Mechanism of Bond Energy Absorption

[SonOfADunn]

When scientists analyze proteins (chains of amino acids), often times light spectroscopy is used. Light is passes through a cuvet containing dissolved protein, and the absorption is measured. My question is: How do bonds absorb energy? What is the actual mechanism?

I have been told that the wavelength of the bond must match that of the radiation being absorbed, but I do not understand this explanation. If the wavelengths match, would we note expect amplification of the bond (constructive interference)? And what does it mean to speak of bonds as "wavelengths"? Is that simply another way of referring to the length of the bond?

 

[SonOfADunn]

Seem to have answered my own question (partially):
http://en.wikipedia.org/wiki/Woodward-Fieser_rules
http://en.wikipedia.org/wiki/Chromophore

But I still don't understand why a molecule seems to act as a single entity and each atom doesn't absorb its own characteristic wavelength. Can someone explain that to me?

 

[haruspex]

Light is emitted in consequence of a net acceleration of charge. Conversely, absorption drives a net acceleration of charge.
Accelerating a neutral atom is not a net acceleration of charge - the +ve and -ve charge accelerations cancel.

An atom can absorb if the wavelength matches an energy gap between one of its electrons and a higher available energy; in the extreme, any energy sufficient to ionise the atom will work.
A molecule can absorb by a change to the bonding of its atoms. H2O can absorb some IR wavelengths because H2O is polar and there are various possible vibration states. O2 and N2 are not polar, so cannot absorb in this way (no net acceleration of charge).

In short, the molecule as a whole can offer energy gaps not offered by its constituent atoms.