12/6/05      
 
Study Guide for BCB 444/544 Final Exam:   Thurs, Dec 15, 9:45-11:45 AM
 
General comments   
Summary of Required Reading:  
            o      Mount        Much of assigned reading in Mount was not covered in class.
                                     The Exam will focus on topics covered in lecture PPTs & Labs.
                                 
                             Chp  9      Gene Prediction
                                                         (only Promoter Prediction, pp 385-400)
                            Chp   8      Prediction of RNA Secondary Structure
                            Chp 10       Protein classification & structure prediction
                            Chp 11       Genome Analysis
                                                        (only pp 496-503; 519- 526; 539-543)
                            Chp 13       Microarray Analysis
                                                        (only pp 611-628; 654-658)
 
o      Cates (Online) RNA Secondary Structure Prediction Module
                            http://cnx.rice.edu/content/m11065/latest/
 
o      Zuker (Online)  Focus on the "strategies" not the details
                            http://www.bioinfo.rpi.edu/~zukerm/lectures/RNAfold-html/  
o      Burge, C, Karlin, S. (1997)  - will not be covered on Final Exam
 
o      Gibbs, R. (2005)
   Deeper Into the Genome  
               Nature 437:1233-1234
    http://www.cs.iastate.edu/~cs544/Papers/HapMapCommentaryNature2005.pdf
 
o      Goldstein, D.B.., Cavalleri, G.L. (2005)
    Genomics: Understanding Human Diversity
    Nature 437:1241-1242
    http://www.cs.iastate.edu/~cs544/Papers/HapMapNews&ViewsNature2005.pdf
 

List of topics

 
The exam will cover topics covered in:
 
              9 Lectures:    PPTS for 10/26 through 11/18 
          3 Labs:        #10, 11, 12
   
       Promoter structure:  prokaryotes vs eukaryotes
         Eukaryotic promoters vs enhancers
         Eukaryotic transcription factors
         Strategies for promoter prediction
                   Requirements for three major strategies
                   FP prediction problem
   
       Levels of RNA structure organization
         Base-pairing in RNA
         RNA types & functions
         Importance of miRNA/siRNAs in gene regulation
                   (not miRNA biogenesis)
                 
         Strategies for structure prediction
         Energy minimization
                   Assumptions, rules, calculations
                   Zuker's Mfold: How does it work?         
         Comparative/co-variation
                   When does it perform better than energy minimization?
   
       Levels of protein structure organization
         Characteristics of amino acids (do not memorize groups!)
         Characteristics of globular proteins
         Secondary structural elements
                   What are major types?
                   What types of bonds stabilize them?
         Tertiary structure
                   What are 6 major classes?
                   Could you recognize an "all alpha" domain?
                            (do not memorize examples!)
         Structure databases: What are 3 main ones?
         Structure classification databases: What are 3 major ones?
         Structure visualization: Cn3D: What can you do with it?
         Structural genomics project: What is goal?

 
      Why are folded proteins only marginally stable?
         What are primary forces involved in folding?
         Protein folding vs inverse folding problem
         Secondary structure prediction
                   (not covered in lecture, only in Lab 10)
         Tertiary structure prediction
                   3 major methods – When use each?
                   What is CASP?
         Threading
                   What are requirements & steps?
                   What is an energy function?  How is it used?
                   What tricks are used by Ho et al to "speed up" threading?
          
         Genomics
                   Genomic sequencing
                            What are two major strategies?
                   Human genome project
                            What have we learned?
                   SNPs
                            What are they & why are they important?
         Experimental approaches:
                   Genome sequencing/assembly
                            Two major strategies
                            What did we learn about human genome?
                   Gnome-wide RNA expression analysis
                            Differential display (digital)
                            Microarrays
                   Genome-wide protein expression analysis
                            What is proteomics?
                            Why analyze proteins instead of RNA?
                                                      will not be covered on the Final Exam
                   
 
         Karlin & Burge will not be covered
             HapMap project
                   What is the goal?
                   What is the significance? Potential applications?
                   What are limitations of HapMap?