Molecular binding is central to cellular regulation, from ligands that bind to receptors, to transcription factors that bind DNA. In this talk I will discuss recent theoretical work on the functional capabilities of binding-based regulatory systems, motivated by the transcriptional control of the model Drosophila gene hunchback by Bicoid. On the one hand, I will discuss the capabilities of allosteric conformational ensembles to integrate information through binding cooperativity. On the other, I will describe a fundamental limit to the generation of sharp sigmoidal responses in the absence of energy expenditure. These findings reveal general regulatory principles in transcription and beyond.