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