MBMB 451A Section 1


New Postings:   

The study guide for the second section is now posted. I will let you know about any more details forthcoming on my part of the exam. Lecture notes have been updated for last two lectures.

Here is a review article on RNA polymerase II and its transcription machinery that I think will be useful: Article

Old Postings:

•How does histone acetylation affect the interactions of histone tails with the nucleosome? How does RNA polymerase II find its correct binding site and is there such a thing as a sigma factor in this case?
•How does the activity of RNA polymerase II get modulated?
•How are RNA polymerase I promoter and transcription factor requirements fundamentally different from RNA polymerase II?
•What is the difference between basal and activated transcription?

Questions for September 29 and October 1, 2009:

•How does histone acetylation affect the interactions of histone tails with the nucleosome?
•Why would RNA polymerase in eukaryotes need to be different than in prokaryotes? Don’t they carry out the same basic process.
•Of the 3 nuclear RNA polymerases which would be the more specialized? Which would require more diversity of action?
•Where does the specificity come in for transcription? How does RNA polymerase II know where to begin?
•How is transcription of particular genes get turned on in response to external stimuli such as stress (heat, starvation, and so on), hormones and other small molecule effectors?
•How different are enhancers from promoter regions? Are different DNA elements used in each?

Questions for September 17, 2009

Find what kind of protein databases are available and be able to discuss their different features? Also look over the last of protein methods and nucleosome notes so that you can discuss it with the class.

Homework is due Sept 16 Wednesday by 5 p.m.

Questions for September 15, 2009

What is reverse phase chromatography and what is it generally used for?

How does gel filtration chromatography work? What is the excluded volume? How good would this approach be for purifying proteins?

What is the difference between Sephadex, Sephacryl, Sepharose, and Superose?

Questions for September 10, 2009:
Why would you need to purify protein? What properties of proteins can be used to separate and purify them from each other? What is column chromatography and how does it apply to protein purification?
What causes proteins to denature?

Homework is due on Wednesday September 9, 2009 by 5 p.m.

Questions for September 8, 2009: What is the difference between interwound and toroidal supercoiling? Give an example of toroidal supercoiling that occurs inside the cell. How many different ways are there to construct recombinant plasmids (hint: try a Google or similar search, also check out Invitrogen)? Why are protein expression vectors useful?  What kind of cells are proteins generally over-expressed in and why?  What are the considerations in vector construction that need to be taken into account with over-expression of a protein?

Questions for September 3, 2009

How does changing the ratio of dideoxynucleotide to deoxynucleotide (i.e. ddATP vs dATP) effect Dideoxy (Sanger) Method of DNA sequencing? Could this effect the range that can be sequenced and why?

How can PCR be used to monitor which version of a particular gene or large alteration in that gene is present in your colony of cells? How could PCR be used to isolate genes that are related to each other be a conserved domain?

Why are cDNA libraries still so important in the era of genomics? 
What information can be derived from cDNA that are not obtained generally by DNA microarrays?
How is DNA supercoiling measured? Which amino acids could be used to recognize the major and minor groove of DNA and to contact the phosphate backbone? How does the lac repressor protein bind DNA?

First homework assignment is to submit a digital photo of yourself by email to psen@siu.edu by August 28, 2009. It is preferred that you submit it as a jpeg file.

Questions for August 27, 2009

1. How do DNA or RNA modifications affect their structure in the following examples?
(A) Methylation of the C5 position of deoxcytidine in DNA
(B) 4-S-deoxythymidine
(C) Inosine
2. What are in vivo examples of non Watson-Crick base pairing?
3. What would a protein be recognizing if it binds to DNA independent of the DNA sequence?
4. What would a protein be recognizing if it binds to DNA in a DNA sequence dependent manner?

.Questions for Septepmber 1, 2009

Find and be ready to discuss how DNA microarrays were used to study a particular problem.  Some keywords that might help are genome-wide expression profiling, cDNA microarrays


  Course Information  
Professor and TA information Course Syllabus Course Material
     
Study Guides Part 1 Part 2

Study Groups

 

   
Lectures
   
  DNA Structure Supercoiling
  DNA methods Part 1 and Part 2 Molecular Cloning
  Protein methods  
  Chromatin Structure
  Transcription Transcription Regulation
  Chromatin/Transcription  
Sample Exams
   
  2007b; 2007; 2006; 2005; 2001  
Exam Key
Exam I Key 2009

 

Homework Keys:
1st Homework - Ans Key

2nd Homework Ans Key

 

3rd Homework  

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Last updated on October 23, 2009.