Fundamentals

Understanding life on a molecular level involves understanding the arrangements of those complex molecular structures, their conforational changes, and how their interactions are regulated and controlled.

Studying these processes will give insight into the fundamental structure and function of life's building blocks, and allow us to study diseases that occur when these carefully calibratd equiliibria fail and where regulation and control no longer function.

Biochemical and biophysical methods and instrumentation can help provide to our understanding, and can help up investigate these biological processes.

Let us review the basics of what we currently understand about matter and energy. This process allows one to visualize how we have come to our current methadology for studying biophysics.

Firstly, we know of the atomic nature of matter, in which atoms and molecules in motion will create heat, pressure, and diffusion. Furthermore, if we are able to measure these parameters, we can gain information of molecular number, size, mass, and shape.

Second, atoms and molecules have a mass and a charge; they will move in response to an external gravitational/centrifugal/electric field. For example, see gel electro-phoresis or gravity purification techniques. Rates of their mmovement in such fields will provide information on molecular mass, charge, size, and shape.

Now, onto electro-magnetic (EM) radiaation. EM Radiation is a light wave/particle (wave/particle duality), with a speed, amplituce, frequency, phase, polarization, absorbance and emission. In its wave form, EM radiation also experiences constructive and destructive interference.

Let us now combine our knownledge of matter and EM radiation (energy). Their interactions can be through elastic and inelastic scattering, absorptiona dn emission, resonance (relationship to electronic or nuclear structure), refraction, diffraction, and reflection.

So, if we use EM radiation or even thermal energy, we can interrogate biological matter to determine information on its structure, dynamics, and their interactions and distances from other biological matter.

Since frequencies of abosrobed or emitted radiation are determined by the electronic and nuclear structure, adn the local enviromament around the atom/molecule, this can lead us to spectroscopic methods.

The sponeneous loss of absorbed radiation will result in either heat or emitted light (fluoresnce or phosphoresnce), which can be used to probe distances by resonsnace transfer.

As a result, instrument can be used to generate the thermal/EM radiaton or centrifugal/electric fields that can be used to interrogate biological material.

Finally, equations and algorithms can quantitively describe how a change in a measureable parameter is related to otherwise undetectable atomic features.

Hydrodynamics

Hydrodyanmic parameters include quantities such as sedimentation and diffusion coefficients, rotational relaxation times, intrinsic viscoity, etc. These parameter allow us to determine how rapidly a molecule translates and rotates in solutions, and how they influence the solution. Additionally, when used in appropriate models, these parameters allow us to determine molecular weight, size, hydration, shape, flexability, conformation, and the degree of association of biological macromolecules.

For more information on hydrodyanmics as described by the inital founders, see:

• H.C. Berg. (1993) Random walks in biology. Princeton University Press, Princeton, NJ

• A. Einstein. (1905) On the motion of small particles suspended in a stationary liquid, as required by the molecular kinetic theory of heat. Annalen der Physik, 17 (8), pp. 549-560. https://doi.org/10.1051/jphysrad:01936007010100

• A. Fick. (1855) On liquid diffusion, Phil. Mag. and Jour. Sci., 10, pp. 31-39.

• F. Perrin. (1936). Brownian motion of an ellipsoid. II. Free rotation and depolarisation of fluorescence: Translation and diffusion of ellipsoidal molecules. J. Phys. Radium, 7 1, pp. 1-11

• T. Svedberg, and K. O. Pedersen. (1940). "The ultracentrifuge." The Ultracentrifuge.

• T. Svedberg. (1926). Nobel Prize Lecture.

• Historical Note of Poiseuille's Law.

There is also a lot of information based on the experimentaton developments that add to this field. These experiments include: dynamic light scattering, nonsecond fluorescence depolarization measurements, fluorescnece correlation spectroscopy, pulsed field gradient NMR, and AUC. But regardless of the technique that are several questions that we can ask about macromolecular structure and function:

1. How many? (value of n for interacting components)

2. How tightly? (binding constants or free energies)

3. Why? (chemical nature of binding site)

4. Where? (physical location of binding site)

5. What of it? (significance of the interaction?)