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This chapter describes the Advanced Technology Program (ATP) through which government acts as entrepreneur. ATP's public financial resources leverage private-sector R＆D. The use of public resources to leverage private-sector R＆D that would not otherwise have been undertaken lessens barriers to innovation and creates a cost-sharing environment conducive for cooperative research.

A variety of different methodologies have been used to probe the kinetics of cross-bridge transitions, e.g. rapid force or displacement transients, transients associated with X-ray diffraction, ATP hydrolysis by contracting muscle fibres, temperature jumps, and pressure jumps. However, these types of approaches are limited in that they do not target specific steps of the cross-bridge mechanism and, as such, produce data which are difficult to interpret. A major advance in our understanding of the mechanism of ATP hydrolysis occurred with the application of transient kinetic analysis to the study of isolated proteins in solution.

This chapter discusses the advantages, problems, and limitations of some in vitro motility assay systems hitherto developed by various researchers. Because of space limitation, it only focuses on assay systems for studying the ATP-dependent actin-myosin sliding responsible for muscle contraction, but not on the ATP-dependent microtubule-kinesin and microtubule-dynein sliding. For the same reason, this chapter aims at giving general readers an idea about the advantages, problems, and limitations of in vitro motility assay techniques as described in selected papers, but it is not an exhaustive survey of the literature.

Living systems create order, and appear to break the Second Law. This chapter explains, and resolves, this apparent paradox, drawing on the concept of coupled reactions (as introduced in Chapters 13 and 16), as mediated by ‘energy currencies’ such as ATP and NADH. The chapter then examines the key energy-capturing systems in biological systems – glycolysis and the citric acid cycle, and also photosynthesis. Topics covered include how energy is captured in the conversion of glucose to pyruvate, the mitochondrial membrane, respiration, electron transport, ATP synthase, chloroplasts and thylakoids, photosystems I and II, and the light-independent reactions of photosynthesis.

All biological operations require the input of energy. In contemporary organisms, energy is harvested by mechanisms that are essentially electrical. Energy transduction relies on the circulation of ions across membranes (usually protons), and on a sophisticated rotary ATP synthase to capture the energy and conserve it as ATP. This chapter begins with an overview of chemiosmotic energy transduction and then poses the question, How did LUCA make a living? Current thinking questions the traditional notion that that LUCA lived off prebiotic organic molecules, and favors geochemical processes, such as the reduction of CO2 by hydrogen gas. One possible habitat for such organisms would be mineral honeycombs laid down by hydrothermal vents. If there is any truth to this hypothesis, then chemiosmotic energy transduction will have been part of LUCA's endowment, and may have evolved under the special circumstances that prevail in those vents. Subsequent evolution will have led to the liberation of cells from their mineral cradle, and the progressive expansion of energy metabolism by the invention of both photosynthesis and respiration.

A more technical chapter in which the author describes the molecular adaptations allowing hyperthermophiles thriving in hell. The chapter starts with reminder of the role of water and carbon in the chemistry of life and the importance of both strong (covalent) and weak chemical bonds in the architecture of macromolecules. The two types of damages affecting these bonds at high temperature, thermodegradation and thermodenaturation, respectively, are discussed, explaining the range of temperatures suitable for life on Earth. The mechanisms protecting proteins, nucleic acids and lipids against thermodegradation and thermodenaturation are described with reminders of the role of these macromolecules in cell physiology. This includes an experiment showing that circular DNA is stable up to 110°C, thanks to topological links between the two DNA strands. RNA is very fragile at high temperature and the author suggests that requirement for messenger RNA stability in eukaryotes could explain why there is no hyperthermophilic eukaryote. Membrane permeability appears to be the Achille’s heel of cells at high temperature and the unique phospholipids of archaea probably explain why most hyperthermophiles belong to this domain. Reading this chapter led you concluding that microbes from hell are not primitive organisms but marvels of adaptation

This chapter describes and elaborates on the energy coupling processes of living systems. First, equilibrium and nonequilibrium systems are discussed, introducing living systems as open, nonequilibrium, and dissipative structures continuously interacting with their surroundings. The roles of thermodynamics and Gibbs free energy as they apply to energy coupling phenomena are then summarized, followed by a discussion of protein structures as playing a crucial role in information processes and energy couplings. The “well-informed” character of living systems and the control of free energy, or exergy, by information are also briefly discussed. Finally, using the linear nonequilibrium thermodynamic approach, energy couplings in ATP production through oxidative phosphorylation and active transport of ions by chemical pumps are discussed as a part of bioenergetics.

Over the past half century of serious research on the origin of life, several schools of thought have emerged that focus on “worlds” and what came first in the pathway to the origin of life. One example is the RNA World, a term coined by Walter Gilbert after the discovery of ribozymes. Other examples include the Iron-Sulfur World of Günther Wächtershäuser and the Lipid World proposed by Doron Lancet and coworkers. Then we have a competition between “metabolism first” and “replication first” schools. The worlds and schools have the positive effect of sharpening arguments and forcing us to think carefully, but they also can lock researchers into defending their individual approaches rather than looking for patterns in a larger perspective. One of the main themes of this book is the notion that the first living cells were systems of functional polymers working together within membranous compartments. Therefore, it is best not to think of “worlds” and “firsts” as fundamentals but instead as components evolving together toward the assembly of an encapsulated system of functional polymers. At first the polymers will be composed of random sequences of their monomers, and the compartments will contain random assortments of polymers. Here, we refer to these structures as protocells which are being produced in vast numbers as they form and decompose in continuous cycles driven by a variety of impinging, free-energy sources. This chapter describes how thermodynamic principles can be used to test the feasibility of a proposed mechanism by which random polymers can be synthesized. There is a current consensus that early life may have passed through a phase in which RNA served as a ribozyme catalyst, as a replicating system, and as a means for storing and expressing genetic information. For this reason, we will use RNA as a model polymer, but condensation reactions also produce peptide bonds and oligopeptides. At some point in the evolutionary steps leading to life, peptides and RNA formed complexes with novel functional properties beyond those of the individual molecular species.

It seems inescapable that at some point primitive cells incorporated chemical reactions related to what we now call metabolism. In all life today, metabolic reactions are driven by sources of chemical or photochemical energy, and each step is catalyzed by enzymes and regulated by feedback systems. There have been multiple proposals for the kinds of reactions that could have been incorporated into early life, but so far there is little consensus about a plausible way for metabolism to begin. This chapter will briefly review the main ideas that are familiar to chemists as solution chemistry but then ask a new question from the epigraph: how can reactions in bulk aqueous solutions be captured in membranous compartments? This question is still virtually unexplored, but I can offer some ideas in the hope of guiding potentially fruitful approaches. Because metabolism is such a complex process, it is helpful to use bullet points to help clarify the discussion. The first is a list of questions that guide the discussion, the second is list of facts to keep in mind, and the third is a list of assumptions that introduce the argument. Questions to be addressed: What are the primary metabolic reactions used by life today? What reactions can occur in prebiotic conditions that are related to metabolism? How can potential nutrient solutes cross membranes in order to support metabolism? How could metabolic systems become incorporated into primitive cellular life? Metabolism can be defined as the activity of catalyzed networks of intracellular chemical reactions that alter nutrient compounds available in the environment into a variety of compounds that are used by living systems. Most of the reactions are energetically downhill, so there is an intimate association between the energy sources available to life and the kinds of reactions that can occur. Here is a summary of energy sources used by life today: Light is by far the most abundant energy source, totaling 1360 watts per square meter as infrared and visible wavelengths. Chemical energy in the form of reduced carbon compounds is made available by photosynthesis.

Are corporate charters and bylaws contracts? What is the scope or subject matter of the corporate contract? Is access to litigation part of the bundle of rights that shareholders purchase when they buy shares in a corporation? This book chapter, “Litigation Rights and the Corporate Contract,” examines how one controversial innovation has pushed courts and legislatures to address these fundamental questions about the nature and scope of the corporate contract. That innovation was the use of corporate charter provisions and bylaws to set the rules for resolving internal disputes, especially for shareholder litigation. The emergence of exclusive forum and fee-shifting bylaws pushed lawmakers to be newly explicit about the role of corporate organizational documents. The questions and initial answers have broad implications, reaching all of the ways charters and bylaws define the relationships within the corporation. The emergence of dispute resolution provisions made them express and potentially urgent.

The energetic costs of terrestrial locomotion are placed in the context of the fuel sources that animals use for generating adenosine triphosphate (ATP) and how these fuel sources affect an animal’s capacity for sustainable aerobic metabolism. Aerobic capacity and energy use are closely linked to an animal’s thermoregulatory strategy. Patterns of energy use across terrestrial gaits, sloped substrates and level ground are examined alongside explanatory models. The energetics of terrestrial locomotion is compared with the energetics of swimming and flight. Whereas the support of an animal’s weight against gravity dominates the cost of moving on land and through air, overcoming resistive forces of drag strongly affects the energy cost of movement through water and air. The physical properties of land, water and air influence how energy use changes with the speed of movement. Given these energetic considerations, animals use different locomotor strategies and mechanisms to avoid fatigue and increase endurance capacity.

Metabolism is driven by redox reactions, in which part of the difference in potential energy between the electron donor and acceptor is used by the organism for its life processes (with the remainder being dissipated as heat). The key process is intermediary metabolism, by which the energy stored in reserves (glycogen, starch, lipid, protein) is transferred to ATP. In aerobic respiration the electrons released from reserves are passed to oxygen, which is thereby reduced to water. Not all ATP regeneration involves oxygen as the final electron acceptor, and not all oxygen is used for ATP regeneration, but oxygen consumption is often the simplest and most practical way to measure the rate of intermediary metabolism and the errors in doing so are believed to be small. The costs of existence, as estimated by resting metabolism, represent only a part (~ 25%) of the daily energy expenditure of organisms. The costs of the organism’s ecology (growth, reproduction, movement and so on) are additional to existence costs. Resting metabolic rate increases with cell temperature, indicating that it costs more energy to maintain a warm cell than it does a cool or cold cell. The temperature sensitivity of resting metabolism is highly conserved across organisms.

Probably no process epitomizes life more than respiration. By respiration we mean the cascade of energy-producing biochemical reactions called oxidative phosphorylation, powered by a gradient of oxidation. Structure and function are intimately connected, forming an entity called a faculty. In this book, we focus on the functional and evolutionary morphology of the respiratory faculty, many of the components of which are older than the first animals, indeed older than life itself. The initial steps until the first animals arose are summarized here in a hypothetical scenario and provided together with an introduction to several other conceptual approaches that we have adhered to throughout this book.

Phytoplankton plays a critical role in determining light fields of the world’s oceans, primarily through absorption of light by photosynthetic pigments (see Chapters 1 to 5). Consequently there has been considerable interest from optical researchers in determining phytoplankton absorption. Conversely, from the biological point of view, this absorption assumes paramount importance because it is the sole source of energy for photosynthesis and thus should be central to direct estimates of primary production. There are two logical parts in determining this effect of phytoplankton and in estimating primary production. One is the estimation of abundance, and the other is estimation of specific effect or specific production rate. The earliest estimates of phytoplankton abundance were based on cell counts. From the time of Francis A. Richards’ Ph.D. dissertation, however, measurement of chlorophyll a concentration per unit of water volume, because of its relative ease, has assumed a central role in abundance estimation. Physiological studies and technological advances in optical instrumentation over the last decade lead me to question whether the continued use of chlorophyll a concentration to estimate phytoplankton abundance was wise either from the viewpoint of narrowing confidence intervals on estimates of absorption and production or from the viewpoint of mechanistic understanding of the processes involved. The measurement of chlorophyll a has become such a routine tool of biological oceanography, however, that the reasons for my heresy require elaboration. Some of the reasons are not too subtle. Chlorophyll a exists with other photosynthetic pigments in organized arrays associated with photosynthetic membranes. The function of these arrays is to harvest photons and transfer their energy to the specialized reaction center complexes that mediate photochemistry (see Chapter 9). The size of the arrays or packages and the ratio of chlorophyll a molecules to other light-harvesting pigments within the packages vary with phytoplankton cell size, total irradiance and its spectral distribution, as well as with other environmental parameters. It is well known that dark-adapted (= light-limited) cells increase their complements of photopigments. This plasticity in pigment packaging is evidenced in the variability of chlorophyll a-specific absorption coefficients. Simple optical models based only on chlorophyll a concentrations cannot be accurate or precise unless the effects of pigment packaging are considered.

This chapter argues that the Omnibus Trade and Competitiveness Act of 1988 (along with the Advanced Technology Program [ATP] that it created) is an example of public sector entrepreneurship, albeit a short-lived one. The chapter begins with a description of the legislative history of the Act, before turning to the reasons for its relatively short duration. Despite its short life, the Act still represents an example of public sector entrepreneurship. After explaining why that is, based on the conceptual structure developed in Chapter 3, the chapter concludes with an analysis of the impact and effectiveness of the Act and an example of ATP-funded research.

As noted earlier and as anticipated by Charles and Francis Darwin it has been argued that plants sense the direction of gravity (gravitropism) by movement of starch granules found in cells called statocytes that contain compartments (organelles) called statoliths. The synthesis of statoliths appears to occur in the plastid (plant organelle) compartments called amyloplasts (Figure 7.1, 1). It has been suggested that this gravitropic signal then leads to movement of plant hormones such as indole-3-acetic acid (auxin) (Figure 7.2), through the phloem opposite to the pull of gravity to promote stem growth. Chloroplasts (Figure 7.1, 2) are cell compartments (plastids or organelles) in which photosynthesis is carried out. The process of photosynthesis, discussed more fully later, is accompanied by the production of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) and inorganic phosphate (Pi) (Figure 7.3). ATP is consumed and converted to ADP and Pi in living systems. The cycle of production and consumption allows ATP to serve as an “energy currency” to pay for the reactions in living systems. Beyond this generally recognized critical function of chloroplasts, it has recently been pointed out that light/dark conditions affect alternative splicing of genes which may be necessary for proper plant responses to varying light conditions. The organelles or plastids which contain the pigments for photosynthesis and the amyloplasts that store starch are only two of many kinds of plastids. Other plastids, leucoplasts for example, hold the enzymes for the synthesis of terpenes, and elaioplasts store fatty acids. Apparently, all plastids are derived from proplastids which are present in the pluripotent apical and root meristem cells. The cell wall (Figure 7.1, 3) is the tough, rigid layer that surrounds cells. It is located on the outside of the flexible cell membrane, thus adding fixed structure. A representation of a portion of the cell wall (as made up of cellulose and peptide cross-linking) is shown below in Figure 7.7. The cells will have different sizes as a function of where they are found (e.g., leaf, stalk, root), but in every case, the cell wall limits the size of the membrane that lies within.

We believe there are important roles for in vivo NMR spectroscopy techniques in studies of protection and treatment in stroke. Perhaps the primary utility of in vivo NMR spectroscopy is to establish the relevance of metabolic integrity, intracellular pH, and intracellular energy stores to concurrent changes occurring both at gross physiological levels (e.g., changes in cerebral blood flow, or blood oxygenation), and at microscopic or cellular levels. It has long been known that the brain is exquisitely sensitive to deprivations of oxygen, glucose, and cerebral blood flow. Routine human surgery on a limb takes place every day with tourniquets stopping all blood flow for up to two hours. In contrast, the deprivation of all blood flow to the brain (global ischemia) for approximately 5 minutes can result in severe, permanent brain damage. Research has gone on for more than 30 years to understand why the brain’s revival time is so much shorter, and to discover brain biochemical interventions that might dramatically extend the brain’s intolerance beyond 5 minutes, and therefore be relevant to protection and treatment of stroke. (Kogure and Hossmann, 1985; 1993) Stroke, defined as a permanent neurologic deficit arising from the death of brain cells, kills ∼ 150,000 people in the U.S.A. each year, and is the third leading cause of death (Feinleib et al., 1993). It is the next malady to escape, once one has dodged death from cardiovascular disease and cancer. Many, if not most, U.S.A. stroke victims will receive neurological clinical care not substantially different from what was provided 30 years ago. Most stroke patients will be put in intensive care units where blood pressure will be regulated and kept in a “safe” range, with the body given supportive care and the brain given an opportunity to heal itself. The problem of stroke is actually quite complex because there are several different kinds of stroke (ischemic, hemorrhagic, etc.), and because numerous systemic physiological factors are of relevance. Nevertheless, exciting advances in brain biochemistry suggest that stroke therapy and prophylaxis are likely to improve dramatically in the near future (Zivin and Choi, 1991).

In December 2, 2010, at 11:16 a.m., I received the first of three emails from students in my biochemistry class, all asking if I had heard the news. A press conference at 11 a.m. had announced that scientists had discovered a bacterium that uses arsenic instead of phosphorus in its DNA. Soon there was a hashtag for this: #arseniclife. We were excited and a little puzzled. I had just lectured about how phosphorus was uniquely useful to DNA. I shrugged and mumbled something about how textbooks can be rewritten. Today, the dust has settled—and the textbook reads the same as ever. DNA is made of phosphorus, never arsenic. That December press conference was followed by two full years of multiple experiments in labs around the world. It confirmed what the textbook said all along, yet the story was well worth it. The “arsenic life” story was never just about microbiology. It’s about science itself, how we know things, and the nature of natural history. Everyone should know this story. It will temper expectations when the next press-conference-induced hashtag makes its way halfway around the world while science is still lacing up its boots. More than that, it shows something deep about what kind of world we live in, something underreported because it is so intricate and comes from so many different places. There is a hidden order that makes some sense of biology and even sociology, and that hidden order is chemistry. All life, from a lakewater bacterium to the neurons firing in your brain as you read this, is hemmed in. It is free to randomly adapt to its surroundings with nearly infinite creativity, but its overall path is as constrained as if it were walking on the deck of a ship crossing the ocean. The ultimate movement, on the scale of billions of years, is shaped by chemical rules. One of these rules is that phosphorus makes good DNA, while arsenic does not. To reach this conclusion, we have to start where the arsenic life story started.