Plant Cell Biology

From Astronomy to Zoology

3rd Edition - November 15, 2024
Author: Randy O. Wayne
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 2 1 4 6 9 - 1
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 1 4 7 0 - 7

Plant Cell Biology: From Astronomy to Zoology, Third Edition connects the fundamentals of plant anatomy, plant physiology, plant growth and development, plant taxonomy, plant… Read more

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Plant Cell Biology: From Astronomy to Zoology, Third Edition connects the fundamentals of plant anatomy, plant physiology, plant growth and development, plant taxonomy, plant biochemistry, plant molecular biology, and plant cell biology. It covers all aspects of plant cell biology without emphasizing any one plant, organelle, molecule, or technique. Although most examples are biased towards plants, basic similarities between all living eukaryotic cells (animal and plant) are recognized and used to best illustrate cell processes. This is a must-have reference for scientists with a background in plant anatomy, plant physiology, plant growth and development, plant taxonomy, and more.

Title of Book
Cover image
Title page
Table of Contents
Copyright
Dedication
Preface to the first edition
Preface to the second edition
Preface to the third edition
Chapter 1. On the nature of cells
1.1 Introduction: what is a cell?
1.2 The basic unit of life
1.3 The chemical composition of cells
1.4 A sense of cellular scale
1.5 The energetics of cells
1.6 Are there limits to the mechanistic view?
1.7 The mechanistic viewpoint and God
1.8 What is cell biology?
1.9 Summary
1.10 Questions
Chapter 2. Plasma membrane
2.1 The cell boundary
2.2 Topology of the cell
2.3 Evidence for the existence of a plasma membrane
2.4 Structure of the plasma membrane
2.5 Isolation of the plasma membrane
2.6 Chemical composition of the plasma membrane
2.7 Transport physiology
2.8 Electrical properties of the plasma membrane
2.9 Characterization of two transport proteins of the plasma membrane
2.9.1 Proton-pumping ATPase
2.9.2 The K+ channel
2.10 Plasma membrane–localized physiological responses
2.10.1 Guard cells
2.10.2 Motor organs
2.10.3 Action potentials
2.10.4 Cell polarization
2.11 Structural specializations of the plasma membrane
2.12 The cytoskeleton–plasma membrane–extracellular matrix continuum
2.13 Summary
2.14 Questions
Chapter 3. Plasmodesmata
3.1 The relationship between cells and the organism
3.2 Discovery and occurrence of plasmodesmata
3.3 Structure of plasmodesmata
3.4 Isolation and composition of plasmodesmata
3.5 Permeability of plasmodesmata
3.6 Summary
3.7 Questions
Chapter 4. Endoplasmic reticulum
4.1 Significance and evolution of the endoplasmic reticulum
4.2 Discovery of the endoplasmic reticulum
4.3 Structure of the endoplasmic reticulum
4.4 Structural specializations that relate to function
4.5 Isolation of RER and SER
4.6 Composition of the endoplasmic reticulum
4.7 Function of the endoplasmic reticulum
4.7.1 Lipid synthesis
4.7.2 Protein synthesis on the endoplasmic reticulum
4.7.3 Protein glycosylation (carbohydrate synthesis)
4.7.4 Calcium regulation
4.7.5 Phenylpropanoid and flavonoid synthesis
4.8 Summary
4.9 Questions
Chapter 5. Peroxisomes
5.1 Discovery of microbodies
5.2 Isolation of peroxisomes
5.3 Composition of peroxisomes
5.4 Function of peroxisomes
5.4.1 β-Oxidation
5.4.2 Photorespiration
5.5 Relationship between glyoxysomes and peroxisomes
5.6 Metabolite channeling
5.7 Other functions
5.8 Biogenesis of peroxisomes
5.9 Evolution of peroxisomes
5.10 Summary
5.11 Questions
Chapter 6. Golgi apparatus
6.1 Discovery and structure of the Golgi apparatus
6.2 Polarity of the Golgi stack
6.3 Isolation of the Golgi apparatus
6.4 Composition of the Golgi apparatus
6.5 Function of the Golgi apparatus
6.5.1 Processing of glycoproteins
6.5.2 Synthesis of carbohydrates
6.5.3 Transport of sugars
6.6 The Mechanism of movement from cisterna to cisterna
6.7 Positioning of the Golgi apparatus
6.8 Summary
6.9 Questions
Chapter 7. The vacuole
7.1 Discovery of the vacuole
7.2 Structure, biogenesis, and dynamic aspects of vacuoles
7.3 Isolation of vacuoles
7.4 Composition of vacuoles
7.5 Transport across the vacuolar membrane
7.5.1 Proton-translocating pumps
7.5.2 ATP-binding cassette transporters or traffic ATPases
7.5.3 Slowly activated vacuolar channels
7.5.4 Water channels
7.6 Functions of the vacuole
7.6.1 Proteolysis and recycling
7.6.2 Taking up space
7.6.3 Storage and homeostasis
7.6.4 Role in turgor generation
7.6.5 Other functions
7.7 Biotechnology
7.8 Summary
7.9 Questions
Chapter 8. Movement within the endomembrane system
8.1 Discovery of the secretory pathway
8.2 Movement to the plasma membrane and the extracellular matrix
8.2.1 Movement between the endoplasmic reticulum and the Golgi apparatus
8.2.2 Movement from the Golgi apparatus to the plasma membrane
8.3 Movement from the endoplasmic reticulum to the Golgi apparatus to the vacuole
8.4 Movement from the endoplasmic reticulum to the vacuole
8.5 Movement from the plasma membrane to the endomembranes
8.5.1 Fluid-phase endocytosis
8.5.2 Receptor-mediated endocytosis
8.5.3 Piggyback endocytosis
8.6 Disruption of intracellular secretory and endocytotic pathways
8.7 Summary
8.8 Questions
Chapter 9. Cytoplasmic structure
9.1 Historical survey of the study of cytoplasmic structure
9.2 Chemical composition of protoplasm
9.3 Physical properties of cytoplasm
9.3.1 Viscosity of the cytoplasm
9.3.1.1 Newtonian fluids
9.3.1.2 Non-Newtonian fluids
9.3.1.3 Experimental approaches to measuring cytoplasmic viscosity
9.3.1.4 The effect of environmental stimuli on cytoplasmic viscosity
9.3.2 Elasticity of the cytoplasm
9.4 Microtrabecular lattice
9.4.1 Function of the microtrabecular lattice in polarity
9.5 Summary
9.6 Questions
Chapter 10. Actin- and microfilament-mediated processes
10.1 Discovery of actomyosin and the mechanism of muscle movement
10.2 Actin in nonmuscle cells
10.2.1 Temporal and spatial localization of actin in plant cells
10.2.2 Biochemistry of actin
10.2.3 Biochemistry of myosins
10.3 Force-generating reactions involving actin
10.3.1 Actomyosin
10.3.2 Polymerization of actin filaments
10.4 Actin-based motility
10.4.1 Cytoplasmic streaming
10.4.2 Chloroplast movements
10.4.3 Cell plate reorientation in Allium
10.4.4 Secretion of vesicles involved in tip growth and auxin-induced growth
10.4.5 Contractile vacuoles
10.5 Role of actin in membrane transport
10.6 Summary
10.7 Questions
Chapter 11. Tubulin and microtubule-mediated processes
11.1 Discovery of microtubules in cilia and flagella and the mechanism of movement
11.2 Microtubules in nonflagellated or nonciliated cells and the discovery of tubulin
11.2.1 Temporal and spatial localization of microtubules in animal and plant cells
11.2.2 Characterization of microtubule-associated motor proteins
11.3 Force-generating reactions involving tubulin
11.3.1 Sliding
11.3.2 Polymerization/depolymerization
11.4 Tubulin-based motility
11.5 Microtubules and cell shape
11.5.1 Apical meristems
11.5.2 Tracheary elements
11.5.3 Guard cells
11.5.4 Extracellular matrix of Oocystis
11.5.5 Mechanism of microtubule-mediated cellulose orientation
11.5.6 Tip-growing cells
11.6 Various stimuli affect microtubule orientation
11.7 Microtubules and cytoplasmic structure
11.8 Intermediate filaments
11.9 Centrin-based motility
11.10 Tensegrity in cells
11.11 Summary
11.12 Questions
Chapter 12. Cell signaling
12.1 The scope of cell regulation
12.2 What is stimulus–response coupling?
12.3 Receptors
12.4 Cardiac muscle as a paradigm for understanding the basics of stimulus–response coupling
12.5 A kinetic description of regulation
12.5.1 Early history of kinetic studies
12.5.2 Kinetics of enzyme reactions
12.5.3 Kinetics of diffusion and dehydration
12.5.4 A thermodynamic analysis of the signal-to-noise problem
12.6 Ca2+ signaling system
12.7 Mechanics of doing experiments to test the importance of Ca2+ as a second messenger
12.8 Specific signaling systems in plants involving Ca2+
12.8.1 Double fertilization
12.8.2 Ca2+-induced secretion in barley aleurone cells
12.8.3 Excitation–cessation of streaming coupling in characean internodal cells
12.8.4 Regulation of turgor in cells
12.8.4.1 Thermodynamic basis of the van’t Hoff Equation
12.8.4.2 Turgor pressure in characean cells
12.8.4.3 Turgor regulation in characean cells
12.9 Phosphatidylinositol signaling system
12.9.1 Components of the system
12.9.2 Phosphatidylinositol signaling in guard cell movement
12.10 The role of ions in cells
12.11 Summary
12.12 Questions
Chapter 13. Chloroplasts
13.1 Discovery of chloroplasts and photosynthesis
13.1.1 Discovery of photosynthesis
13.1.2 Discovery and structure of chloroplasts
13.2 Isolation of chloroplasts
13.3 Composition of the chloroplasts
13.4 Thermodynamics and bioenergetics in photosynthesis
13.4.1 Laws of thermodynamics
13.4.2 Molecular free energy of some photosynthetic processes
13.4.3 Molecular free energy of oxidation–reduction reactions
13.4.3.1 Measurement of the electrical potential across a membrane
13.4.3.2 Measurement of the pH difference across a membrane
13.5 Organization of the thylakoid membrane and the light reactions of photosynthesis
13.5.1 Photosystem complexes
13.5.1.1 Charge separation
13.5.1.2 Photosystem II complex
13.5.1.3 Photosystem I complex
13.5.2 Cytochromeb6-f complex
13.5.3 ATP synthase
13.5.4 Light reactions of photosynthesis
13.6 Physiological, biochemical, and structural adaptations of the light reactions
13.7 Fixation of carbon
13.8 Reduction of nitrate and the activation of sulfate
13.9 Chloroplast movements and photosynthesis
13.10 Genetic system of plastids
13.11 Biogenesis of plastids
13.12 Summary
13.13 Questions
Chapter 14. Mitochondria
14.1 Discovery of the mitochondria and their function
14.1.1 History of the study of respiration
14.1.2 History of the structural studies in mitochondria
14.2 Isolation of mitochondria
14.3 Composition of mitochondria
14.3.1 Proteins
14.3.2 Lipids
14.4 Cellular geography of mitochondria
14.5 Chemical foundation of respiration
14.5.1 Fitness of adenosine triphosphate as a chemical energy transducer
14.5.1.1 Free energy, enthalpy, and entropy
14.5.1.2 Resonance structures of phosphates
14.5.1.3 The principle of the common intermediate
14.5.2 Glycolysis
14.5.2.1 The discovery of the glycolytic pathway
14.5.2.2 Metabolic channeling in glycolysis
14.5.3 Cellular respiration
14.5.3.1 Biochemistry of the Krebs cycle
14.5.3.2 Biochemistry of the electron transport chain
14.5.3.3 Oxidative phosphorylation
14.5.3.4 Thermodynamics of oxidative phosphorylation
14.5.3.5 The alternative oxidase
14.5.3.6 Historical aspects of cellular respiration
14.6 Other functions of the mitochondria
14.7 Genetic system in mitochondria
14.8 Biogenesis of mitochondria
14.9 Summary
14.10 Questions
Chapter 15. Origin of organelles
15.1 Autogenous origin of organelles
15.2 Endosymbiotic origin of chloroplasts and mitochondria
15.3 Origin of peroxisomes, centrioles, and cilia
15.4 Ongoing process of endosymbiosis
15.5 Primordial host cell
15.6 Symbiotic DNA
15.7 Summary
15.8 Questions
Chapter 16. The nucleus
16.1 The discovery of the nucleus and its role in heredity, systematics, and development
16.2 Isolation of nuclei
16.3 Structure of the nuclear envelope and matrix
16.4 Chemistry of chromatin
16.5 Morphology of chromatin
16.6 Cell cycle
16.7 Chromosomal replication
16.8 Transcription
16.9 Nucleolus and ribosome formation
16.10 Other membraneless compartments
16.11 Summary
16.11 Questions
Chapter 17. Ribosomes and proteins
17.1 Nucleic acids and protein synthesis
17.2 Protein synthesis
17.3 Protein activity
17.4 Protein targeting
17.5 Protein–protein interactions
17.6 Protein degradation
17.7 Structure of proteins
17.8 Functions of proteins
17.9 Techniques of protein purification
17.10 Plants as bioreactors to produce proteins for vaccines
17.11 Summary
17.12 Questions
Chapter 18. The origin of life
18.1 Spontaneous generation
18.2 Concept of vitalism
18.3 The origin of the universe
18.4 Geochemistry of the early earth
18.5 Prebiotic evolution
18.6 The earliest darwinian ancestor and the last common ancestor
18.7 Diversity in the biological world
18.8 The origin of consciousness
18.9 Concept of time
18.10 Summary
18.11 Questions
Chapter 19. Cell division
19.1 Mitosis
19.1.1 Prophase
19.1.2 Prometaphase
19.1.3 Metaphase
19.1.4 Anaphase
19.1.4.1 The sliding filament hypothesis
19.1.4.2 Microtubule depolymerization and poleward flux theories
19.1.4.3 The motile kinetochore model
19.1.4.4 Actin
19.1.4.5 Double insurance and functional redundancy
19.1.5 Telophase
19.2 Regulation of mitosis
19.3 Energetics of mitosis
19.4 Division of organelles
19.5 Cytokinesis
19.5.1 Cell plate formation
19.5.2 Isolation of cell plates
19.5.3 Orientation of the cell plate
19.6 Summary
19.7 Questions
Chapter 20. Extracellular matrix
20.1 Relationship of the extracellular matrix of plant and animal cells
20.2 Isolation of the extracellular matrix of plants
20.3 Chemical composition and architecture of the extracellular matrix
20.4 Extracellular matrix–plasma membrane–cytoskeletal continuum
20.5 Biogenesis of the extracellular matrix
20.5.1 Plasma membrane
20.5.2 Cytoskeleton
20.5.3 Endomembrane system
20.5.4 Self-assembly of the extracellular matrix
20.6 Permeability of the extracellular matrix
20.7 Mechanical properties of the extracellular matrix
20.8 Cell expansion
20.8.1 Forces, pressures, and stresses and their relationship to strain
20.9 Summary
20.10 “Epilog”
20.11 Questions
Chapter 21. Omic science: Platforms and pipelines
21.1 One, two, three, infinity
21.2 Genomics
21.2.1 The relationship between a trait and the sequence of DNA
21.2.2 Sequencing DNA by synthesis
21.2.2.1 Sequencing by measuring the incorporation of radioactive deoxyribonucleotides into a primer-template
21.2.2.2 Analysis of the incorporation of radioactive dideoxyribonucleotides into a primer-template using gel electrophoresis
21.2.2.3 Analysis of the incorporation of fluorescent dideoxyribonucleotides into a primer-template using gel electrophoresis and automated detection
21.2.2.4 Using polymerase chain reaction to clone DNA outside of microorganisms
21.2.2.5 Massively parallel analysis of the incorporation of deoxyribonucleotides into a primer-template using pyrosequencing
21.2.2.6 Massively parallel sequencing by hybridization
21.2.2.7 Massively parallel analysis of the incorporation of reversible fluorescent dideoxyribonucleotides into a primer-template
21.2.2.8 Single-molecule real-time sequencing analysis of the incorporation of fluorescent dideoxyribonucleotides into a primer-template
21.2.2.9 Single-molecule real-time DNA sequencing using nanopore technology
21.2.2.10 Sequenced genomes, phylogenomics, and resequencing
21.2.2.11 Metagenomics
21.2.3 Gene discovery and annotation
21.2.3.1 The golden age of molecular biology
21.2.3.2 The golden age of biotechnology
21.2.3.3 Methods used for gene discovery
21.2.4 Targeted characterization of the genome
21.2.4.1 Exomics: exome enrichment using hybridization
21.2.4.2 Epigenomics: detecting cytosine modification using bisulfite conversion
21.2.4.3 Finding transcription-factor-specific promoters using ChIP-Seq
21.2.5 The postgenomic era: functional genomics
21.3 Transcriptomics
21.3.1 Microarrays
21.3.2 RNA-seq
21.4 Proteomics
21.4.1 Characterizing the proteome using polyacrylamide gel electrophoresis
21.4.2 Sequencing of a polypeptide by stepwise degradation
21.4.3 Sequencing of a polypeptide by mass spectrometry
21.4.4 Characterizing the proteome by mass spectrometry
21.5 Interactomics
21.6 Metabolomics
21.7 Phenomics
21.8 Pan-omics
21.9 Single-cell omics
21.10 One, two, three … infinity revisited
21.11 Summary
21.12 Questions
Appendix 1. SI units, constants, variables, and geometrical formulas
1 SI units
2 Constants
3 Variables
4 Geometrical formulae
Appendix 2. A cell biologist’s view of non-newtonian physics
Appendix 3. Calculation of the total transverse force and its relation to stress
Appendix 4. Laboratory exercises
1 Laboratory 1: introduction to the light microscope
1.1 Bright-field microscopy: establish Köhler illumination on the Olympus BH-2
1.2 Measurements with a microscope
1.3 Observations of cells and organelles using bright-field microscopy
1.4 Observations of cells using dark-field microscopy
2 Laboratory 2: phase-contrast, polarization, and differential interference contrast microscopy
2.1 Observation of cells with phase-contrast microscopy
2.2 Observation of cells with polarization microscopy
2.3 Differential interference contrast microscopy (demonstration)
3 Laboratory 3: fluorescence microscopy
3.1 Setting up Köhler illumination with incident light
3.2 Observe organelles (e.g., mitochondria and/or peroxisomes) in tobacco cells transformed with organelle-targeted GFP
3.3 Visualizing organelles with fluorescent organelle-selective stains
4 Laboratory 4: photomicrography
5 Laboratory 5: membrane permeability
5.1 Determination of the osmotic permeability coefficient of the plasma membrane of Chara corallina
5.2 Measurement of the reflection coefficient of nonelectrolytes
5.3 Determination of the permeability of living cells to acids and bases
5.4 Observation of spatial heterogeneity of the proton pump in the plasma membrane of Chara
6 Laboratory 6: cell diversity and cell motility
6.1 Observation of cells with your microscope
6.2 Observation of giant cells using the dissecting microscope
6.3 Using cytoskeletal inhibitors to probe cell motility
6.4 Observing actin filaments in onion epidermal cells
Appendix 5. Science: logos, intellectual intuition, and first principles
Logos: the underlying order of the natural world
Mathematizing knowledge
How do we know that our knowledge is true?
The connection and distinction between dialectical and scientific inquiry
First principles
On being and becoming
Experimental science
Getting to know the logos of the cell through experiment
Logos, êthos, and pathos
Bibliography
Index

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