How We See: Retinal and a Single Double Bond

Everything you have ever seen started with a remarkably small chemical event: a single carbon–carbon double bond in a small molecule called retinal twisting from one shape to another. It happens in less than a trillionth of a second, it can be triggered by just one photon, and it turns light into an electrical signal the brain can read. Vision is a story of photochemistry, geometric isomerism and molecular amplification, and it’s one of the most elegant pieces of chemistry in the body.

The light sensor: rhodopsin

The retina at the back of the eye contains two kinds of light-sensitive cells:

• Rods, about 90 million per eye, extremely sensitive and responsible for dim-light, black-and-white vision.
• Cones, about 5 million per eye, less sensitive but responsible for colour and fine detail.

Each rod contains stacks of membrane discs packed with a protein called rhodopsin (visual purple). Rhodopsin has two parts:

1. Opsin, a protein of 348 amino acids that snakes back and forth across the membrane seven times.
2. 11-cis-retinal, a small molecule tucked inside the protein.

Retinal is attached to opsin through a covalent bond: its aldehyde group (–CHO) reacts with the –NH₂ on the side chain of a lysine residue to form a Schiff base (an imine, C=N). In rhodopsin this nitrogen is protonated, giving C=NH⁺, and that positive charge matters a great deal for the colour of light the molecule absorbs.

Retinal: a conjugated chain

Retinal (C₂₀H₂₈O) is made from vitamin A. Its structure is a six-membered ring attached to a chain of carbons with alternating single and double bonds. This alternation creates a conjugated system: the π electrons are spread along the chain rather than locked in individual double bonds.

Conjugation lowers the energy gap between the highest occupied and lowest unoccupied molecular orbitals. The longer the conjugated chain, the smaller the gap and the longer the wavelength of light absorbed. Free retinal absorbs in the ultraviolet, around 380 nm. Once bound in rhodopsin, with the protonated Schiff base and the charged amino acids surrounding it, the absorption shifts to about 500 nm — green-blue light, right in the middle of the visible spectrum. The protein “tunes” the chromophore.

The key event: cis to trans

In the dark, retinal sits in rhodopsin with a cis double bond between carbons 11 and 12. The chain is bent at this point, and the kink fits neatly into the protein pocket.

When a photon of suitable energy is absorbed, an electron is promoted into an antibonding π* orbital. In that excited state, the C11=C12 bond loses much of its double-bond character, so rotation around it becomes possible. The molecule twists, and when it relaxes back to the ground state it’s in the all-trans form — a straight chain.

11-cis-retinal + photon → all-trans-retinal

This photoisomerisation is one of the fastest chemical reactions known in biology: the first photoproduct forms in about 200 femtoseconds (2 × 10⁻¹³ s). It’s also efficient: roughly two-thirds of absorbed photons cause isomerisation (a quantum yield of about 0.65).

Why does a change in one bond matter? Because the straight all-trans chain no longer fits the pocket that was shaped for the bent cis form. It’s like forcing a straightened paperclip into a slot made for a bent one. The strain pushes on the surrounding protein, and opsin rearranges through a series of intermediates over microseconds to milliseconds. The final active form is called metarhodopsin II.

This is geometric isomerism doing real work. If cis–trans isomerism has only ever been a textbook exercise for you, the rod cell is the best example of why it matters (see isotopes, ions, isomers and allotropes).

Amplification: from one photon to a signal

A single activated rhodopsin can’t send a signal to the brain on its own. The rod amplifies it through an enzyme cascade — a chain in which each step multiplies the effect of the last.

1. Transducin: metarhodopsin II activates a G protein called transducin by causing it to swap GDP for GTP. One activated rhodopsin can switch on dozens to hundreds of transducin molecules before it’s shut off.
2. Phosphodiesterase (PDE): each activated transducin switches on a PDE enzyme.
3. cGMP hydrolysis: PDE breaks down cyclic GMP (cGMP), a small messenger molecule. Each PDE can destroy on the order of a thousand cGMP molecules per second.
4. Ion channels close: in the dark, cGMP holds sodium channels in the rod’s membrane open, so positive ions flow in continuously (the “dark current”). As cGMP falls, the channels close.
5. Hyperpolarisation: the inside of the rod becomes more negative, and the cell reduces its release of the neurotransmitter glutamate. Downstream neurons read this drop as “light”.

It’s an unusual design: rods are most active in the dark and switch off in light. The amplification is so large that a rod can reliably respond to a single photon — one of the most sensitive detectors known.

Switching off

A detector that stays on is useless, so the cascade has off switches:

• Rhodopsin kinase adds phosphate groups to activated rhodopsin, and a protein called arrestin then binds and blocks it.
• Transducin has built-in GTPase activity, which slowly hydrolyses its GTP back to GDP and inactivates it.
• An enzyme called guanylate cyclase rebuilds cGMP, reopening the channels. Its activity is controlled by calcium levels, which fall when the channels close — a feedback loop that also helps the eye adapt to bright light.

Recycling retinal: the visual cycle

After activation, all-trans-retinal is released from opsin. It can’t be used again until it’s converted back to the 11-cis form. This happens mainly in the neighbouring retinal pigment epithelium:

1. All-trans-retinal is reduced to all-trans-retinol (vitamin A) by an enzyme using NADPH.
2. Retinol is esterified with a fatty acid.
3. An enzyme called an isomerohydrolase converts the ester into 11-cis-retinol.
4. This is oxidised back to 11-cis-retinal, which returns to the rod and recombines with opsin.

Rebuilding rhodopsin is relatively slow, which is why it takes around 20 to 30 minutes for your eyes to reach full sensitivity in the dark after bright light. Bright light “bleaches” much of the rhodopsin, and the visual cycle needs time to restore it.

Colour: same chromophore, different proteins

Humans with typical colour vision have three types of cone, each with its own opsin. All three use the same 11-cis-retinal. The difference is in the amino acids surrounding it, which alter the electric field around the conjugated chain and shift its absorption peak:

Receptor	Peak absorption (approx.)
S cones (“blue”)	420 nm
Rods (rhodopsin)	498 nm
M cones (“green”)	530 nm
L cones (“red”)	560 nm

The brain compares signals from the three cone types to work out colour. The genes for the M and L opsins sit next to each other on the X chromosome and are very similar, which is why red–green colour blindness is common and much more frequent in males.

Vitamin A and night blindness

Because retinal is made from vitamin A (retinol), which the body gets from animal foods or makes from β-carotene in orange and green vegetables, a shortage of vitamin A reduces the amount of rhodopsin in rods. The first symptom is night blindness — difficulty seeing in dim light. Severe deficiency damages the cornea and is still a major cause of preventable childhood blindness in parts of the world. Carrots won’t give you night vision beyond normal, but they do supply the raw material for it (see vitamins and their chemistry).

Common misconceptions

• “Light is absorbed by the whole protein.” It’s absorbed by retinal; the protein tunes the wavelength.
• “Light turns the rod on.” Light turns the rod’s dark current off; the signal is a decrease in neurotransmitter release.
• “Colour receptors use different pigments.” They all use 11-cis-retinal; only the opsin differs.
• “The isomerisation is slow chemistry.” It’s among the fastest reactions known, taking a few hundred femtoseconds.

Key takeaways

• Rhodopsin = opsin protein + 11-cis-retinal, joined through a protonated Schiff base.
• A photon causes cis → trans isomerisation at C11=C12 in about 200 fs, straining and activating the protein.
• A cascade (transducin → PDE → cGMP) amplifies the signal enormously, closing sodium channels and hyperpolarising the rod.
• Retinal is recycled via vitamin A in the visual cycle; dark adaptation reflects this rebuilding.
• Colour vision uses the same chromophore tuned to different wavelengths by different opsins.

For the light physics behind this, see photons and energy levels; for another pigment that captures light, see chlorophyll.