Bacteria thermodynamics

Before we describe the chemistry of the compartments involved, note that like prokaryotes, a number of oxidative enzymes are found in the cytoplasm but they do not release damaging chemicals (see Section 6.10). We also observed that such kinds of kinetic compartments are not enclosed by physical limitations such as membranes. We have also mentioned that increased size itself makes for kinetic compartments if diffusion is restricted. In this section, we see many additional advantages of eukaryotes from those given in Section 7.4. How deceptive it can be to use just the DNA, the all-embracing proteome, metabolome or metallome in discussing evolution without the recognition of the thermodynamic importance of compartments and their concentrations These data could be useful both here and in simpler studies of single-compartment bacteria even in the analysis of species but not much information is available. 

Daughney CJ, Fein JB, Yee N (1998) A comparison of the thermodynamics of metal adsorption onto two common bacteria. Chem Geol 144 161-176... 

The bacteria in our example promote Reaction 18.7 at a rate given by Equation 18.15, the thermodynamically consistent form of the Monod equation,... 

We can expect the sulfide produced by the bacteria to react with the iron in solution to form mackinawite (FeS), a precursor to pyrite (FeS2). The mineral is not in the default thermodynamic database, so we add to the file the reaction... 

On the other hand, the uptake of colloidal iron has been studied in greater detail. For example, some bacteria have been demonstrated to reduce ferric oxide particles to increase iron bioavailability [341,342], As was observed in Section 5.2.4, Fe reaction kinetics with metal carriers are thought to be rate-limiting. In the presence of colloidal iron, the thermodynamic stability or... 

Kelly DP. 1999. Thermodynamic aspects of energy conservation by chemolithotrophic sulfur bacteria in relation to the sulfur oxidation pathways. Arch Microbiol 171 219-29. 

Biological reductive dissolution by Shewanella putrifaciens of Fe oxides in material from four Atlantic pleistocene sediments (ca. 1.5-41 g/kg Fe oxides) was compared with that of the synthetic analogues (ferrihydrite, goethite, hematite) (Zachara et al. 1998). In the presence of AQDS as an electron shuttle, the percentage of bio-reduc-tion of the three oxides was increased from 13.3 %(fh) 9.2%(gt) and 0.6%(hm) to 94.6% 32.8% and 9.9% with part of the Fe formed being precipitated as vivianite and siderite, but not as magnetite. The quinone was reduced to hydroquinone which in turn, and in agreement with thermodynamics, reduced the Fe as it had much better access to the oxide surface than did the bacteria themselves. 

A beauty of thermodynamics is that it is not concerned with the detailed processes, and its predictions are independent of such details. Thermodynamics predicts the extent of a reaction when equilibrium is reached, but it does not address or care about reaction mechanism, i.e., how the reaction proceeds. For example, thermodynamics predicts that falling tree leaves would decompose and, in the presence of air, eventually end up as mostly CO2 and H2O. The decomposition could proceed under dry conditions, or under wet conditions, or in the presence of bacteria, or in a pile of tree leaves that might lead to fire. The reaction paths and kinetics would be very different under these various conditions. Because thermodynamics does not deal with the processes of reactions, it cannot provide insight on reaction mechanisms. 

Thermodynamic considerations suggest that in oxygenated seawater, arsenic should exist almost entirely as arsenate (71). It was apparent from the early work on arsenic in seawater, however, that arsenite was also present in significant concentrations and could at times predominate over arsenate (7,8, 72, 73). Marine bacteria (74) and marine phytoplankton (75) were shown to reduce arsenate to arsenite, thereby providing an explanation for the observed As(III)/As(V) ratio in seawater. The compounds MMA and DMA also occur in seawater, generally as minor constituents (9, 34, 71, 76). The concentrations of As(III), MMA, and DMA are positively correlated with primary productivity,... 

Most nitroreductases found in bacteria to date fall into this type I category. Type I nitroreductive transformations may be limited by the first of two electron transfers in a tight sequence of one-electron transfers since the enzymatic rates correlate with the corresponding (ArN02) (see Eq. 14-32) values (Riefler and Smets, 2000). However, it has also been noted that the free energies of the one-electron and two-electron reductions correlate with one another, and therefore this thermodynamic data may not distinguish between the one- vs. two-electron possibilties (Nivinskas et al., 2001). 

Photosynthesis occurs only in plants, algae, and some bacteria, but all forms of life are dependent on its products. In photosynthesis, electromagnetic energy from the sun is used as the driving force for a thermodynamically unfavorable chemical reaction, the synthesis of carbohydrates from C02 and H20 (Equation E9.1). 

It may also be noted that the pE values indicate the thermodynamic possibility of N2 reduction accompanied by CH20 oxidation. This is the gross mechanism mediated by nonphotosynthetic nitrogen-fixing bacteria. 

Like the various forms of iron, NOM apparently serves as both bulk reductant and mediator of reduction as well as bulk reductant (recall section 2.2.2). NOM also can act as an electron acceptor for microbial respiration by iron reducing bacteria (26), thereby facilitating the catabolism of aromatic hydrocarbons under anaerobic conditions (103). In general, it appears that NOM can mediate electron transfer between a wide range of donors and acceptors in environmental systems (104,105). In this way, NOM probably facilitates many redox reactions that are favorable in a thermodynamic sense but do not occur by direct interaction between donor and acceptor due to unfavorable kinetics. 

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