Hierarchical Architecture of Plants
The dynamics and structural organisation of photosynthetic organisms covers more than 10 orders of magnitude in space and up to 26 orders of magnitude in time, ranging from the pm-dimension of electronic orbitals up to plants that are tens of meters large and from the fs dynamics of light absorption to the life time of trees that can span thousands of years. Our aim is to contribute to our understanding of the complicated hierarchical network of communication that enables the stability of such structures over time.
In the following chapters, we will focus on the role of ROS as a messenger product and substrate in its contribution to communication and feedback in hierarchical networks. The described formalism of rate equations will be an approach to model such behaviour in the form of communication trees or flux diagrams that will make the observed behaviour understandable with reference to only the basic molecular entities of the system. Top down messaging in such systems occurs in the form of regulated gene expression that is originally caused by macroscopic parameters. One example is the regulation of genes by MAPKs that respond to ROS that are produced under high light conditions. In that sense the high light condition changes the protein environment in cells and is therefore a type of top-down communication in the plant. Generally all kind of feedback loops, from macroscopic structures to the microscopic environment, are top down. Such feedback does not necessarily need to target the basic molecular level. However, looking at the regulation of genes, the composition and, consequently, the behaviour of molecules on the microscopic level is partially induced from the macroscopic level.
These phenomena might also be constraints that develop from collective behaviour that are behind the structure parameters or the slaving principle mentioned in the first chapter. Plants turn out to be the optimized system for such consideration on the way to explain living matter as they exhibit features of top down signalling without the need to model consciousness or focus on the emergence of consciousness as plants do not seem to exhibit consciousness in a measurable way.
It is proposed that the ability to react to external stimuli by active mobility strategies is a necessary prerequisite to develop a strategic and existential advantage from consciousness and therefore supports its emergence. This assumption is in agreement with psychoinformatic studies performed in cognitive sciences such as e.g. the proposition of the anticipatory drive (Butz et al., 2003).
Figure 50 presents a schematic overview on the hierarchical organisation of structures that form the photosynthetic organism (e.g. a photosynthetic tree of 10 m) that is a sum of its cells (typically 10-100 pm). The photosynthesis takes place inside the leaves which are formed by an inhomogeneous 3-dim. array of cells on the pm-scale. The single cell is the smallest organized form that is still named “living system”. It is a whole organism and all higher individual organisms are formed by a symbiotic biosystem of such cells.
In eukaryotic organisms the cells contain chloroplasts (chloroplasts have very different sizes and geometries, see e.g. (Hader, 1999) where photosynthesis takes place inside the thylakoid membrane. The cells contain the endoplasmatic reticulum that connects ribosomes and the cell organelles, i.e. mitochondria, chloroplasts, the nucleus and the vacuole. Additional minor components like hormones, proteins, free DNA and RNA and a number of different small molecules are not shown in Figure 50. The chloroplasts have their own DNA, lipid droplets, starch, ribosomes and they contain the Grana stacks of the thylakoid membrane. The thylakoid membrane is formed by a lipid bilayer with hydrophilic surface. Inside the thylakoid membrane the lipophilic environment contains the membrane proteins. They are hydrophobic and therefore bound to the membrane (membrane intrinsic proteins).
Figure 51 schematically shows the substructure of the chloroplasts containing the thylakoid membrane where the photosynthetic pigment- protein-complexes are located as membrane intrinsic proteins.
Figure 50. Hierarchic structures of green plants. The chloroplasts contain the Grana stacks of the thylakoid membrane where photosynthesis takes place.
Figure 51. Membrane proteins inside the lipid double membrane of the thylakoids.
The dynamics of the thylakoid membrane is assumed to have impact on the transient changes of the quantum yield of photochemical light transformation. Therefore the thylakoid membrane is typically the highest organised structure taken into account for the description of fluorescence measurements that cover a time scale up to several ms after light excitation like single flash induced transient fluorescence yield measurements in whole cells of Chlorella pyrenoidosa Chick or higher plants (Belyaeva et al., 2008, 2011, 2014, 2015).
The photosynthetic reactions leading to CO2-fixation comprise the light driven reactions which take place inside the thylakoid membrane and the “dark” reactions which take place inside the chloroplast stroma (indicated as a red cycle process in Figure 51).The thylakoid membrane divides the aqueous phases of the chloroplasts into the thylakoid lumen and the chloroplast stroma. Protons released into the thylakoid lumen and protons transferred from the stroma into the lumen form a transmembrane electrochemical potential difference which drives the adenosine triphosphate (ATP) synthase that phosphorylates adenosine diphosphate to the energy rich compound ATP required as free energy source in the dark reaction for carbon reduction.
The “light” reaction performs the exploitation of solar energy by highly functionalized PPCs. Solar energy represents the unique Gibbs free energy source of the biosphere on earth. The Gibbs free energy is converted into high energetic chemical compounds via the process of photosynthesis. This goal is achieved in a perfect manner by incorporation of suitable chromophores into protein matrices. The PPCs are optimized to energy absorption and transfer producing the high energetic compounds ATP and NADPH.