The main concern of plant physiology is the causality of functions. A basic property of life is metabolism. Therefore, we may distinguish functions of biochemistry and fUnctions of development.
A major distinction of biochemical functions is dissimilation and assimiliation. Dissimilation breaks down substrates for energy metabolism and also for the formation of monomeric building blocks for the synthesis of macromolecules. Assimiliation in photosynthetically active plants is the most noble character of plants because the strictly auto-trophic plants can build up their entire organic biomass from inorganic precursors, not only carbon compounds from carbon dioxide and water in photosynthesis, but also nitrogen- and sulfur-containing organic molecules from inorganic ammonia and nitrate, sulfate and sulfide. This is of eminent basic ecological importance as it is the only pathway for the entry of inorganic matter into the organic biomass on Earth.
Dissimilative processes are fermentation in the cytoplasm and respiration in the mitochondria breaking down carbohydrates and serving energy metabolism as well as providing building stones for the synthesis of proteins and lipids. Similarly the breakdown of proteins and lipids (fatty acids) to their monomeric building stones are dissimilative processes which also can considerably contribute to energy metabolism in the case of lipids. The major assimilative process is photosynthesis. The biosynthesis of structural and functional macromolecules uses the monomeric building stones of organic bases and pentoses (five-carbon sugars) for polynucleic acids, amino acids for proteins, various monomeric sugars for polysaccharides, and activated acetic acid (acetyl-coenzyme A) for lipids. A list of important compounds in the biochemistry of plants and their functions is given in Table 1. The major role of polynucleic acids is in storage, transmittance, and active use of genetic information. Proteins serve structural functions but are particularly important as biocatalyzers in enzymatic reactions. Lipids together with proteins build up the lipoprotein biomembranes. Carbohydrates have major structural functions in the cell walls of plants and, in this way, also are the basis of the formation of wood in the stems of plants and the trunks of large trees.
In addition, we must note that plants are the most inventive biochemists we can imagine. They can produce a vast diversity of natural products some of which may be classified as terpenoids, phenolic compounds and organic bases, and alkaloids (Table 1 ). Among the latter the stimulating compounds of coffee, tea, and tobacco as well as drugs such as atropine, chinine, curare, opium, cocaine, mescaline, and coniine, are well known.
Having mentioned the separate biochemical functions of cytoplasm, mitochondria, and chloroplasts above, it should be evident that metabolism in plant cells is compartmentalized. This is possible by the separating functions of membranes concealing the compartments. However, like any good border such membrane borders must not block off the various compartments hermetically from each other. On the contrary, they must allow a controlled and regulated cooperation of compartments. This is provided by transport proteins crossing the membranes,
Table 1 Important chemical compounds and their major functions in plants
Primary metabolism and functions
Monosaccharides (pentoses, C5; hexoses, C6)
Activated acetyl Glycerol
Fatty acids Lipids
Biocatalyzers Structure (membranes) Storage
Structure (membranes) Storage (fats)
Organic bases, pentoses (ribose) (deoxyribose)
Natural products and their functions Terpenoids Isopentenyl-
Phenolic Phenol compounds
Amino acids Organic bases
Polynucleic acids Ribonucleic acid (RNA) Deoxyribonucleic acid (DNA)
(C40), poly- (C500 -5000) terpenes Flavons Flavonols
Phytohormones, scent compounds, pigments, defense, resins
Electron transport Pigments
Structure (the lignin of wood) Defense
Nitrogen storage that is, carriers and channels for substrates mediating the exchange between the compartments. Separate biochemical and physiological functions of the organs leaves, roots, and flowers need translocation in the long-distance transport pathways of the phloem for assimilates and the xylem for water plus mineral nutrients.
Analytical techniques have now advanced to the extent that one can collect information about entire complements of various compounds. We call this 'omics', such as genomics deciphering entire genomes, transcriptomics covering gene transcripts, proteomics analyzing sets of proteins, and metabolomics assessing occurrence of metabolites. This is very descriptive of the functional system of organisms and provides huge sets of data. New theoretical approaches are developed to digest this information for the quest of understanding causality, for example, network dynamics (Figure 1).
The life cycle of higher plants comprises germination of seeds, growth, flowering, fertilization, and sexual reproduction forming seeds. Since plants normally cannot move around and are bound to a given location their orientations in space also are largely given by developmental processes. These processes involve increases in plant size and mass by assimilation. However, life cycles also require the most complex differentiations. These are regulated by effectors which can be external or internal control parameters and which evoke differential activation/inactivation of genes. External control parameters are environmental cues linking developmental functions to ecological responses. Internal control parameters among others are various phy-tohormones controlling different developmental functions. External and internal control parameters interact. There are primary and secondary messengers. All of this is interwoven in signaling networks of an extraordinarily high degree of complexity, an example of which is shown in Figure 2 where the signal transduction pathways from an effector to the phosphorylation of proteins are depicted. Protein phosphorylation is an essential element in differential gene regulation as well as directly in cellular metabolic functions.
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