Biochemistry - Chemical Reactions in the Living Cell, Volume 2 - D. Metzler 1980



Enzymes: Cellular Protein Catalysts

Enzymes: Protein Catalysts of Cells

Fundamentals of Enzyme Kinetics

First-Order Reactions

Enzyme Turnover Number

Enzymes: The Protein Catalysts of Cells

Second-Order Reactions

Enzymes: Protein Catalysts of Cells

Reversible Chemical Reactions

Enzymes: The Protein Catalysts of Cells

Formation and Transformation of the ES Complex

Enzymes: Protein Catalysts of Cells

Linear Forms of Rate Equations

Diffusion and the Number of Active Collisions between Enzyme and Substrate

The "Cell Effect" and Molecular Rotation

Reversible Enzymatic Reactions

Reactions Involving Two or More Substrates

Enzymes: Protein Catalysts of the Cell

Kinetics of Rapid Reactions

Enzymes: Protein Catalysts of Cells

Enzyme Inhibition and Activation

Competitive Inhibitors

Noncompetitive Inhibition and Activation

Using Inhibitors to Study Mechanisms of Enzymatic Reactions

Enzymes: Protein Catalysts of the Cell

Agonists and Antagonists

Enzymes: Protein Catalysts of Cells

Isotope Exchange at Equilibrium

Enzymes: Cellular Protein Catalysts

Allosteric Effectors and Enzyme Conformation Changes

Enzymes: Protein Catalysts of the Cell

Regulatory Subunits

Enzymes: The Protein Catalysts of Cells

Cell Growth Rate

Enzymes: Cellular Protein Catalysts

Specificity of Enzyme Action

Enzyme Specificity

Complementarity of Substrate and Enzyme Surfaces

Enzymes: Protein Catalysts of Cells

Prochiral Centers

Enzymes: Protein Catalysts of the Cell

Stereochemical Numbering

Enzymes: Protein Catalysts of Cells

Mechanisms of Enzymatic Catalysis

Transition State

Quantitative Transition State Theory

Transition-State Analogue Inhibitors

Microscopic Reversibility

Enzymes: The Protein Catalysts of Cells

Acid-Base Catalysis

Enzymes: Protein Catalysts of Cells

Covalent Catalysis

Enzymes: Protein Catalysts of the Cell

Proximity and Orientation Effects

Conclusions

Enzymes: Cellular Protein Catalysts

Regulation of Enzymatic Activity

Key Enzymes

Enzymes: Protein Catalysts of the Cell

Genetic Control of Enzyme Synthesis

Enzymes: The Protein Catalysts of Cells

Spatial Compartmentalization: Isolated Compartments and Organized Assemblies

Enzymes: Protein Catalysts of the Cell

Regulation of Enzyme Activity

Enzymes: Protein Catalysts of Cells

Hormones

Amplification of Regulatory Signals

Enzymes: Cellular Protein Catalysts

Cross-Regulation

Enzymes: Protein Catalysts of Cells

Species Differences in Regulatory Mechanisms

Enzyme Classification

References

Types of reactions catalyzed by enzymes

Brief overview of some metabolic pathways

Initiating reaction or activation of metabolites

A brief overview of selected metabolic pathways

ß-Oxidation

Types of Enzyme-Catalyzed Reactions

A Brief Overview of Some Metabolic Pathways

Electron Transport Chain. Oxidative Phosphorylation

Types of reactions catalyzed by enzymes

A brief overview of selected metabolic pathways

Tricarboxylic acid cycle

A brief overview of certain metabolic pathways

Glycolysis

Brief overview of some metabolic pathways

Fermentation

A brief overview of certain metabolic pathways

Biosynthesis

Brief overview of selected metabolic pathways

Photosynthesis

Types of enzyme-catalyzed reactions

Classification of enzymatic reactions

Types of reactions catalyzed by enzymes

Nucleophilic substitution reactions (Type 1 reactions)

Factors affecting the rates of substitution reactions

Nucleophilic substitution reactions at saturated carbon atoms

Types of enzyme-catalyzed reactions

Mechanism of double displacement reactions

Carbonium ions

Glycogen phosphorylase

Types of reactions catalyzed by enzymes

Other enzymes acting on glycosides

Substitution reactions at carbonyl groups

Types of enzyme-catalyzed reactions

Chymotrypsin and trypsin

Types of reactions catalyzed by enzymes

Pepsin

Papain

Involvement of metal ions in the action of proteinases: Carboxypeptidase A

Acyltransferases

Substitution at the phosphorus atom

Phosphatases

Types of Reactions Catalyzed by Enzymes

Substitution at the Phosphorus Atom

Ribonuclease

Types of enzyme-catalyzed reactions

Substitution at the phosphorus atom

Pentavalent intermediates and permutational rearrangements in substitution at the phosphorus atom

Types of reactions catalyzed by enzymes

Metaphosphate formation

Micrococcal (staphylococcal) nuclease

Kinases

Types of enzyme-catalyzed reactions

Nuclear relaxation induced by paramagnetic ions

Types of Reactions Catalyzed by Enzymes

Substitution at the Phosphorus Atom

Adenylyl Cyclase and Cyclic AMP

Types of reactions catalyzed by enzymes

Substitution at the phosphorus atom

Mutases

Multiple displacement reactions and the coupling of ATP cleavage reactions with endergonic processes

Transfer of phosphate, pyrophosphate, and adenylyl groups from ATP

Types of enzyme-catalyzed reactions

Multiple displacement reactions and the coupling of ATP cleavage with endergonic processes

Acyl phosphates

Types of reactions catalyzed by enzymes

Multiple displacement reactions and the coupling of ATP cleavage reactions with endergonic processes

General mechanism of formation of thioesters, esters, and amides

Multiple displacement reactions and coupling of ATP cleavage reactions with endergonic processes

CoA transferases

Conformational changes induced by phosphorylation

Sulfate transfer

Addition and elimination reactions

Addition to polarized double bonds (Type 2.A reaction, Table 7-1)

Carbonic anhydrase

Imines

Types of Reactions Catalyzed by Enzymes

Addition and Elimination Reactions

Stereochemistry and Designation of Faces of Trigonal Carbon Atoms

Types of reactions catalyzed by enzymes

Addition and elimination reactions

Addition to a double bond conjugated with a carbonyl group (Type 2.B reactions)

Types of Enzyme-Catalyzed Reactions

Addition and Elimination Reactions

Addition to double bonds adjacent to carboxyl groups

Types of Reactions Catalyzed by Enzymes

Addition to Isolated Double Bonds

Types of reactions catalyzed by enzymes

Addition and elimination reactions

Conjugated elimination

Types of Reactions Catalyzed by Enzymes

Addition and Elimination Reactions

Decarboxylation-Coupled Elimination

Types of reactions catalyzed by enzymes

Addition and elimination reactions

Reversibility of addition and elimination reactions

Types of Reactions Catalyzed by Enzymes

Enolic Intermediates in Isomerization Reactions

Types of reactions catalyzed by enzymes

Enolic intermediates in isomerization reactions

Ketol-isomerases

Diffusion-controlled proton transfer

Types of Enzyme-Catalyzed Reactions

Enolic Intermediates in Isomerization Reactions

Ring Opening Catalyzed by Isomerases

Types of reactions catalyzed by enzymes

Enolic intermediates in isomerization reactions

Other sugar phosphate isomerases

Types of enzyme-catalyzed reactions

∆5-3-Ketosteroid isomerase and other enzymes catalyzing 1,3-proton migration

Types of Enzyme-Catalyzed Reactions

Enolic Intermediates in Isomerization Reactions

Internal Oxidation-Reduction Reactions Proceeding via Dehydration to Enol or Enol Phosphate

Types of Reactions Catalyzed by Enzymes

ß-Cleavage and Condensation

Substitution at the Carbonyl Group (Type 5.A Reactions)

Types of reactions catalyzed by enzymes

ß-Cleavage and condensation

Addition of an enolate anion to a carbonyl group or to imines (type 5.B reactions)

Types of Reactions Catalyzed by Enzymes

ß-Cleavage and Condensation

Addition of an enolate ion to carbon dioxide (Type 5.B reaction and its reverse)

Types of enzyme-catalyzed reactions

Selected isomerization and rearrangement reactions

Types of reactions catalyzed by enzymes

References

Coenzymes - specific natural specialized reagents

Coenzymes - specialized natural reagents

ATP and nucleotide "handles"

Coenzymes — specialized natural reagents

Coenzyme A and Phosphopantetheine

Isolation of a New Coenzyme

Coenzymes — special naturally occurring specialized reagents

Coenzyme A and phosphopantetheine

Structure and function of coenzyme A

Acyl carrier proteins and phosphopantetheine

Coenzymes: Specialized Natural Reagents

Bound biotin acting as a prosthetic group

Coenzymes: specialized natural reagents

Mechanism of biotin action

Other properties of biotin-dependent enzymes

Coenzymes are specialized natural reagents

Avidin

Coenzymes: Specialized Natural Reagents

Bound Biotin Acting as a Prosthetic Group

Attachment of Biotin to Apoenzymes

Coenzymes – specialized natural reagents

Thiamine diphosphate

Coenzymes - special natural specialized reagents

Mechanism of α-cleavage

Coenzymes — specialized natural reagents

Enzymatic reactions involving thiamine

Coenzymes - specialized natural reagents

The role of thiamine coenzymes in nerve cell function

Coenzymes: specialized natural reagents

Pyridoxal phosphate

Coenzymes are specialized natural reagents of a unique kind.

Pyridoxal phosphate as a catalyst

The primary function of pyridoxal phosphate

Coenzymes - special natural specialized reagents

Pyridoxamine phosphate in the role of coenzyme

Coenzymes — special naturally occurring specialized reagents

Stereochemistry of PLP-dependent enzymes

Coenzymes – specialized natural reagents of a distinct kind

Observed changes in the optical properties of the coenzyme

Coenzymes are specialized natural reagents of a unique type.

Elucidating a detailed picture of the mechanism of a PLP-dependent enzyme

Coenzymes - specialized natural reagents

Keto acids and other unusual electrophilic centers

Decarboxylases

Coenzymes – specialized natural reagents

Threonine dehydratase

Coenzymes - specialized natural reagents

Urocanase

Coenzymes – specialized natural reagents of a unique kind

Proline reductase

Coenzymes - specialized natural reagents

Histidine and phenylalanine deaminases (ammonia-lyases)

Coenzymes: specialized natural reagents

Hydrogen-transfer coenzymes

Coenzymes – unique, specialized natural reagents

Pyridine nucleotide coenzymes and dehydrogenases

Coenzymes are specialized natural reagents of a unique kind.

Direct hydrogen atom transfer

Coenzymes: specialized natural reagents

Alcohol dehydrogenases

Coenzymes – specialized natural reagents

Conformational changes accompanying the catalytic action of dehydrogenases

Coenzymes — special naturally occurring specialized reagents

Glutamate dehydrogenase

Coenzymes - special naturally occurring specialized reagents

Glyceraldehyde-3-phosphate dehydrogenase and ATP formation in fermentation reactions

Coenzymes - specialized natural reagents of a distinct kind

Other dehydrogenases

Coenzymes – specialized natural reagents

Some unusual chemical properties of pyridine nucleotides

Coenzymes - specialized natural reagents

Analogues of pyridine nucleotides

Coenzymes: specific, naturally occurring specialized reagents

Flavin Coenzymes

Coenzymes - specialized natural reagents

Flavin coenzymes

Flavoproteins and their redox potentials

Coenzymes — specialized naturally occurring reagents

Typical dehydrogenation reactions catalyzed by flavoproteins

Coenzymes – special natural specialized reagents

Covalently bound and other modified flavin coenzymes

Coenzymes — special naturally occurring specialized reagents

Flavin Coenzymes

Mechanism of Action of Flavin Dehydrogenases

Coenzymes - special natural specialized reagents

Flavin coenzymes

Semireduced flavins

Coenzymes - specialized natural reagents

Metal-flavin complexes and metalloflavoproteins

Reactions of reduced flavins with oxygen

Coenzymes - special natural specialized reagents

Light absorption

Coenzymes - specialized natural reagents of a distinct type

Lipoic acid and oxidative decarboxylation of α-keto acids

Coenzymes - specialized natural reagents

Lipoic acid and the oxidative decarboxylation of α-keto acids

Chemical reactions involving lipoic acid

Coenzymes: Specialized Natural Reagents

Lipoic Acid and Oxidative Decarboxylation of α-Keto Acids

Enzymatic Function

Coenzymes - specialized natural reagents

Lipoic acid and oxidative decarboxylation of α-keto acids

Pyruvate : ferredoxin oxidoreductase

Oxidative decarboxylation by hydrogen peroxide

Coenzymes: Specialized Natural Reagents

Lipoic Acid and the Oxidative Decarboxylation of α-Keto Acids

Pyruvate-Formate-Lyase Reaction

Cleavage of α-Keto Acids and Substrate-Level Phosphorylation

Coenzymes - specialized natural reagents

Tetrahydrofolic acid and other pterin coenzymes

Coenzymes — special naturally occurring specialized reagents

Coenzyme forms of folic acid

Coenzymes: Specialized Natural Reagents

Tetrahydrofolic Acid and Other Pterin Coenzymes

Dihydrofolate Reductase

Coenzymes - specialized natural reagents of a distinct type

Tetrahydrofolic acid and other pterin coenzymes

Single-carbon groups and compounds in metabolic processes

Coenzymes are specialized natural reagents

Coenzyme forms of vitamin B12

Reduction of cyanocobalamin and synthesis of alkylcobalamins

Coenzymes: Specialized Natural Reagents

Coenzyme Forms of Vitamin B12

Three Reactions of Non-Enzymatic Cleavage of Vitamin B12 Coenzyme Forms

Coenzymes: specific natural specialized reagents

Coenzyme forms of vitamin B12

Enzymatic functions of B12 coenzymes

Coenzymes - specialized natural reagents

Ribonucleotide reductase

Coenzymes are specialized natural reagents of a unique kind.

Substrate isomerization

Coenzymes – unique specialized natural reagents

Stereochemistry of the action of vitamin B12-dependent enzymes

Coenzymes: specialized natural reagents of unique function

Methyl group transfer reactions

Coenzymes: specialized natural reagents

Methane synthesis

Coenzymes: Special Natural Specialized Reagents

References

Organization of Metabolism: Catabolic Pathways

Fatty Acid Oxidation

Beta-Oxidation

Branched-Chain Fatty Acids

Oxidation of Saturated Hydrocarbons

Alpha- and Omega-Oxidation

Oxidation of Unsaturated Fatty Acids

Carnitine and Mitochondrial Permeability

Ketone Bodies

The Tricarboxylic Acid Cycle

An Efficient Pathway for Cleaving Strong Bonds

Tricarboxylic Acid Cycle

Synthesis of the Regenerating Substrate Oxaloacetate

General Properties of Catalytic Cycles

Regulation of the Cycle

The Tricarboxylic Acid Cycle

Catabolism of Intermediates of the Tricarboxylic Acid Cycle

Oxidation Pathways Linked to the Tricarboxylic Acid Cycle

γ-Aminobutyrate Shunt

Oxidation Pathways Associated with the Tricarboxylic Acid Cycle

Dicarboxylic Acid Cycle

Oxidation of oxalate to CO2 via formate

Catabolism of Propionyl-CoA and Propionate

Catabolic Pathways Involving the Formation of Malonate Semialdehyde

The Methylmalonyl Pathway of Propionate Utilization

Catabolism of Sugars

Glycolysis

ATP Generation Coupled to Substrate Oxidation

Pentose Phosphate Pathways

Carbohydrate Catabolism

Entner-Doudoroff Pathway

Fermentation: "Life Without Oxygen"

Fermentation Based on the Embden-Meyerhof Pathway

Mixed Acid Fermentation

Propionic Acid Fermentation

Butyric Acid and Butanol Fermentation

Fermentation of Ethanol and Acetate to Butyrate and Caproate

Fermentation Based on the Phosphogluconate and Pentose Phosphate Pathways

References

How electrons meet oxygen, how ATP is generated in the process, and other related phenomena

Historical Background

Hemoproteins

Some names worth remembering

How electrons meet oxygen, how ATP is formed in the process, and some related phenomena

Hemes

How electrons meet oxygen, how ATP is generated in the process, and other related phenomena.

Functions of hemoproteins

How electrons encounter oxygen, how ATP is generated in the process, and related phenomena.

Oxygen-transporting proteins

Cytochromes

How electrons meet oxygen, how ATP is generated in the process, and related phenomena

Catalase and peroxidases

How electrons meet oxygen, how ATP is formed in the process, and some related phenomena

Non-heme iron proteins

On how electrons meet oxygen, how ATP is generated in the process, and on several related phenomena

Quinones as hydrogen carriers

How electrons meet oxygen, how ATP is generated in the process, and some related phenomena

Electron transport chain and oxidative phosphorylation

Mitochondrial architecture

How electrons meet oxygen, how ATP is formed in the process, and other related phenomena.

Electron Transport Chain and Oxidative Phosphorylation

Chemical Activity of Mitochondria

How electrons meet oxygen, how ATP is generated in the process, and related phenomena

Electron transport chain and oxidative phosphorylation

Sequence of electron carrier function

How electrons meet oxygen, how ATP is formed in the process, and some related phenomena

Electron Transport Chain and Oxidative Phosphorylation

Stoichiometry and Sites of Oxidative Phosphorylation

Respiratory Control, Uncoupling, and Exchange Reactions

How electrons meet oxygen, how ATP is generated in the process, and some related phenomena

Thermodynamics and "Reverse Electron Flow"

On how electrons meet oxygen, how ATR is generated in the process, and some related phenomena

Electron transport chain and oxidative phosphorylation

Reconstitution of phosphorylating particles

On how electrons meet oxygen, how ATR is formed in the process, and some related phenomena

Theories of oxidative phosphorylation and model experiments

Energy-dependent processes in mitochondria

On how electrons meet oxygen, how ATR is generated in the process, and some related phenomena

Transport across mitochondrial membranes

Utilization of energy from inorganic reactions

How electrons meet oxygen, how ATP is generated in the process, and other related phenomena

Reduced inorganic compounds as respiratory substrates

How electrons meet oxygen, how ATP is formed in the process, and some related phenomena

Utilization of the energy of inorganic reactions

Anaerobic respiration

How electrons encounter oxygen, how ATP is generated in the process, and some related phenomena

Oxygenases and hydroxylases

How electrons meet oxygen, how ATP is formed in the process, and related phenomena

Dioxygenases

How electrons encounter oxygen, how ATP is formed in the process, and related phenomena.

Monooxygenases

How electrons encounter oxygen, how ATP is generated in the process, and related phenomena.

Desaturation of fatty acids

References

Biosynthesis: How New Molecules Are Formed

Metabolic Loops and Biosynthetic Families

Metabolic Loops

Metabolic loops and biosynthetic families

Key intermediates and biosynthetic families

Utilization of ATP Energy

Biosynthesis; how new molecules are formed

Utilization of ATP energy

Group activation

Biosynthesis: how new molecules are formed

Pyrophosphate hydrolysis

Biosynthesis: How New Molecules Are Formed

Utilization of ATP Energy

Coupling of phosphorylation with sequential phosphatase cleavage

Carboxylation and Decarboxylation; Fatty Acid Synthesis

The Role of Reducing Agents in Biosynthetic Reactions

Reversal of the Oxidative Phase by a Strong Reducing Agent

Biosynthesis; how new molecules are formed

The role of reducing agents in biosynthetic reactions

Fructose in spermatozoa

Biosynthesis: How New Molecules Are Formed

The Role of Reducing Agents in Biosynthetic Reactions

Regulation of the Reducing Capacity of Systems Containing NAD and NADP

Biosynthesis: how new molecules are formed

The role of reducing agents in biosynthetic reactions

Reduced ferredoxin in reductive biosynthesis

Biosynthesis of monomers

The role of carbonyl groups in chain formation and cleavage

Biosynthesis: How New Molecules Are Formed

Biosynthesis of Monomers

Starting from CO2

Biosynthesis; how new molecules are formed

Biosynthesis of monomers

Biosynthesis from formate, formaldehyde, and methanol

Glyoxylate cycle

Biosynthesis of glucose (gluconeogenesis)

Biosynthesis: How New Molecules Are Formed

Biosynthesis of Monomers

Construction of Hydrocarbon Chains from Two-Carbon Units

Keto acid chains. The elongation process

Decarboxylation as a Driving Force in Biosynthesis

Stabilization and Termination of Chain Growth via Cyclization

Formation of Branched Chains

Polymer Biosynthesis and Modification

Characteristic Features of Biosynthesis

Biosynthesis; how new molecules are formed

Biosynthesis of polymers and their modification

Irreversible modification and catabolism of polymers

Polymer biosynthesis and modification

Hydroxylation and other modifications of connective tissue proteins

Biosynthesis: How New Molecules Are Formed

Regulation of Biosynthetic Processes

An Overview of Cellular Metabolism

Glycogen and Blood Glucose

Biosynthesis: how new molecules are formed

Regulation of biosynthetic processes

Synthesis and catabolism of glycogen

Biosynthesis: How New Molecules Are Formed

Regulation of Biosynthetic Processes

Phosphofructokinase: A Key Regulatory Enzyme

Gluconeogenesis

Substrate Cycles

The Starvation State

Ketosis

Lipogenesis

References

Biosynthesis; how new molecules are formed

Selected pathways of carbohydrate and lipid metabolism

Interconversions of monosaccharides

Biosynthesis: How New Molecules Are Formed

Selected Pathways of Carbohydrate and Lipid Metabolism

Galactose Metabolism

Selected pathways of carbohydrate and lipid metabolism

Interconversions of nucleotide sugars

Biosynthesis: how new molecules are formed

Certain specific pathways of carbohydrate and lipid metabolism

Inositol and D-glucuronic acid

Biosynthesis: How New Molecules Are Formed

Selected pathways of carbohydrate and lipid metabolism

Transformations of fructose-6-phosphate

Synthesis of deoxysugars

Synthesis and Utilization of Oligosaccharides

Polysaccharide Synthesis

Highly Specific Transferases

Chain Elongation via Insertion

Biosynthesis: how new molecules are formed

Polysaccharide synthesis

Lipid carriers

Biosynthesis: How New Molecules Are Formed

Polysaccharide Synthesis

Cellulose and Chitin

Intracellular Degradation of Polysaccharides and Glycolipids

Biosynthesis; how new molecules are formed

Intracellular degradation of polysaccharides and glycolipids

Glycolipids

Biosynthesis: How New Molecules Are Formed

Intracellular Degradation of Polysaccharides and Glycolipids

Can Lysosomal Storage Diseases Be Cured?

Special Aspects of Fatty Acid Metabolism

Biosynthesis; how new molecules are formed

Special aspects of fatty acid metabolism

Unsaturated fatty acids and their transformation products

Biosynthesis: How New Molecules Are Formed

Cell surface lipids

Biosynthesis; how new molecules are formed

Prostaglandins

Metabolism of triglycerides, phospholipids, and glycolipids

Regulation of triglyceride metabolism

Synthesis of phospholipids and glycolipids

Biosynthesis: How New Molecules Are Formed

Metabolism of Triglycerides, Phospholipids, and Glycolipids

Ether-linked Lipids

Biosynthesis: how new molecules are formed

Metabolism of triglycerides, phospholipids, and glycolipids

Sphingolipids

Biosynthesis: How New Molecules Are Formed

Polyketides

Biosynthesis; how new molecules are formed

Polyprenyl (isoprenoid) compounds

Biosynthesis: How New Molecules Are Formed

Polyprenyl (Isoprenoid) Compounds

Terpenes

Polypretyl (Isoprenoid) Compounds

Formation of Symmetrical Terpenes, Squalene, and Phytoene

Polyprenyl (Isoprenoid) Compounds

Carotenes and Their Derivatives

Polyprenyl Side Chains

Biosynthesis; how new molecules are formed

Steroid compounds

Biosynthesis of sterols

Biosynthesis: How New Molecules Are Formed

Steroid Compounds

Cholesterol Metabolism

Steroid Hormones

Other Steroids

Biosynthesis: how new molecules are formed

Steroid compounds

References