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Chapter 13 Blog: Gene Regulation (Kimberley)

Page history last edited by KimberleyHausheer 12 years, 1 month ago


A.  Daily Blog


     Chapter 13 is about gene regulation, which is the ability for cells to express genes when they are needed. This conserves energy and ensures genes are expressed the correct cell type and at the correct stage in development.

      Gene regulation differs in prokaryotes and eukaryotes. In prokaryotes, gene regulation focuses on nutrient, and gas availability in the environment. Because prokaryotes are single celled and live everywhere, their main concern is surviving. They do not have a homeostatic environment like eukaryotes do. Therefore, gene regulation helps them to respond to nutrients in the environment. In eukaryotes, gene regulation focuses on cell differentiation. All eukaryotic cells have the same genome, which is their set of genes, however many of them have different proteomes, which is the collection of proteins they make. The proteome of a cell is what makes one a skin cell and the other a nerve cell. Cell regulation determines the proteome. Gene regulation in eukaryotes also enables multicellular organisms to progress through developmental stages. Certain genes are expressed at certain stages in life. In the book, they give the example of embryonic development. In this case, different globin genes are expressed because during development more oxygen is needed.

     Gene Regulation can occur at different points in the process from DNA to protein. Gene regulation most commonly occurs during transcription. How much mRNA is made from genes is regulated. When a gene is “turned off” little or no MRNA is made from it. When a gene is “turned on” it is transcribed in mRNA. This is the most efficient way because cells avoid wasting energy when the product of the gene is not needed. It can also be regulated when mRNA is translated into protein and at the protein or post-translational level. In eukaryotes, because there is an extra step during transcription genes can also be regulated during mRNA processing.

     Regulation of transcription in bacteria is similar to eukaryotes but much simpler. In prokaryotes, genes are organized into groups called operons. The operons are transcribed into mRNA as a polycistronic mRNA, which encodes more than one protein. Each operon consists of a regulatory region and a coding region. The regulatory region includes a promoter, operator, and a CAP site. The promoter region is where the RNA polymerase binds. The operator and CAP site are switches where regulatory transcription factors bind.  There are two kinds of regulatory transcription factors, activators and repressors. Repressors inhibit transcription and bind to the operator. Activators increase the rate of transcription and bind to the CAP site. The coding region of an operon consists of the genes that the operon will turn “on” or “off.”

     Gene regulation during transcription is eukaryotes is very different. The main point, like in everything comparing these two cell types, the eukaryote version is more complicated. In eukaryotes there are no operons and every gene is organized individually. Additionally, there is no switch that turns the gene on or off, instead there is a variety of factors that affect the expression of the gene. This is called combinatorial control.     

      For eukaryotes the promoter is made up of a TATA box, transcriptional start site, and regulatory elements. The core promoter is made of the TATA box and the transcriptional start site. The transcriptional start site is where transcription actually begins. The TATA box is a sequence upstream from the start site which helps to determine the exact starting point of transcription. The regulatory elements are positioned about 50 to 100 base paris upstream. There are two kinds, enhancers and silencers. Enhancers help RNA polymerase to begin transcription. Silencers prevent transcription of a given gene when its expression is not needed.  

     Researchers have identified three types of proteins that play a role in initiating transcription at the core promoter of structural genes. These are RNA polymerase II, five different proteins called general transcription factors (GTFs), and a large protein complex called mediator. RNA polymerase II and the general transcription factors meet at the TATA box and create the preinitiation complex. The mediator wraps itself around the GTFs, this controls the rate at which RNA polymerase can begin to transcribe RNA at the transcriptional start site. Activators and repressors can affect transcription in three ways. They can work by binding to the enhancer or silencer region and helping it along. An activator can also bind with a coactivator and then to the mediator which causes polymerase II to work to the elongation process faster. A repressor works the opposite way.  A third way that regulatory transcription factors influence transcription is by recruiting proteins that change the position of a gene to make it accessible


Reference: This information was all found from the ConnectPlus website which has the 2nd edition of the textbook "Biology" and the lectures instructed by Dr. Weber.


B.  Useful Materials

This is a short five minute video that explains the lac operon. I learned from playing this video many times in a row that lactose is a disaccharide made up of glucose and galactose. In order for lactose to be useful, the cell must cleave the disaccharide in two. This is done by b-galactosidase, which is an enzyme that is produced when the lac operon is turned on.  However this is not necessary if glucose is abundant. Then it explains the rest of the process how the repressor is made and where it binds, etc. In addition to the audio lecture part, there are simple pictures that help to show what the guy in the audio is explaining. It is very straightforward and easy to understand. Although it mentions CAP and how it must bind to cAMP in order for transcription to occur it does not mention the CAP binding site.

Added: Jan. 30 Source: Youtube



This image shows the  lac operon, a well known operon that is turned on when there is a not a sufficient amount of glucose and lactose is used as a food source instead. This operon and process is also discussed in the video, but I thought this picture showed a good representation of how the CAP binding site and the operator, both the switches that regulate transcription, work together. Because they were explained differently in the book, I was a little confused with how they worked together if they did at all. The first image shows a good representation of the different parts of the operon, showing where the operator and CAP binding site are on the the gene. The other images help you to understand when the repressor binds and when the CAP binds.

Added: Jan 30 Source:http://www.nvo.com/jin/scrapbookcell/view.nhtml?profile=scrapbookcell&UID=10032




A 1,064 bp fragment from the promotor region of the Col11a2 gene drive lacZ expression not only in cartilage bit also in osteoblasts adjacent to regions undergoing both endochronal and intramembranous ossification in mouse embryos

This article explains how a promotor fragment, consisting of 1,064 bp is linked to a beta-galactosidase gene and used to prepare transgenic mice. Three different things were tested in the mice:cartilaginous tissues in 15.5-day-old mouse embryos, in osteoprogenitors within developing periosteum, and in osteoblasts within mineralized bone. Although I am not sure what those three things are this is a good thing. The results suggest that the fragment, with the help of b-galactosidase can cause tissue specific expression in the Col11a2 gene. This applies to what we have learned in a few ways. It refer to different parts of a structural gene like the promotor, the binding site for RNA polymerase. It also refers to b-galactosidase, which I learned in the video above is an enzyme that breaks down lactose and is encoded by the lacZ gene in E. coli. It also refers to different developmental stages in the mouse, which is one of the main ways gene regulation is used in eukaryotes.

Added: Jan 30 Source: PubMed




Comments (1)

Derek Weber said

at 12:18 am on Feb 16, 2011

This is really nice work Kim. The summaries are detailed. Keep with this format.

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