Plant Biochemistry

The fully revised and expanded fourth edition of Plant Biochemistry presents the latest science on the molecular mechanisms of plant life. The book not only covers the basic principles of plant biology, such as photosynthesis, primary and secondary metabolism, the function of phytohormones, plant genetics, and plant biotechnology, but it also addresses the various commercial applications of plant biochemistry. Plant biochemistry is not only an important field of basic science explaining the molecular function of a plant, but is also an applied science that is in the position to contribute to the solution of agricultural and pharmaceutical problems. Plants are the source of important industrial raw material such as fat and starch but they are also the basis for the production of pharmaceutics. It is expected that in the future, gene technology will lead to the extensive use of plants as a means of producing sustainable raw material for industrial purposes. As such, the techniques and use of genetic engineering to improve crop plants and to provide sustainable raw materials for the chemical and pharmaceutical industries are described in this edition. The latest research findings have been included, and areas of future research are identified. Offers the latest research findings in a concise and understandable manner. Presents plant metabolism in the context of the structure and the function of plants. Includes more than 300 two-color diagrams and metabolic schemes. Covers the various commercial applications of plant biochemistry. Provides extensive references to the recent scientific literature. Plant Biochemistry......Page 2 Copyright......Page 3 Dedication......Page 4 Preface......Page 5 Introduction......Page 7 A leaf cell consists of several metabolic compartments......Page 9 The cell wall consists mainly of carbohydrates and proteins......Page 12 Plasmodesmata connect neighboring cells......Page 15 Vacuoles have multiple functions......Page 17 Plastids have evolved from cyanobacteria......Page 19 Mitochondria also result from endosymbionts......Page 23 Peroxisomes are the site of reactions in which toxic intermediates are formed......Page 25 The endoplasmic reticulum and golgi apparatus form a network for the distribution of biosynthesis products......Page 26 Functionally intact cell organelles can be isolated from plant cells......Page 30 Various transport processes facilitate the exchange of metabolites between different compartments......Page 32 Translocators catalyze the specific transport of metabolic substrates and products......Page 34 Metabolite transport is achieved by a conformational change of the translocator......Page 36 Aquaporins make cell membranes permeable for water......Page 39 Ion channels have a very high transport capacity......Page 40 Porins consist of sheet structures......Page 45 How did photosynthesis start?......Page 51 The energy content of light depends on its wavelength......Page 53 Chlorophyll is the main photosynthetic pigment......Page 55 Light absorption excites the chlorophyll molecule......Page 58 An antenna is required to capture light......Page 62 How is the excitation energy of the photons captured in the antennae and transferred to the reaction centers?......Page 64 The function of an antenna is illustrated by the antenna of photosystem II......Page 65 Phycobilisomes enable cyanobacteria and red algae to carry out photosynthesis even in dim light......Page 68 The photosynthetic machinery is constructed from modules......Page 73 A reductant and an oxidant are formed during photosynthesis......Page 77 The basic structure of a photosynthetic reaction center has been resolved by X-ray structure analysis......Page 78 X-ray structure analysis of the photosynthetic reaction center......Page 80 The reaction center of Rhodopseudomonas viridis has a symmetric structure......Page 81 How does a reaction center function?......Page 83 Two photosynthetic reaction centers are arranged in tandem in photosynthesis of algae and plants......Page 87 Water is split by photosystem II......Page 90 Photosystem II complex is very similar to the reaction center in purple bacteria......Page 94 Mechanized agriculture usually necessitates the use of herbicides......Page 96 Iron atoms in cytochromes and in iron-sulfur centers have a central function as redox carriers......Page 98 The electron transport by the cytochrome-b6/f complex is coupled to a proton transport......Page 101 The number of protons pumped through the cyt-b6/f complex can be doubled by a Q-cycle......Page 104 Photosystem I reduces NADP+......Page 106 The light energy driving the cyclic electron transport of PS I is only utilized for the synthesis of ATP......Page 109 In the absence of other acceptors electrons can be transferred from photosystem I to oxygen......Page 110 Regulatory processes control the distribution of the captured photons between the two photosystems......Page 114 Excess light energy is eliminated as heat......Page 116 ATP is generated by photosynthesis......Page 121 A proton gradient serves as an energy-rich intermediate state during ATP synthesis......Page 122 The electron chemical proton gradient can be dissipated by uncouplers to heat......Page 125 H+-ATP synthases from bacteria, chloroplasts, and mitochondria have a common basic structure......Page 127 X-ray structure analysis of the F1 part of ATP synthase yields an insight into the machinery of ATP synthesis......Page 131 The synthesis of ATP is effected by a conformation change of the protein......Page 133 In photosynthetic electron transport the stoichiometry between the formation of NADPH and ATP is still a matter of debate......Page 136 V-ATPase is related to the F-ATP synthase......Page 137 Biological oxidation is preceded by a degradation of substrates to form bound hydrogen and CO2......Page 140 Mitochondria are the sites of cell respiration......Page 141 Mitochondria form a separated metabolic compartment......Page 142 Pyruvate is oxidized by a multienzyme complex......Page 143 Acetate is completely oxidized in the citrate cycle......Page 147 A loss of intermediates of the citrate cycle is replenished by anaplerotic reactions......Page 149 How much energy can be gained by the oxidation of NADH?......Page 151 The mitochondrial respiratory chain shares common features with the photosynthetic electron transport chain......Page 152 The complexes of the mitochondrial respiratory chain......Page 154 Electron transport of the respiratory chain is coupled to the synthesis of ATP via proton transport......Page 158 Mitochondrial proton transport results in the formation of a membrane potential......Page 160 Mitochondrial ATP synthesis serves the energy demand of the cytosol......Page 161 Plant mitochondria have special metabolic functions......Page 162 Mitochondria can oxidize surplus NADH without forming ATP......Page 163 NADH and NADPH from the cytosol can be oxidized by the respiratory chain of plant mitochondria......Page 165 Compartmentation of mitochondrial metabolism requires specific membrane translocators......Page 166 CO2 assimilation proceeds via the dark reaction of photosynthesis......Page 169 Ribulose bisphosphate carboxylase catalyzes the fixation of CO2......Page 172 The oxygenation of ribulose bisphosphate: a costly side-reaction......Page 174 Activation of ribulose bisphosphate carboxylase/oxygenase......Page 176 The reduction of 3-phosphoglycerate yields triose phosphate......Page 178 Ribulose bisphosphate is regenerated from triose phosphate......Page 180 Besides the reductive pentose phosphate pathway there is also an oxidative pentose phosphate pathway......Page 187 Reduced thioredoxins transmit the signal “illumination” to the enzymes......Page 191 The thioredoxin modulated activation of chloroplast enzymes releases a built-in blockage......Page 193 Multiple regulatory processes tune the reactions of the reductive pentose phosphate pathway......Page 194 Ribulose 1,5-bisphosphate is recovered by recycling 2-phosphoglycolate......Page 198 The NH4+ released in the photorespiratory pathway is refixed in the chloroplasts......Page 204 Peroxisomes have to be provided with external reducing equivalents for the reduction of hydroxypyruvate......Page 206 A “malate valve” controls the export of reducing equivalents from the chloroplasts......Page 208 The peroxisomal matrix is a special compartment for the disposal of toxic products......Page 210 How high are the costs of the ribulose bisphosphate oxygenase reaction for the plant?......Page 211 There is no net CO2 fixation at the compensation point......Page 212 The photorespiratory pathway, although energy-consuming, may also have a useful function for the plant......Page 213 The uptake of CO2 into the leaf is accompanied by an escape of water vapor......Page 215 Malate plays an important role in guard cell metabolism......Page 217 Complex regulation governs stomatal opening......Page 219 The diffusive flux of CO2 into a plant cell......Page 221 C4 plants perform CO2 assimilation with less water consumption than C3 plants......Page 224 The CO2 pump in C4 plants......Page 225 C4 metabolism of the NADP-malic enzyme type plants......Page 227 C4 metabolism of the NAD-malic enzyme type......Page 231 C4 metabolism of the phosphoenolpyruvate carboxykinase type......Page 233 Enzymes of C4 metabolism are regulated by light......Page 235 C4 plants include important crop plants but also many persistent weeds......Page 236 Crassulacean acid metabolism allows plants to survive even during a very severe water shortage......Page 237 CO2 fixed during the night is stored as malic acid......Page 238 Photosynthesis proceeds with closed stomata......Page 240 C4 as well as CAM metabolism developed several times during evolution......Page 242 Polysaccharides are storage and transport forms of carbohydrates produced by photosynthesis......Page 244 Large quantities of carbohydrate can be stored as starch in the cell......Page 245 Starch is synthesized via ADP-glucose......Page 249 Degradation of starch proceeds in two different ways......Page 251 Surplus of photosynthesis products can be stored temporarily in chloroplasts as starch......Page 254 Sucrose synthesis takes place in the cytosol......Page 256 Fructose 1,6-bisphosphatase is an entrance valve of the sucrose synthesis pathway......Page 258 Sucrose phosphate synthase is regulated by metabolites and by covalent modification......Page 262 Trehalose is an important signal mediator......Page 263 In some plants assimilates from the leaves are exported as sugar alcohols or oligosaccharides of the raffinose family......Page 264 Fructans are deposited as storage compounds in the vacuole......Page 267 Cellulose is synthesized by enzymes located in the plasma membrane......Page 271 Synthesis of callose is often induced by wounding......Page 272 Cell wall polysaccharides are also synthesized in the Golgi apparatus......Page 273 Nitrate assimilation is essential for the synthesis of organic matter......Page 275 The reduction of nitrate to NH3 proceeds in two reactions......Page 276 Nitrate is reduced to nitrite in the cytosol......Page 278 The reduction of nitrite to ammonia proceeds in the plastids......Page 279 The fixation of NH4+ proceeds in the same way as in the photorespiratory cycle......Page 280 The oxidative pentose phosphate pathway in leucoplasts provides reducing equivalents for nitrite reduction......Page 282 Nitrate assimilation is strictly controlled......Page 284 Nitrate reductase is also regulated by reversible covalent modification......Page 285 14-3-3 proteins are important metabolic regulators......Page 286 There are great similarities between the regulation of nitrate reductase and sucrose phosphate synthase......Page 287 CO2 assimilation provides the carbon skeletons to synthesize the end products of nitrate assimilation......Page 288 The synthesis of glutamate requires the participation of mitochondrial metabolism......Page 290 Biosynthesis of proline and arginine......Page 291 Aspartate is the precursor of five amino acids......Page 293 Acetolactate synthase participates in the synthesis of hydrophobic amino acids......Page 295 Glyphosate acts as a herbicide......Page 299 A large proportion of the total plant matter can be formed by the shikimate pathway......Page 301 Glutamate is the precursor for chlorophylls and cytochromes......Page 302 Protophorphyrin is also precursor for heme synthesis......Page 304 Nitrogen fixation enables plants to use the nitrogen of the air for growth......Page 308 Legumes form a symbiosis with nodule-inducing bacteria......Page 309 Metabolic products are exchanged between bacteroids and host cells......Page 312 Dinitrogenase reductase delivers electrons for the dinitrogenase reaction......Page 314 Plants improve their nutrition by symbiosis with fungi......Page 319 N2 fixation can proceed only at very low oxygen concentrations......Page 317 The arbuscular mycorrhiza is widespread......Page 320 Root nodule symbioses may have evolved from a pre-existing pathway for the formation of arbuscular mycorrhiza......Page 321 Sulfate assimilation proceeds primarily by photosynthesis......Page 324 Sulfate assimilation has some parallels to nitrogen assimilation......Page 325 Sulfate is activated prior to reduction......Page 326 Sulfite reductase is similar to nitrite reductase......Page 327 H2S is fixed in the amino acid cysteine......Page 328 Glutathione serves the cell as an antioxidant and is an agent for the detoxification of pollutants......Page 329 Xenobiotics are detoxified by conjugation......Page 330 Phytochelatins protect the plant against heavy metals......Page 331 S-Adenosylmethionine is a universal methylation reagent......Page 333 Excessive concentrations of sulfur dioxide in the air are toxic for plants......Page 335 Phloem transport distributes photoassimilates to the various sites of consumption and storage......Page 337 There are two modes of phloem loading......Page 339 Phloem transport proceeds by mass flow......Page 341 Sink tissues are supplied by phloem unloading......Page 342 The glycolysis pathway plays a central role in the utilization of carbohydrates......Page 343 Products of nitrate assimilation are deposited in plants as storage proteins......Page 349 Globulins are the most abundant storage proteins......Page 350 Prolamins are formed as storage proteins in grasses......Page 351 Special proteins protect seeds from being eaten by animals......Page 352 Synthesis of the storage proteins occurs at the rough endoplasmic reticulum......Page 353 Proteinases mobilize the amino acids deposited in storage proteins......Page 356 Lipids are membrane constituents and function as carbon stores......Page 358 Polar lipids are important membrane constituents......Page 359 The fluidity of the membrane is governed by the proportion of unsaturated fatty acids and the content of sterols......Page 360 Membrane lipids contain a variety of hydrophilic head groups......Page 362 Sphingolipids are important constituents of the plasma membrane......Page 363 Triacylglycerols are storage compounds......Page 365 Acetyl CoA is a precursor for the synthesis of fatty acids......Page 367 Acetyl CoA carboxylase is the first enzyme of fatty acid synthesis......Page 370 Further steps of fatty acid synthesis are also catalyzed by a multienzyme complex......Page 372 The first double bond in a newly synthesized fatty acid is formed by a soluble desaturase......Page 374 Glycerol 3-phosphate is a precursor for the synthesis of glycerolipids......Page 377 The ER membrane is the site of fatty acid elongation and desaturation......Page 380 Some of the plastid membrane lipids are synthesized via the eukaryotic pathway......Page 381 Triacylglycerols are synthesized in the membranes of the endoplasmatic reticulum......Page 383 Plant fat is used for human nutrition and also as a raw material in industry......Page 384 Plant fats are customized by genetic engineering......Page 385 Storage lipids are mobilized for the production of carbohydrates in the glyoxysomes during seed germination......Page 387 The glyoxylate cycle enables plants to synthesize hexoses from acetyl CoA......Page 389 Reactions with toxic intermediates take place in peroxisomes......Page 391 Lipoxygenase is involved in the synthesis of oxylipins, which are defense and signal compounds......Page 392 Secondary metabolites often protect plants from pathogenic microorganisms and herbivores......Page 398 Plants synthesize phytoalexins in response to microbial infection......Page 399 Plant defense compounds can also be a risk for humans......Page 400 Alkaloids comprise a variety of heterocyclic secondary metabolites......Page 401 Some plants emit prussic acid when wounded by animals......Page 403 Some wounded plants emit volatile mustard oils......Page 404 Plants protect themselves by tricking herbivores with false amino acids......Page 405 A large diversity of isoprenoids has multiple functions in plant metabolism......Page 408 Acetyl CoA is a precursor for the synthesis of isoprenoids in the cytosol......Page 410 Pyruvate and D-glyceraldehyde-3-phosphate are the precursors for the synthesis of isopentyl pyrophosphate in plastids......Page 412 Prenyl transferases catalyze the association of isoprene units......Page 413 Some plants emit isoprenes into the air......Page 415 Many aromatic compounds derive from geranyl pyrophosphate......Page 416 Farnesyl pyrophosphate is the precursor for the synthesis of sesquiterpenes......Page 418 Steroids are synthesized from farnesyl pyrophosphate......Page 419 Oleoresins protect trees from parasites......Page 421 Carotene synthesis delivers pigments to plants and provides an important vitamin for humans......Page 422 A Prenyl chain renders compounds lipid-soluble......Page 423 Proteins can be anchored in a membrane by prenylation......Page 424 Dolichols mediate the glucosylation of proteins......Page 425 Isoprenoids are very stable and persistent substances......Page 426 Phenylpropanoids comprise a multitude of plant secondary metabolites and cell wall components......Page 429 Phenylalanine ammonia lyase catalyzes the initial reaction of phenylpropanoid metabolism......Page 431 Monooxygenases are involved in the synthesis of phenols......Page 432 Phenylpropanoid compounds polymerize to macromolecules......Page 434 Lignans act as defense substances......Page 435 Lignin is formed by radical polymerization of phenylpropanoid derivatives......Page 436 Suberins form gas- and water-impermeable layers between cells......Page 438 Some stilbenes are very potent natural fungicides......Page 440 Flavonoids have multiple functions in plants......Page 442 Anthocyanins are flower pigments and protect plants against excessive light......Page 444 Tannins bind tightly to proteins and therefore have defense functions......Page 445 Multiple signals regulate the growth and development of plant organs and enable their adaptation to environmental conditions......Page 448 G-proteins act as molecular switches......Page 449 Small G-proteins have diverse regulatory functions......Page 450 Ca2+ is a component of signal transduction chains......Page 451 The phosphoinositol pathway controls the opening of Ca2 channels......Page 452 Calmodulin mediates the signal function of Ca2 ions......Page 454 Phosphorylated proteins are components of signal transduction chains......Page 455 Phytohormones contain a variety of very different compounds......Page 457 Auxin stimulates shoot elongation growth......Page 458 Gibberellins regulate stem elongation......Page 461 Cytokinins stimulate cell division......Page 464 Abscisic acid controls the water balance of the plant......Page 466 Ethylene makes fruit ripen......Page 467 Brassinosteroids control plant development......Page 469 Systemin induces defense against herbivore attack......Page 471 A small protein causes the alkalization of cell culture medium......Page 472 Defense reactions are triggered by the interplay of several signals......Page 473 Salicylic acid and jasmonic acid are signal molecules in pathogen defense......Page 474 Phytochromes function as sensors for red light......Page 476 Phototropin and cryptochromes are blue light receptors......Page 479 A plant cell has three different genomes......Page 483 In the nucleus the genetic information is divided among several chromosomes......Page 484 The DNA of the nuclear genome is transcribed by three specialized RNA polymerases......Page 487 The transcription of structural genes is regulated......Page 488 Promoter and regulatory sequences regulate the transcription of genes......Page 489 Small (sm)RNAs inhibit gene expression by inactivating messenger RNAs......Page 490 The transcription of structural genes requires a complex transcription apparatus......Page 491 The formation of the mature messenger RNA requires processing......Page 493 DNA polymorphism yields genetic markers for plant breeding......Page 497 Individuals of the same species can be differentiated by restriction fragment length polymorphism......Page 498 The RAPD technique is a simple method for investigating DNA polymorphism......Page 501 The polymorphism of micro-satellite DNA is used as a genetic marker......Page 503 Transposable DNA elements roam through the genome......Page 504 Viruses are present in most plant cells......Page 505 Retrotransposons are degenerated retroviruses......Page 508 Plastids possess a circular genome......Page 509 The transcription apparatus of the plastids resembles that of bacteria......Page 512 The mitochondrial genome of plants varies largely in its size......Page 513 Mitochondrial RNA is corrected after transcription via editing......Page 516 Male sterility of plants caused by the mitochondria is an important tool in hybrid breeding......Page 517 Protein biosynthesis occurs in three different locations of a cell......Page 523 Protein synthesis is catalyzed by ribosomes......Page 524 A peptide chain is synthesized......Page 525 The translation is regulated......Page 529 Proteins attain their three-dimensional structure by controlled folding......Page 530 The folding of a protein is a multistep process......Page 531 Proteins are protected during the folding process......Page 532 Chaperones bind to unfolded proteins......Page 533 Most of the proteins imported into the mitochondria have to cross two membranes......Page 536 The import of proteins into chloroplasts requires several translocation complexes......Page 539 Proteins are imported into peroxisomes in the folded state......Page 542 Proteins are degraded by proteasomes in a strictly controlled manner......Page 543 Biotechnology alters plants to meet requirements of agriculture, nutrition and industry......Page 547 A gene library is required for the isolation of a gene......Page 548 A gene library can be kept in phages......Page 550 A gene library can also be propagated in plasmids......Page 551 A clone is identified by antibodies which specifically detect the gene product......Page 553 A clone can also be identified by DNA probes......Page 555 Genes encoding unknown proteins can be functionally assigned by complementation......Page 556 Agrobacteria can transform plant cells......Page 558 The Ti plasmid contains the genetic information for tumor formation......Page 560 Ti-Plasmids are used as transformation vectors......Page 562 A new plant is regenerated after the transformation of a leaf cell......Page 565 Protoplasts can be transformed by the uptake of DNA......Page 567 Plastid transformation to generate transgenic plants is advantageous for the environment......Page 569 Selected promoters enable the defined expression of a foreign gene......Page 571 Genes can be turned off via plant transformation......Page 572 Plant genetic engineering can be used for many different purposes......Page 574 Plants are protected against some insects by the BT protein......Page 575 Plants can be protected against viruses by gene technology......Page 577 Nonselective herbicides can be used as a selective herbicide by the generation of herbicide-resistant plants......Page 578 Genetic engineering is used to produce renewable resources for industry......Page 579 Genetic engineering provides a chance for increasing the protection of crop plants against environmental stress......Page 580 The introduction of transgenic cultivars requires a risk analysis......Page 581 Index......Page 583 A Leaf Cell Consists of Several Metabolic Compartments The Use of Energy from Sunlight by Photosynthesis is the Basis of Life on Earth Photosynthesis is an Electron Transport Process ATP is Generated by Photosynthesis Mitochondria are the Power Station of the Cell The Calvin Cycle Catalyzes Photosynthetic CO2 Assimilation In the Photorespiratory Pathway Phosphoglycolate Formed by the Oxygenase Activity of RubisCo is Recycled Photosynthesis Implies the Consumption of Water Polysaccharides are Storage and Transport Forms of Carbohydrates Produced by Photosynthesis Nitrate Assimilation is Essential for the Synthesis of Organic Matter Nitrogen Fixation Enables the Nitrogen in the Air to be Used for Plant Growth Sulfate Assimilation Enables the Synthesis of Sulfur Containing Substances Phloem Transport Distributes Photoassimilates to the Various Sites of Consumption and Storage Products of Nitrate Assimilation are Deposited in Plants as Storage Proteins Glycerolipids are Membrane Constituents and Function as Carbon Stores Secondary Metabolites Fulfill Specific Ecological Functions in Plants Large Diversity of Isoprenoids has Multiple Funtions in Plant Metabolism Phenylpropanoids Comprise a Multitude of Plant Secondary Metabolites and Cell Wall Components Multiple Signals Regulate the Growth and Development of Plant Organs and Enable Their Adaptation to Environmental Conditions A Plant Cell has Three Different Genomes Protein Biosynthesis Occurs at Different Sites of a Cell Gene Technology Makes it Possible to Alter Plants to Meet Requirements of Agriculture, Nutrition, and Industry.