We have examined the pre-steady state reduction kinetics of the Saccharomyces cerevisiae cytochrome bc 1 complex by menaquinol in the presence and absence of endogenous ubiquinone to elucidate the mechanism of triphasic cytochrome b reduction. With cytochrome bc 1 complex from wild type yeast, cytochrome b reduction was triphasic, consisting of a rapid partial reduction phase, an apparent partial reoxidation phase, and a slow rereduction phase. Absorbance spectra taken by rapid scanning spectroscopy at 1-ms intervals before, during, and after the apparent reoxidation phase showed that this was caused by a bona fide reoxidation of cytochrome b and not by any negative spectral contribution from cytochrome c 1 . With cytochrome bc 1 complex from a yeast mutant that cannot synthesize ubiquinone, cytochrome b reduction by either menaquinol or ubiquinol was rapid and monophasic. Addition of ubiquinone restored triphasic cytochrome b reduction, and the duration of the reoxidation phase increased as the ubiquinone concentration increased. When reduction of the cytochrome bc 1 complex through center P was blocked, cytochrome b reduction through center N was biphasic and was slowed by the addition of exogenous ubiquinone. These results show that ubiquinone residing at center N in the oxidized cytochrome bc 1 complex is responsible for the triphasic reduction of cytochrome b.Although the protonmotive Q cycle mechanism of the cytochrome bc 1 complex is generally well understood (1-3), the redox behavior of cytochrome b during pre-steady state reduction of the bc 1 complex is not fully understood. Cytochrome b reduction is triphasic, consisting of a rapid partial reduction phase, a partial reoxidation phase, and a slow rereduction phase. This behavior is puzzling, because the reoxidation phase occurs while reduced substrate is still available, and continued reduction of cytochrome b would be expected.Previous examinations of the pre-steady state reduction kinetics of the bc 1 complex were limited to single wavelength kinetics, and the spectral data, when collected, extended over time ranges that were long relative to the half-times of the reactions (4 -9). The substrates used in these studies, succinate, duroquinol, trimethylquinol, and ubiquinol, have relatively high redox potentials and reduce only a small percentage of cytochrome b. This is of concern because the high redox potential may predispose these substrates to oxidize cytochrome b and thus introduce artifacts into the pre-steady state kinetics in the absence of a low potential reductant.Several explanations for the triphasic reduction have been put forth. One proposal is that ubiquinone formed at center P is not in rapid equilibration with the quinone pool and oxidizes cytochrome b at center N (5, 10). Crystal structures of the mitochondrial cytochrome bc 1 complexes show a pear-shaped and dimeric integral membrane protein that extends ϳ80 Å into the matrix and ϳ30 Å into the intermembrane space (11, 12). There are two large cavities within the bc 1 dimer that lin...