FTIR difference spectroscopy provides a unique approach to study directly protonation/deprotonation events of carboxylic acids involved in the photochemical cycle of membrane proteins, such as the bacterial photosynthetic reaction center (RC). In this work, we review the data obtained by light-induced FTIR difference spectroscopy on the first electron transfer to the secondary quinone Q(B) in native RCs and a series of mutant RCs. We first examine the approach of isotope-edited FTIR spectroscopy to investigate the binding site of Q(B). This method provides highly specific IR vibrational fingerprints of the bonding interactions of the carbonyls of Q(B) and Q(B)(-) with the protein. The same isotope-edited IR fingerprints for the carbonyls of neutral Q(B) have been observed for native Rhodobacter sphaeroides RCs and several mutant RCs at the Pro-L209, Ala-M260, or Glu-L212/Asp-L213 sites, for which X-ray crystallography has found the quinone in the proximal position. It is concluded that at room temperature Q(B) occupies a single binding site that fits well the description of the proximal site derived from X-ray crystallography and that the conformational gate limiting the rate of the first electron transfer from Q(A)(-)Q(B) to Q(A)Q(B)(-) cannot be the movement of Q(B) from its distal to proximal site. Possible alternative gating mechanisms are discussed. In a second part, we review the contribution of the various experimental measurements, theoretical calculations, and molecular dynamics simulations which have been actively conducted to propose which amino acid side chains near Q(B) could be proton donors/acceptors. Further, we show how FTIR spectroscopy of mutant RCs has directly allowed several carboxylic acids involved in proton uptake upon first electron transfer to Q(B) to be identified. Owing to the importance of a number of residues for high efficiency of coupled electron transfer reactions, the photoreduction of Q(B) was studied in a series of single mutant RCs at Asp-L213, Asp-L210, Asp-M17, Glu-L212, Glu-H173, as well as combinations of these mutations in double and triple mutant RCs. The same protonation pattern was observed in the 1760-1700 cm(-1) region of the Q(B)(-)/Q(B) spectra of native and several mutant (DN-L213, DN-L210, DN-M17, EQ-H173) RCs. However, it was drastically modified in spectra of mutants lacking Glu at L212. The main conclusion of this work is that in native RCs from Rb. sphaeroides, Glu-L212 is the only carboxylic acid residue that contributes to proton uptake at all pH values (from pH 4 to pH 11) in response to the formation of Q(B)(-). Another important result is that the residues Asp-L213, Asp-L210, Asp-M17, and Glu-H173 are mostly ionized in the Q(B) state at neutral pH and do not significantly change their protonation state upon Q(B)(-) formation. In contrast, interchanging Asp and Glu at L212 and L213 (i.e., in the so-called swap mutant) led to the identification of a novel protonation pattern of carboxylic acids: at least four individual carboxylic acids were affected by Q(B) reduction. The pH dependence of IR carboxylic signals in the swap mutant demonstrates that protonation of Glu-L213 occurred at pH >5 whereas that of Asp-L212 occurred over the entire pH range from 8 to 4. In native RCs from Rhodobacter sphaeroides, a broad positive IR continuum around 2600 cm(-1) in the Q(B)(-)/Q(B) steady-state FTIR spectrum in (1)H(2)O was assigned to delocalized proton(s) in a highly polarizable hydrogen-bonded network. The possible relation of the IR continuum band to the carboxylic acid residues and to bound water molecules involved in the proton transfer pathway was investigated by testing the robustness of this band to different mutations of acids. The presence of the band is not correlated with the localization of the proton on Glu-L212. The largest changes of the IR continuum were observed in single and double mutant RCs where Asp-L213 is not present. It is proposed that the changes observed in the mutant RCs with respect to native RCs reflect the specific role of bound protonated water molecule(s) located in the vicinity of Asp-L213 and undergoing hydrogen-bond changes in the network.