Molecular Mechanisms of Photosynthesis. Robert E. Blankenship
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pigments: structure and spectroscopy
The lifeblood of a photosynthetic organism is its pigments. Without them, light cannot be absorbed, and therefore energy cannot be stored. There are a remarkable number of pigments found in different photosynthetic organisms, and they serve a variety of functional roles. In this chapter, we will learn about the different types of pigments, with an emphasis on how the chemical and spectroscopic properties of the pigments are determined by their structures and the functions that they perform in the photosynthetic process. The chlorophylls are named a–f, and the bacteriochlorophylls a–g, in order of their discovery. In addition, we will consider carotenoids and bilins, the two other major classes of photosynthetic pigments.
Chlorophylls have long been investigated (Scheer, 1991; Grimm et al., 2006). The word chlorophyll was first used by Pelletier and Caventou in 1818 to describe the green pigments that are involved in photosynthesis in higher plants. Three Nobel prizes have been given at least in part for studies on the structural determination of chlorophyll. Richard Wilstätter was honored in 1915 for his work that established the major features of the chlorophyll structure, including the empirical formula and the presence of magnesium (Mg). Hans Fischer was awarded the 1930 Nobel prize in part because he determined the complete structure, and Robert Woodward received the 1965 prize in part for his work that culminated in the total synthesis of chlorophyll.
4.1 Chemical structures and distribution of chlorophylls and bacteriochlorophylls
The empirical chemical formula for chlorophyll a is C55H72N4O5Mg. This simple representation is entirely inadequate to convey the essential properties of this extraordinary molecule. The structural formula for chlorophyll a is shown in Fig. 4.1. It is a squarish planar molecule, about 10 Å on a side. A space‐filling model of chlorophyll a is shown in Fig. 4.2. The Mg atom in the center of the planar portion is coordinated to four nitrogen atoms. The nitrogens are each part of a substructural element of the molecule that is derived from pyrrole, a cyclic organic compound with a nitrogen atom in a five‐membered ring with four carbons. For this reason, chlorophylls and related compounds are often referred to as tetrapyrroles. A fifth ring is formed in the lower right corner, and a long hydrocarbon tail is attached to the lower left (in the standard representation). Chemically, the chlorophylls are related to the porphyrins, which are also tetrapyrroles, but the porphyrins are generally more symmetric molecules.
Figure 4.1 Numbering schemes for chlorophylls and bacteriochlorophylls. Chlorophyll a is shown, although the same basic numbering scheme applies to all chlorophyll‐type pigments. Left: the current IUPAC standard system. Right: the older Fischer numbering system. Hydrogen atoms are not shown.
Figure 4.2 Space filling model of chlorophyll a. Carbon is shown as black, hydrogen as white, oxygen as red, nitrogen as blue, and magnesium as orange.
The five rings in chlorophylls are lettered A through E, and the substituent positions on the macrocycle are numbered clockwise, beginning in ring A, as shown in Fig. 4.1, according to the officially recognized International Union of Pure and Applied Chemistry (IUPAC) nomenclature. An older nomenclature known as the Fischer system is also shown in Fig. 4.1. All of the older literature uses the Fischer nomenclature, so it is necessary to be conversant with both systems. In this book, the IUPAC system will be used exclusively.
By convention, the y molecular axis of all chlorophylls is defined as passing through the N atoms of rings A and C, with the x axis passing through the N atoms in rings B and D. The z axis is perpendicular to the plane of the macrocycle. An extensive delocalized π electron system extends over most of the molecule, with the exception of ring D, in which the C‐17–C‐18 double bond is reduced to a single bond. The tail is formed by condensation of four five‐carbon isoprene units and is then esterified to ring D. It is often called the phytyl tail, after the polyisoprenoid alcohol precursor phytol that is attached during biosynthesis. It is also sometimes called the isoprenoid tail.
Most of the chlorophylls are classified chemically as chlorins rather than porphyrins, by virtue of the reduced ring D. Most of the bacteriochlorophylls are similarly called bacteriochlorins, because of the reduction of both rings B and D. All chlorophylls and bacteriochlorophylls contain the extra ring E, which is called the isocyclic ring.
Most chlorophyll‐type pigments contain three chiral carbon atoms, C‐132, C‐17, and C‐18. Bacteriochlorophyll a contains two additional chiral centers, C‐7 and C‐8. In all cases, the stereochemical fidelity of the biosynthetic enzymes is extremely high, so the compounds found in cells are a single species and not mixtures of diastereomers (except as noted below).
Figure 4.3 Chemical structures of chlorophylls a, b, c, d, and f. R1, R2, etc. refer to ring substituents. In some cases, more than one possible group can be found at some positions.
The structures of all major chlorophylls and bacteriochlorophylls are shown in Figs. 4.3 and 4.4. The distribution of photosynthetic pigments in different classes of photosynthetic organisms is given in Table 4.1.
Figure 4.4 Chemical structures of bacteriochlorophylls a, b, c, d, e, f, and g.
4.1.1 Chlorophyll a
Chlorophyll a is found in all known eukaryotic photosynthetic organisms. Among prokaryotes, it is found in large quantities only in the cyanobacteria (including the prochlorophytes), although traces of chlorophyll a or minor variants are found in some anoxygenic bacteria, where it is thought to have an important function as an intermediate in the electron transport chain. Some prochlorophytes contain divinyl chlorophyll a, in which the substituent at the C‐8 position on ring B is vinyl instead of ethyl.
Table 4.1 Distribution of chlorophylls and bacteriochlorophylls
| Type of organism | Chl a | Chl b | Chl c | Chl d,f | BChl a |
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