Introduction, resources, and questions

Conjugated system in biology                                                                        Spring 2013


  • To be able to explain how conjugated systems lead to absorption of photons
  • To apply this explanation to the ability of rhodopsin to absorb light
  • To explain why particular opsin-retinal combinations can only absorb particular, narrow ranges of light
  • To be able to explain how the interaction between all-trans-retinal and opsin can be “tuned” to produce rhodopsin-like molecules that absorb a range of different wavelengths of light
  • To be able to provide a general explaination of how the phenomenon of light absorption leads to change inside cells in the retina (“phototransduction”)



Cells in the retina contain visual pigments:  macromolecules that absorb specific wavelengths of light. These visual pigments – also called photoreceptor molecules – are in the membranes of cells in the retina. Rhodopsin is an example of a photoreceptor molecule. It consists of a protein and a non-protein organic molecule called retinal.

 Read descriptions of how rhodopsin functions here:

Other links and images are included at the end of this documents as additional resources.

Chapter 15 in your text has a section on conjugated systems and absorption of light. Another great resource is this discussion of conjugated systems at chemguide.


Part I.

You must be able to respond to the questions below, and familiar with the topics listed. Your goal is to be able to read an article titled Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal, by Wang et al. (2012).

Here are a couple of places to start. These articles are descriptions of the research by Wang et al. (2012) that are written for a more general audience:

Redder Than Red, T. P. Sakmar. Science. 7 December 2012:  Vol. 338 no. 6112 pp. 1299-1300.  DOI: 10.1126/science.1231589

Scientists engineer a spectrum of artificial pigments to understand how animals see in color, R. Williams. The Scientist. December 6, 2012

Design and Discovery: Extreme Red Shift - Structure-guided mutagenesis of a protein-chromophore complex enables engineering of prediction-defying red shift. StructuralBiology Knowledgebase (SBKB). [doi:10.1038/sbkb.2012.123]

  • What does the protein component of rhodopsin look like at the molecular scale?
  • Where is rhodopsin in the cell?
  • What amino acid forms a “Schiff base” and creates a link between the protein and 11-cis-retinal
    • Why is the molecule retinal?
  • Why does 11-cis-retinal change shape when it absorbs a photon?
    • What role does this change in shape play in helping us see?
  • Why does the combination of opsin and 11-cis-retinal absorb only photons of a narrow range of energies?


Part II.

What hypothesis was tested by the authors of the following article?

Wang et al. (2012) Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal, Science 7 December 2012: 1340-1343. Supplementary material for this article is available in a separate pdf.

  • Describe details of the interaction between protein and alkene
  • How do these particular interactions lead to the ability of slightly different protein-chromophore combinations to absorb different colors of light?
    • Use your understanding of conjugation in polyenes, including the concepts of HOMO and LUMO, to help answer this question.
  • What do the authors mean by the phrase in their title “tuning electronic absorption”? What are they tuning, and how are they performing this tuning?
  • Use CN3D to create an illustration that helps show how the electronic absorption of the protein-chromophore combination was “tuned”

Examples of Schiff base in rhodopsin

Structural representations of retinal associated with opsin or opsin-like proteins

Single-letter amino acid abbreviations (find amino acid structures here)

Last modified: Thursday, April 18, 2013, 11:15 AM