Genetic and biochemical studies have identified RNA polymerase II (Pol II) activity mutants that alter catalysis, which we use as tools to investigate transcription mechanisms. Gene expression consequences due to altered Pol II activity in vivo are complex. We find that alteration of Pol II catalysis decreases Pol II occupancy and reporter gene expression in vivo. Both reduced and increased activity Pol II mutants lead to apparent reduction in elongation rate in vivo in a commonly used chromatin IP assay, and we identify a confounding variable affecting interpretation of this assay. Pol II mutant effects on gene expression are exacerbated with increased promoter strength and gene length. mRNA degradation rates for a reporter gene are altered in Pol II mutant strains, with magnitude of half-life increases correlating both with mutants' growth and gene expression defects. Prior work has suggested that altered Pol II elongation sensitizes cells to nucleotide depletion. We reexamine this hypothesis and find that Pol II activity mutants and several elongation factor mutants respond to GTP starvation similarly to wild type and that putative elongation defects are not likely to drive the cellular response to limiting GTP.