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CHAPTER 5 - BINDING

D:  BINDING AND THE
CONTROL OF GENE TRANSCRIPTION

BIOCHEMISTRY - DR. JAKUBOWSKI

Last Updated: 03/30/16

Learning Goals/Objectives for Chapter 5D:  After class and this reading, students will be able to

  • describe general mechanisms of how a gene for a given protein might be negatively and positively regulated at the level of gene transcription;
  • describe the structure/function/role of promoters, response elements, RNA polymerase, transcription factors, nucleosomes, histone proteins, epigenetic modifications of DNA in gene transcription;
  • explain the differences (structural, Kds) between specific and nonspecific binding of a ligand to a macromolecule, at the structural level;
  • describe the structural features of both proteins and DNA that result in specific and nonspecific binding;
  • describe and give examples of how post-translational modifications of proteins and epigenetic modifications of DNA can alter gene expression;
  • explain how the apparent Kd for a protein binding to DNA can be altered by the presence of another protein bound to DNA at a proximal site
  • describe the basis of RNA interference in gene expression

D2.  Control of Transcription in Prokaryotes

The regulation of the genes involved in lactose utilization won Jacob and Monod (of MWC fame) the Nobel Prize. Lactose can be used as the sole source of carbon by E. Coli. Three genes are required for lactose utilization, beta-galactosidase (lac Z, cleaves lactose to Gal and Glc), galactoside permease (lac Y, transports Lac into the cell) and thiogalactoside transacetylase (lac A, function unknown). These genes follow one another on the DNA, and have 1 promoter region. On transcription and translation, one long poly-protein is made, which is cleaved post-translationally to form the individual proteins.

Figure:  FUNCTION OF PROTEINS IN GALACTOSE UTILIZATION  

In addition, another gene, the Gal repressor, is found just upstream of the Gal utilization genes. It has its own promoter (PI).  A gene cluster, including promoter and any regulatory DNA sequences is called an operon, for example, the Lac operon. In this case, transcription from the operon is induced in response to a molecular signal - i.e. the presence of lactose, or allolactose. The signal binds to the repressor protein, which is bound to the operator DNA, which in the absence of the signal inhibits transcription. When the signal, in this case allolactose or another beta-galactosides, such as isopropylthiogalactoside (IPTG), binds to the repressor protein, a conformation change occurs in the repressor, resulting in a higher Kd for the operator DNA, and subsequent dissociation of the repressor-galactoside complex. Transcription ensues.

Figure:  IPTG and Lactose Structures

IPTG is an inducer of the lac operon but is not a substrate for the enzymes produced.

Figure:  INDUCTION OF LAC OPERON

Many analogous but distinct methods are used to control gene transcription in prokaryotes. The control of lac operon transcription is but one example.

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