This open-access textbook is an excellent introduction to systems biology, which has developed rapidly in recent years. It discusses the processes in living organisms in an integrated way, enabling the reader to understand the fundamental principles and cause-effect relationships in biology and biochemistry. The authors have chosen an original but at the same time clear way of presenting the topics, repeatedly drawing comparisons and models from the macroscopic world and making the reader aware of the unity of the laws of physics, chemistry and biology.
The fully updated 2nd edition also contains information that has only become available as a result of the increase in knowledge in recent years. This includes information on tumorigenesis, where significant progress has been made due to the explosive development of genetic knowledge as well as bioengineering with a highly effective technique adopted from the solutions of the bacterial world, such as CRISPR/CAS.
This richly illustrated book is essential for postgraduate students and scientists of the following disciplines: biology, biotechnology, medicine, bioinformatics, robotics and automation, biocybernetics, and biomedical engineering. It is also an exciting read for anyone interested in biology.
Author(s): Leszek Konieczny, Irena Roterman-Konieczna, Paweł Spólnik
Edition: 2
Publisher: Springer
Year: 2023
Language: English
Pages: 268
City: Cham
Preface
Preface to Second Edition
Acknowledgments
Introduction
Contents
1: The Structure and Function of Living Organisms
1.1 General Physiochemical Properties of Biological Structures
1.1.1 Small-Molecule Structures and Polymers
1.1.2 The Biological Purpose of Cellular and Organism Structures
1.1.3 Supporting Structures
1.1.3.1 Cellular Supporting Structures
1.1.3.2 Cellular Shielding Structures
1.1.3.3 Extracellular Supporting Structures
1.1.3.4 Polysaccharides as Supporting Structures
1.1.4 Structures Associated with Biological Functions
1.1.5 Energy and Information Storage Structures
1.2 Self-Organization
1.3 Hypothesis
1.3.1 Protein Folding Simulation Hypothesis: Late-Stage Intermediate-Role of Water
Suggested Reading
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
2.6 Energy Conversion Efficiency in Biological Processes
2.7 Entropic Effects
2.8 Energy Requirements of Organisms
Suggested Reading
3: Information: Its Role and Meaning in Organisms
3.1 Information as a Quantitative Concept
3.2 Reliability of Information Sources
3.2.1 Steady-State Genetics
3.2.2 Replication and Its Reliability
3.2.2.1 Telomeres
3.2.2.2 Function-Oriented Organization of the Genome
3.2.3 Gene Expression and Its Fidelity
3.2.3.1 Nuclear Pores
3.2.3.2 Protein Synthesis and Degradation
3.2.4 Epigenetics
3.2.5 Development Genetics (Embryogenesis and Regeneration): The Principles of Cell Differentiation
3.2.5.1 Molecular Licensing of Genes for Transcription
3.2.5.2 Specificity of Epigenetic Processes
3.2.5.3 External Control of Cell Proliferation and Differentiation: Embryonic Development
3.2.6 The Genetics of Evolution
3.2.6.1 Combinatorial Changes as a Diversity-Promoting Strategy
3.2.6.2 Directed Mutability: Hotspot Genes
3.2.6.3 Gene Collaboration and Hierarchy
3.3 Types of Information Conveyed by DNA
3.4 Information Entropy and Mechanisms Assisting Selection
3.5 Indirect Storage of Genetic Information
3.5.1 Self-Organization as a Means of Exploiting Information Associated with the Natural Direction of Spontaneous Processes
3.5.1.1 Formation of Organized Structures as a Means of Reducing the Necessary Quantity of Information
3.5.1.2 Reducing the Need for Genetic Information by Substituting Large Sets of Random Events for Directed Processes
3.5.1.3 Exploiting Systemic Solutions as a Means of Restricting Information Requirements
3.6 The Role of Information in Interpreting Pathological Events
3.7 Hypothesis
3.7.1 Protein Folding Simulation Hypothesis: Early-Stage Intermediate Form
Suggested Reading
4: Regulation in Biological Systems
4.1 The Cell and the Organism
4.2 The Principle and Mechanism of Automatic Intracellular Regulation
4.2.1 Cellular Receptors
4.2.2 Cellular Effectors
4.3 Regulatory Coupling Between Cells and Organisms: Hierarchical Properties of Regulation
4.4 Regulatory Mechanisms on the Organism Level
4.4.1 Signal Encoding
4.4.2 Signal Amplification
4.4.3 Cascade Amplifier
4.4.4 Positive Feedback Loop
4.4.5 Signal Attenuation
4.4.6 Signal Inactivation
4.4.7 Discrimination
4.4.8 Coordinating Signals on the Organism Level
4.4.9 Extracellular Process Control
4.4.10 Cell Population Control
4.5 Development Control
4.6 Basic Principles of Regulation in Biology
4.7 Regulation Levels
4.8 Hypothesis
4.8.1 Proteome Construction Hypothesis
Suggested Reading
5: Interrelationship 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 Relation 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)
5.5.1 The Structural Underpinnings of Interrelationship
5.5.2 The Role of Common Metabolite in Complex Process Coordination
5.5.3 Signal Effectiveness and the Structuring of Mutual Relations in Metabolism
5.5.4 Interrelationship in Times of Crisis: Safety Valves
5.6 Specialization of Cell Interrelationship
5.7 Microbiome
5.8 Bacterial Bioengineering Techniques
5.9 Hypothesis
5.9.1 Carcinogenesis
5.9.2 The Criteria of Life
Suggested Reading
