Relative to each promoter, where would you predict phosphorylated OmpR would bind the ompC and ompF genes?

The APETALA1:GUS line you were given is a transcriptional fusion. Given that APETALA1 encodes a transcription factor, where might you expect to detect the expression of a translational reporter gene fusion?

IIVY is a LysR regulator, and it helps control transcription of a neighboring gene, ilvC. IlvY can either bend the DNA and block RNAP's access to ilvC's -35 promoter site, or it can allow access to the ilvC -35 site, thereby promoting ilvC transcription. What determines whether llvY is repressing or activating transcription from the ilvC promoter? The presence of the co-inducer acetolactate - acetolactate binds to llvY and changes llvY's shape such that it doesn't block the -35 of the ilvC promoter. IlvY represses ilvC transcription when the IlvC protein is bound to llvY, and it activates ilvC transcription when the lvC protein is not present to bind to llvY. The presence of the co-inducer valine - when valine is present, it binds llvY and causes llvY to repress transcription from the ilvC promoter. The presence of the co-inducer acetolactate - acetolactate induces negative supercoiling at the ilvC promoter, which represses ilvC transcription.

Using baker's yeast it is possible to generate point mutations that destroy the kinase activity of CDK9/P-TEFB protein kinase. When genome-wide ChIP studies using anti-phosphorylated CTD antibodies and RNA-seq analysis of the mRNA purified from these cells were performed it was found that RNA Polymerase II was present in the 5' region of the coding regions of most protein coding genes, but mRNA levels were reduced for all genes tested. The cells that had this mutation were very sick and the mutation caused many of the cells to die. The abundance of mature mRNAs was lower than in non-mutant cells, and often lower than the levels of their corresponding pre-mRNA. Some of the mature mRNAs had short poly A tails and some were detected with none at all. Based on this information: Provide one reason why this mutation in CDK9 affects the levels of mature mRNAs?

CD3 is a signaling protein that is typically found only in the plasma membrane of immune system T lymphocytes. CD3 is composed of several different polypeptides, including a gamma chain, CD3γ. Scientists analyzed the promoter of the CD3γ chain gene for regulatory sequences that might have positive or negative effects on expression of the gene. The scientists cloned fragments of the CD3γ gene that included the first transcribed nucleotides plus up to 789 nucleotides of upstream regulatory sequences into plasmids in which the gene for the firefly enzyme luciferase immediately follows the fragments. The plasmids were then introduced into a line of T lymphocytes (Figure 1), and the cells were allowed to grow for a short while. Because the regulatory sequences of the CD3γ gene immediately precede the luciferase gene in the plasmids, the activity, either positive or negative, of the regulatory sequences affected the amount of luciferase gene expression by the T lymphocytes. Luciferase…