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

     Chapter thirteen went over gene regulation. Gene regulation is responsible for many things like cell differentiation and conservation of cellular resources. Usually the cell would use proteins and/or other molecules to turn off/on (and in the case of eukaryotes, modify the level of transcription) its genes.

     Bacteria have their genes grouped together by function. This group is called an operon. Besides the genes that code for proteins the operon consists of a promoter and an operator. In the popular example that our book uses the lac operon also contains a CAP site, which increases the rate of transcription, before the promoter. The promoter is where RNA polymerase binds to, to start transcription. The operator is the site where the repressor protein would bind to, to inhibit transcription. The CAP site is where the CAP(catabolite activator protein) would bind to. Normally the lac operon is inhibited by its repressor due the lack of lactose and the abundance of glucose in the environment. But when there is a lack of glucose and lactose present in the environment the cAMP, produced when there is a lack of glucose, would bind to CAP which binds to the CAP site and the lactose would bind to the repressor thus preventing it from binding to the operator. The result of this is the polycistronic mRNA being transcribed.

     Eukaryotes on the other hand do not group their genes together and thus each gene is regulated individually. Each gene has a promoter region and the structural gene. Most promoter regions contain a region for regulatory elements, a TATA box and a transcriptional start site. The TATA box is a region containing Thymine and Adenine. The transcriptional start site is where... transcription starts. These two regions make up the core promoter region, which is where RNA polymerase and general transcription factors(GTFs) assemble and bind to in order to start transcription. The regulatory elements region is found upstream of the core promoter. These can either be enhancers, which bind to activators to increase the rate of transcription, or silencers, which bind to repressors that decrease the rate of transcription. Also, since eukaryotes pack their DNA using histones the DNA is unaccessible to RNA polymerase. This vastly reduces the rate of transcription and can only countered by the unpackaging of the DNA. Through a combination of these factors, levels of transcription begin to form. This is called combinatorial control.

B.  Useful Materials

Item 1:

Gene Regulation in Eukaryotes (added 1/30/11) This website goes over the chapter section for gene regulation in eukaryotes and it even provides an analogy for you if you do not understand what the core promoter and the upstream regulatory elements do. There is also a link at the bottom for the section that talks about gene regulation in prokaryotes.

Item 2:

(added 1/30/11)

This video goes over the popular lac operon in E. coli. This is for the people who have a hard time learning from a wall of text and prefer digital representations of the molecules and processes that regulate this operon.

Article:

Chronic ecstasy use increases neurotrophin-4 gene expression and protein levels in the rat brain.

Link: http://www.ncbi.nlm.nih.gov/pubmed/21273656

     This article shows how the environment can influence gene expression. The scientists injected ecstasy into the brain stem, cerebellum, and cerebral hemispheres for five days. After the five days they tested for the amount of NT-4 protein levels and rate of transcription for the NT-4 protein. The results show that there was an increase of NT-4 protein and an increased rate of transcription for the NT-4 protein in the aforementioned areas.