What Determines a Protein’s Color and Its Function?

The vibrant red of blood and the deep green of plant leaves are colors produced by proteins, the molecular machines that perform countless jobs inside living things. While these well-known examples are full of color, the vast majority of proteins are not. This contrast is determined by how these complex molecules are built and how they interact with light.

Why Most Proteins Are Colorless

The color of any substance is determined by which wavelengths of visible light it absorbs and which it reflects. Our eyes perceive the reflected light as color. Proteins are constructed from smaller building blocks called amino acids, linked together by chemical connections known as peptide bonds. These core components are the primary structures of every protein.

The chemical bonds within these components are very stable and absorb light in the ultraviolet (UV) spectrum, which is invisible to the human eye. Because these building blocks do not absorb light in the visible range, they do not produce any perceivable color.

As a result, a solution of purified protein in water will appear clear, much like salt dissolved in water. If that same protein solution were dried, the resulting substance would be a white powder. This colorless state is true for the overwhelming majority of proteins found across all forms of life.

The Origin of Color in Proteins

For a protein to have color, it must contain a specific component that can absorb visible light. This light-absorbing part of a molecule is called a chromophore. Most proteins gain their color not from their own amino acid structure, but by incorporating other molecules or atoms that act as chromophores, allowing them to interact with the visible light spectrum.

Many colored proteins rely on non-protein helper molecules, called prosthetic groups, which are frequently the source of the color. A classic example is hemoglobin, the protein that makes blood red. Hemoglobin’s color comes from a complex ring-like molecule called heme, which has an iron atom at its center. This heme group absorbs blue-green light, reflecting red light back to our eyes. Similarly, a class of proteins called flavoproteins appear yellow because they contain a flavin group that absorbs blue light.

Another source of color comes from proteins that directly bind to individual metal ions. Unlike hemoglobin, where the iron is part of a larger heme structure, some proteins bind metals without an elaborate molecular cage. Hemocyanin, a protein used by some invertebrates like octopuses and crabs to transport oxygen, is a prime example. When an oxygen molecule binds, the copper atoms change their electronic properties, causing the protein to turn a distinct blue.

In rare cases, a protein can generate color from its own structure without any external helper molecules or metal ions. The Green Fluorescent Protein (GFP), originally found in jellyfish, is a well-known example. Within GFP, three specific amino acids undergo a chemical reaction that requires oxygen. This reaction links the amino acids to form a new structure that functions as a chromophore, giving the protein its green fluorescence.

The Functional Role of Colored Proteins

A protein’s color is often directly linked to its biological function. The mechanisms that produce color, such as binding metal ions or containing light-absorbing groups, are frequently the same ones the protein uses to carry out its work, making the color a direct consequence of its molecular action.

For hemoglobin, the iron atom within the red-pigmented heme group is what binds to oxygen. As blood circulates and releases oxygen to the tissues, the electronic state of the iron atom changes slightly. This shift alters how the heme group absorbs light, causing the color to change from a bright scarlet red in arteries (oxygenated) to a deeper red in veins (deoxygenated). The red color is a byproduct of its oxygen-transporting capability.

In plants, the connection between color and function is also direct. Chlorophyll-binding proteins are green because the chlorophyll molecule they hold absorbs light in the red and blue parts of the spectrum for photosynthesis. The unused green light is reflected, which is why we see leaves as green. This captured light energy is then converted into chemical energy for the plant.

The Green Fluorescent Protein (GFP) is a unique case where its color has been repurposed by science. In the lab, its color is its function for researchers. Scientists can attach the gene for GFP to the gene of another, colorless protein they want to study. When the cell manufactures the target protein, it also produces GFP attached to it, allowing researchers to track the location and movement of their protein of interest within a living cell by observing its fluorescence.