Biophysics
Biophysics applies the laws and methods of physics to the study of biological systems. It has only recently emerged as a subdivison of physics and as such, it represents one of the most specialized area of study in physics.
Its range of applicability is broad and seeks to gain understanding of every aspect of the biological world. Major areas of current interest are very diversified and include: bioenergetics, biophysical theory and modeling, cell biophysics, membrane, muscle and contractility, nucleic acid research, photobiophysics, imaging and supramolecular assemblies.
Today, it is becoming increasingly difficult to distinguish among biochemistry, genetics, biophysics, chemistry, and all the other sciences investigating biological phenomena since these almost always involve an overlap of approaches and conceptualizations. What is then the contribution of physics to biophysics? First, biophysics is responsible for the development of new methods of investigation to address the mechanisms of biological processes at every level. For example, the contribution of x-ray crystallography to understanding the structure and function of macromolecular assemblies as large as viruses or ribosomes is now acknowledged. Spectroscopy is also used to investigate structure-function relationships. Nuclear magnetic resonance (NMR) is a complementary approach that provides not only structural knowledge about biomolecules, but also provides insights in intramolecular dynamics. Electron microscopy and image processing also allows visualization of biological molecular structure. And this arsenal of physical methods is constantly supplemented by newer techniques
Second, physics, more than any other science, provides a conceptual framework of choice for dealing with biological phenomena. This is due to the universality of its laws on time and space time-scales compatible with the processes under investigation. Another contribution of physics lies in its ability to reduce complex systems to models that can be treated theoretically and compared with experiment. An example is provided by molecular biophysics that reduces biological phenomena to a set of algorithms forming a consistent whole into which a biomolecular assembly can fit. In this sense, it is similar to thermodynamics which also provides a logical framework for the occurrence of all physical phenomena described by a few laws.
Biophysics can then be considered as the interface between two apparently different views of nature, those of physics and those of biology. One of the interacting surfaces is turned towards biological investigations and the other towards the concepts, models and methods of physics. The biophysical interface then serves the purpose of providing quantitative interpretations for biological phenomena using the laws of physics, as shown by the following examples.
In the physics of the inanimate world, the first law of thermodynamics is concerned with the bulk behavior of matter. In biophysics, thermodynamics is used to predict the position of equilibrium in a system and the energy changes involves in biological processes such as enzyme catalyzed reactions, the mechanical work performed by muscles, the electrical work required to charge nerve membranes, the chemical work involved in the synthesis of biomolecules or in the emission of light by phosphorescent marine organisms. Another example is provided by the field of protein dynamics. As in the physical world, motion is of crucial importance at the molecular level of biology. Detailed studies of the atomic motions of proteins and nucleic acids are of relatively recent origin and it is now recognized that an appreciation of molecular flexibility and dynamics is essential to the understanding of the activity of biomolecules and to the design of new molecules with specific uses, such as drugs or vaccines.
A variety of biophysical methods are available to study the dynamics of biomolecules, one being molecular dynamics simulation, in which the classical equations of motion for the atoms in the sytem are solved by numerical techniques for time intervals ranging from the picosecond to the nanosecond range. The second method is normal mode analysis, in which the motion is described as a superposition of harmonic vibrations whose characteristics depend on the shape of the potential energy surface near an energy minimum. These theoretical approaches have the advantage that the models can be experimentally verified using vibrational spectroscopy techniques.
Another active area of biophysical research concerns the study of the interactions involving charged, polar and polarizable groups of atoms in proteins. This is important, because they are believed to be responsible for biomolecular recognition and assembly processes, as well as fundamental biochemical processes such as electron and energy transfer. Recent advances in understanding electric field effects lead to viewing proteins as dynamic assemblies that can control and reorganize their charge distribution, provided by their amino acid constituents. Since proteins are also dynamic systems undergoing constant fluctuations, the electric fields generated by a protein are also changing and it has been proposed that this is how proteins adopt the conformations required for their biological function.
It can be said that biophysics is now firmly at the forefront of the studies presently investigating the most important problems in biology, such as the protein folding problem (how do proteins fold their long amino acid sequence into their characteristic and functionally important structure?), the molecular recognition problem (how can an inhibitor bind to the HIV-1 virus?), the long-range electron-transfer problem (how are electrons transferred by protein active centers over long distances?), to name but a few.
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