Organic Chemistry I For Dummies
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For many students of organic chemistry, it’s easy to become bogged down in the minutiae of organic molecules and their reactions and forget that organic compounds actually form the backbone of all living things.

For example, when learning about alkenes (carbon-carbon double bonds) and their properties, you learn that two stereoisomers are often possible — the cis isomer, where two substituents are oriented off the same side of the double bond, and the trans isomer, where the two substituents are oriented off the opposite side of the double bond. These cis and trans isomers do not interconvert at room temperature without some sort of chemical reaction taking place, so these cis and trans isomers represent different compounds.

Nature takes advantage of the three-dimensional differences between cis and trans isomers for double bonds in the chemistry of vision. Within the retinas of our eyes, we have photoreceptor cells (called rods and cones) that are responsible for detecting all the light that we see. Within these photoreceptor cells are a class of proteins called opsins, which are responsible for vision. Bound within these opsin proteins is a small organic light-absorbing molecule (or chromophore) called retinal. Retinal is a polyene organic compound, meaning that this molecule contains multiple alkene functional groups.

When a photon strikes this retinal chromophore and the light energy is absorbed by retinal, this light energy is used to cause one of the alkenes in retinal to undergo a cis to trans configuration change. This configuration change causes a change in the conformation (the three-dimensional shape) of the opsin protein, which in turn begins a cascade that leads to an electrical signal being sent down the optic nerve toward the visual cortex part of the brain. This electrical signal is then used by the brain to construct the visual image of what we’re seeing.

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Arthur Winter, PhD, is the author of the popular Organic Chemistry Help! website and Organic Chemistry I For Dummies. His professional focus is on the chemistry of magneto-organic materials.

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