Cell signaling pathways direct cell growth and differentiation during development and the improper growth and proliferation of cancer cells largely by directing the transcription of genes and the translation of these transcripts into proteins. Chapters 1 and 2 address the cellular properties of a new class of inhibitors of the mammalian Target of Rapamycin (mTOR) kinase. mTOR sits at the hub of an important growth factor sensing pathway and its activity controls the translation of proteins important for cell growth and proliferation. Rapamycin is a small molecule natural product and an allosteric inhibitor of mTOR which is commonly used as an immunosupressant and is being investigated for the treatment of cancer. Rapamycin has even been shown to extend lifespan in mice. New inhibitors that target the active site of mTOR have very different cellular effects than rapamycin and may prove useful in the treatment of human diseases and cancer. Chapter 3 examines the effects of isoform specific PI3-K inhibitors on insulin signaling. Discovering specific inhibitors of protein and lipid kinases requires testing many inhibitors against many kinases. When we assay kinases \invitro, we use a nitrocellulose membrane to capture the phosphorylated substrate. Chapter 4 describes an image analysis program specifically designed to analyze membrane capture kinase assays. Chapter 5 investigates the adaptability of the highly conserved interface between a homeodomain transcription factor and its target gene. Homeodomain transcription factors are highly conserved regulators of metazoan body development that control development by binding to DNA and regulating the transcription of their target gens. Adaptability of homeodomain transcription factor binding is examined in Chapter 5 though the biochemical, biophysical and structural characterization of an adapted mutant of the engrailed homeodomain.