Allophycocyanin vs. Phycocyanin

What's the Difference?

Allophycocyanin and Phycocyanin are both types of phycobiliproteins found in cyanobacteria and certain types of algae. They play crucial roles in the process of photosynthesis by capturing light energy and transferring it to chlorophyll for conversion into chemical energy. While both pigments have a similar structure and function, there are some key differences between them. Allophycocyanin absorbs light at longer wavelengths, appearing red or orange, while Phycocyanin absorbs light at shorter wavelengths, giving it a blue or green color. Additionally, Allophycocyanin is typically found in higher concentrations in cyanobacteria, whereas Phycocyanin is more abundant in algae. Overall, these pigments contribute to the vibrant colors seen in cyanobacteria and algae and are essential for their survival and growth.


StructureHexameric proteinHexameric protein
Found inCyanobacteria, red algaeCyanobacteria, red algae
Wavelength absorption650-660 nm620-640 nm

Further Detail


Allophycocyanin and phycocyanin are two types of phycobiliproteins found in cyanobacteria and certain algae. These pigments play a crucial role in photosynthesis, capturing light energy and transferring it to chlorophyll for the production of carbohydrates. While both allophycocyanin and phycocyanin share similarities in their structure and function, they also possess distinct attributes that set them apart. In this article, we will explore and compare the various characteristics of allophycocyanin and phycocyanin.


Allophycocyanin and phycocyanin are both composed of protein subunits that bind chromophores, which are responsible for their characteristic blue-green color. However, their specific structures differ slightly. Allophycocyanin consists of two types of subunits, α and β, arranged in a hexameric structure. Each subunit contains a covalently attached phycocyanobilin chromophore. On the other hand, phycocyanin is composed of only one type of subunit, α, and forms a trimeric structure. Each α subunit also carries a phycocyanobilin chromophore. These structural differences contribute to variations in their spectral properties and stability.

Spectral Properties

When it comes to spectral properties, allophycocyanin and phycocyanin exhibit distinct absorption and fluorescence characteristics. Allophycocyanin has a higher absorption peak around 650-660 nm, allowing it to absorb light more efficiently in the red region of the spectrum. This property makes allophycocyanin particularly useful in applications that require red-shifted fluorescence, such as flow cytometry. Phycocyanin, on the other hand, has a lower absorption peak around 620-640 nm, making it more suitable for blue-shifted fluorescence detection. These differences in absorption spectra make allophycocyanin and phycocyanin complementary tools in various research applications.


Both allophycocyanin and phycocyanin serve as light-harvesting pigments in photosynthetic organisms. They capture light energy and transfer it to chlorophyll molecules, which then convert it into chemical energy through photosynthesis. However, allophycocyanin and phycocyanin have different roles within the light-harvesting complex. Allophycocyanin is primarily involved in capturing and transferring light energy from phycobilisomes to the reaction centers, where the actual photosynthesis takes place. Phycocyanin, on the other hand, acts as a linker pigment, connecting the phycobilisomes to the photosystem complexes. This distinction in function highlights the cooperative nature of these pigments in optimizing light absorption and energy transfer.


Due to their unique properties, allophycocyanin and phycocyanin find applications in various fields of research and industry. Allophycocyanin's red-shifted fluorescence makes it particularly valuable in flow cytometry, where it can be used as a fluorescent label for cell sorting and analysis. Its high quantum yield and photostability also make it suitable for fluorescence microscopy and immunoassays. Phycocyanin, with its blue-shifted fluorescence, is commonly used in applications such as protein labeling, immunohistochemistry, and as a natural food colorant. Its antioxidant and anti-inflammatory properties have also led to its use in nutraceuticals and cosmetics.


Stability is an important consideration when working with phycobiliproteins. Both allophycocyanin and phycocyanin are sensitive to factors such as temperature, pH, and light exposure. However, allophycocyanin generally exhibits higher stability compared to phycocyanin. This increased stability is attributed to its hexameric structure and the presence of two different subunits. The additional subunit in allophycocyanin provides structural stability and protects the chromophores from degradation. Phycocyanin's trimeric structure, while less stable, offers advantages in terms of solubility and ease of purification. The stability differences between allophycocyanin and phycocyanin should be considered when selecting the appropriate pigment for specific applications.


In conclusion, allophycocyanin and phycocyanin are two important phycobiliproteins that play crucial roles in light harvesting and energy transfer in photosynthetic organisms. While they share similarities in their function and chromophore composition, their structural differences result in distinct spectral properties, stability, and applications. Allophycocyanin's hexameric structure, red-shifted absorption, and higher stability make it well-suited for certain fluorescence-based techniques, while phycocyanin's trimeric structure and blue-shifted absorption offer advantages in other applications. Understanding the attributes of allophycocyanin and phycocyanin allows researchers to harness their unique properties for a wide range of scientific and industrial purposes.

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