercup Family Buttercup Subfamily Buttercup Tribe Buttercup Lesser Spearwort Lesser Spearwort</p> <p>SUPERORDER Magnoliidae ORDER FAMILY SUBFAMILY TRIBE GENUS SPECIES SUBSPECIES VARIETY Ranunculares Ranunculaceae Ranunculoideae Ranunculeae Ranunculus (Ranunculus) flammula (Ranunculus flammula) subsp. flammula</p> <p>(Ranunculus flammula subsp. flammula) var. tenuifolius Narrow-leaved Lesser Spearwort</p> <p>The traditional ways of classifying plants have been based on the visible physical characterists of the plant. However, since the discovery of DNA, plant scientists have been trying to classify plants more accurately, and to group them according to the similarities of their DNA. This has led to major changes in plant classification, as scientists have discovered that some plants have more in common with other plants which do not look the same, and that other plants which look similar have very different DNA make-up.</p> <p>Citric acid cycleFrom Wikipedia, the free encyclopedia (Redirected from Krebs cycle) Jump to: navigation, search</p> <p>Overview of the citric acid cycle The citric acid cycle also known as the tricarboxylic acid cycle (TCA cycle), the Krebs cycle, or recently in certain former Soviet Bloc countries the Szent-Gyrgyi-Krebs cycle[1][2] is a series of enzyme-catalysed chemical reactions, which is of central importance in all living cells, especially those that use oxygen as part of cellular respiration. In eukaryotic cells, the citric acid cycle occurs in the matrix of the mitochondrion. In aerobic organisms, the citric acid cycle is part of a metabolic pathway involved in the chemical conversion of carbohydrates, fats and proteins into carbon dioxide and water to generate a form of usable energy. Other relevant reactions in the pathway include those in glycolysis and pyruvate oxidation before the citric acid cycle, and oxidative phosphorylation after it. In addition, it provides precursors for many compounds including some amino acids and is therefore functional even in cells performing fermentation. Its centrality to many paths of biosynthesis suggest that it was one of the earliest formed parts of the cellular metabolic processes, and may have formed abiogenically.[3]</p> <p>The components and reactions of the citric acid cycle were established in the 1930s by seminal work from the Nobel laureates Albert Szent-Gyrgyi and Hans Adolf Krebs.</p> <p>Contents[hide] </p> <p>1 A simplified view of the process 2 Steps 3 Products 4 Regulation 5 Major metabolic pathways converging on the TCA cycle 6 Interactive pathway map 7 See also 8 Notes 9 External links</p> <p>[edit] A simplified view of the process</p> <p>The citric acid cycle begins with the transfer of a two-carbon acetyl group from acetylCoA to the four-carbon acceptor compound (oxaloacetate) to form a six-carbon compound (citrate). The citrate then goes through a series of chemical transformations, losing two carboxyl groups as CO2. The carbons lost as CO2 originate from what was oxaloacetate, not directly from acetyl-CoA. The carbons donated by acetyl-CoA become part of the oxaloacetate carbon backbone after the first turn of the citric acid cycle. Loss of the acetyl-CoA-donated carbons as CO2 requires several turns of the citric acid cycle. However, because of the role of the citric acid cycle in anabolism, they may not be lost, since many TCA cycle intermediates are also used as precursors for the biosynthesis of other molecules.[4] Most of the energy made available by the oxidative steps of the cycle is transferred as energy-rich electrons to NAD+, forming NADH. For each acetyl group that enters the citric acid cycle, three molecules of NADH are produced. Electrons are also transferred to the electron acceptor Q, forming QH2. At the end of each cycle, the four-carbon oxaloacetate has been regenerated, and the cycle continues.</p> <p>[edit] StepsTwo carbon atoms are oxidized to CO2, the energy from these reactions being transferred to other metabolic processes by GTP (or ATP), and as electrons in NADH and QH2. The NADH generated in the TCA cycle may later donate its electrons in oxidative phosphorylation to drive ATP synthesis; FADH2 is covalently attached to succinate dehydrogenase, an enzyme functioning both in the TCA cycle and the mitochondrial electron transport chain in oxidative</p> <p>phosphorylation. FADH2, therefore, facilitates transfer of electrons to coenzyme Q, which is the final electron acceptor of the reaction catalyzed by the Succinate:ubiquinone oxidoreductase complex, also acting as an intermediate in the electron transport chain.[5] The citric acid cycle is continuously supplied with new carbon in the form of acetyl-CoA, entering at step 1 below.[6] Substrates Products Enzyme Citrate synthase Reaction type Aldol condensation Dehydration reversible isomerisation Hydration Oxidation generates NADH (equivalent of 2.5 ATP) Comment irreversible, extends the 4C oxaloacetate to a 6C molecule</p> <p>Oxaloacetate + Citrate + 1 Acetyl CoA + CoA-SH H2O 2 Citrate cis-Aconitate + H2O</p> <p>Aconitase cis-Aconitate + 3 Isocitrate H2O Oxalosuccinate Isocitrate + 4 + NAD+ NADH + H + Isocitrate dehydrogenase 5 Oxalosuccinate Ketoglutarate + CO2</p> <p>rate-limiting, irreversible Decarboxylation stage, generates a 5C molecule irreversible stage, Succinyl-CoA generates NADH Ketoglutarate + + -Ketoglutarate Oxidative 6 (equivalent of 2.5 ATP), NAD+ + NADH + H+ + dehydrogenase decarboxylation regenerates the 4C chain CoA-SH CO2 (CoA excluded) or ADPATP instead Succinyl-CoA Succinate + Succinyl-CoA substrate-level of GDPGTP,[5] 7 + CoA-SH + synthetase phosphorylation generates 1 ATP or GDP + Pi GTP equivalent uses FAD as a prosthetic group (FADFADH2 in Fumarate + the first step of the Succinate + Succinate 8 ubiquinol Oxidation reaction) in the ubiquinone (Q) dehydrogenase (QH2) enzyme,[5] generates the equivalent of 1.5 ATP Fumarate + 9 L-Malate Fumarase Hydration H2O reversible (in fact, L-Malate + Oxaloacetate + Malate equilibrium favors 10 Oxidation NAD+ NADH + H+ dehydrogenase malate), generates NADH (equivalent of</p> <p>2.5 ATP) Mitochondria in animals, including humans, possess two succinyl-CoA synthetases: one that produces GTP from GDP, and another that produces ATP from ADP.[7] Plants have the type that produces ATP (ADP-forming succinyl-CoA synthetase).[6] Several of the enzymes in the cycle may be loosely-associated in a multienzyme protein complex within the mitochondrial matrix.[8] The GTP that is formed by GDP-forming succinyl-CoA synthetase may be utilized by nucleoside-diphosphate kinase to form ATP (the catalyzed reaction is GTP + ADP GDP + ATP).[5]</p> <p>[edit] ProductsProducts of the first turn of the cycle are: one GTP (or ATP), three NADH, one QH2, two CO2. Because two acetyl-CoA molecules are produced from each glucose molecule, two cycles are required per glucose molecule. Therefore, at the end of two cycles, the products are: two GTP, six NADH, two QH2, and four CO2 Description The sum of all reactions in the citric acid cycle is: Combining the reactions occurring during the pyruvate oxidation with those occurring during the citric acid cycle, the following overall pyruvate oxidation reaction is obtained: Combining the above reaction with the ones occurring in the course of glycolysis, the following overall glucose oxidation reaction (excluding reactions in the respiratory chain) is obtained: Reactants Acetyl-CoA + 3 NAD+ + Q + GDP + Pi + 2 H2O Products CoA-SH + 3 NADH + 3 H+ + QH2 + GTP + 2 CO2</p> <p>Pyruvate ion + 4 4 NADH + 4 H+ + NAD + Q + GDP + + QH2 + GTP + 3 Pi + 2 H2O CO2 Glucose + 10 NAD+ + 2 Q + 2 ADP + 2 GDP + 4 Pi + 2 H2O 10 NADH + 10 H+ + 2 QH2 + 2 ATP + 2 GTP + 6 CO2</p> <p>The above reactions are balanced if Pi represents the H2PO4- ion, ADP and GDP the ADP2- and GDP2- ions, respectively, and ATP and GTP the ATP3- and GTP3- ions, respectively. The total number of ATP obtained after complete oxidation of one glucose in glycolysis, citric acid cycle, and oxidative phosphorylation is estimated to be between 30 and 38. A recent assessment of the total ATP yield with the updated proton-to-ATP ratios provides an estimate of 29.85 ATP per glucose molecule.[9]</p> <p>[edit] RegulationAlthough pyruvate dehydrogenase is not technically a part of the citric acid cycle, its regulation is included here.</p> <p>The regulation of the TCA cycle is largely determined by substrate availability and product inhibition. NADH, a product of all dehydrogenases in the TCA cycle with the exception of succinate dehydrogenase, inhibits pyruvate dehydrogenase, isocitrate dehydrogenase, ketoglutarate dehydrogenase, and also citrate synthase. Acetyl-coA inhibits pyruvate dehydrogenase, while succinyl-CoA inhibits succinyl-CoA synthetase and citrate synthase. When tested in vitro with TCA enzymes, ATP inhibits citrate synthase and -ketoglutarate dehydrogenase; however, ATP levels do not change more than 10% in vivo between rest and vigorous exercise. There is no known allosteric mechanism that can account for large changes in reaction rate from an allosteric effector whose concentration changes less than 10%.[10] Calcium is used as a regulator. It activates pyruvate dehydrogenase, isocitrate dehydrogenase and -ketoglutarate dehydrogenase.[11] This increases the reaction rate of many of the steps in the cycle, and therefore increases flux throughout the pathway. Citrate is used for feedback inhibition, as it inhibits phosphofructokinase, an enzyme involved in glycolysis that catalyses formation of fructose 1,6-bisphosphate,a precursor of pyruvate. This prevents a constant high rate of flux when there is an accumulation of citrate and a decrease in substrate for the enzyme. Recent work has demonstrated an important link between intermediates of the citric acid cycle and the regulation of hypoxia-inducible factors (HIF). HIF plays a role in the regulation o...</p>