Plant Biochemistry

Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
Preface
First Edition Preface
Chapter 1 Introduction to Plant Biochemistry
Chapter 2 Approaches to Understanding Metabolic Pathways
What We Need to Understand a Metabolic Pathway
Chromatography
Electrophoresis
The Use of Isotopes
Current Research Techniques Using a Range of Molecular Biology Approaches
The Generation of Mutant Plants
Plant Transformation Techniques
Epigenetic Modification in Plants
The Functional Identification of Unknown Genes Has Been a Major Biological Challenge
The Impact of Metabolic Flux on Plant Metabolism
Coarse and Fine Metabolic Control
Metabolic Control Analysis Theory
Compartmentation: Keeping Competitive Reactions Apart
Understanding Plant Metabolism in the Individual Cell
The Isolation of Organelles
Summary
Bibliography
Chapter 3 Plant Cell Structure
Plant Organs and Tissues Consist of Communities of Cells
Cell Structure Is Defined by Membranes
The Plasma Membrane: The Cell Boundary that Controls Transport Into and Out of the Cell
Vacuoles and the Tonoplast Membrane
The Endomembrane System
Cell Walls Serve to Limit Osmotic Swelling of the Enclosed Protoplast
The Nucleus Contains the Cell’s Chromatin within a Highly Specialized Structure, the Nuclear Envelope
Mitochondria Are Ubiquitous Organelles, Which Are the Site of Cellular Respiration
Peroxisomes House Vital Biochemical Pathways for Many Plant Cell Processes
Plastids Are an Integral Feature of All Plant Cells
Summary
Bibliography
Chapter 4 Light Reactions of Photosynthesis
Basic Features of the Photochemical Process
Pigments Capture Light Energy and Convert it to a Flow of Electrons
Photosystem II Splits Water to Form Protons and Oxygen and Reduces Plastoquinone to Plastoquinol
The Q-Cycle Uses Plastoquinol to Pump Protons and Reduce Plastocyanin
Photosystem I Catalyzes a Second Light Excitation Event
ATP Synthase Utilizes the Proton Motive Force to Generate ATP
Cyclic Photophosphorylation Generates ATP Independently of Water Oxidation and NADPH Formation
Mechanisms for Adjusting to Erratic Solar Irradiation
Summary
Bibliography
Chapter 5 Photosynthetic Carbon Assimilation
Photosynthetic Carbon Assimilation Produces Most of the Biomass on Earth
Carbon Dioxide Enters the Leaf Through Stomata, but Water Is also Lost in the Process
Carbon Dioxide Is Converted to Carbohydrates Using Energy Derived from Sunlight
The Calvin–Benson Cycle Is Used by All Photosynthetic Eukaryotes to Convert Carbon Dioxide to Carbohydrate
Discovery of the Calvin–Benson Cycle
There Are Three Phases in the Calvin–Benson Cycle
Calvin–Benson Cycle Intermediates May Be Used to Make Other Photosynthetic Products
The Calvin–Benson Cycle Is Autocatalytic and Produces More Substrate Than It Consumes
Calvin–Benson Cycle Activity and Light-Regulation
Rubisco is a Highly Regulated Enzyme
Rubisco Oxygenase: The Starting Point for the Photorespiratory Pathway
The Photorespiratory Pathway Operates via Reactions in the Chloroplast, Peroxisome, and Mitochondria
The Isolation and Analysis of Mutants and the Photorespiratory Pathway
Photorespiration May Provide Essential Amino Acids and Protect against Environmental Stress
Photorespiration Uses ATP and Reductant
Photorespiration and the Loss of Photosynthetically Fixed Carbon
Photorespiration Is a Target for Modification to Improve Crop Productivity
C4 Photosynthesis Reduces Photorespiratory Carbon Losses by Concentrating Carbon Dioxide Around Rubisco
Spatial Separation of the Two Carboxylases Occurs in C4 Leaves
Stages of C4 Photosynthesis and Variations of the Basic Pathway
Some of the C4 Pathway Enzymes Are Light-Regulated
Decreasing Global Carbon Dioxide Concentrations Caused Rapid Evolution of C4 Photosynthesis
C3–C4 Intermediate Species May Represent an Evolutionary Stage Between C3 and C4 Plants
The C4 Pathway Can Exist in Single Cells of Some Species
Crassulacean Acid Metabolism Is a Photosynthetic Pathway Particularly Well-Suited to Arid Environments
Temporal Separation of the Carboxylases in CAM
Crassulacean Acid Metabolism as a Flexible Pathway
Phosphoenolpyruvate Carboxylase in Crassulacean Acid Metabolism Plants Is Regulated by Protein Phosphorylation
Crassulacean Acid Metabolism Is Thought to Have Evolved Independently on Several Occasions
C3, C4, and CAM Photosynthetic Pathways: Advantages and Disadvantages
C3, C4, and CAM Plants Differ in Their Facility to Discriminate Between Different Isotopes of Carbon
Summary
Bibliography
Chapter 6 Respiration
Overview of Respiration
The Main Components of Plant Respiration
Plants Need Energy and Precursors for Subsequent Biosynthesis
Glycolysis Is the Major Pathway That Fuels Respiration
Hexose Sugars Enter into Glycolysis and Are Converted into Fructose 1,6-Bisphosphate
Fructose 1,6-Bisphosphate Is Converted to Pyruvate
Alternative Reactions Provide Flexibility to Plant Glycolysis
Plant Glycolysis Is Regulated by a Bottom-Up Process
Metabolic Complex Formation (Metabolons) May Affect Glycolytic Flux
Glycolysis Supplies Energy and Reducing Power for Biosynthetic Reactions
The Availability of Oxygen Determines the Fate of Pyruvate
The Oxidative Pentose Phosphate Pathway Is an Alternative Catabolic Route for Glucose Metabolism
The Irreversible Oxidative Decarboxylation of Glucose 6-Phosphate Generates NADPH
The Second Stage of the Oxidative Pentose Phosphate Pathway Returns Any Excess Pentose Phosphates to Glycolysis
All or Part of the OPPP Is Duplicated in the Plastids and Cytosol
The Tricarboxylic Acid Cycle Is Located in the Mitochondria
Pyruvate Oxidation Marks the Link Between Glycolysis and the Tricarboxylic Acid Cycle
The Product of Pyruvate Oxidation, Acetyl CoA, Enters the Tricarboxylic Acid Cycle via the Citrate Synthase Reaction
Substrates for the Tricarboxylic Acid Cycle Are Derived Mainly from Carbohydrates
The Tricarboxylic Acid Cycle Serves a Biosynthetic Function in Plants and Can Function in a Non-Cyclic Manner
The TCA Cycle Is Sensitive to Mitochondrial NADH/NAD+ and ATP/ADP Ratios
A Thioredoxin/NADPH Redox System Regulates a Number of Tricarboxylic Acid Cycle Enzymes and Other Mitochondrial Proteins
The Mitochondrial Electron Transport Chain Oxidizes Reducing Equivalents Produced in Respiratory Substrate Oxidation and Produces ATP
There are Five Main Protein Complexes of the Electron Transport Chain
Plant Mitochondria Possess Additional Respiratory Proteins That Provide a Branched Electron Transport Chain
Plant Mitochondria Contain Four Additional NAD(P)H Dehydrogenases
Plant Mitochondria Contain an Alternative Oxidase That Transfers Electrons from QH2 to Oxygen and Provides a Bypass of the Cytochrome Oxidase Branch
The Alternative Oxidase Is a Dimer of Two Identical Polypeptides with a Non-Heme Iron Center
Alternative Oxidase Isoforms in Plants Are Encoded by Discrete Gene Families
Alternative Oxidase Activity Is Regulated by 2-Oxo Acids and by Reduction and Oxidation
The Alternative Oxidase Adds Flexibility to the Operation of the Mitochondrial Electron Transport Chain
The Alternative Oxidase May Prevent the Formation of Damaging Reactive Oxygen Species within the Mitochondria
Alternative Oxidase Appears to Play a Role in the Response of Plants to Environmental Stresses
Alternative Oxidase and NADH Oxidation Can Operate Under Low ADP/ATP
Plant Mitochondria Contain Uncoupling Proteins
ATP Synthesis in Plant Mitochondria Is Coupled to the Proton Electrochemical Gradient That Forms During Electron Transport
ATP Synthase Uses the Proton Motive Force to Generate ATP
Mitochondrial Respiration Interacts with Photosynthesis and Photorespiration in the Light
Supercomplexes May Form between Components of the Electron Transport Chain, but Their Physiological Significance Remains Uncertain
Summary
Bibliography
Chapter 7 Synthesis and Mobilization of Storage and Structural Carbohydrates
Role of Carbohydrate Metabolism in Higher Plants
Sucrose Is the Major Form of Carbohydrate Transported from Source to Sink Tissue
Sucrose Phosphate Synthase Is an Important Control Point in the Sucrose Biosynthetic Pathway in Plants
Sensing, Signaling, and Regulation of Carbon Metabolism by Fructose 2,6-Bisphosphate
Fructose 2,6-Bisphosphate Enables the Cell to Regulate the Operation of Multiple Pathways of Plant Carbohydrate Metabolism
Fructose 2,6-Bisphosphate as a Regulatory Link between the Chloroplast and the Cytosol
Sucrose Breakdown Occurs via Sucrose Synthase and Invertase
Starch Is the Principal Storage Carbohydrate in Plants
Starch Synthesis Occurs in Plastids of Both Source and Sink Tissues
Starch Formation Occurs in Water-Insoluble Starch Granules in the Plastids
The Composition and Structure of Starch Affects the Properties and Functions of Starches
Starch Degradation Varies in Different Plant Organs
The Nature and Regulation of Starch Degradation Is Poorly Understood
Transitory Starch Is Remobilized Initially by a Starch Modifying Process That Takes Place at the Granule Surface during the Dark Period
The Regulation of Starch Degradation Is Unclear
Fructans Are Probably the Most Abundant Storage Carbohydrates in Plants after Starch and Sucrose
A Model Has Been Proposed for the Biosynthesis of the Different Fructan Molecules Found in Plants
Fructan-Accumulating Plants Are Abundant in Temperate Climate Zones with Seasonal Drought or Frost
Trehalose Biosynthesis Is Not Just Limited to Resurrection Plants
Trehalose Biosynthesis in Higher Plants and Its Role in the Regulation of Carbon Metabolism
Plant Cell Wall Polysaccharides
Synthesis of Cell Wall Sugars and Polysaccharides
Cellulose
Matrix Components Consist of Branched Polysaccharides
Expansins and Extensins, Proteins That Play Both Enzymatic and Structural Roles in Cell Expansion
Lignin
Summary
Bibliography
Chapter 8 Nitrogen and Sulfur Metabolism
Nitrogen and Sulfur Must Be Assimilated in the Plant
Apart from Oxygen, Carbon, and Hydrogen, Nitrogen Is the Most Abundant Element in Plants
Nitrogen Fixation: Some Plants Obtain Nitrogen from the Atmosphere via a Symbiotic Association with Bacteria
Symbiotic Nitrogen Fixation Involves a Complex Interaction between Host Plant and Microorganism
Nodule-Forming Bacteria (Rhizobiaceae) Are Composed of the Three Genera Rhizobium, Bradyrhizobium, and Azorhizobium
The Nodule Environment Is Generated by Interaction between the Legume Plant Host and Rhizobia
Nitrogen Fixation Is Energy Expensive, Consuming Up to 20% of All Photosynthates Generated
Mycorrhizae Are Associations Between Soil Fungi and Plant Roots That Can Enhance the Nitrogen Nutrition of the Plant
Most Higher Plants Obtain Nitrogen from the Soil in the Form of Nitrate
Higher Plants Have Multiple Nitrate Carriers with Distinct Properties and Regulation Mechanisms
Nitrate Reductase Catalyzes the Reduction of Nitrate to Nitrite in the Cytosol of Root and Shoot Cells
The Production of Nitrite Is Rigidly Controlled by the Expression, Catalytic Activity, and Degradation of NR
Nitrite Reductase, Localized in the Plastids, Catalyzes the Reduction of Nitrite to Ammonium
Plant Cells Have the Capacity to Transport Ammonium Ions
Ammonium Is Assimilated into Amino Acids
Sulfate Is Relatively Abundant in the Environment and Serves as a Primary Sulfur Source for Plants
The Assimilation of Sulfate
Adenosine 5′-Phosphosulfate Reductase Is Composed of Two Distinct Domains
Sulfite Reductase Is Similar in Structure to Nitrite Reductase
Sulfation Is an Alternative Minor Assimilation Pathway Incorporating Sulfate into Organic Compounds
Amino Acid Biosynthesis Is Essential for Plant Growth and Development
Carbon Flow Is Essential for Maintaining Amino Acid Production
The Form of Nitrogen Transported Through the Xylem Differs across Species
Aminotransferase Reactions Are Central to Amino Acid Metabolism as They Distribute Nitrogen from Glutamate to Other Amino Acids
Asparagine, Aspartate, and Alanine Biosynthesis
Glycine and Serine Biosynthesis
The Aspartate Family of Amino Acids: Lysine, Threonine, Isoleucine, and Methionine
The Branched-Chain Amino Acids Valine and Leucine
Sulfur-Containing Amino Acids Cysteine and Methionine
Glutamine, Arginine, and Proline Biosynthesis
The Biosynthesis of the Aromatic Amino Acids: Phenylalanine, Tyrosine, and Tryptophan
Histidine Biosynthesis
Large Amounts of Nitrogen Can Be Present in Non-Protein Amino Acids
Plant Storage Proteins: Why Do Plants Store Proteins and What Sort of Proteins Do They Store?
Vicilins and Legumins Are the Main Storage Proteins in Many Dicotyledonous Plants
Prolamins Are Major Storage Proteins in Cereals and Grasses
2S Albumins Are Important but Minor Components of Seed Proteins
Where Are Seed Proteins Synthesized and How Do They Reach Their Storage Compartment?
Protein Stores Are Degraded and Mobilized during Seed Germination
Vegetative Organs Store Proteins, Which Are Very Different from Seed Proteins
The Potato, a Major Temperate-Climate Crop
Tropical Roots and Tubers: Sweet Potato, Yams, Taro, and Cassava
Despite Their Diversity, Storage Proteins Share Common Characteristics
Summary
Bibliography
Chapter 9 Lipid Biosynthesis
Overview of Lipids
Fatty Acid Biosynthesis Occurs through the Sequential Addition of Two Carbon Units
The Condensation of Nine Two-Carbon Units Is Necessary for the Assembly of an 18C Fatty Acid
The Assembly of an 18C Fatty Acid from Acetyl CoA Using Type II Fatty Acid Synthase Requires 48 Reactions and the Involvement of at Least 12 Different Proteins
Acyl-ACP Utilization in the Plastid
Source of NADPH and ATP to Support Fatty Acid Biosynthesis
Glycerolipids Are Formed from the Incorporation of Fatty Acids to the Glycerol Backbone
Phosphatidic Acid, Produced in the Plastids or Endoplasmic Reticulum, Is a Central Intermediate in Glycerolipid Biosynthesis
Lipids Function in Signaling and Defense
The Products of the Oxidation of Lipids and the Resulting Metabolites Are Collectively Known as Oxylipins
A Waxy Cuticle Coats All Land Plants
Biosynthesis of Very-Long-Chain Fatty Acid Wax Precursors
Role of Suberin as a Hydrophobic Layer
Storage Lipids Are Primarily a Storage Form of Carbon and Chemical Energy
Important Role of Transcriptional Regulation of Fatty Acid Biosynthesis in Oil Seeds
Release of Fatty Acids from Acyl Lipids
The Breakdown of Fatty Acids Occurs via Oxidation at the β Carbon and Subsequent Removal of Two Carbon Units
Summary
Bibliography
Chapter 10 Alkaloids
Plants Produce a Vast Array of Chemicals That Deter or Attract Other Organisms
Alkaloids Are a Chemically Diverse Group That All Contain Nitrogen and a Number of Carbon Rings
Alkaloids Are Widespread in the Plant Kingdom and Are Particularly Abundant in the Solanaceae
Functions of Alkaloids in Plants and Animals
The Challenges and Complexity of Alkaloid Biosynthetic Pathways
Amino Acids as Precursors in the Biosynthesis of Alkaloids
Terpenoid Indole Alkaloids Are Made from Tryptamine and the Terpenoid Secologanin
Isoquinoline Alkaloids Are Produced from Tyrosine and Include Many Valuable Drugs such as Morphine and Codeine
Tropane Alkaloids and Nicotine Are Found Mainly in the Solanaceae
Pyrollizidine Alkaloids Are Found in Four Main Families
Purine Alkaloids as Popular Stimulants and as Poisons and Feeding Deterrents against Herbivores
The Diversity of Alkaloids Has Arisen through Evolution Driven by Herbivore Pressure
Gene Duplication Followed by Mutation Is Thought to Be a Major Factor in the Evolution of the Alkaloid Biosynthesis Pathways
The Distribution of Enzymes between Different Cell Types Allows for Further Chemical Diversity
There Is No Simple Taxonomic Relationship in the Distribution of Different Classes of Alkaloids
Summary
Bibliography
Chapter 11 Phenolics
Plant Phenolic Compounds Are a Diverse Group with a Common Aromatic Ring Structure and a Range of Biological Functions
The Simple Phenolics Include Simple Phenylpropanoids, Coumarins, and Benzoic Acid Derivatives
The More Complex Phenolics Include the Flavonoids, Which Have a Characteristic Three-Membered A-, B-, C-Ring Structure
Lignin Is a Complex Polymer Formed Mainly from Monolignol Units
The Tannins Are Phenolic Polymers That Form Complexes with Proteins
Most Plant Phenolics Are Synthesized from Phenylpropanoids
The Shikimic Acid Pathway Provides the Aromatic Amino Acid Phenylalanine from Which the Phenylpropanoids Are All Derived
The Shikimic Acid Pathway Is Regulated by Substrate Supply and End-Product Inhibition and Is Affected by Wounding and Pathogen Attack
The Core Phenylpropanoid Pathway Provides the Basic Phenylpropanoid Units That Are Used to Make Most of the Phenolic Compounds in Plants
Flavonoids Are Produced from Chalcones, Formed from the Condensation of p-Coumaroyl CoA and Malonyl CoA
Simple Phenolics from the Basic Phenylpropanoid Pathway Are Used in the Biosynthesis of the Hydrolyzable Tannins
Lignin Is a Complex Polymer Formed from Subunits That Are Synthesized from Phenylalanine in the General Phenylpropanoid Pathway
Summary
Bibliography
Chapter 12 Terpenoids
Terpenoids Are a Diverse Group of Essential Oils That Are Formed from the Fusion of Five-Carbon Isoprene Units
Terpenoids Serve a Wide Range of Biological Functions
The Biosynthesis of Terpenoids
Stage 1. Formation of the Core Five-Carbon Isopentenyl Diphosphate Unit Can Occur via Two Distinct Pathways: The Mevalonic Acid (MVA) Pathway and the Methylerythritol 4-Phosphate (MEP) Pathway
Stage 2. Prenyltransferases Combine the Five-Carbon IPP and DMAPP Units to Form a Range of Terpenoid Precursors
Stage 3. Terpene Synthases Convert the Terpenoid Precursors GPP, FPP, and GGPP into the Basic Terpenoid Groups
Stage 4. The Modification of the Basic Terpenoid Skeletons Produces a Vast Array of Terpenoid Products
Subcellular Compartmentation Is Important in the Regulation of Terpenoid Biosynthesis
Summary
Bibliography
Index