Protons, movement

An asymmetric hydrogen bond is common even where a proton coordinates two equivalent anions. The rc-bond repulsive forces between two coordinated anions tend to prohibit a close X-H-X separation, so competition between the two equivalent anions for the shorter X-H bond may set up a double-well potential for the equilibrium proton position between the two coordinated anions. With oxide anions, an O-H-O separation greater than 2.4 A sets up a double-well potential and creates an asymmetric hydrogen bond, which we represent as O-H O. Although displacement toward one anion may be energetically equivalent to a displacement toward the other, one well is made deeper than the other by an amount AH, as a result of the motion of the proton from the centre of the bond. 

2p states (Potier, 1983). Formation of symmetric hydrogen bonds tends to occur with F ions or where two equivalent oxide ions are strongly polarised to the opposite side by neighbouring cations. The dioxonium ion, for example, consists of two water molecules bonded by a symmetric hydrogen bond, but the O-H-O bond angle may be bent by as much as 6°. 

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Fi re 12.6 Schematic diagram Illustrating the proton movements in the photocycle of bacteriorhodopsin. The protein adopts two main conformational states, tense (T) and relaxed (R). The T state binds trans-tetinal tightly and the R state binds c/s-retinal. (a) Stmcture of bacteriorhodopsin in the T state with hflus-retinal bound to Lys 216 via a Schiff base, (b) A proton is transferred from the Schiff base to Asp 85 following isomerization of retinal and a conformational change of the protein. 

Component Molecular Size Number of Peptide Subunits Prosthetic Croups Topology in Inner Membrane Abundance in Inner Membrane (nmol per mg Protein. Data for Cardiac Mitochondria) Proton Movements (the Stoichiometry is Discussed in Appendix 3)... 

In Chapter H, we introduce a second definition of acids and bases, the Lewis definition, which focuses attention on electron movement rather than proton movement Until then, acid-base always means proton transfer."... 

C21-0030. The reaction between CO2 and H2 O to form carbonic acid (H2 CO3) can be described in two steps formation of a Lewis acid-base adduct followed by Brcjmsted proton transfer. Draw Lewis structures illustrating these two steps, showing electron and proton movement by curved arrows. 

Quite apart from the molecular structure of the channel it must also allow proton movement in only one direction and a pumping mechanism. Stoeckenius 236 has proposed an ingenious means by which the Schiff base linkage of the protein and retinal performs both these functions. 

The proton motion from Asp27 to 04 comprises a trajectory of approximately 0.6 A (Figure 6). There is a decrease in the free energy due to the surroundings, which corresponds to nearly 4.5 kcal/mol of stabilization by the protein. Further stabilization occurs as the 04-H04 bond rotates toward the N5 atom, which corresponds to a proton movement of about 1.4 A (Figure 6b)... 

Because proton movements are distinct, the general principles developed for the conduction of other ions in electrolytes need to be modified for protonic conduction. 

Since the membrane is stationary, only the water and protons move in the membrane system. The simplest membrane models either neglect the water movement or treat it as a known constant. For the proton movement, the simplest treatment is to use Ohm s law (eq 16 in differential form)... 

As mentioned, the reaction distribution is the main effect on the catalyst-layer scale. Because of the facile kinetics (i.e., low charge-transfer resistance) compared to the ionic resistance of proton movement for the HOR, the reaction distribution in the anode is a relatively sharp front next to the membrane. This can be seen in analyzing Figure 10, and it means that the catalyst layer should be relatively thin in order to utilize the most catalyst and increase the efficiency of the electrode. It also means that treating the anode catalyst layer as an interface is valid. On the other hand, the charge-transfer resistance for the ORR is relatively high, and thus, the reaction distribution is basically uniform across the cathode. This means... 

There are numerous cases of assisted diffusion but the simplest is that of proton movements in carbonic anhydrase. I do not think that I follow the problem that Professor Mayer has defined. 

Zhang and Styring421 discussed the possibility of a so-called low barrier H-bond between Yz and a nearby base, His (Dl-190), in which proton movement could also occur at very low temperatures. 

Intermediate-level review of the role of an internal chain of water molecules in proton movement through this protein. 

How is proton movement into the cell coupled with lactose uptake Extensive genetic studies of the lactose transporter have established that of the 417 residues in the protein, only 6 are absolutely essential for cotransport of H+ and lactose—some for lactose binding, others for proton transport. Mutation in either of two residues (Glu325 and Arg302 Fig. 11-43) results in a protein still able to catalyze facilitated diffusion of lactose... 

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. 

The mitochondria of plants have an externally oriented NADH dehydrogenase that can transfer electrons directly from cytosolic NADH into the respiratory chain at the level of ubiquinone. Because this pathway bypasses the NADH dehydrogenase of Complex I and the associated proton movement, the yield of ATP from cytosolic NADH is less than that from NADH generated in the matrix (Box 19-1). 

Like Complex III of mitochondria, cytochrome b6f conveys electrons from a reduced quinone—a mobile, lipid-soluble carrier of two electrons (Q in mitochondria, PQb in chloroplasts)—to a water-soluble protein that carries one electron (cytochrome c in mitochondria, plastocyanin in chloroplasts). As in mitochondria, the function of this complex involves a Q cycle (Fig. 19-12) in which electrons pass, one at a time, from PQBH2 to cytochrome bs. This cycle results in the pumping of protons across the membrane in chloroplasts, the direction of proton movement is from the stromal compartment to the thylakoid lumen, up to four protons moving for each pair of electrons. The result is production of a proton gradient across the thylakoid membrane as electrons pass from PSII to PSI. Because the volume of the flattened thylakoid lumen is small, the influx of a small number of protons has a relatively large effect on lumenal pH. The measured difference in pH between the stroma (pH 8) and the thylakoid lumen (pH 5) represents a 1,000-fold difference in proton concentration—a powerful driving force for ATP synthesis. 

FIGURE 19-55 Dual roles of cytochrome b6f and cytochrome c6 in cyanobacteria. Cyanobacteria use cytochrome bsf, cytochrome c6, and plastoquinone for both oxidative phosphorylation and photophosphorylation. (a) In photophosphorylation, electrons flow (top to bottom) from water to NADP+. (b) In oxidative phosphorylation, electrons flow from NADH to 02. Both processes are accompanied by proton movement across the membrane, accomplished by a Q cycle. 

FIGURE 19-58 Comparison of the topology of proton movement and ATP synthase orientation in the membranes of mitochondria, chloroplasts, and the bacterium E. coli. In each case, orientation of the proton gradient relative to ATP synthase activity is the same. 

One may arise by deprotonation of the reacting -NH2 group of the aminoacyl-tRNA (Eq. 29-1, step c). Conformational changes,387e which may be induced by proton movements, may also be encompassed within the array of pH-independent equilibria. 

Phosphorylation Is Driven by Proton Movements Electron Transport Creates an Electrochemical Potential Gradient for Protons across the Inner Membrane... 

The mechanism of proton translocation in complexes I and IV is not yet understood. Here, the electron-transfer reactions may cause protein conformational changes that open gates for proton movement first on one side of the membrane and then on the other. 

Proton movements do not have much effect on the equilibrium constant for the formation of ATP from bound ADP and P, on the synthase. Instead, they affect the release of ATP from the enzyme. The nucleotides evidently are bound in an environment that favors formation of ATP, and proton movements change the enzyme s conformation in such a way that the ATP is released. 

Proton movement back out through the thylakoid membrane is conducted by an ATP-synthase, and this movement drives the formation of ATP. The chloroplast ATP-synthase is structurally very similar to the mitochondrial ATP-synthase (see fig. 14.24). Its head-piece (CF ... 

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