Physics of Life (2022) / Chapter Skim
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1 What Physics Problems Do Organisms Need to Solve?
1 What Physics Problems Do Organisms Need to Solve?
Pages 47-87
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From page 47... ...
, although it is more precise to say that evolution has selected organisms that achieve effective solutions to these problems. One of the central problems in biological physics is to turn qualitative notions of function into precise physical concepts.
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From page 48... ...
efficient energy theoretical ideas on conversion; nanoscale thermodynamics and linear and rotary motors. information on small scales and away from equilibrium.
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Parts of this understanding now are well established, providing a solid foundation for exploration of quantum effects in other biologi cal processes. From a historical perspective, the emergence of this understanding straddles the emergence of biological physics as a part of physics, and thus some of the crucial insights are seen now as part of mainstream biology, or perhaps part of biophysics as a biological science.
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From page 50... ...
More generally, photosynthetic organisms contain many more chlorophyll molecules than those involved directly in the chemical reactions driven by light, leading to the picture of a large "antenna" composed of many chlo rophylls, absorbing light and funneling energy to a "reaction center" that contains only a handful of these molecules. The problem of energy transfer in the photosynthetic antenna would recapture the attention of the physics community in the 21st century, with the first direct evidence that the process involves quantum mechanical coherence.
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From page 51... ...
These results are in marked contrast to typical chemical reactions, where rates are exponentially sensitive to temperature changes, following the Arrhenius law. This is a sign that quantum mechanical effects are important, and through the 1970s and 1980s, the biological physics community reached a relatively complete under standing of this.
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From page 52... ...
In large molecules such as the photosynthetic reaction center, there is a mix of high frequency and low frequency vibrations, and this can lead to the anomalous patterns of temperature dependence seen in this system. Thus, electron transfer in photosynthesis depends on an interplay of classical and quantum dynamics, at biologically relevant tem peratures.
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From page 53... ...
Efficient hydrogen transfer in biological molecules thus depends on an interplay between classical and quantum dynamics, in many ways parallel to the case of photosynthetic electron transfer. scales comparable to the initial electron transfer rate.
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. Even beyond its in trinsic importance, the physics of how the photosynthetic reaction center captures the energy of sunlight thus provides an entrance point for studying mechanisms of energy conversion that are shared across all forms of life on Earth.
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letters to nature Drosophila is weak in resting intact muscle, which is consistent with its relatively disordered appearance in electron micrographs21. tilting and release of myosin heads on actin target zones during the (A)
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. The biological physics community made a major effort to develop these single molecule manipulation experiments, which have now been exported to the broader community of biologists.
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They are driven by the world's smallest rotary engine, as schematized in Figure 1.4. As noted above, this motor is powered directly by the difference in chemical potential for protons FIGURE 1.3 Single molecule experiments help us to understand molecular motors, including force generation in muscle.
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From page 58... ...
showing the protein components of the motor and its anchoring in the cell membranes. Structure of core components (top right)
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From page 59... ...
This rotation is visible in single molecules that are fixed to a glass slide and running "backward," degrading ATP molecules to pump protons, as in Figure 1.5. Strikingly, unlike the linear motors myosin and kinesin, which have irreversible cycles and convert only a fraction of the energy from ATP into mechanical work, the ATP synthases are nearly 100 percent efficient; they are thus reversible and can be run in either direction (i.e., to consume or to produce ATP)
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From page 60... ...
Single molecule measurements have provided an extraordinarily direct and precise view of this information processing, as discussed in Chapter 2. As explained there, an important function for many of these molecules is "proofread ing," whereby the cell expends energy to achieve fidelity of information transmis sion beyond what would be possible from the equilibrium thermodynamic speci ficity of molecular interactions alone.
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From page 61... ...
The effort to explore these nanomachines has led to the development of new methods for single molecule measurement and manipulation, and to sharp new theoretical ideas about the relations between ther modynamics and information on small scales and away from equilibrium. These developments in biological physics are continuous with a broader renaissance in non-equilibrium statistical mechanics (Chapter 5)
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From page 62... ...
More profoundly, at very low Reynolds number, the viscous forces from the surrounding fluid balance the active forces that an organism generates in order to move, and this balance is enforced moment by moment. As a consequence, as the organism goes through one cycle of movement -- one rotation of a bacterial flagellum, one beat of a eukaryotic cilium, one full squirm or writhe
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From page 63... ...
SOURCE: Reproduced from E.M. Purcell, 1977, Life at low Reynolds number, American Journal of Physics 45:3, https://doi.org/10.1119/1.10903, with the permission of the American As sociation of Physics Teachers.
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. Both brains and leaves devote considerable resources to their vasculature, and the biological physics community has explored whether there might be general physi cal principles governing the distribution of these resources.
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. This theoretical work raises questions about how to characterize the "loopiness" of flow networks, and how such networks could develop.
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This example also illustrates how the questions asked by the biological physics community connect to questions asked by neurobiologists, engineers, control theorists, and others, as explored more fully in Part II of this report. Faced with the wide range of questions associated even with one movement, many physicists and biologists have made progress by constraining animal behavior so that some more limited set of movements could be studied more precisely.
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From page 67... ...
In many ways, the challenge ethologists raise is paradigmatic for modern biological physics: Can the complexity of a living system be tamed in its functional context? In the spirit of physicists' approaches to other complex prob lems, the goal is not just to build better tools for characterizing behavior, but to discover some underlying principles that govern these complex dynamics.
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From page 68... ...
These measurements reveal highly stereotyped responses on time scales of tens of milliseconds, which can be understood in terms of feedback from gyroscopic sensors called halteres. Perspective The motion of organisms through fluids -- from swimming bacteria to soar ing birds -- has long provided inspiration for the physics community, pushing our
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From page 69... ...
Altun, edi tor of www.wormatlas.org, https://en.wikipedia.org/wiki/Caenorhabditis_elegans, Creative Commons license CC BY-SA 2.5. understanding into new regimes and far eclipsing what human-made machines can accomplish.
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From page 70... ...
In fact, flies are equipped with a pair of small vibrating ing; and the search for physical principles governing more complex movements in CD ðαÞ ≈ CD ðα0 Þ þ C0D ðα0 Þ · ðα − α0 Þ, where α0 ¼ 45° and C0D ðα0 Þ organs called halteres that act as gyroscopic sensors (3)
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From page 71... ...
The absorption of one photon triggers a change in the struc ture of one rhodopsin molecule. As in photosynthesis, the first molecular events that follow photon absorption happen within trillionths of a second, so fast that these events compete with the loss of quantum mechanical coherence.
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From page 72... ...
Figure sive flash was four times brigh N CASCADE the electrical current for this r closed all the channels in the o Figure 4(c) shows superimposed d the rod outer segment as a and completely shut off the cur cident photons to a change in brief light flashes recorded from a Dim flashes produced respons igate the biophysical mecha- the average of 4–5 individual r lasted about 5 seconds.
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From page 73... ...
But a single molecule makes transitions between states at random times, and this randomness would be passed through the cascade, ultimately resulting in a highly variable current across the cell membrane. Such variability would make it impossible for cells to report reliably that different numbers of photons had been counted; in fact the current pulses in response to single photons are stereotyped and reproducible.
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From page 74... ...
The commonality of vesicle release mechanisms was crucial in the identification of the key protein molecules involved in the process, which was recognized by a Nobel Prize in 2013. Today, vesicle release is studied with the full range of experimental methods from the biological physics community, down to the single molecule level.
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A challenge for the coming decade is to determine whether these physical principles can predict the dynamics of signal processing at synapses in the retina more generally. Molecule Counting Photon counting is not the only example where biological signaling systems encounter fundamental physical limits to performance.
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Clément, 2020, 3D spatial exploration by E coli echoes motor temporal variability, Physical Review X 10:021004, Creative Commons License Attribution 4.0 International (CC BY 4.0)
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From page 77... ...
This detailed mecha nistic understanding was built using a combination of experimental methods from biology and physics, for example using genetic engineering to make fluorescent analogs of crucial molecular components and monitoring their interaction through measurements of energy transfer. These developments have gone hand in hand with increasingly precisely theoretical descriptions of the system, which have been used, for example, to address questions about the relations between energy dissipa tion and signal-to-noise ratio, which are much more general.
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FIGURE 1.13 The hair cells of the inner ear generate electrical signals in response to displacement of their "hairs" or stereocilia.
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These essentially parameter-free predictions are consistent with classical perceptual observations on "combination tones," and with direct measure ments on hair cells. Perspective This discussion of just three of the very many sensing systems that organisms possess has revealed deep principles.
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From page 80... ...
At the same time, pattern formation in living systems poses qualitatively new challenges, driving the search for new physical principles that can explain these beautiful phenomena. Allometry The first spatial structures of plants and animals that attracted human attention were the most macroscopic, and it would take into the 20th century to state the problem of how these are encoded by the underlying molecules.
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This approach from the biological physics commu nity parallels single molecule experiments aimed at understanding force generation in muscle (see Figure 1.3) , the synthesis of ATP from the flux of protons across a membrane (see Figure 1.5)
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From page 82... ...
117:10673, Creative Commons License CC BY-NC-ND 4.0.
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From page 83... ...
In many cases, including the well-studied Escherichia coli, the overall structure of the cell is supported in part by a polymer of protein molecules that wraps the cell, underneath its membrane, with a helical structure. This helix has a radius essentially equal to the radius of the cell itself, many hundreds of times larger than the diameter of the constituent protein molecules.
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From page 84... ...
de Boer, 1999, Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli, Proceedings of the National Academy of Sciences U.S.A. 96:4971, Creative Commons License CC BY-NC-ND 4.0.
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From page 85... ...
While the inanimate world provides many examples of pattern formation, some of which may remind us of patterns in living systems, these patterns do not scale. Perhaps this is one more example of life finding new physics.
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From page 86... ...
In presenting his work, Turing also gave voice to an approach that resonates strongly with many members of the biological physics community even today: A mathematical model of the growing embryo will be described. This model will be a simplification and an idealization, and consequently a falsification.
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From page 87... ...
It will be exciting to see how the examples of self-assembly and pattern formation guide the search for more general physical principles that address this challenge.
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