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Chapter 13 Blog: Gene Regulation (Nicole)

Page history last edited by Nicole Lee 13 years, 5 months ago

A. Chapter 13 Blog (Gene Regulation)


     So far the class has discussed topics pertaining to Chapter 13, gene regulation.  On the first day, the class discussed the regulation of transcription in eukaryotes.  Transcription in eukaryotes thinly follows the same principles that are found of the prokaryotes.  two main examples are: 


  1. the Activator and repressor proteins influence the ability of RNA polymerase to initiate transcription
  2. many are regulated by small effector molecules 

Although the transcription of both eukaryotes and prokaryotes may seem like they are completely similar, they also have important differences.  In eukaryotes, their genes are almost ALWAYS recognized separately, and the regulation process is much more intricate.  This is due to the fact that the prokaryotes are single celled organisms and they have far less genes to be regulated than eukaryotes.  In prokaryotes, the genes that have similar functions are turned off all at once, or turned on all at once, and they are grouped together.  This is done to conserve energy.  In eukaryotes, there are far too many genes for that to happen.  There are many levels of activation and repressing.   

     The class also discussed combinitorial control.  Combinitorial contol occurs when one or more activator proteins may stimulate the ability of RNA polymerase to initiate transcription and when one or more repressor proteins may inhibit the ability of RNA polymerase to initiate transcription.  The function of activators and repressors may be modulated inseveral ways.  These include the binding of small effector molecules, protein- protein interactions, and covalent modifications.  Activator proteins are necessary to promote the loosening up of the region in the chromosome where a gene is located thereby making it easier for the gene to be recognized and transcribed by RNA polymerase.  DNA methylation usually inhibits transcription, either by preventing the binding of an activator protein or by recruiting proteins that cause the DNA to become more compact.

     The class also discussed the 3 features found in most promoters.  As a recap, promoters are where transcription starts.  The three features that are found in MOST, but not all promoters are the TATA box, the transcription start site, and the regulatory ( or the response) elements.  The TATA box goes from 5’-TATAAAA-3’.  There are 25 base pairs upstream from the transcriptional start site, and this determines the precise starting point for transcription.  The transcription start site on the other hand is where transcription obviously begins.  Transcription (just as a re-cap) is when a DNA sequence is copied into an RNA sequence.  Most importantly, transcription does not permanently alter the structure of DNA.  When the transcription start site forms with the TATA box, it forms the core promoter.  When by itself, this results in low lever basal transcription.  The last of the three features found in most promoters is the regulatory or response elements.  

     The class also then briefly discussed about the 3 proteins that are needed for transcription.  These 3 include RNA polymerase II, 5 different general transcription factors, and large protein complex called the mediator.  The mediator ( as a re- cap) is composed of several proteins that bind to each other to form an elliptical-shaped complex that partially wraps around RNA polymerase II and the GTFs.  The mediator derives its name from the observation that it mediates interactions between the preinitiation complex and regulatory transcription factors such as activators or repressors that bind to enhancers or silencers.  The function of the mediator is to control the rate at which RNA polymerase can begin to transcribe RNA at the transcriptional start site.  The class then ended the discussion of chapter 13 by talking about the role of transcription factors and how they promote tf, and in return the tf promotes polymerase.  

     My experience with chapter 13 was an extremely interesting one.  Before the semester began I had read over the material and I took notes.  However, when I got to class and we discussed the topics, I was taken back that I knew most of the facts yet not all.  The class really helped me to understand the missing parts in my knowledge.  One thing that helped me understand the material was the lecture on the TATA box.  I now understand the concept and why it is so important that the TATA box must conform with the transcription start site to form the core promoter.  However, one thing that I was confused in the discussion was methylation.  I understand that methylation inhibits gene transcription, but I do not understand how it may play a role in silencing.  I will review over my notes taken during the lecture and from my readings, review over the book, and if I still can not find my answer I will email the professor.  




B.  Useful Materials

This first useful material is a video briefly describing the process of transcription and translation.  The video relates to the topic of chapter 13 because a lot of the information is based upon the process of transcription and translation.  Transcription is the process in which a DNA sequence is copied into an RNA sequence.  One of the most important factors both mentioned in the video and in the book is that transcription does NOT change the configuration of the structure of the DNA.  Translation is when the nucleotides that match up with the original strand are scanned, and the matching proteins (amino acids) are attracted and attached.  This correlates with the chapter material because this is a crucial part of gene regulation and gene expression.  


This second useful information tool is a short and sweet video on the TATA binding protein.  This relates to the chapter because the class mostly focused it's attention on the importance of this  structure (the TATA)  The RNA polymerase binds to the promoter.  One of the most crucial parts of this initiation process is the recognition of the TATA sequence.  The TATA sequence (which is described in the video) is a short stretch of DNA which is rich in thymine and adenine nucleotides.  This video helped me understand how the TATA box gets binded to subunit of polymerase.  Without this video, I believe my understanding of the TATA box and it's function would be very limited.  I highly recommend that anyone who is having trouble understanding the concept of not only the TATA box itself but also what is made of should watch this video.


C. Article



     This article is about the differential patterns of histone acetylation in inflammatory bowel diseases.  I chose this article because the class briefly described the histone acetylation.  Histone acetylation is when there is a removal of the COCH3.  The article talks about post- translational modifications of histones (mostly about acetylation) which is associated with the regulation of inflammatory gene expression.  The scientists used two models of inflammation of both the bowel and the biopsy samples of patients which acquired Crohn's disease.  They did this to study the expression of acetylated histones 3 and 4 in inflamed mucosa.  An experiment involving these two took place and the results showed that histone acetylation is associated with inflammation.  This also may show a therapeutic target for mucosal inflammation. 





Comments (1)

Derek Weber said

at 12:22 am on Feb 16, 2011

Let's discuss methylation. Great job on this. Keep this formatting going forward.

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