Short Story ⬡ Biochemistry

The Landscape Created by Pigment Molecules

Understanding the origin of color and light energy harvesting through photosynthetic pigments, conjugated double bonds, and light absorption and reflection.

  • #pigments
  • #conjugated double bonds
  • #photosynthesis
  • #absorption spectrum
  • #excited state

"Why are leaves green?"

Toma was looking at trees outside the window.

"Chlorophyll," Rei answered. "Because it reflects green light."

Kana looked puzzled. "But isn't it used for photosynthesis?"

"Sharp," Rei smiled. "Reflecting green means not absorbing green."

"That's wasteful," Toma said.

"Evolutionary choice," Rei explained. "Red and blue light were energetically optimal."

Milia showed an absorption spectrum. High peaks in red and blue regions. Green is low.

"Pigments are selective," Rei continued. "Molecular structure determines which light is absorbed."

Kana wrote in her notebook. "What kind of structure?"

"Conjugated double bonds," Rei drew a molecule. "Double bonds alternating."

"What does that do?"

"Electrons spread across the whole molecule. Called delocalization."

Toma looked at the diagram. "Electrons can move freely?"

"To some extent. That narrows the energy level spacing."

Kana thought. "Energy levels?"

"The steps of energy electrons can take. When narrow, they can transition with visible light energy."

Milia drew a diagram. Ground state and excited state.

"When absorbing a photon, electrons jump to upper level," Rei explained.

"After jumping?"

"Several paths. Lost as heat, transfer energy to another molecule, or emit as light."

Toma asked. "Fluorescence?"

"Yes. When returning from excited state, emit light. Energy is slightly reduced, so longer wavelength."

Kana understood. "That's why fluorescence is more reddish than original color."

"Stokes shift," Rei acknowledged.

Milia showed another pigment. Carotenoid. Orange color.

"This absorbs blue-green and reflects red-orange," Rei explained.

"Autumn leaf color," Toma said.

"Yes. In autumn, chlorophyll breaks down and carotenoids stand out."

Kana was moved. "Color is chemistry."

"All chemistry," Rei said. "Visible color is evidence of molecular structure."

"Beautiful evidence."

"Exactly. But in photosynthesis, there's more meaning than color."

Milia showed her notebook. "Antenna complex"

"Multiple pigments cooperate," Rei explained. "Capture light across wide wavelength range and send to reaction center."

"Teamwork?" Toma said.

"Yes. One pigment alone is inefficient. Various pigments utilize entire sunlight."

Kana looked at the diagram. "Chlorophyll a, b, carotenoid, phycobilin..."

"Each absorbs different wavelengths," Rei continued. "Concentrate collected energy at reaction center P700 or P680."

"What's P?"

"Pigment. 700 and 680 are absorption wavelengths in nanometers."

Toma was impressed. "Well thought out."

"3 billion years of optimization," Rei said. "From cyanobacteria to plants, refined system."

Milia wrote a question. "Why are red algae red?"

"Phycoerythrin," Rei answered. "Absorbs green and yellow light. In deep sea, red light doesn't reach."

Kana understood. "Pigments adapted to environment."

"Yes. Shallow sea has chlorophyll, deep sea has phycobilin. Adaptation to light quality."

Toma looked outside the window. "The green world is actually rainbow-colored."

"Invisible colors carry energy," Rei said quietly.

Milia smiled.

"The landscape created by pigment molecules," Kana murmured.

"Selecting light, gathering energy," Toma continued.

"Beyond what's visible, there's a molecular world," Rei concluded.

The four gazed at the greenery outside. In the leaves, countless pigment molecules capture light and support life. Color is the most beautiful picture chemistry draws.