Quantum biology

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Quantum biology is the study of applications of quantum mechanics and theoretical chemistry to biological objects and problems. Many biological processes involve the conversion of energy into forms that are usable for chemical transformations, and are quantum mechanical in nature. Such processes involve chemical reactions, light absorption, formation of excited electronic states, transfer of excitation energy, and the transfer of electrons and protons (hydrogen ions) in chemical processes, such as photosynthesis, olfaction and cellular respiration. [1]

Contents

Quantum biology may use computations to model biological interactions in light of quantum mechanical effects. [2] Quantum biology is concerned with the influence of non-trivial quantum phenomena, [3] which can be explained by reducing the biological process to fundamental physics, although these effects are difficult to study and can be speculative. [4]

History

Quantum biology is an emerging field; most of the current research is theoretical and subject to questions that require further experimentation. Though the field has only recently received an influx of attention, it has been conceptualized by physicists throughout the 20th century. It has been suggested that quantum biology might play a critical role in the future of the medical world. [5] Early pioneers of quantum physics saw applications of quantum mechanics in biological problems. Erwin Schrödinger's 1944 book What is Life? discussed applications of quantum mechanics in biology. [6] Schrödinger introduced the idea of an "aperiodic crystal" that contained genetic information in its configuration of covalent chemical bonds. He further suggested that mutations are introduced by "quantum leaps". Other pioneers Niels Bohr, Pascual Jordan, and Max Delbruck argued that the quantum idea of complementarity was fundamental to the life sciences. [7] In 1963, Per-Olov Löwdin published proton tunneling as another mechanism for DNA mutation. In his paper, he stated that there is a new field of study called "quantum biology". [8]

Applications

Photosynthesis

Diagram of FMO complex. Light excites electrons in an antenna. The excitation then transfers through various proteins in the FMO complex to the reaction center to further photosynthesis. FMO Complex Simple Diagram.jpg
Diagram of FMO complex. Light excites electrons in an antenna. The excitation then transfers through various proteins in the FMO complex to the reaction center to further photosynthesis.

Organisms that undergo photosynthesis absorb light energy through the process of electron excitation in antennae. These antennae vary among organisms. For example, bacteria use ring-like antennae, while plants use chlorophyll pigments to absorb photons. Photosynthesis creates Frenkel excitons, which provide a separation of charge that cells convert into usable chemical energy. The energy collected in reaction sites must be transferred quickly before it is lost to fluorescence or thermal vibrational motion.

Various structures, such as the FMO complex in green sulfur bacteria, are responsible for transferring energy from antennae to a reaction site. FT electron spectroscopy studies of electron absorption and transfer show an efficiency of above 99%, [9] which cannot be explained by classical mechanical models like the diffusion model. Instead, as early as 1938, scientists theorized that quantum coherence was the mechanism for excitation energy transfer.

Scientists have recently looked for experimental evidence of this proposed energy transfer mechanism. A study published in 2007 claimed the identification of electronic quantum coherence [10] at −196 °C (77 K). Another theoretical study from 2010 provided evidence that quantum coherence lives as long as 300 femtoseconds at biologically relevant temperatures (4 °C or 277 K) . In that same year, experiments conducted on photosynthetic cryptophyte algae using two-dimensional photon echo spectroscopy yielded further confirmation for long-term quantum coherence. [11] These studies suggest that, through evolution, nature has developed a way of protecting quantum coherence to enhance the efficiency of photosynthesis. However, critical follow-up studies question the interpretation of these results. Single molecule spectroscopy now shows the quantum characteristics of photosynthesis without the interference of static disorder, and some studies use this method to assign reported signatures of electronic quantum coherence to nuclear dynamics occurring in chromophores. [12] [13] [14] [15] [16] [17] [18] A number of proposals emerged trying to explain unexpectedly long coherence. According to one proposal, if each site within the complex feels its own environmental noise, the electron will not remain in any local minimum due to both quantum coherence and thermal environment, but proceed to the reaction site via quantum walks. [19] [20] [21] Another proposal is that the rate of quantum coherence and electron tunneling create an energy sink that moves the electron to the reaction site quickly. [22] Other work suggested that geometric symmetries in the complex may favor efficient energy transfer to the reaction center, mirroring perfect state transfer in quantum networks. [23] Furthermore, experiments with artificial dye molecules cast doubts on the interpretation that quantum effects last any longer than one hundred femtoseconds. [24]

In 2017, the first control experiment with the original FMO protein under ambient conditions confirmed that electronic quantum effects are washed out within 60 femtoseconds, while the overall exciton transfer takes a time on the order of a few picoseconds. [25] In 2020 a review based on a wide collection of control experiments and theory concluded that the proposed quantum effects as long lived electronic coherences in the FMO system does not hold. [26] Instead, research investigating transport dynamics suggests that interactions between electronic and vibrational modes of excitation in FMO complexes require a semi-classical, semi-quantum explanation for the transfer of exciton energy. In other words, while quantum coherence dominates in the short-term, a classical description is most accurate to describe long-term behavior of the excitons. [27]

Another process in photosynthesis that has almost 100% efficiency is charge transfer, again suggesting that quantum mechanical phenomena are at play. [18] In 1966, a study on the photosynthetic bacteria Chromatium found that at temperatures below 100 K, cytochrome oxidation is temperature-independent, slow (on the order of milliseconds), and very low in activation energy. The authors, Don DeVault and Britton Chase, postulated that these characteristics of electron transfer are indicative of quantum tunneling, whereby electrons penetrate a potential barrier despite possessing less energy than is classically necessary. [28]

Seth Lloyd is also notable for his contributions to this area of research.

DNA mutation

Deoxyribonucleic acid, DNA, acts as the instructions for making proteins throughout the body. It consists of 4 nucleotides guanine, thymine, cytosine, and adenine. [29] The order of these nucleotides gives the “recipe” for the different proteins.

Whenever a cell reproduces, it must copy these strands of DNA. However, sometimes throughout the process of copying the strand of DNA a mutation, or an error in the DNA code, can occur. A theory for the reasoning behind DNA mutation is explained in the Lowdin DNA mutation model. [30] In this model, a nucleotide may change its form through a process of quantum tunneling. [31] Because of this, the changed nucleotide will lose its ability to pair with its original base pair and consequently changing the structure and order of the DNA strand.

Exposure to ultraviolet lights and other types of radiation can cause DNA mutation and damage. The radiations also can modify the bonds along the DNA strand in the pyrimidines and cause them to bond with themselves creating a dimer. [32]

In many prokaryotes and plants, these bonds are repaired to their original form by a DNA repair enzyme photolyase. As its prefix implies, photolyase is reliant on light in order to repair the strand. Photolyase works with its cofactor FADH, flavin adenine dinucleotide, while repairing the DNA. Photolyase is excited by visible light and transfers an electron to the cofactor FADH-. FADH- now in the possession of an extra electron gives the electron to the dimer to break the bond and repair the DNA. This transfer of the electron is done through the tunneling of the electron from the FADH to the dimer. Although the range of the tunneling is much larger than feasible in a vacuum, the tunneling in this scenario is said to be “superexchange-mediated tunneling,” and is possible due to the protein's ability to boost the tunneling rates of the electron. [30]

Vibration theory of olfaction

Olfaction, the sense of smell, can be broken down into two parts; the reception and detection of a chemical, and how that detection is sent to and processed by the brain. This process of detecting an odorant is still under question. One theory named the “shape theory of olfaction” suggests that certain olfactory receptors are triggered by certain shapes of chemicals and those receptors send a specific message to the brain. [33] Another theory (based on quantum phenomena) suggests that the olfactory receptors detect the vibration of the molecules that reach them and the “smell” is due to different vibrational frequencies, this theory is aptly called the “vibration theory of olfaction.”

The vibration theory of olfaction, created in 1938 by Malcolm Dyson [34] but reinvigorated by Luca Turin in 1996, [35] proposes that the mechanism for the sense of smell is due to G-protein receptors that detect molecular vibrations due to inelastic electron tunneling, tunneling where the electron loses energy, across molecules. [35] In this process a molecule would fill a binding site with a G-protein receptor. After the binding of the chemical to the receptor, the chemical would then act as a bridge allowing for the electron to be transferred through the protein. As the electron transfers through and that usually would be a barrier for the electrons and would lose its energy due to the vibration of the molecule recently bound to the receptor, resulting in the ability to smell the molecule. (This "sentence" has no subject - someone please fix this clause.) [35] [36]

While the vibration theory has some experimental proof of concept, [37] [38] there have been multiple controversial results in experiments. In some experiments, animals are able to distinguish smells between molecules of different frequencies and same structure, [39] while other experiments show that people are unaware of distinguishing smells due to distinct molecular frequencies. [40] However, it has not been disproven, and has even been shown to be an effect in olfaction of animals other than humans such as flies, bees, and fish.[ citation needed ]

Vision

Vision relies on quantized energy in order to convert light signals to an action potential in a process called phototransduction. In phototransduction, a photon interacts with a chromophore in a light receptor. The chromophore absorbs the photon and undergoes photoisomerization. This change in structure induces a change in the structure of the photo receptor and resulting signal transduction pathways lead to a visual signal. However, the photoisomerization reaction occurs at a rapid rate, in under 200 femtoseconds, [41] with high yield. Models suggest the use of quantum effects in shaping the ground state and excited state potentials in order to achieve this efficiency. [42]

Quantum vision implications

Experiments have shown that the sensors in the retina of human eye is sensitive enough to detect a single photon. [43] Single photon detection could lead to multiple different technologies. One area of development is in quantum communication and cryptography. The idea is to use a biometric system to measure the eye using only a small number of points across the retina with random flashes of photons that “read” the retina and identify the individual. [44] This biometric system would only allow a certain individual with a specific retinal map to decode the message. This message can not be decoded by anyone else unless the eavesdropper were to guess the proper map or could read the retina of the intended recipient of the message. [45]

Enzymatic activity (quantum biochemistry)

Enzymes may use quantum tunneling to transfer electrons long distances. It is possible that protein quaternary architecture may have evolved to enable sustained quantum entanglement and coherence. [46] More specifically, they can increase the percentage of the reaction that occurs through hydrogen tunneling. [47] Tunneling refers to the ability of a small mass particle to travel through energy barriers. This ability is due to the principle of complementarity, which hold that certain objects have pairs of properties that cannot be measured separately without changing the outcome of measurement. Electrons have both wave and particle properties, so they can pass through physical barriers as a wave without violating the laws of physics. Studies show that long distance electron transfers between redox centers through quantum tunneling plays important roles in enzymatic activity of photosynthesis and cellular respiration. [48] [49] For example, studies show that long range electron tunneling on the order of 15–30 Å plays a role in redox reactions in enzymes of cellular respiration. [50] Without quantum tunneling, organisms would not be able to convert energy quickly enough to sustain growth. Even though there are such large separations between redox sites within enzymes, electrons successfully transfer in a generally temperature independent (aside from extreme conditions) and distance dependent manner. [47] This suggests the ability of electrons to tunnel in physiological conditions. Further research is needed to determine whether this specific tunneling is also coherent.

Magnetoreception

Magnetoreception refers to the ability of animals to navigate using the inclination of the magnetic field of the earth. [51] A possible explanation for magnetoreception is the entangled radical pair mechanism. [52] [53] The radical-pair mechanism is well-established in spin chemistry, [54] [55] [56] and was speculated to apply to magnetoreception in 1978 by Schulten et al.. The ratio between singlet and triplet pairs is changed by the interaction of entangled electron pairs with the magnetic field of the earth. [57] In 2000, cryptochrome was proposed as the "magnetic molecule" that could harbor magnetically sensitive radical-pairs. Cryptochrome, a flavoprotein found in the eyes of European robins and other animal species, is the only protein known to form photoinduced radical-pairs in animals. [51] When it interacts with light particles, cryptochrome goes through a redox reaction, which yields radical pairs both during the photo-reduction and the oxidation. The function of cryptochrome is diverse across species, however, the photoinduction of radical-pairs occurs by exposure to blue light, which excites an electron in a chromophore. [57] Magnetoreception is also possible in the dark, so the mechanism must rely more on the radical pairs generated during light-independent oxidation.

Experiments in the lab support the basic theory that radical-pair electrons can be significantly influenced by very weak magnetic fields, i.e. merely the direction of weak magnetic fields can affect radical-pair's reactivity and therefore can "catalyze" the formation of chemical products. Whether this mechanism applies to magnetoreception and/or quantum biology, that is, whether earth's magnetic field "catalyzes" the formation of biochemical products by the aid of radical-pairs, is undetermined for two reasons. The first is that radical-pairs may need not be entangled, the key quantum feature of the radical-pair mechanism, to play a part in these processes. There are entangled and non-entangled radical-pairs. However, researchers found evidence for the radical-pair mechanism of magnetoreception when European robins, cockroaches, and garden warblers, could no longer navigate when exposed to a radio frequency that obstructs magnetic fields [51] and radical-pair chemistry. To empirically suggest the involvement of entanglement, an experiment would need to be devised that could disturb entangled radical-pairs without disturbing other radical-pairs, or vice versa, which would first need to be demonstrated in a laboratory setting before being applied to in vivo radical-pairs.


Other biological applications

Other examples of quantum phenomena in biological systems include the conversion of chemical energy into motion [58] and brownian motors in many cellular processes. [59]

Biological Homing.

Biological homing is a theory that there is a long-range quantum mechanical force between complimentary pairs of biological molecules (60 Meggs WJ.  Biological homing: Hypothesis for a quantum effect that leads to the existence of life.  Medical Hypotheses 1998;51:503.506.

). Examples of complimentary pairs of biological molecules are enzymes and substrates, hormones and receptors, and antibodies and surface proteins on micro-organisms. A demonstration has been given if complimentary molecules have identical charge distributions, but with positive and negative charges reversed on the two molecules, the probability of quantum interaction is proportional to the square of the number of charges.

Related Research Articles

Fluorescence Emission of light by a substance that has absorbed light

Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, than the absorbed radiation. The most striking example of fluorescence occurs when the absorbed radiation is in the ultraviolet region of the spectrum, and thus invisible to the human eye, while the emitted light is in the visible region, which gives the fluorescent substance a distinct color that can be seen only when exposed to UV light. Fluorescent materials cease to glow nearly immediately when the radiation source stops, unlike phosphorescent materials, which continue to emit light for some time after.

Photosynthesis Biological process to convert light into chemical energy

Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. This chemical energy is stored in carbohydrate molecules, such as sugars and starches, which are synthesized from carbon dioxide and water – hence the name photosynthesis, from the Greek phōs, "light", and sunthesis, "putting together". In most cases, oxygen is also released as a waste product. Most plants, algae, and cyanobacteria perform photosynthesis; such organisms are called photoautotrophs. Photosynthesis is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth.

Photochemistry Sub-discipline of chemistry

Photochemistry is the branch of chemistry concerned with the chemical effects of light. Generally, this term is used to describe a chemical reaction caused by absorption of ultraviolet, visible light (400–750 nm) or infrared radiation (750–2500 nm).

Photosystem II First protein complex in light-dependent reactions of oxygenic photosynthesis

Photosystem II is the first protein complex in the light-dependent reactions of oxygenic photosynthesis. It is located in the thylakoid membrane of plants, algae, and cyanobacteria. Within the photosystem, enzymes capture photons of light to energize electrons that are then transferred through a variety of coenzymes and cofactors to reduce plastoquinone to plastoquinol. The energized electrons are replaced by oxidizing water to form hydrogen ions and molecular oxygen.

Photosystem I Second protein complex in photosynthetic light reactions

Photosystem I is one of two photosystems in the photosynthetic light reactions of algae, plants, and cyanobacteria. Photosystem I is an integral membrane protein complex that uses light energy to catalyze the transfer of electrons across the thylakoid membrane from plastocyanin to ferredoxin. Ultimately, the electrons that are transferred by Photosystem I are used to produce the high energy carrier NADPH. The combined action of the entire photosynthetic electron transport chain also produces a proton-motive force that is used to generate ATP. PSI is composed of more than 110 cofactors, significantly more than Photosystem II.

Chlorophyll <i>a</i> Chemical compound

Chlorophyll a is a specific form of chlorophyll used in oxygenic photosynthesis. It absorbs most energy from wavelengths of violet-blue and orange-red light, and it is a poor absorber of green and near-green portions of the spectrum. Chlorophyll does not reflect light but chlorophyll-containing tissues appear green because green light, diffusively reflected by structures like cell walls, becomes enriched in the reflected light. This photosynthetic pigment is essential for photosynthesis in eukaryotes, cyanobacteria and prochlorophytes because of its role as primary electron donor in the electron transport chain. Chlorophyll a also transfers resonance energy in the antenna complex, ending in the reaction center where specific chlorophylls P680 and P700 are located.

The vibration theory of smell proposes that a molecule's smell character is due to its vibrational frequency in the infrared range. This controversial theory is an alternative to the more widely accepted docking theory of olfaction, which proposes that a molecule's smell character is due to a range of weak non-covalent interactions between its protein odorant receptor, such as electrostatic and Van der Waals interactions as well as H-bonding, dipole attraction, pi-stacking, metal ion, Cation–pi interaction, and hydrophobic effects, in addition to the molecule's conformation.

CIDNP, often pronounced like "kidnip", is an nuclear magnetic resonance (NMR) technique that is used to study chemical reactions that involve radicals. It detects the non-Boltzmann nuclear spin state distribution produced in these reactions as enhanced absorption or emission signals.

Photodissociation, photolysis, or photodecomposition is a chemical reaction in which a chemical compound is broken down by photons. It is defined as the interaction of one or more photons with one target molecule. Photodissociation is not limited to visible light. Any photon with sufficient energy can affect the chemical bonds of a chemical compound. Since a photon's energy is inversely proportional to its wavelength, electromagnetic waves with the energy of visible light or higher, such as ultraviolet light, x-rays and gamma rays are usually involved in such reactions.

Photosynthetic reaction centre

A photosynthetic reaction center is a complex of several proteins, pigments and other co-factors that together execute the primary energy conversion reactions of photosynthesis. Molecular excitations, either originating directly from sunlight or transferred as excitation energy via light-harvesting antenna systems, give rise to electron transfer reactions along the path of a series of protein-bound co-factors. These co-factors are light-absorbing molecules such as chlorophyll and phaeophytin, as well as quinones. The energy of the photon is used to excite an electron of a pigment. The free energy created is then used to reduce a chain of nearby electron acceptors, which have progressively higher redox-potentials. These electron transfer steps are the initial phase of a series of energy conversion reactions, ultimately resulting in the conversion of the energy of photons to the storage of that energy by the production of chemical bonds.

A light-harvesting complex consists of a number of chromophores which are complex subunit proteins that may be part of a larger super complex of a photosystem, the functional unit in photosynthesis. It is used by plants and photosynthetic bacteria to collect more of the incoming light than would be captured by the photosynthetic reaction center alone. The light which is captured by the chromophores is capable of exciting molecules from their ground state to a higher energy state, known as the excited state. This excited state does not last very long and is known to be short-lived. Light-harvesting complexes are found in a wide variety among the different photosynthetic species. The complexes consist of proteins and photosynthetic pigments and surround a photosynthetic reaction center to focus energy, attained from photons absorbed by the pigment, toward the reaction center using Förster resonance energy transfer.

Spin chemistry is a sub-field of chemistry and physics, positioned at the intersection of chemical kinetics, photochemistry, magnetic resonance and free radical chemistry, that deals with magnetic and spin effects in chemical reactions. Spin chemistry concerns phenomena such as chemically induced dynamic nuclear polarization (CIDNP), chemically induced electron polarization (CIDEP), magnetic isotope effects in chemical reactions, and it is hypothesized to be key in the underlying mechanism for avian magnetoreception and consciousness.

Photoprotection is the biochemical process that helps organisms cope with molecular damage caused by sunlight. Plants and other oxygenic phototrophs have developed a suite of photoprotective mechanisms to prevent photoinhibition and oxidative stress caused by excess or fluctuating light conditions. Humans and other animals have also developed photoprotective mechanisms to avoid UV photodamage to the skin, prevent DNA damage, and minimize the downstream effects of oxidative stress.

Fenna–Matthews–Olson complex

The Fenna–Matthews–Olson (FMO) complex is a water-soluble complex and was the first pigment-protein complex (PPC) to be structure analyzed by x-ray spectroscopy. It appears in green sulfur bacteria and mediates the excitation energy transfer from light-harvesting chlorosomes to the membrane-embedded bacterial reaction center (bRC). Its structure is trimeric (C3-symmetry). Each of the three monomers contains eight bacteriochlorophyll a molecules. They are bound to the protein scaffold via chelation of their central magnesium atom either to amino acids of the protein or water-bridged oxygen atoms.

Graham R. Fleming is a Professor of Chemistry at the University of California, Berkeley and member of the Kavli Energy NanoScience Institute based at UCB.

Light-dependent reactions Photosynthetic reactions

In photosynthesis, the light-dependent reactions take place on the thylakoid membranes. The inside of the thylakoid membrane is called the lumen, and outside the thylakoid membrane is the stroma, where the light-independent reactions take place. The thylakoid membrane contains some integral membrane protein complexes that catalyze the light reactions. There are four major protein complexes in the thylakoid membrane: Photosystem II (PSII), Cytochrome b6f complex, Photosystem I (PSI), and ATP synthase. These four complexes work together to ultimately create the products ATP and NADPH.

The evolution of photosynthesis refers to the origin and subsequent evolution of photosynthesis, the process by which light energy is used to assemble sugars from carbon dioxide and water, releasing oxygen as a waste product. The process of photosynthesis was discovered by Jan Ingenhousz, a Dutch-born British physician and scientist, first publishing about it in 1779.

Light harvesting materials harvest solar energy that can then be converted into chemical energy through photochemical processes. Synthetic light harvesting materials are inspired by photosynthetic biological systems such as light harvesting complexes and pigments that are present in plants and some photosynthetic bacteria. The dynamic and efficient antenna complexes that are present in photosynthetic organisms has inspired the design of synthetic light harvesting materials that mimic light harvesting machinery in biological systems. Examples of synthetic light harvesting materials are dendrimers, porphyrin arrays and assemblies, organic gels, biosynthetic and synthetic peptides, organic-inorganic hybrid materials, and semiconductor materials. Synthetic and biosynthetic light harvesting materials have applications in photovoltaics, photocatalysis, and photopolymerization.

David Nathan Beratan is an American chemist and physicist, the R.J. Reynolds Professor of Chemistry at Duke University. He has secondary appointments in the departments of Physics and Biochemistry. He is the Director of the Center for Synthesizing Quantum Coherence, a NSF Phase I Center for Chemical Innovation.

Adiabatic electron transfer

Adiabatic electron-transfer is the basis of oxidation-reduction processes, which are ubiquitous in nature in both the inorganic and biological spheres. The mechanism of these reactions—the simplest of which proceed without making or breaking chemical bonds—remained unknown until the mid 1950s, when several independent theoretical studies showed that it was due to modulation of coupling between electronic and vibrational motions. According to his Royal Society election citation, Noel Hush's research in the area of homogeneous and heterogeneous electron transfer showed that electron transfer occurring during a collision between a molecule and either another molecule or else an electrode surface occurs adiabatically on a continuous potential-energy surface, and that electron transfer can occur by either optical or thermal mechanisms with the corresponding rates being closely connected.

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