Systems Biology (eBook)

Foreword  Introduction  1. THE STRUCTURE AND FUNCTION OF LIVING ORGANISMS 1.1 General physiochemical properties of biological structures The biological purpose of cellular and organism structures Supporting structures Cellular supporting structures Cellular shielding structures Extracellular supporting structures    Polysaccharides as supporting structures Structures associated with biological functions Energy and information storage structures 1.2 Self-organization 1.3 Hypothesis - Protein folding simulation hypothesis  - late stage intermediate – role of water 2. ENERGY IN BIOLOGY – Demand and Use 2.1 General principles of thermodynamics 2.2 Biological energy sources – synthesis of water 2.3 ATP synthesis 2.4 Photosynthesis 2.5 Direct and indirect exploitation of energy sources Direct way (direct coupling of spontaneous and non-spontaneous processes to an energy source)Indirect way (indirect coupling between non-spontaneous processes and sources of energy) 2.6 Energy conversion efficiency in biological processes 2.7 Entropic effects 2.8 Energy requirements of organisms  3. INFORMATION – Its Role and Meaning in Organisms 3.1 Information as a quantitative concept 3.2 Reliability of information sources Steady-state genetics Replication and its reliability Gene expression and its fidelity Development genetics (embryogenesis and regeneration) – the principles of cell differentiation - epigeneticsMolecular licensing of genes for transcription Specificity of epigenetic processes External control of cell proliferation and differentiation – embryonic development The genetics of evolution Combinatorial changes as a diversity-promoting strategy Directed mutability: hotspot genes Gene collaboration and hierarchy 3.3 Types of information conveyed by DNA 3.4 Information entropy and mechanisms assisting selection        Intermediate storage of genetic information Self-organization as a means of exploiting information associated with the natural direction of spontaneous processes Formation of organized structures as a means of reducing the necessary quantity of information Reducing the need for genetic information by substituting large sets of random events for directed processes Exploiting systemic solutions as a means of restricting information requirements         3.5 The role of information in interpreting pathological events3.6 Hypothesis - Protein folding early stage intermediate 4. REGULATION IN BIOLOGICAL SYSTEMS 4.1 The cell and the organism 4.2 The principle and mechanism of automatic intracellular regulation Cellular receptors Cellular effectors 4.3 Regulatory coupling between cells and organisms – hierarchical properties of regulation 4.4 Regulatory mechanisms on the organism level Signal encodingSignal amplification Positive feedback loop Signal attenuationSignal inactivationDiscrimination Coordinating signals on the organism level Extracellular process controlCell population control 4.5 Development control 4.6 Basic principles of regulation in biology 4.7 Regulation levels 4.8 Hypothesis - Proteome construction hypothesis 5. INTERRELATIONSHIPS IN ORGANIZED BIOLOGICAL SYSTEMS 5.1 The need of mutual relations in biological systems 5.2 Cooperation and coordination 5.3 The characteristics of process coordination in individual cells and organisms5.4 Mutual relationship between cells and the organism – activation and inhibition of enzymes (rapid effects) 5.5 Mutual support between cells and the organism – interdependence related to gene expression (slow effects) The structural underpinnings of interrelationship The role of common metabolite in complex process coordination Signal effectiveness and the structuring of mutual relations in metabolism Interrelationship in times of crisis – safety valves 5.6 Specialization of cell interrelationships 5.7 Hypothesis - The criteria of life