The protein BFGF (basic fibroblast growth factor) was studied with fluorescence spectroscopy. We previously showed that heparin, which is a cofactor needed for receptor binding, induced marked enhancement of fluorescence from the single tryptophan residue which is located in the receptor binding region. We now find that heparin also markedly quenches tyrosine fluorescence. Since there are multiple tyrosine residues, the result shows extensive conformational change induced by heparin. Widespread rather than local structural change may be required for BFGF to bind to its receptor. Studies were carried out on basic mechanisms in fluorescence. Using fluorescence spectroscopy, it was found that chloride ion enhances the rate of protonation of excited-state serotonin and related 5- hydroxyindoles. The finding shows that chloride acts as a counterion, within the solvent shell of positively charged indoles, thereby facilitating approach of a proton. The phenomenon can serve as a model for chloride modulation of biomolecule reactivity, and could serve as a basis for a fluorescence assay for chloride. In a separate study, fluorescence decay kinetics and spectra were measured for proteins and peptides to test the generally accepted axiom that lifetime and quantum yield are directly proportional. This rule fails in the case of tryptophan fluorescence of proteins. Possible explanations for this finding include several type of excited-state interactions and static quenching.