CONTENTSCONTENTS

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10Introduction xii

Chapter 1: Biochemical Reactions 1Historical Overview of Biochemistry 2 Joseph Priestley 3 Jean Senebier 8The Chemistry and Reactions of Cells 9

Chemical Composition of Living Matter 9Nutritional Components 12The Breakdown of Chemicals 14Metabolism and Heat 15

Basic Concepts of Chemical Reactions 16

Synthesis 17The Conservation of Matter 17Energy Considerations 19Kinetic Considerations 21

Chapter 2: Classifying and Studying Chemical Reactions 24

Classifying Chemical Reactions 24Classifi cation by Type of Product 24

Svante August Arrhenius 29 Johannes Nicolaus Brønsted 33 Gilbert N. Lewis 35

Classifi cation by Reaction Outcome 37Classifi cation by Reaction Mechanism 42

The Study of Biochemical Reactions 44Centrifugation and Electrophoresis 46Chromatography and Isotopes 46

Mikhail Semyonovich Tsvet 47

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59Chapter 3: The Chemical Reactions of Cells 49

The Unity of Life 49Biological Energy Exchanges 52

The Carrier of Chemical Energy 52Catabolism 55

Sir Hans Adolf Krebs 60Anabolism 61Integration of Catabolism and Anabolism 63

The Study of Metabolic Pathways 66 George Wells Beadle 69 Edward L. Tatum 72

Chapter 4: The Fragmentation of Complex Molecules 74

The Catabolism of Glucose 75Glycolysis 75

Gustav Georg Embden 76 Otto Meyerhof 77 Archibald V. Hill 79 Axel Hugo Teodor Theorell 85

The Catabolism of Sugars Other Than Glucose 90

The Catabolism of Lipids (Fats) 93Fate of Glycerol 94Fate of Fatty Acids 95

The Catabolism of Proteins 100Removal of Nitrogen 101Disposal of Nitrogen 103Oxidation of the Carbon Skeleton 108

Chapter 5: The Combustion of Food Materials 109

Fritz Albert Lipmann 110

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133The Oxidation of Molecular Fragments 110

The Oxidation of Pyruvate 111The TCA Cycle 113

Isomerization 118Biological Energy Transduction 120

ATP as the Currency of Energy Exchange 121

Free Energy 124 J. Willard Gibbs 126

Energy Conservation 127

Chapter 6: The Biosynthesis of Cell Components and Regulation of Metabolism 135

The Stages of Biosynthesis and Utilization of ATP 136The Supply of Biosynthetic Precursors 137

Anaplerotic Routes 139Growth of Microorganisms on TCA Cycle Intermediates 141

The Synthesis of Building Blocks 143 Bernardo Alberto Houssay 143

Sugars 144 Carl Cori and Gerty Cori 145

Lipid Components 149Amino Acids 156Nucleotides 157

The Synthesis of Macromolecules 162

Carbohydrates and Lipids 162Nucleic Acids and Proteins 168

Regulation of Metabolism 169Fine Control 170Coarse Control 178

Chapter 7: The Transformation of Light Into Chemical Energy 181

Early Observations of Photosynthesis 182 Jan Ingenhousz 183Overall Reaction of Photosynthesis 184Basic Products of Photosynthesis 186Evolution of Photosynthesis 187Factors That Infl uence the Rate of Photosynthesis 189

Light Intensity and Temperature 189Carbon Dioxide 190Water 191

Leaf 192Minerals 194Internal Factors 194

Energy Effi ciency of Photosynthesis 195Chloroplasts, the Photosynthetic Units of Green Plants 198

Structural Features 199Chemical Composition of Lamellae 200

Coenzyme 203

Chapter 8: The Process of Photosynthesis 204

The Light Reactions 204Light Absorption and Energy Transfer 204

Fluorescence 205The Pathway of Electrons 206Evidence of Two Light Reactions 208Photosystems I and II 210Quantum Requirements 210206

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The Conversion of Light Energy to ATP 211 Peter Dennis Mitchell 213Carbon Fixation and Reduction 214

Elucidation of the Carbon Pathway 214

Melvin Calvin 216The Reductive Pentose Phosphate Cycle 218Regulation of the Cycle 220Products of Carbon Reduction 221Photorespiration 222Carbon Fixation via C4 Acids 222

The Molecular Biology of Photosynthesis 224

Chapter 9: Bioluminescence and Light Reactions 226

Bioluminescence 226 Edmund Newton Harvey 227

The Role of Bioluminescence in Behaviour 227

Anglerfi sh 228The Role of Bioluminescence in Metabolism 230The Range and Variety of Bioluminescent Organisms 230

Luciferin 231Biochemical Events of Light Emission 236The Signifi cance of Bioluminescence in Research 237

Biological Effects of Visible and Ultraviolet Light 239

Intrinsic Action 241Photodynamic Action 242

Chromatophore 243

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238 Effects on Development and Biologic Rhythms 244

Conclusion 245

Glossary 248Bibliography 250Index 252

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7 Introduction 7

The significance of chemical reactions and their role in modern science was made evident in 2010 when biologists synthesized a functional DNA sequence from scratch. The sequence was the genome of a bacterium called Mycoplasma mycoides. The researchers transplanted the synthetic sequence into the cell of a different bacterium and demonstrated that the synthetic DNA was functional when new colonies of M. mycoides began to grow.

Although the scientists who created the synthetic cell pushed the boundary of biochemistry to make something new, they built this accomplishment on the discoveries of earlier biochemists, starting with the work of Robert Boyle in the 1650s. Boyle felt that the goal of chemistry was to determine what chemical components made up various substances. Later scientists focused not only on the composition of substances but also on the mecha-nisms and products of different chemical reactions.

Biochemists concern themselves with the chemical reactions of life, and their research has transformed eso-teric topics such as cellular metabolism into more familiar topics such as stem cell research and dietary recommenda-tions. Biochemistry’s far reaches extend to advancements in the fields of medicine, nutrition, agriculture, and dis-ease. Even though scientists have greatly added to the body of work generated by the first biochemists, many unsolved mysteries remain. This volume will explore the mysterious and complex world of the chemical reactions that make life possible.

A chemical reaction is a process in which the atoms of chemical elements or chemical compounds are rear-ranged to form different substances as products. To express what happens when new substances are created, or synthesized, from other elements or compounds, sci-entists use chemical equations. Many chemical equations

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can be found in this book. In a chemical equation depict-ing the reaction of two or more substances, the same number of atoms of each kind must appear on both sides of the equation. The reactions of different elements remain the same whether they happen within a living being or not. But living organisms are unique. They can use energy found in their environments to move, grow, and reproduce. The chemical process that allows living things to extract energy from foods and other sources, and that allows the organisms to use this energy to create new cells, is called metabolism. Chemical reactions are considered endothermic if heat energy is absorbed and exothermic if heat is released.

There are four ways to classify a chemical reaction: by product type, by reactant type, by reaction outcome, and by reaction mechanism. A reaction can be placed in more than one category. One example of a reaction by product type is a gas-forming reaction, such as the combination of calcium and hydrochloric acid to produce carbon dioxide. Classification by reactant type is used to distin-guish between reactions based on the types of chemical substances involved in a reaction. For example, oxidation-reduction reactions make use of reactants that are capable of donating or receiving electrons. In contrast, acid-base reactions involve reactants that are capable of donating or receiving protons. Many different kinds of reactions are categorized by reaction outcome. Examples include decomposition reactions, in which molecules break up into simpler parts; substitution reactions, in which atoms in a molecule are replaced by other atoms; and elimina-tion and addition reactions, in which one molecule is subtracted from or added to another. The classification of reactions by reaction mechanism is based on the different ways in which atoms can be rearranged during the forma-tion of molecules. For example, chain reactions occur in

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sequential steps, and each step results in the production of a chemically active component known as a reagent. Photolysis reactions, which are also distinguished based on reaction mechanism, are facilitated by the absorption of electromagnetic radiation. One example of a photoly-sis reaction is the decomposition of ozone into oxygen in the atmosphere.

The study of biochemical reactions involves sophis-ticated instruments for measuring and quantifying data. For example, biochemists use centrifuges to separate sus-pended particles and molecules in solution. Centrifugal force can be used to separate red cells from blood plasma and to separate the various parts of cells, such as the nuclei, mitochondria, and ribosomes, from one another. Another separation technique used in biochemical stud-ies is electrophoresis. In this technique, a liquid is placed under the influence of an electric field to separate the electrically charged particles of amino acids and pro-teins for study. The abnormal hemoglobin in sickle-cell anemia, a molecular disease, was discovered through the use of electrophoresis. The use of chromatography, in which the varying solubility of substances in solvents is measured, has been used to help scientists determine the exact composition of the amino acids in a protein. It also gives estimates of the weight of different molecules. Scientists have developed techniques to “label” biological compounds with isotopes (radioactive elements) so they can study the process of metabolism as the compounds undergo chemical change. To measure the isotope-labeled compounds, they have also developed special radioactive detection devices.

The main cellular chemical processes are similar among all living things. Proteins make up all living things. Many of these proteins work as catalysts, allowing chemi-cal reactions to happen efficiently.

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Almost all organisms use DNA (deoxyribonucleic acid) to transfer genetic information to their offspring. Those that do not use DNA as their carrier of genetic informa-tion use RNA (ribonucleic acid) instead. Although the genetic code itself is variable among organisms, the chem-ical reactions that govern the expression and activity of DNA and RNA are similar.

The first law of thermodynamics (the study of the rela-tionship between heat, work, temperature, and energy) posits that energy can be neither created nor destroyed. Living organisms simply transform energy from one form (most often from the Sun) to another and thereby trans-fer energy through biological systems. Biological energy exchange, therefore, involves organisms absorbing useful energy (free energy) and returning less useful energy to the environment, usually as heat. Catabolism and anabo-lism are opposing pathways involved in energy exchange. Catabolism breaks down large molecules into smaller ones, whereas anabolism constructs large molecules from smaller units.

Only a small portion of the energy contained in food is released when the food is fragmented, or broken down into small molecules. In order to yield energy, food must undergo oxidation (the removal of electrons). Oxidation is essential to cellular respiration, the process by which organisms mix oxygen with food molecules, such as car-bohydrates, lipids (fats), and proteins, to create chemical energy that can be used by cells. This process also discards carbon dioxide and water as waste products. Cellular res-piration helps produce ATP (adenosine triphosphate), the major energy-carrying molecule found in living organisms. Through a complicated molecular reaction, ATP supplies energy for growth, movement, and other functions.

Since the amount of ATP in a cell is limited, it must be constantly replaced and conserved. Therefore, cells

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contain separate locations where ATP is generated and consumed. In most animals, plants, and fungi, ATP is synthesized in the membranes of mitochondria—tiny rod-shaped organelles found within cells. Since bacteria do not have mitochondria, this chemical process is incor-porated into the plasma membrane.

Even though the most important source of energy for cellular processes is the carbohydrate sugar called glu-cose, the value of fatty acids as an energy source cannot be underestimated. Half the energy used by vital organs in vertebrates comes from lipids, and hibernating animals use fatty acids as virtually their sole source of energy.

To balance the process of metabolism, the catabolism of energy-yielding molecules must be counterbalanced by the biosynthesis (anabolism) of cellular components. Anabolism occurs in two main steps. First, intermediate compounds are directed away from catabolic pathways and toward pathways that yield small molecules for the building blocks of macromolecules. Then, the building blocks combine, yielding proteins, nucleic acids, lipids, and polysaccharides. This second stage involves the pres-ervation of genetic information for cells and tissues.

Photosynthesis is another important process involv-ing the chemical reactions of life. Green plants and certain other organisms convert light energy into chemical energy by transforming water, carbon dioxide, and min-erals into oxygen and energy-rich organic compounds. In addition to sustaining life on Earth, photosynthesis also helps yield the coal, oil, and gas (the so-called fossil fuels) that support industrial processes used in human societ-ies. The increase in global human population and the consequent rise in demand for these natural resources has created a severe imbalance between the rate of con-sumption and the rate of natural production through photosynthesis. Today, the former far outpaces the latter.

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Agricultural and industrial advancements have increased the efficiency of photosynthetic output to help meet some of these demands, but much work is still needed to prevent the depletion of Earth’s natural resources. The field of molecular biology has been particularly useful in discovering solutions to these problems. For example, in focusing on the manipulation of plant DNA, molecu-lar biologists have been able to accelerate the process of photosynthesis in certain plant species.

Chemically speaking, photosynthesis is an oxidation-reduction process in which electrons are removed from one molecule and gained by another molecule. In plant photosynthesis, the removed electrons and hydrogen ions eventually are transferred to carbon dioxide. The carbon dioxide is then reduced to organic products. Carbohydrates, in the form of starch and the sugar sucrose, are usually the organic end products in most green cells. Early studies of photosynthesis incorrectly named carbohydrates as the only product of photosynthesis, but scientists now known that amino acids, proteins, lipids, and pigments can also be synthesized during the process. Light energy is stored as chemical energy in the organic products formed, resulting from the difference in bond energy between the reactants and the products of photosynthesis.

The rate of photosynthesis varies among plant species and is dependent on environmental factors such as light levels, carbon dioxide supply, temperature, water supply, and mineral availability. Light and temperature work in tandem to determine the rate of photosynthesis. At low to medium light, the rate is independent of temperature influence, but as light intensity increases to high levels, the rate becomes increasingly dependent on temperature. The rate of reaction increases when carbon dioxide levels increase. In land plants, water affects the rate of photo-synthesis by indirectly interfering with the carbon dioxide

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levels in a plant. The plant’s stomates (small holes in the leaf epidermis) close to prevent the exit of water vapour as a conservation method in arid climates. Closure of the stomates, however, prevents entry of carbon dioxide, thus slowing the rate of photosynthesis.

The percentage of solar energy stored is considerably less than the maximum energy efficiency of photosyn-thesis. Several factors account for this discrepancy. Most of the sunlight travels in wavelengths too long to be absorbed. Also, additional chemical processes in plants, such as cellular respiration, consume stored energy. Bright sunlight causes the synthesis of extra sugar and starch, inhibiting photosynthesis. Any sunlight received outside the growing season goes unused, further diminishing the percentage of stored solar energy.

Chloroplasts are the site of plant photosynthesis. The size and number of chloroplasts varies among plant spe-cies. Chloroplasts are composed of internal membranes, called lamellae, whose edges are joined to form thylakoids, which are necessary for the formation of ATP. The lamel-lar membranes can permit a charge that can be used as a source of chemical or electrical energy. The lamellae are made up of lipids and proteins. Some of the lipids are chlorophyll molecules responsible for absorbing light and transferring its energy to other chlorophyll molecules that then convert light energy to chemical energy. Some of the lamellae’s protein molecules contain metal atoms required for the catalytic activity essential to photosynthesis.

Light reacts differently in various biological systems. Some organisms can store light for energy production but can also suffer negative effects from overexposure to light. Bioluminescence occurs when an organism or controlled biological system emits light, such as the illu-minating signals of fireflies. This rare ability occurs when chemical energy is converted into radiant energy in a

7 Introduction 7

completely efficient manner. Light production in organ-isms is sometimes a form of protection, as in some marine animals that emit luminous clouds to confuse predators. Primitive bacteria and other lower organisms may have originally used bioluminescence as a means of remov-ing toxic oxygen in a period when oxygen levels in the atmosphere were once very low. Biologists have used bio-luminescence to study the production of ATP in certain organisms, resulting in a better understanding of cellular energy conversion.

The study of chemical reactions is an ongoing pro-cess, one in which discovery and the implementation of new findings are intimately associated with the devel-opment of new technologies. Recent discoveries have opened new inquiries into the metabolic activities that take place in human cells. This volume will allow readers to explore the early discoveries of the first biochemists and to trace these developments and their impact, ulti-mately leading to a deeper understanding of life on Earth.

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