Pigments and absorption spectra

Pigments are molecules with their own characteristic absorption spectra in response to light. The perceived color of the pigment depends upon the wavelengths of light that are not absorbed.

A chromophore is the moiety within the pigment molecule that is responsible for the molecule's color. The chromophore possesses two orbitals whose difference in energy falls within the light spectrum. Thus, a photon of incident light is able to excite an electron from its ground-state orbital to the excited state.

Chromophores typically exist as conjugated pi systems or metal complexes:
1. In conjugated pi systems, electron excitation occurs between pi orbitals spread across alternating single and double bonds. Examples of conjugate pi chromophores are retinenes, azo compounds, lycopene, β-carotene, and anthocyanins.
2. Metal complex chromophores possess share d-orbitals between transition metals (with incomplete d-shells) and ligands. Examples of such chromophores are the chlorophylls, hemoglobin, and hemocyanin.

Commonly, chromophores comprise four pyrrole rings;
a. open chain pyrroles without a metal atom: phytochromes and phycobilins, carotenoids
b. pyrroles arranged as a porphyrin ring with a central metal atom: chlorophylls, bacteriochlorophylls

Chlorophyll absorbs all wavelengths of visible light except green, which it reflects, producing the green color of leaves. Various chlorophylls and accessory pigments have characteristic absorption spectra. The action spectrum of photosynthesis relates to the relative electron-exciting effectiveness of different wavelengths of light.

When a pigment absorbs light energy, either:
a. energy is dissipated as heat, or
b. energy is re-emitted immediately at a longer wavelength (fluorescence), or
c. "exciton" energy is passed from one molecule of chlorophyll to another in the photosynthetic antenna, and
d. an energetic electron is ejected by a pair of chlorophylls at the reaction center, initiating the electron transport chain that generates concentration gradients and the energy-storage molecules employed by the Calvin cycle to generate glucose and starch.

Chlorophyll triggers the photosynthetic chemical reactions of 'c' and 'd' only when it is associated with proteins embedded in a membrane (as in a chloroplast) or with the membranous infoldings of photosynthetic prokaryotes such as Cyanobacteria and Prochlorobacteria.

Accessory pigments include chlorophyll b and chlorophylls c, d, and e in algae and protistans, plus xanthophylls, and carotenoids. Non-chlorophyll accessory pigments absorb light energy at wavelength that do not stimulate chlorophyll. The energy absorbed by accessory pigments is funnelled to the reaction center for conversion into chemical energy.



Beta-carotene is a yellow carotenoid pigment. Phycobilins are water-soluble pigments, so they are found in the cytoplasm, or in the stroma of the chloroplast. Phycolibins occur in Cyanobacteria (phycocyanin and phycoerythrin) and the "red algae", the Rhodophyta (phycoerythrin). Bacteriochlorophylls (Bchl) is slightly different chemically from plant chlorophyll – one of the porphyrin rings is saturated – and it absorbs light of longer wavelength (lower energy) than chlorophylls. The bacteriochlorophyll b of Rhodopseudomonas viridis absorbs light of wavelength 960 nm.

The ability to absorb some energy from the longer, more penetrating wavelengths probably confered an advantage to early photosynthetic algae below the upper zone of the sea (photic or euphotic or epipelagic). Depending upon clarity of water, the shorter, high energy wavelengths penetrate very little below 5 meters in sea water (euphotic zone).

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External link External link Pigments and absorption spectra

Antenna and Reaction Center

Highly simplified diagram of antenna system and reaction center (right).

A photon of light energy travels across the rings of the thylakoid membrane-embedded protein-chlorophyll-pigment complex until it reaches the closely-paired chlorophyll molecules of thereaction center, where it excites an electron which passes to an electron acceptor.

Theoretical and Computational Biophysics at UC Irvine: click image at left of page for audiovisual of light harvesting complexes & reaction centers of PSUs. Quantum Biology of the PSU .

PSI and PSII differ in wavelength of light absorbed and in the utilization of energy delivered to the electron acceptor. In the chloroplasts of green plants, transduced energy is utilized in the generation of ATP for PSII, and NADPH for PSI. Ultimately, the chemical energy of ATP and NADPH is employed in the production of glucose, which is stored in starch granules.

3D reaction center Rhodopsedoumonas viridis : External link Antenna and Reaction Center

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Bacteriochlorophylls

The chlorophylls of bacteria – bacteriochlorophylls – differ both chemically and in absortption spectra from those of cyanobacteria and chloroplasts.

Chemical differences involve the phytol side chain, groups attached to the porhyrin ring, and the saturation of one pyrrole subunit of the porphyrin ring. At right - bacteriochlorophyll a with superimposed (color) location of variable R groups. Image of bacteriochlorophyll-protein complex, Prosthecochloris Aestuarii.

Table ~ structure of bacteriochlorophylls : molecular diagrams chlorophyll proteins :

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Chlorophylls and accessory pigments

A space-fill model of chlorophyll a (left), and a ball and stick model of chlorophyll a (right). A magnesium ion (green) lies at the centre of the ring structure)

grey - carbon / white - hydrogen / blue - nitrogen / red - oxygen / green - magnesium

The porphyrin ring is a complex of four heterocyclic pyrrole rings, which chelates Mg (green area in ball and stick model at left). The electron cloud associated with the porphyrin ring is available to harness incident light.

.. Chime animation of Chlorophyll a spinning



A phytol side chain is attached to the porphyrin ring. This side chain anchors the molecule into the photosynthetic thylakoid membrane. Chlorophylls a and b differ only in the character of the R1 group attached to the Mg-porphyrin ring moiety of the molecule: -CH3 for chlorophyll a, and -COH for chlorophyll b. Bacteriochlorophylls possess different side chains and different groups attached to the porphyrin rings.

Chlorophyll a: green plants, algae, Cyanobacteria.
Chlorophyll b: green algae, plants
Chlorophyll b: dinoflagellates, photosynthetic Chromista

The overall reaction of photosynthesis is:
6H2O + 6CO2 --> C6H12O6+ 6O2

Although the reaction formula is simple, reaction mechanics of photosynthesis are complex.

See also: Structure and Reactions of Chlorophyll External link Chlorophylls and accessory pigments

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Carotenoids

The carotenoids are an important group of pigments in bacteria, algae and higher plants, where they function as accessory light-harvesting pigments covering regions of the visible spectrum not utilized by (bacterio)chlorophylls. The carotenoid pigments exhibit strong light absorption in the blue portion of the visible spectrum. For example, lutein has its maximum absorption at 450 nm, cryptoxanthin at 453 nm, and zeaxanthin at 454 nm.
Beta-carotene is made up of eight isoprene units, which are cyclized at each end.

As accessory pigments, carotenoids participate in photoinduced electron transfer processes – they cannot transfer sunlight energy directly to the photosynthetic pathway, but pass their absorbed energy to (bacterio)chlorophylls. Carotenoids also protect against excessive light by quenching both singlet and triplet states of (bacterio)chlorophylls. The carotenoids are brightly colored in the portion of the visible spectrum where their absorbency is low and wavelengths are transmitted or reflected (red to yellow). The yellow colour of many flowers is due to carotenoid-containing chromoplasts, which are usually devoid of chlorophyll.

Ball-stick model of beta-carotene (above).

The numerous compounds in the carotenoid group are tetraterpenes, containing 40 C-atoms in eight isoprene residues. Within the carotenoids are carotenes (pure carbohydrates without additional groups) and the xanthophylls (carotenoids containing oxygen). Oxyfunctionalization of various carotenoids leads to a large number of xanthophylls in which the function may be a carbonyl, epoxy, formyl, hydroxyl, methoxyl, or oxo group. The backbone of carotenoid chains comprises conjugated double bonds – alternating single and double carbon bonds – that forms a conjugated p-electron system. Beta-carotene is made up of eight isoprene units, which are cyclized at each end.

Carotenoids exhibit a diversity of function that is unmatched by any other classes of natural pigments. This is directly related to their unique spectroscopic properties, which result from the structure of the carotenoid molecule. Absorption in the blue portion of the electromagnetic spectrum results from transition to the second excited state S2. The fundamental laws of photophysics ensure that after being promoted to the S2, or other higher energy states, a carotenoid molecule rapidly relaxes to the lowest singlet state. The lifetime of the lowest singlet state is determined by the conjugation length of carotenoids and varies from 300 ps for short conjugated chains to ~1 ps for the longest.

The carotenoids spheroidene and rhodopin glucoside are found in the light-harvesting complexes 1 and 2 (LH1 and LH2) of purple bacteria, and the LHCII light-harvesting complex of plants. LHCII complexes also contain carotenoid species such as violaxanthin, lutein, neoxanthin, and zeaxanthin. The carbonyl carotenoids contribute a substantial part of Earth's photosynthetic CO2 fixation. Carbonyl carotenoids such as peridinin, fucoxanthin or siphonaxanthin, occur in various taxonomic groups of oceanic photosynthetic organisms, including the light-harvesting antennae of algae. Fucoxanthin confers a brown color to kelp and other brown algae, and to the diatoms.

The carotenoids provide a source of vitamin A Retinoids are a group of natural and synthetic analogues of retinal (vitamin A), and their activity is important during the development of the embryo and in postnatal life. The macula of the human retina contains high amounts of the xanthophyll carotenoids lutein and zeaxanthin. It is generally believed that these two carotenoids provide protection against age-related macular degeneration (AMD), which is the leading cause of blindness among the elderly. Many studies point to the health benefits of a diet rich in beta-carotene and other carotenoids, which are found in fruits and vegetables that are yellow, orange, or red in color. However, contrary to earlier expectations, not only do beta-carotene supplements not prevent lung cancer in people at high risk for the disease, they appear to increase rates of the disease, particularly among smokers. http://www.cancer.gov/clinicaltrials/results/final-CARET1204

External link Carotenoids

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Phycobilins

Phycobilins are complex photoreceptor pigments – open-chain tetrapyrroles that are structurally related to mammalian bile pigments. Phytochromes are phycobilin-protein pigments involved in floral induction. There are two classes of phycobilins and they occur only in Cyanobacteria and Rhodophyta. The phycobilin component is similar to the porphyrins without a metallic atom. Water-soluble phycobilin pigments are found in the stroma of the chloroplast. In at least two groups of algae, phycobiliproteins are aggregated in a highly ordered protein complex called a phycobilisome (PBS), making these phycobilins unique among photosynthetic pigments.

Phycobilisomes are attached to the cytosol (stromal) face of the thylakoid. Extending into the cytosol, the phycobilisomes consist of a cluster of phycobilin pigments including phycocyanin (blue) and phycoerythrin (red) attached by their phycobiliproteins. These particles serve as light-energy antennae for photosynthesis. Phycobilisomes preferentially funnel light energy into photosystem II for the splitting of water and generation of oxygen. While many photosynthetic eubacteria possess photosystem I to oxidize reduced molecules such as H2S, only Cyanobacteria have photosystem II. The evolution of photosystem II apparently occured in Cyanobacteria.

The bluish pigment phycocyanin is found in Cyanobacteria, giving them their misleading common name of "blue-green algae". Different species of cyanobacteria possess differing ratios of phyocyanin and phycoerythrin. Cyanobacteria such as Hammatoidea, Heterohormogonium, Albrightia, Scytonematopsis, Thalopophila, Myxocarcina and Colteronema confer colors from red to purple on thermal springs and geyser pools. The ratio of phycocyanin and phycoerythrin can be environmentally altered. Cyanobacteria which are raised in green light typically develop more phycoerythrin and become red. The same Cyanobacteria grown in red light become bluish-green. This reciprocal color change has been named 'chromatic adaptation’.

Phycoerythrin is an accessory photoreceptor pigment found in the Rhodophyta ("red algae"). Phycoerythrin is associated with chlorophyll in the Rhodophyta, and enables them to be photosynthetically efficient in deep water where blue light predominates. The longer wavelength red portion of the spectrum that activate green chlorophyll pigments do not penetrate the deeper water of the photic zone, so green algae cannot survive at depth where red algae thrive.

Three major classes of photosynthetic pigments occur among the algae: chlorophylls, carotenoids (carotenes and xanthophylls) and phycobilins. The phycobilins and the carotenoid peridinin are water soluble. In the Cryptophyta, the phycobilin pigments are found in the spaces between the thylakoids, not in phycobilisomes as they are in the Cyanobacteria and Rhodophyta. Alpha-carotene, and the xanthophyll, diatoxanthan, combine with the proteinaceous phycobilin pigments phycoerythrin and phycocyanin. Chlorophyll-a and chlorophyll-c1 are the main photosynthetic pigments of the Cryptophyta, and chlorophyll-b is never present.

The photosynthesizing ability of eukaryotes was made possible by one or more endosymbiotic associations between heterotrophic eukaryotes and photosynthetic prokaryotes (or their descendents). Several primary endosymbioses occurred between eukaryotes and blue green algae. In one of the lineages, the photosynthetic organism lost much of its genetic independence and became functionally and genetically integrated as plastids – chloroplasts within the host cell. At least two types of protists – chloroarachniophytes and cryptomonads –acquired 'plastids' by forming symbioses with eukaryotic algae. Such acquisitions are referred to as secondary symbioses.

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External links Phycobilins : Phycobiliproteins :