Botany online 1996-2004. No further update, only historical document of botanical science!

Ions and Small Molecules

The sum of all biochemical processes is called metabolism. It is distinguished between primary and secondary metabolism. The primary metabolism contains all pathways necessary to keep the cell alive. In the secondary metabolism, compounds are produced and broken down that are essential for the whole organism.

The cell's compounds can be grouped into three different classes: inorganic ions, small organic molecules and macromolecules. Macromolecules comprise again three classes of molecules: proteins, polysaccharides and nucleic acids

"It has already been recognized earlier that we have explained nothing of a plant's life as long as we have not detected the physical or chemical processes that it relies on and exactly for this it is imperative that we start our studies with the simplest case, the single cell. That we will never gain a clear picture, if we start from the back, is understood considering the great complications of most chemico-physical phenomenons." (from: M. J. SCHLEIDEN: Grundzüge der wissenschaftlichen Botanik, 1842 (Rudiments of Scientific Botany))

The Bohr model of the atom, often called the planetary model. As shown for a hydrogen atom, the Bohr model envisions the nucleus of the atom occupying a fixed position at the center of an atomic system with the electron revolving around the nucleus in the same way that a planet revolves around the sun. Actually most of the atom is empty space, and the electron repesents the state as a moving cloud

© Thomas A. NEWTON

For the understanding of biochemical and molecular biological processes as metabolism, differentiation, growth and inheritance, the knowledge of the molecules involved is imperative. They consist of atoms (Periodic Table of the Elements) that are arranged according to a clear set of rules. According to the theory of combinations, any number of molecules should exist but actually only those are known that have been synthesized during the last 100-150 years in chemical research laboratories or those whose structure could be ascertained. Limiting are on one hand the potential experimental effort and on the other hand financial resources. The number and nature of chemical compounds in plant cells is determined from a very different point of view although efficiency and economy are decisive, too.

Cell specific molecules are generated via a number of intermediate products from simple precursors, others again are broken down or rearranged. The sum of all biochemical processes is called metabolism. During evolution, just such pathways have developed and been maintained that produce functional molecules actually needed by the cell or the organism.

It is distinguished between the primary and the secondary metabolism. The primary metabolism also called basic metabolism contains all pathways and products that are essential for the cell itself. Besides some specific pathways of plants (like photosynthesis) and micro-organisms, the reactions of the primary metabolism are nearly identical in all organisms (plants, animals, micro-organisms). This fact can be regarded as a proof that their evolution was already largely accomplished before diversification into the different cells and organisms happened.

The secondary metabolism produces molecules that are not that important for the survival of the cell itself but much more so for that of the whole organism. Especially in plants, such pathways play an important part. They lead to products like flower colours, scents and flavours, stabilizing elements, toxic components, etc.

From the chemical point of view, the compounds of cells can be grouped into three categories: the inorganic ions (mineral nutrients), the small organic molecules and the macromolecules. Below, the most important representatives will be introduced in the order mentioned above. When enumerating the organic molecules, the chemically simply structured carbohydrates that are the basic compounds for the slightly more complex derivatives occurring in cells will be reviewed, too.

Out of the large number of the mineral nutrients contained in the soil, some are taken up selectively by the plant. The rather common aluminium for example is not used although many plant species are able to accumulate it. For an understanding of the organic molecules, a knowledge of the structure of saturated and unsaturated aliphatic hydrocarbons and the derived alcohols, aldehydes, organic acids and esters is imperative. The structures of sugars and their biosynthetic precursors, the aromatic hydrocarbons and heterocyclic rings as well as the amino acids and lipids are also important.

The macromolecules are grouped into three classes, polysaccharides, proteins and nucleic acids. They are usually linear polymers that consist of a small amount of monomers. Real branching occurs only in polysaccharides. A decisive aspect in the explanation of the function of these molecules is founded on the formation of many so-called weak bonds or interactions that stabilize the linear molecules in complex, three-dimensional conformations.

The Kyoto Encyclopedia of Genes and Genomes (KEGG) - develops into an ultimate source for biochemical data such as formulas, names and positions within metabolic pathways of biologically important compounds and for metabolic pathways, in addition to those of enzyme nomenclature, amino acid - and nucleotide sequences . All other relevant international databases can be accessed through the DBGET Database Links and through . Essential parts of the database are mirrored in Botany online . All graphical elements within the metabolic pathway maps are clickable. Not-mirrored files, search devices and updates can be accessed only if online.

© Peter v. Sengbusch - Impressum