Systems Biology

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 - epigenetics

Molecular 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        

3.6 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 encoding

Signal amplification

Positive feedback loop

Signal attenuation

Signal inactivation

Discrimination

Coordinating signals on the organism level

Extracellular process control

Cell 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 organisms

5.4 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