Bacterial reactions

Figure Bl.15.16. Two-pulse ESE signal intensity of the chemically reduced ubiqumone-10 cofactor in photosynthetic bacterial reaction centres at 115 K. MW frequency is 95.1 GHz. One dimension is the magnetic field value Bq, the other dimension is the pulse separation x. The echo decay fiinction is anisotropic with respect to the spectral position.

BittI R, van der Est A, Kamlowski A, Lubitz W and Stehlik D 1994 Time-resolved EPR of the radical pair bacterial reaction centers. Observation of transient nutations, quantum beats and... 

Vos M H, Jones M R, Hunter C N, Breton J and Martin J-L 1994 Coherent nuclear dynamics at room temperature in bacterial reaction centers Proc. Natl Acad. Sci. USA 91 12 701-5... 

Jean J M, Chan C-K and Fleming G R 1988 Electronic energy transfer in photosynthetic bacterial reaction centers Isr. J. Chem. 28 169-75... 

Figure 12.13 Photosynthetic pigments are used hy plants and photosynthetic bacteria to capture photons of light and for electron flow from one side of a membrane to the other side. The diagram shows two such pigments that are present in bacterial reaction centers, bacteriochlorophyll (a) and ubiquinone (b). The light-absorbing parts of the molecules are shown in yellow, attached to hydrocarbon "tails" shown in green.

In the bacterial reaction center the photons are absorbed by the special pair of chlorophyll molecules on the periplasmic side of the membrane (see Figure 12.14). Spectroscopic measurements have shown that when a photon is absorbed by the special pair of chlorophylls, an electron is moved from the special pair to one of the pheophytin molecules. The close association and the parallel orientation of the chlorophyll ring systems in the special pair facilitates the excitation of an electron so that it is easily released. This process is very fast it occurs within 2 picoseconds. From the pheophytin the electron moves to a molecule of quinone, Qa, in a slower process that takes about 200 picoseconds. The electron then passes through the protein, to the second quinone molecule, Qb. This is a comparatively slow process, taking about 100 microseconds. 

Sulfides and disulfides can be produced by bacterial reactions in the marine environment. 2-Dimeth-ylthiopropionic acid is produced by algae and by the marsh grass Spartina alternifolia, and may then be metabolized in sediment slurries under anoxic conditions to dimethyl sulfide (Kiene and Taylor 1988), and by aerobic bacteria to methyl sulfide (Taylor and Gilchrist 1991). Further details are given in Chapter 11, Part 2. Methyl sulfide can also be produced by biological methylation of sulfide itself (HS ). Carbon radicals are not the initial atmospheric products from organic sulfides and disulfides, and the reactions also provide an example in which the rates of reaction with nitrate... 

Ceccarelli, M. Marchi, M., Simulation and modeling of the Rhodobacter spaeroides bacterial reaction center, J. Phys. Chem. B 2003,107, 1423-1431... 

The spectroscopy and dynamics of photosynthetic bacterial reaction centers have attracted considerable experimental attention [1-52]. In particular, application of spectroscopic techniques to RCs has revealed the optical features of the molecular systems. For example, the absorption spectra of Rb. Sphaeroides R26 RCs at 77 K and room temperature are shown in Fig. 2 [42]. One can see from Fig. 2 that the absorption spectra present three broad bands in the region of 714—952 nm. These bands have conventionally been assigned to the Qy electronic transitions of the P (870 nm), B (800 nm), and H (870 nm) components of RCs. By considering that the special pair P can be regarded as a dimer of two... 

In the study of the ultrafast dynamics of photosynthetic bacterial reaction centers, we are concerned with the photoinduced electron transfer [72]... 

Figure 3. The bacterial reaction-center protein model from Rhodopseudomonas sphaeroides the structure and positioning of components are highly speculative.

Prior to the introduction of ion-selective electrode techniques, in situ monitoring of free copper (II) in seawater was not possible due to the practical limitations of existing techniques (e.g., ligand competition and bacterial reactions). Ex situ analysis of free copper (II) is prone to experimental error, as the removal of seawater from the ocean can lead to speciation of copper (II). Potentially, a copper (II) ion electrode is capable of rapid in situ monitoring of environmental free copper (II). Unfortunately, copper (II) has not been used widely for the analysis of seawater due to chloride interference that is alleged to render the copper nonfunctional in this matrix [288]. 

B. A. Heller, D. Holten, C. Kirmaier, Effects of Asp Residues near the L-Side Pigments in Bacterial Reaction Centers , Biochemistry 1996, 35,15418-15427. 

Anaerobic bacterial reactions are much slower and produce only a fraction of the energy produced by aerobic activity. Alternate electron acceptors are generally consumed in a stepwise process ... 

As pointed out in Ref. [4], no entropy variation appears in the description given by the harmonic model, apart from the weak contribution arising from the frequency shifts of the oscillators. The applications of this model are then a priori restricted to redox reactions in which entropic contributions can be neglected. We shall see in Sect. 3 that the current interpretations of most electron transfer processes which take place in bacterial reaction centers are based on this assumption. 

Some authors have described the time evolution of the system by more general methods than time-dependent perturbation theory. For example, War-shel and co-workers have attempted to calculate the evolution of the function /(r, Q, t) defined by Eq. (3) by a semi-classical method [44, 96] the probability for the system to occupy state v]/, is obtained by considering the fluctuations of the energy gap between and 11, which are induced by the trajectories of all the atoms of the system. These trajectories are generated through molecular dynamics models based on classical equations of motion. This method was in particular applied to simulate the kinetics of the primary electron transfer process in the bacterial reaction center [97]. Mikkelsen and Ratner have recently proposed a very different approach to the electron transfer problem, in which the time evolution of the system is described by a time-dependent statistical density operator [98, 99]. 

It is evident that the preceding considerations do not apply to all biological electron transfer systems. Even in the bacterial reaction center, the transfer between the two quinones Qa Qbj which takes place over 18 A [18], is characterized in Rhodobacter sphaeroides by a large entropic contribution, which has been attributed to the high solvent exposure of Qg [126]. By using the activation energy value reported in Ref. [126], two very different X values may be deduced from Eq. (23) = 0.1 eV and Aj = 2.5 eV. The previous considerations... 

Fig. 4. Schematic representation of the bacterial reaction center (R. sphaeroides). The two branches are noted A, B in studies on R. viridis. Center-to-center distances are reported from Refs. [18, 21], The approximate position of the cytochrome is indicated. The simplified notations P, B, H are used in the text...

A recent study (Booth PJ, Crystall B, Giorgi LB, Barber J, Klug DR, Porter G (1990) Biochim. Biophys. Acta 1016 141) has shown that the free energy difference of the primary electron transfer is dominated by entropic contributions in photosystem II reaction centers as in bacterial reaction centers (Woodbury NWT, Parson WW (1984) Biochim. Biophys. Acta 767 345), so that the interpretation of the rate temperature dependenee should be revised. 

Until a recent x-ray diffraction study (17) provided direct evidence of the arrangement of the pigment species in the reaction center of the photosynthetic bacterium Rhodopseudomonas Viridis, a considerable amount of all evidence pertaining to the internal molecular architecture of plant or bacterial reaction centers was inferred from the results of in vitro spectroscopic experiments and from work on model systems (5, 18, 19). Aside from their use as indirect probes of the structure and function of plant and bacterial reaction centers, model studies have also provided insights into the development of potential biomimetic solar energy conversion systems. In this regard, the work of Netzel and co-workers (20-22) is particularly noteworthy, and in addition, is quite relevant to the material discussed at this conference. 

EPR studies of paramagnetic species occurring in the bacterial reaction centre (bRC) have been comprehensively reviewed in this series by Weber45. This chapter covered the literature up to 1999, and also gave an introduction into structure and function of this interesting membrane protein. Due to an enormous international research effort (for leading references see ref. 3, 46-52 many of the questions about the structure and function of the bRC were already answered by the end of the last millennium. Advanced EPR techniques have... 

J. Breton and A. Vermeglio (eds.), The Photosynthetic Bacterial Reaction Center -Structure and Dynamics , Plenum Press, New York and London, 1988. 

Zheng, Z., Dutton, P.L. and Gunner, M.R. (2010) The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers. Proteins Struct. Fund. Bioinform., 78 (12), 2638-2654. 

Fig. 1. A. Noise level expressed in milli optical density, obtained after 1 minute of data acquisition. B. Time dependent absorption change of the keto group of the primary donor of the bacterial reaction center, at 1685 cm 1 and 1715 cm 1 upon excitation at 600 nm, noise level 30 pOD, measured in the Lissajous scanner. The solid line through the data points is a fit with = 3.8 ps, t2 = 16 ps, t3 = 4 ns and t5 = oc. The time scale is linear up to 3 ps and logarithmic thereafter.

In Purple Bacterial Reaction Centers, Electrons Move from P870 to Bacteriopheophytin and Then to Quinones... 

Although the structures of the plant reaction centers are not yet known in detail, photosystem II reaction centers resemble reaction centers of purple bacteria in several ways. The amino acid sequences of their two major polypeptides are homologous to those of the two polypeptides that hold the pigments in the bacterial reaction center. Also, the reaction centers of photosystem II contain a nonheme iron atom and two molecules of plastoquinone, a quinone that is closely related to ubiquinone (see fig. 15.10), and they contain one or more molecules of pheophytin a and several... 

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