In the first section of this page, you will write a daily summary of that day's class.  For example in  your chapter 2 blog, your first entry should be titled 9/3/10.  You should then write a one or two paragraph summary of that day's lecture, outlining the major points.  In the second section, you are required to add two items (link to a website, video, animation, student-created slide show, student-created PowerPoint presentation) and one journal article pertaining to a topic in this chapter.  A one-paragraph summary must accompany each item describing the main idea and how it applies to the lecture topic.  Please see the PBWorks help guide for assistance embedding video and other items directly in the page.  I will also produce a how-to video on using tables to wrap text around items and other useful tips.  Please see the syllabus for organization and grading details.

A.  Daily Blog

January 27, 2011

     Chapter 13 explains gene regulation in a cell.  All cells, in an organism, contain the same genome, or genetic information, but they have a different proteom, collection of proteins made.  This is because different genes are expressd in different cells.  Those genes encode for different proteins.  Gene expression in cell then must be regulated to ensure that the right genes are being expressed.  Gene regulation differs in prokaryotes and eukaryotes. In prokaryotes, genes are arranged in groups called operons.  These genes code for protein that have similar roles in the cell.  These genes are controlled by a promoter and operator located upstream of the genes.  The promoter provides a binding site for RNA polymerase.  The operator is the binding site for regulatory transcription factors.  These factors include activators and repressors.  Activators "turn on" transcription the genes and repressors "turn off" transcription of the genes.  The lac operon, for example, is a set of genes that fucntion in the catabolizm of lactose.  The lac operon is usually turned off.  It turns on when lactose is present.  lacZ, lacY, and lacA are the genes that code for the protein that break down lactose.  lacP is the promoter site where RNA polymerase binds. lacO is the operator; here the lac repressor binds.  The lac repressor is synthesized from the lac regulatory gene. In the absence of lactose, this repressor binds to lacO, enabling RNA polymerase to go on with transcription.  When lactose is present, it binds to the repressor, making it inactive and unable to bind to lacO. The trp operon contains genes that function in the anabolism of tryptophan.  This operon is generally on; it is turned off in the presence of tryptophan. When tryptophan is absent, RNA polymerase binds to the promoter site and transcribes the genes. At this point, the repressor is inactive. When tryptophan is present, it binds to the repressor making it active. The repressor then binds to the operator and halts transcription.

     Regulation of gene expression in eukaryotes is more complex then in prokaryotes. Eukaryote genes are controlled individually, each with its own promoter. The promoter consists of a TATA box, a transcriptional start site, and regulatory elements.  The TATA box provides a starting region for transcription. Regulatory elements include enhancers and silencers. Enhancers promote transcription and silencers prevent transcription. General transcription factors bind to the promoter, with RNA polymerase, and helps it bind to DNA to being transcription.  This region is called the preinitiation complex. A mediator binds to this complex and controls the rate of transcription at the start site. Activators and repressors bind to the enhancer region located several nucleotides upstream.  To enhance transcription, an activator binds to the enhancer region and a coactivator binds to the activator. The DNA is then folded so that the enhancer region and preinitiation complex are in close proximity. The coactivator then binds to the mediator. Stimulating it to increase transcription. Repressors follow the same steps, but they decrease the rate of transcription.

B.  Useful Materials

• http://www.ncbi.nlm.nih.gov/pubmed/21448808 
• This article explains epistasis, which is the contact of two genetic alleles. This is used to explain the great genetic variation in people.

The preinitiation complex consists of RNA polymerase and general transcription factors. This complex is located on the promoter of a gene. The mediator wraps around this complex. The activator and repressor, bound to enhancer region, bind to the mediator and either increases or decreases transcription.