Plant biochemistry

1 A leaf cell consists of several metabolic compartments 1 1.1 The cell wall gives the plant cell mechanical stability 4 The cell wall consists mainly of carbohydrates and proteins 4 Plasmodesmata connect neighboring cells 7 1.2 Vacuoles have multiple functions 9 1.3 Plastids have evolved from cyanobacteria 10 1.4 Mitochondria also result from endosymbionts 15 1.5 Peroxisomes are the site of reactions in which toxic intermediates are formed 16 1.6 The endoplasmic reticulum and Golgi apparatus form a network for the distribution of biosynthesis products 18 1.7 Functionally intact cell organelles can be isolated from plant cells 22 1.8 Various transport processes facilitate the exchange of metabolites between different compartments 24 1.9 Translocators catalyze the specific transport of substrates and products of metabolism 26 Translocators have a common basic structure 29 Aquaporins make cell membranes permeable for water 31 1.10 Ion channels have a very high transport capacity 32 1.11 Porins consist of b-sheet structures 37 Further reading 40 2 The use of energy from sunlight by photosynthesis is the basis of life on earth 45 2.1 How did photosynthesis start? 45 2.2 Pigments capture energy from sunlight 47 The energy content of light depends on its wavelength 47 Chlorophyll is the main photosynthetic pigment 49 2.3 Light absorption excites the chlorophyll molecule 52 The return of the chlorophyll molecule from the first singlet state to the ground state can proceed in different ways 55 2.4 An antenna is required to capture light 56 How is the excitation energy of the photons, which have been captured in the antennae, transferred to the reaction centers? 58 The function of an antenna can be illustrated using the antenna of photosystem II as an example 59 Phycobilisomes enable cyanobacteria and red algae to carry out photosynthesis even in dim light 62 Further reading 66 3 Photosynthesis is an electron transport process 67 3.1 The photosynthetic machinery is constructed from modules 67 3.2 A reductant and an oxidant are formed during photosynthesis 71 3.3 The basic structure of a photosynthetic reaction center has been resolved by X-ray structure analysis 72 X-ray structure analysis of the photosynthetic reaction center 74 The reaction center of Rhodopseudomonas viridis has a symmetric structure 75 3.4 How does a reaction center function? 77 3.5 Two photosynthetic reaction centers are arranged in tandem in photosynthesis of algae and plants 81 3.6 Water is split by photosystem II 84 Photosystem II complex is very similar to the reaction center in purple bacteria 88 Mechanized agriculture usually necessitates the use of herbicides 90 3.7 The cytochrome-b6/f complex mediates electron transport between photosystem II and photosystem I 92 Iron atoms in cytochromes and in iron-sulfur centers have a central function as redox carriers 92 The electron transport by the cytochrome-b6/f complex is coupled to a proton transport 95 The number of protons pumped through the cyt-b6/f complex can be doubled by a Q-cycle 98 3.8 Photosystem I reduces NADP 99 In cyclic electron transport by PS I light energy is used for the synthesis of ATP only 103 3.9 In the absence of other acceptors electrons can be transferred from photosystem I to oxygen 104 3.10 Regulatory processes control the distribution of the captured photons between the two photosystems 108 Excess light energy is eliminated as heat 110 Further reading 112 xii Contents 4 ATP is generated by photosynthesis 115 4.1 A proton gradient serves as an energy-rich intermediate state during ATP synthesis 116 4.2 The electron chemical proton gradient can be dissipated by uncouplers to heat 119 The chemiosmotic hypothesis was proved experimentally 121 4.3 H+-ATP synthases from bacteria, chloroplasts, and mitochondria have a common basic structure 121 X-ray structure analysis of the F1 part of ATP synthase yields an insight into the machinery of ATP synthesis 125 4.4 The synthesis of ATP is effected by a conformation change of the protein 127 In photosynthetic electron transport the stoichiometry between the formation of NADPH and ATP is still a matter of debate 130 H+-ATP synthase of chloroplasts is regulated by light 130 V-ATPase is related to the F-ATP synthase 131 Further reading 132 5 Mitochondria are the power station of the cell 135 5.1 Biological oxidation is preceded by a degradation of substrates to form bound hydrogen and CO2 135 5.2 Mitochondria are the sites of cell respiration 136 Mitochondria form a separated metabolic compartment 137 5.3 Degradation of substrates for biological oxidation takes place in the matrix compartment 138 Pyruvate is oxidized by a multienzyme complex 138 Acetate is completely oxidized in the citrate cycle 141 A loss of intermediates of the citrate cycle is replenished by anaplerotic reactions 144 5.4 How much energy can be gained by the oxidation of NADH? 145 5.5 The mitochondrial respiratory chain shares common features with the photosynthetic electron transport chain 147 The complexes of the mitochondrial respiratory chain 149 5.6 Electron transport of the respiratory chain is coupled to the synthesis of ATP via proton transport 153 Mitochondrial proton transport results in the formation of a membrane potential 155 Mitochondrial ATP synthesis serves the energy demand of the cytosol 156 Contents xiii 5.7 Plant mitochondria have special metabolic functions 157 Mitochondria can oxidize surplus NADH without forming ATP 158 NADH and NADPH from the cytosol can be oxidized by the respiratory chain of plant mitochondria 159 5.8 Compartmentation of mitochondrial metabolism requires specific membrane translocators 160 Further reading 162 6 The Calvin cycle catalyzes photosynthetic CO2 assimilation 165 6.1 CO2 assimilation proceeds via the dark reaction of photosynthesis 166 6.2 Ribulose bisphosphate carboxylase catalyzes the fixation of CO2 168 The oxygenation of ribulose bisphosphate: a costly side-reaction 170 Ribulose bisphosphate carboxylase/oxygenase: special features 172 Activation of ribulose bisphosphate carboxylase/oxygenase 172 6.3 The reduction of 3-phosphoglycerate yields triose phosphate 174 6.4 Ribulose bisphosphate is regenerated from triose phosphate 176 6.5 Besides the reductive pentose phosphate pathway there is also an oxidative pentose phosphate pathway 183 6.6 Reductive and oxidative pentose phosphate pathways are regulated 187 Reduced thioredoxins transmit the signal for “illumination” to enzyme proteins 187 The thioredoxin modulated activation of chloroplast enzymes releases an inbuilt blockage 189 An abundance of further regulatory processes ensures that the various steps of the reductive pentose phosphate pathway are matched 190 Further reading 192 7 In the photorespiratory pathway phosphoglycolate formed by the oxygenase activity of RubisCo is recycled 195 7.1 Ribulose 1,5-bisphosphate is recovered by recycling 2-phosphoglycolate 195 7.2 The NH4 + released in the photorespiratory pathway is refixed in the chloroplasts 201 7.3 For the reduction of hydroxypyruvate, peroxisomes have to be provided with external reducing equivalents 203 xiv Contents Reducing equivalents are taken up into the peroxisomes via a malate-oxaloacetate shuttle 203 Mitochondria export reducing equivalents via a malate-oxaloacetate shuttle 205 A “malate valve” controls the export of reducing equivalents from the chloroplasts 205 7.4 The peroxisomal matrix is a special compartment for the disposal of toxic products 207 7.5 How high are the costs of the ribulose bisphosphate oxygenase reaction for the plant? 208 7.6 There is no net CO2 fixation at the compensation point 209 7.7 The photorespiratory pathway, although energy-consuming, may also have a useful function for the plant 210 Further reading 211 8 Photosynthesis implies the consumption of water 213 8.1 The uptake of CO2 into the leaf is accompanied by an escape of water vapor 213 8.2 Stomata regulate the gas exchange of a leaf 215 Malate plays an important role in guard cell metabolism 215 Complex regulation governs stomatal opening 217 8.3 The diffusive flux of CO2 into a plant cell 219 8.4 C4 plants perform CO2 assimilation with less water consumption than C3 plants 222 The CO2 pump in C4 plants 223 C4 metabolism of the NADP-malic enzyme type plants 225 C4 metabolism of the NAD-malic enzyme type 229 C4 metabolism of the phosphoenolpyruvate carboxykinase type 231 Kranz-anatomy with its mesophyll and bundle sheath cells is not an obligatory requirement for C4 metabolism 233 Enzymes of C4 metabolism are regulated by light 233 Products of C4 metabolism can be identified by mass spectrometry 234 C4 plants include important crop plants but also many of the worst weeds 234 8.5 Crassulacean acid metabolism makes it possible for plants to survive even during a very severe water shortage 235 CO2 fixed during the night is stored in the form of malic acid 236 Photosynthesis proceeds with closed stomata 238 C4 as well as CAM metabolism has been developed several times during evolution 240 Further reading 240 Contents xv 9 Polysaccharides are storage and transport forms of carbohydrates produced by photosynthesis 243 Starch and sucrose are the main products of CO2 assimilation in many plants 244 9.1 Large quantities of carbohydrate can be stored as starch in the cell 244 Starch is synthesized via ADP-glucose 248 Degradation of starch proceeds in two different ways 250 Surplus photosynthesis products can be stored temporarily in chloroplasts by starch synthesis 253 9.2 Sucrose synthesis takes place in the cytosol 255 9.3 The utilization of the photosynthesis product triose phosphate is strictly regulated 257 Fructose 1,6-bisphosphatase functions as an entrance valve for the pathway of sucrose synthesis 257 Sucrose phosphate synthase is regulated not only by metabolites but also by covalent modification 261 Partitioning of assimilates between sucrose and starch is due to the interplay of several regulatory mechanisms 262 9.4 In some plants assimilates from the leaves are exported as sugar alcohols or oligosaccharides of the raffinose family 263 9.5 Fructans are deposited as storage substances in the vacuole 265 9.6 Cellulose is synthesized by enzymes located in the plasma membrane 269 Synthesis of callose is often induced by wounding 271 Cell wall polysaccharides are also synthesized in the Golgi apparatus 271 Further reading 271 10 Nitrate assimilation is essential for the synthesis of organic matter 275 10.1 The reduction of nitrate to NH3 proceeds in two partial reactions 276 Nitrate is reduced to nitrite in the cytosol 278 The reduction of nitrite to ammonia proceeds in the plastids 279 The fixation of NH4 + proceeds in the same way as in photorespiration 280 10.2 Nitrate assimilation also takes place in the roots 282 The oxidative pentose phosphate pathway provides reducing equivalents for nitrite reduction in leucoplasts 282 10.3 Nitrate assimilation is strictly controlled 284 The synthesis of the nitrate reductase protein is regulated at the level of gene expression 285 xvi Contents Nitrate reductase is also regulated by reversible covalent modification 285 14-3-3 Proteins are important metabolic regulators 286 The regulation of nitrate reductase and of sucrose phosphate synthase have great similarities 287 10.4 The end-product of nitrate assimilation is a whole spectrum of amino acids 288 CO2 assimilation provides the carbon skeletons to synthesize the end-products of nitrate assimilation 288 The synthesis of glutamate requires the participation of mitochondrial metabolism 290 Biosynthesis of proline and arginine 291 Aspartate is the precursor of five amino acids 293 Acetolactate synthase participates in the synthesis of hydrophobic amino acids 295 Aromatic amino acids are synthesized via the shikimate pathway 299 Glyphosate acts as an herbicide 299 A large proportion of the total plant matter can be formed by the shikimate pathway 301 10.5 Glutamate is precursor for synthesis of chlorophylls and cytochromes 302 Protophorphyrin is also a precursor for heme synthesis 304 Further reading 306 11 Nitrogen fixation enables the nitrogen in the air to be used for plant growth 309 11.1 Legumes form a symbiosis with nodule-forming bacteria 310 The formation of nodules is due to a regulated interplay of the expression of specific bacteria and plant genes 313 Metabolic products are exchanged between bacteroids and host cells 313 Nitrogenase reductase delivers electrons for the nitrogenase reaction 315 N2 as well as H+ are reduced by dinitrogenase 316 11.2 N2 fixation can proceed only at very low oxygen concentrations 318 11.3 The energy costs for utilizing N2 as a nitrogen source are much higher than for the utilization of NO3 - 320 11.4 Plants improve their nutrition by symbiosis with fungi 320 The arbuscular mycorrhiza is widespread 321 Ectomycorrhiza supplies trees with nutrients 322 Contents xvii 11.5 Root nodule symbioses may have evolved from a preexisting pathway for the formation of arbuscular mycorrhiza 322 Further reading 323 12 Sulfate assimilation enables the synthesis of sulfur-containing substances 325 12.1 Sulfate assimilation proceeds primarily by photosynthesis 325 Sulfate assimilation has some parallels to nitrogen assimilation 326 Sulfate is activated prior to reduction 327 Sulfite reductase is similar to nitrite reductase 328 H2S is fixed in the form of cysteine 329 12.2 Glutathione serves the cell as an antioxidant and is an agent for the detoxification of pollutants 330 Xenobiotics are detoxified by conjugation 331 Phytochelatins protect the plant against heavy metals 332 12.3 Methionine is synthesized from cysteine 333 S-Adenosylmethionine is a universal methylation reagent 334 12.4 Excessive concentrations of sulfur dioxide in air are toxic for plants 335 Further reading 336 13 Phloem transport distributes photoassimilates to the various sites of consumption and storage 339 13.1 There are two modes of phloem loading 341 13.2 Phloem transport proceeds by mass flow 343 13.3 Sink tissues are supplied by phloem unloading 344 Starch is deposited in plastids 345 The glycolysis pathway plays a central role in the utilization of carbohydrates 345 Further reading 350 14 Products of nitrate assimilation are deposited in plants as storage proteins 353 14.1 Globulins are the most abundant storage proteins 354 14.2 Prolamins are formed as storage proteins in grasses 355 14.3 2S-Proteins are present in seeds of dicot plants 356 14.4 Special proteins protect seeds from being eaten by animals 356 14.5 Synthesis of the storage proteins occurs at the rough endoplasmic reticulum 357 xviii Contents 14.6 Proteinases mobilize the amino acids deposited in storage proteins 360 Further reading 360 15 Glycerolipids are membrane constituents and function as carbon stores 363 15.1 Polar glycerolipids are important membrane constituents 364 The fluidity of the membrane is governed by the proportion of unsaturated fatty acids and the content of sterols 365 Membrane lipids contain a variety of hydrophilic head groups 367 Sphingolipids are important constituents of the plasma membrane 368 15.2 Triacylglycerols are storage substances 369 15.3 The de novo synthesis of fatty acids takes place in the plastids 372 Acetyl CoA is the precursor for the synthesis of fatty acids 372 Acetyl CoA carboxylase is the first enzyme of fatty acid synthesis 375 Further steps of fatty acid synthesis are also catalyzed by a multienzyme complex 377 The first double bond in a newly formed fatty acid is formed by a soluble desaturase 379 Acyl-ACP formed as product of fatty acid synthesis in the plastids serves two purposes 382 15.4 Glycerol 3-phosphate is a precursor for the synthesis of glycerolipids 382 The ER membrane is the site of fatty acid elongation and desaturation 385 Some of the plastid membrane lipids are formed via the eukaryotic pathway 386 15.5 Triacylglycerols are formed in the membranes of the endoplasmic reticulum 388 Plant fat is used not only for nutrition but also as a raw material in industry 389 Plant fats are customized by genetic engineering 390 15.6 During seed germination, storage lipids are mobilized for the production of carbohydrates in the glyoxysomes 392 The glyoxylate cycle enables plants to synthesize hexoses from acetyl CoA 393 Reactions with toxic intermediates take place in peroxisomes 395 15.7 Lipoxygenase is involved in the synthesis of oxylipins, which are acting as defense and signal substances 396 Further reading 401 Contents xix 16 Secondary metabolites fulfill specific ecological functions in plants 403 16.1 Secondary metabolites often protect plants from pathogenic microorganisms and herbivores 403 Microbes can be pathogens 404 Plants form phytoalexins in response to microbial infection 404 Plant defense substances can also be a risk for humans 405 16.2 Alkaloids comprise a variety of heterocyclic secondary metabolites 406 16.3 Some plants emit prussic acid when wounded by animals 408 16.4 Some wounded plants emit volatile mustard oils 409 16.5 Plants protect themselves by tricking herbivores with false amino acids 410 Further reading 411 17 A large diversity of isoprenoids has multiple functions in plant metabolism 413 17.1 Higher plants have two different synthesis pathways for isoprenoids 415 Acetyl CoA is the precursor for the synthesis of isoprenoids in the cytosol 415 Pyruvate and D-glycerinaldehyde-3-phosphate are the precursors for the synthesis of isopentyl pyrophosphate in plastids 417 17.2 Prenyl transferases catalyze the association of isoprene units 418 17.3 Some plants emit isoprenes into the air 420 17.4 Many aromatic substances are derived from geranyl pyrophosphate 421 17.5 Farnesyl pyrophosphate is the precursor for the formation of sesquiterpenes 423 Steroids are synthesized from farnesyl pyrophosphate 424 17.6 Geranylgeranyl pyrophosphate is the precursor for defense substances, phytohormones, and carotenoids 426 Oleoresins protect trees from parasites 426 Carotene synthesis delivers pigments to plants and provides an important vitamin for humans 427 17.7 A prenyl chain renders substances lipid-soluble 428 Proteins can be anchored in a membrane by prenylation 429 Dolichols mediate the glucosylation of proteins 430 17.8 The regulation of isoprenoid synthesis 431 17.9 Isoprenoids are very stable and persistent substances 431 Further reading 432 xx Contents 18 Phenylpropanoids comprise a multitude of plant secondary metabolites and cell wall components 435 18.1 Phenylalanine ammonia lyase catalyzes the initial reaction of phenylpropanoid metabolism 437 18.2 Monooxygenases are involved in the synthesis of phenols 438 18.3 Phenylpropanoid compounds polymerize to macromolecules 440 Lignans act as defense substances 442 Lignin is formed by radical polymerization of phenylpropanoid derivatives 443 Suberins form gas- and water-impermeable layers between cells 444 Cutin is a gas- and water-impermeable constituent of the cuticle 446 18.4 For the synthesis of flavonoids and stilbenes a second aromatic ring is formed from acetate residues 446 The stilbenes include very potent natural fungicides 446 18.5 Flavonoids have multiple functions in plants 448 18.6 Anthocyanins are flower pigments and protect plants against excessive light 450 18.7 Tannins bind tightly to proteins and therefore have defense functions 451 Further reading 453 19 Multiple signals regulate the growth and development of plant organs and enable their adaptation to environmental conditions 455 19.1 Signal chains known from animal metabolism also function in plants 456 G-proteins act as molecular switches 456 Small G-proteins have diverse regulatory functions 457 Ca++ acts as a messenger in signal transduction 458 The phosphoinositol pathway controls the opening of Ca++ channels 459 Calmodulin mediates the messenger function of Ca++ ions 461 Phosphorylated proteins form elements of signal transduction 462 19.2 Phytohormones comprise a variety of very different compounds 464 19.3 Auxin stimulates shoot elongation growth 465 19.4 Gibberellins regulate stem elongation 468 19.5 Cytokinins stimulate cell division 471 19.6 Abscisic acid controls the water balance of the plant 473 19.7 Ethylene makes fruit ripen 474 Contents xxi 19.8 Plants also contain steroid and peptide hormones 476 Brassinosteroids control plant development 476 Various phytohormones are polypeptides 478 Systemin induces defense against herbivore attack 478 Phytosulfokines regulate cell proliferation 479 19.9 Defense reactions are triggered by the interplay of several signals 479 19.10 Light sensors regulate growth and development of plants 481 Further reading 485 20 A plant cell has three different genomes 491 20.1 In the nucleus the genetic information is divided among several chromosomes 492 The DNA sequences of plant nuclear genomes have been analyzed in a dicot and a monocot plant 495 20.2 The DNA of the nuclear genome is transcribed by three specialized RNA polymerases 495 The transcription of structural genes is regulated 496 Promoter and regulatory sequences regulate the transcription of genes 497 Transcription factors regulate the transcription of a gene 498 Micro-RNAs inhibit gene expression by inactivating messeger RNAs 498 The transcription of structural genes requires a complex transcription apparatus 499 The formation of the messenger RNA requires processing 501 rRNA and tRNA are synthesized by RNA polymerase I and III 503 20.3 DNA polymorphism yields genetic markers for plant breeding 505 Individuals of the same species can be differentiated by restriction fragment length polymorphism 506 The RAPD technique is a simple method for investigating DNA polymorphism 508 The polymorphism of micro-satellite DNA is used as a genetic marker 511 20.4 Transposable DNA elements roam through the genome 511 20.5 Most plant cells contain viruses 513 Retrotransposons are degenerated retroviruses 515 20.6 Plastids possess a circular genome 516 The transcription apparatus of the plastids resembles that of bacteria 520 xxii Contents 20.7 The mitochondrial genome of plants varies largely in its size 520 Mitochondrial DNA contains incorrect information that is corrected after transcription 524 Male sterility of plants caused by the mitochondria is an important tool in hybrid breeding 525 Further reading 529 21 Protein biosynthesis occurs at different sites of a cell 531 21.1 Protein synthesis is catalyzed by ribosomes 532 A peptide chain is synthesized 534 Specific inhibitors of the translation can be used to decide whether a protein is encoded in the nucleus or the genome of plastids or mitochondria 537 The translation is regulated 537 21.2 Proteins attain their three-dimensional structure by controlled folding 538 The folding of a protein is a multistep process 539 Proteins are protected during the folding process 540 Heat shock proteins protect against heat damage 541 Chaperones bind to unfolded proteins 541 21.3 Nuclearly encoded proteins are distributed throughout various cell compartments 544 Most of the proteins imported into the mitochondria have to cross two membranes 545 The import of proteins into chloroplasts requires several translocation complexes 547 Proteins are imported into peroxisomes in the folded state 550 21.4 Proteins are degraded in a strictly controlled manner by proteasomes 551 Further reading 554 22 Gene technology makes it possible to alter plants to meet requirements of agriculture, nutrition, and industry 557 22.1 A gene is isolated 558 A gene library is required for the isolation of a gene 558 A gene library can be kept in phages 560 A gene library can also be kept in plasmids 562 A gene library is screened for a certain gene 563 A clone is identified by antibodies against the gene product 563 A clone can also be identified by DNA probes 565 Contents xxiii Genes encoding unknown proteins can be isolated by complementation 566 Genes can be tracked down with the help of transposons or T-DNA 568 22.2 Agrobacteria have the ability to transform plant cells 568 The Ti plasmid contains the genetic information for tumor formation 570 22.3 Ti plasmids are used as transformation vectors 572 A new plant is regenerated following transformation of a leaf cell 575 Plants can be transformed by a modified shotgun 577 Protoplasts can be transformed by the uptake of DNA 578 The use of plastid transformation for genetic engineering of plants is of advantage for the environment 579 22.4 Selection of appropriate promoters enables the defined expression of an inserted gene 581 Gene products are directed into certain subcellular compartments by targeting sequences 582 22.5 Genes can be turned off by transformation 582 22.6 Plant genetic engineering can be used for many different purposes 585 Plants are selectively protected against some insects by the BT protein 585 Plants can be protected against viruses by gene technology 587 The generation of fungus-resistant plants is still at an early stage 588 Nonselective herbicides can be used as selective herbicide following the generation of herbicide-resistant plants 588 Plant genetic engineering is used for the improvement of the yield and quality of crop products 589 Genetic engineering is used to produce raw material for industry and pharmaceuticals 589 Genetic engineering provides a chance for increasing the protection of crop plants against environmental stress 590 The introduction of transgenic cultivars requires a risk analysis 591 Further reading 591 Index 595