Isoprenoid side chains

The isoprenoid side chains of quinones are biosynthesized mainly by the mevalonic acid pathway from acetyl-CoA. Another pathway to biosynthesizing isoprenoids is the so-called non-mevalonate ronte by which isopentenyldiphosphate (IPP) is formed from glyceraldehyde 3-phosphate and pyrnvate. The key molecule is the famesyl-diphosphate (FPP) that accepts other IPP molecules to form polyprenyl diphosphates. 

IUPAC-IUB Commission on Biochemical Nomenclature (CBN). Nomenclature of qui-nones with isoprenoid side-chains recommendations (1973). Arch. Biochim. Biophys. 1974, 165, 1-8. 

The role of ubiquinone (coenzyme Q, 4) in transferring reducing equivalents in the respiratory chain is discussed on p. 140. During reduction, the quinone is converted into the hydroquinone (ubiquinol). The isoprenoid side chain of ubiquinone can have various lengths. It holds the molecule in the membrane, where it is freely mobile. Similar coenzymes are also found in photosynthesis (plastoquinone see p. 132). Vitamins E and K (see p. 52) also belong to the quinone/hydroquinone systems. 

Nomenclature of quinones with isoprenoid side chains Eur. J. Biochem. (1975) 53, 15-18... 

Chemistry.—The chemical structures of several bacterial menaquinones (MKs) with partly saturated isoprenoid side-chains have been studied. Spectroscopic (u.v., i.r., m.s., and H n.m.r.) and chromatographic data have been recorded for the tetrahydro-MK8 and -MK9 mixture of some nocardioform and coryneform bacteria.The main component tetrahydro-MK9 has the second and third iso-prene residues from the quinone ring saturated, i.e. has structure (159), 2-... 

In addition to NAD and flavoproteins, three other types of electron-carrying molecules function in the respiratory chain a hydrophobic quinone (ubiquinone) and two different types of iron-containing proteins (cytochromes and iron-sulfur proteins). Ubiquinone (also called coenzyme Q, or simply Q) is a lipid-soluble ben-zoquinone with a long isoprenoid side chain (Fig. 19-2). The closely related compounds plastoquinone (of plant chloroplasts) and menaquinone (of bacteria) play roles analogous to that of ubiquinone, carrying electrons in membrane-associated electron-transfer chains. Ubiquinone can accept one electron to become the semi-quinone radical ( QH) or two electrons to form ubiquinol (QH2) (Fig. 19-2) and, like flavoprotein carriers, it can act at the junction between a two-electron donor and a one-electron acceptor. Because ubiquinone is both small and hydrophobic, it is freely diffusible within the lipid bilayer of the inner mitochondrial membrane and can shuttle reducing equivalents between other, less mobile electron carriers in the membrane. And because it carries both electrons and protons, it plays a central role in coupling electron flow to proton movement. 

All Parts of Ubiquinone Have a Function In electron transfer, only the quinone portion of ubiquinone undergoes oxidation-reduction the isoprenoid side chain remains unchanged. What is the function of this chain ... 

In 1955, R. A. Morton and associates in Liverpool announced the isolation of a quinone which they named ubiquinone for its ubiquitous occurrence.484 485 It was characterized as a derivative of benzoquinone attached to an unsaturated polyprenyl (isoprenoid) side chain (Fig. 15-24). In fact, there is a family of ubiquinones that from bacteria typically contains six prenyl units in its side chain, while most ubiquinones from mammalian mitochondria contain ten. Ubiquinone was also isolated by F. L. Crane and associates using isooctane extraction of mitochondria. These workers proposed that the new quinone, which they called coenzyme Q, might participate in electron transport. As is described in Chapter 18, this function has been fully established. Both the name ubiquinone and the abbreviation Q are in general use. A subscript indicates the number of prenyl units, e.g., Q10. Ubiquinones can be reversibly reduced to the hydro-quinone forms (Fig. 15-24), providing a basis for their function in electron transport within mitochondria and chloroplasts.486 490... 

Nomenclature of Quinones with Isoprenoid Side-Chains http //www.chem.qmul. ac. Lik/i upac/misc/q uinone. html... 

Iron protoporphyrin IX (heme) is found in the b-type cytochromes and in hemoglobin and myoglobin. In heme c, cysteine residues of the protein (R) are attached covalently by thioether links to the two vinyl (—CH=CH2) groups of protoporphyrin IX. Heme c is found in the c cytochromes. In heme A, which is found in the a cytochromes, a 15-carbon isoprenoid side chain is attached to one of the vinyls, and a formyl group replaces one of the methyls. 

Figure 14. Variation in the carbon number distribution of the bicyclic terpenoid sulfides as a function of depth as shown by the m/z =183 fragmentograms from the SIR-GC/MS experiment. All traces are normalized to the most abundant peak. The oils vary from a heavy Cretaceous oil (Lloydminster) to a light Devonian oil (Leduc). Increasing thermal maturity results in the gradual loss of the isoprenoid side chain until in the Leduc the C13 compound dominates the distribution. Note the intensity distribution of the peaks. Minima occur at C12, C17, and C23. (Reproduced from Ref. 10 with permission. Copyright 1986, Pergamon Journals Ltd.)...

Answer The long isoprenoid side chain makes ubiquinone very soluble in lipids and allows it to diffuse in the semifluid membrane. This is important because ubiquinone transfers electrons from Complexes I and II to Complex III, all of which are embedded in the inner mitochondrial membrane. 

Some amendments to the IUPAC-IUB rules for carotenoid nomenclature have been made, in particular to include the 7-ring end-group (1) and some C37 (trinor) carotenoids.1 Rules have also been presented for the nomenclature of quinones with isoprenoid side-chains.2... 

An important question is Are the cytokinins present in tRNA incorporated intact into tRNA, in a manner like all other nucleoside triphosphates that are polymerized in the synthesis of tRNA, or does the presence of the cytokinins result from alkylation (transfer of isoprenoid side chain) of existing adenosine moieties already present in preformed tRNA In fact, experimental evidence has been reported for both processes (21,22). But the amounts of actual incorporation were very small, and the observed incorporation may be merely the result of transcriptional errors. Meanwhile, the evidence for cytokinin moieties in tRNA arising by alkylation of specific adenosine residues in preformed tRNA is conclusive (23). 

Isoprenoids are one of the largest classes of natural products that comprise at least 35,000 reported members (48). Many of these compounds play crucial roles in human metabolism as hormones, vitamins (vitamins A, D, E and K), quinine-type cofactors of respiratory chain enzymes (ubiquinone), membrane constituents, and functionally important side chains of signal cascade proteins (Fig. 11). Chlorophyll (17, Fig. 2) and heme a (18) have isoprenoid side chains. 

Szkopinska A, Ubiquinone. Biosynthesis of quinone ring and its isoprenoid side chain. Intracellular localization. Acta Biochim. Polonica. 2000 47 469 80. 

We have already encountered several molecules that contain isoprenoid side chains. The C30 hydrocarbon side chain of vitamin K important molecule in clotting (Section 10.5,7). is built from 6 isoprene (C5) units. Coenzyme Q in the... 

The tocopherols and tocotrienols are generally not the major components of vegetable oil, but their presence is vital for stabilizing the unsaturated fatty acids of these oils against oxidative deterioration (39). Their structures are based on a chroman head with two rings, one phenolic and one heterocyclic, and a phytyl tails isoprenoid side chain at C-2. The phytyl tail is saturated in the case of... 

Figure 5. Chromanol ring and isoprenoid side chains in tocopherols, tocotrienols (n = 3), and plastochromanol-8 (n=8, R)=H, R2=CH3 ) in vegetable oils (for systematic names, see Table 6).

The respiratory complexes diffuse laterally in the membrane with diffusion coefficients of 8 X 10 °-2 X 10 cm s [81-83]. Cytochrome c and ubiquinone have been quoted to diffuse at a velocity (10 cm s ) comparable to that of phospholipid molecules [84,85]. However, the bulky isoprenoid side chain of Q may slow down its mobility [86] in chromatophores, which may be compared with mitochondria, a mobility of 10 cm s has been estimated [87]. Overfield and... 

---