Bioenergetics

A Bridge Across Life and Universe

Davor Juretic

• Publisher: CRC Press
• Year: 2021
• ISBN:
  9781351172745
• Edition: 1
• Topic: Ciencias biológicas
• Subtopic: Biología celular

Bioenergetics deals with the very first energy transformation steps performed by living cells. Increased dissipation is the primary effect of processing external energy packages. Enzyme-supported charge separation is the minor but essential outcome for maintaining life. This book explores the usefulness of dissecting the entropy production of enzymes involved in cellular defenses, fermentation, respiration, and photosynthesis, assuming that tightly regulated dissipation is the hallmark of life.

Researchers, educators, and students of life sciences can find in this text many examples of how we can use the interdisciplinary approach to study cells' virtuoso ability to connect the microscopic to the macroscopic world. Each chapter is a self-contained unit with a glossary and selected references for further reading.

Chapter 1 Mitchell’s Chemiosmotic Theory

The Background

DOI: 10.1201/9781351172769-1

1.1 The background and early developments

Present-day bioenergetics, systems biology, and cell biophysics are moving ever closer to the thermodynamics of irreversible processes, while initial expectations after the Second World War about the importance of the quantum biology approach did not come true yet. Quantum phenomena, such as tunneling and ultrafast nondissipative transitions, are relevant for the detailed discussion of photosynthesis and enzyme kinetics, for example. I do not doubt that life evolved ways and means for utilizing the quantum peculiarities like entanglement, superposition, wave-like properties, and tunneling, which even the best physicists don’t know how to detect or employ at room temperatures. Some physicists argue for the need to use quantum physics in explaining consciousness. But on the whole, my viewpoint is closer to Delbrück’s thoughts. Physicist Max Delbrück is today a legendary person among biologists due to the thoughtfulness of his contributions and developed methods in biology. However, in spite of being one of the pioneers in quantum physics applications, he did not use quantum physics in biology, and he had great respect for the wisdom of living species. In one 1949 lecture, he asserted: “You cannot expect to explain such a wise old bird as life in a few words.” He had in mind the billions of years through which biological evolution created even the thinnest living particles, like bacterial viruses named phages, which he liked to use in his research. We must admit that on the mesoscopic and larger scale of macromolecules, cellular organelles, and cells, the classical physics predominates, and irreversible thermodynamics is the only physics subdiscipline allowing for irreversibility, evolution, and free-energy transduction, that are crucial attributes of biochemical processes in every living cell.

The first push in this direction was due to Aaron Katchalsky, Ilya Prigogine, Hermann Haken, Terrel Hill, and many other researchers from 1950 to 1980, who built upon the firm foundation for near-equilibrium irreversible thermodynamics by Lars Onsager, the winner of the 1968 Nobel Prize in Chemistry (Onsager 1931a, b). Although still of limited extent, these new physics developments were essential for a better understanding of complex biological structures and processes. General organizing, evolution, or selection principles from physics were not found during that period, which was not a disappointment to molecular biologists (they did not expect anything else in addition to Darwinian evolution and selection). Still, it was a disappointment to physicists, whose natural inclination is to derive as many predictions as possible from as simple and as general natural law as possible.

Another line of research focused on solving the problem of how oxidative or photosynthetic phosphorylation works. In that research field, Peter Mitchell (1920–1992) became my hero during the PhD thesis research I performed at the Penn. State Univ. from 1972 to 1976. Physicists love to see grand unification ideas either in their or in unrelated research topics. Peter was not a physicist, but he united membrane biochemistry with the biochemistry of soluble proteins, electrochemistry with biochemistry, mitochondrial with microbiological cytochrome research, respiration with photosynthesis, ion gradients with vectorial chemistry, electron transfer with active transport of protons, including conversions among electrical, osmotic, and chemical forms of energy (Mitchell 1977b). All these unifications led to the natural development of membrane bioenergetics as a mature research field. Remarkably, when his chemiosmotic hypothesis was published in 1961 (Mitchell 1961a, b) there was a little experimental evidence for it (Slater 1994). Mitchell’s speculative and visionary intuition was vindicated later in experiments performed by him, his collaborator Jennifer Moyle, and other scientists. It turned out that the chemiosmotic theory by Peter Mitchell, the Nobel Prize winner in Chemistry 1978, was an excellent inspiration for numerous experiments probing the build-up of the electrochemical proton gradient (Mitchell 1979a ,b). The chemiosmotic proposal initially contained some errors in mechanistic details. The chairman of the committee, which recommended Mitchell for the Nobel Prize in 1978, felt obligated to defend their decision with words: ‘‘Mitchell was right only on the phenomenological and not on the mechanistic level’’ (Malmström 2000).

One of my favorite books is: “Surely You’re Joking, Mr. Feynman!” (Feynman 1985). The title could have been expressed as the question: ‘‘Are you serious, Mr. Feynman?” Except for the scientist’s name, the question is identical to the one published by Leslie Orgel in the Nature journal: ‘‘Are you serious, Dr Mitchell?” (Orgel 1999). Mitchell’s ideas seemed bizarre as Orgel commented, or chemically unattractive as put more kindly by Boyer (Prebble 2013), or weighted with perplexing physics as implicitly stated by Slater: “I did not understand why Mitchell believed that the translocation of protons contributed both to the pH difference and the potential across the membrane” (Slater 1994). Mitchell explained in the 1970s (Mitchell 1977b) why transmembrane nanomotors are sensing both the chemical and electric components of the electrochemical driving force across the membrane (see Chapter 6). Presently, the recapitulation of his arguments can be found in many textbooks or, for instance, in the review paper about the concept of the membrane proton well (also introduced by Peter Mitchell) (Mulkidjanian 2006) and the review paper about ATP synthase (Junge and Nelson 2015). However, in the 1960s, it was certainly disconcerting for research leaders in oxidative phosphorylation to give up their preconceived ideas because of the hypothesis that has come from an outsider to that field. Also, not enough experimental evidence has been accumulated to endanger their pet theories.

Contemporary research leaders considered as relevant the metabolic expertise in cell-free preparations of enzymes with as little membraneous contamination as possible. Mitchell did not agree. He was an expert in membranes, ion transport through membranes, and cytochromes embedded in the microbial cytoplasmic membrane (Mitchell and Moyle 1956). In his opinion, other integral membrane proteins also acted as enzymes or power-generating units: “(Membranes) contain the power-generating and power-consuming modules that are plugged through it and make contact with each other through the aqueous conductors on either side.” (Mitchell 1991). He maintained this same opinion from the 1950s, and it gradually become widely accepted, but some of his other prescient proposals were contested before and after his Nobel Prize.

Mitchell’s no-bull style in speaking and writing did not help. One example is the statement from his Nobel lecture: “By 1965, the field of oxidative phosphorylation was littered with the smouldering conceptual remains of numerous exploded energy-rich chemical intermediates” (Mitchell 1979b). Mitchell referred to the prevalent high-energy intermediate hypothesis for oxidative phosphorylation in the 1950s (Slater 1953), which was still the main framework for the unsuccessful experiments to find such intermediates in the 1960s. Characteristically, he stated: “The elusive character of the ‘energy-rich’ intermediates of the orthodox chemical coupling hypothesis would be explained by the fact that these intermediates do not exist” (Mitchell 1961a). A relatively small investment of his family money into Mitchell’s private research institution, the Glynn House (see section 1.5), saved taxpayers from the USA and other countries of much greater additional useless spending of millions of dollars for funding research about the identity of the ‘energy-rich’ intermediates (Rich 2008). Fundamental physical and chemical principles needed for the development of Mitchell’s ideas were just around the corner or already present for some time in the scientific literature as free ingredients that only had to be recognized.

1.2 Living cells are equally brilliant chemists and physicists

The irreversible thermodynamics provided another main line of development for the concept of vectorial metabolism. It suggested some interesting answers about the question of why living cells are at the same time highly ordered and highly powerful entropy producers. It must be admitted that the intuition of Nobelist Ilya Prigogine was on the right track when he introduced the concept of dissipative structures (Glansdorff and Prigogine 1971, Prigogine and Lefever 1973), the structures spontaneously arising whenever there is a pressing need to increase the system’s entropy production (due to increased driving force for instance). It appears that we do have something in common with such dissipative structures as whirlpools, eddies, tornadoes, and dust devils. However, for such a complex system as a living cell, the description in terms of dissipative structure is so abstract that it leaves out all details on how dissipation is performed, by what structures, and why it is functionally essential for a cell to have high dissipation.

There is no doubt that biological macromolecules are often capable of producing the increase in dissipation for many orders of magnitudes when stimulated with appropriate metabolites or free energy packages. The same nucleic acids or protein macromolecules are inert when outside the cellular environment. They can even form crystals in the hands of skilled biochemists interested in performing the X-ray crystallography to study their structure. We learn nothing new if we name all biomolecules as dissipative structures. But an excellent capability to regulate the dissipation level can be regarded as unique to living system bioenergetics.

“The living cell is a chemist,” used to say my PhD thesis mentor, Prof. Alec Keith. One might add that each living cell, visible only under a microscope, is the best chemist in the whole world capable of speeding up some reactions for 10 to 20 orders of magnitude, and without the help of high temperatures. We have equally good reason to consider living cells as genius physicists. Simple bacterial cells are capable of creating and maintaining the strongest possible electric field across their cytoplasmic membrane. Just a little stronger field would ensure the cell’s self-destruction. Cell’s ability to separate charges is responsible for creating the electrochemical proton gradient or protonmotive force, which was mentioned before in the introductory chapter.

For a long time, biochemists did not appreciate that living cells are brilliant physicists, well versed not only in the synthesis of complex organic compounds but also in the art of charge separation and simultaneous generation of strong electric fields. Three domains of life, Archaea, Bacteria, and Eukaryota, generate similarly strong fields of 30 million volts per meter, corresponding to that discharged by a bolt of lightning. However, eukaryotic cells reserve their mitochondria organelles for creating such strong electric fields, while prokaryotic cells use their cytoplasmic membrane for the same purpose. It took the visionary disposition of Peter Mitchell to recognize the common energy-transduction principle of bacteria, mitochondria, and chloroplasts.

1.3 The chemiosmotic hypothesis

The powerhouses of our cells are organelles named mitochondria, while plant cells have chloroplasts too. Mitchell assumed that cells and organelles need an electrochemical proton gradient for ATP synthesis. He called it the protonmotive force (pmf). The ATP-synthase is a membrane-embedded protein, which couples the pmf and directional proton transport to ATP synthesis. Experiments in his and many other laboratories established the importance of charge separation ability in prokaryotes, mitochondria, and chloroplasts. Mitchell also recognized the importance of topologically closed membrane and vectorial active transport of protons by integral membrane proteins acting as proton pumps. Charge separation would be impossible if a bioenergetic membrane with proton pumps is not topologically closed and impermeable to protons. It would also be impossible if some input force d...

Table of contents

• Cover Page
• Title Page
• Copyright Page
• Preface
• Table of Contents
• Introduction
• 1. Mitchell’s Chemiosmotic Theory: The Background
• 2. Membrane Bioenergetics in a Nutshell
• 3. Irreversible Thermodynamics and Coupled Biochemical Reactions
• 4. What is Life?
• 5. Some Answers to Schrödinger’s Questions
• 6. Protonmotive Force
• 7. Membrane Proteins
• 8. The Maximum Entropy Production: Applications in the Bioenergetics of Bacterial Photosynthesis
• 9. Coupling Thermodynamics with Biological Evolution through Bioenergetics
• 10. Perfect Enzymes, According to Biochemists
• 11. ATP Synthase Molecular Motor
• 12. Bacteriorhodopsin: Light-harvesting Movie Star
• 13. The Protonmotive Force in Geochemistry and the Origin Question: Is the Origin of Bioenergetics Connected with the Origin of Life?
• 14. Integrating Glycolysis with Oxidative Phosphorylation by Hexokinases
• 15. Bioenergetics of the Brain, Aging, and Cancer Cells as Bridged by a-synuclein
• 16. Retrospections, Contrasting Viewpoints, Incentives, Challenges, Prospects, and Conclusions
• Index