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EXAM III: Points to ponder

Topics Emphasized since Exam II:

Structure and Function of DNA polymerase III;
Trombone model of replication
Structure, function, and interactions of subunits of the holoenzyme.

Sources and types of DNA damage
Repair schemes for different types of damage, including mechanisms and components involved in each process. 
Special emphasis on MutS structure and function (see Obmolova 2000 paper).

Homologous recombination:

• Holliday model of strand invasion, branch migration, and Holliday junction resolution for single and double strand breaks.
• Difference between patch and splice recombination products and how they are generated.
  
• Structure and function of proteins that mediate the recombination process in prokaryotes and eukaryotes.

Telomeres and telomerase:

• Telomeres:  structure and purpose.
• Telomerase:  structure and function.
• How telomere length and capping state relate to cell division (Blackburn 2000 review).
• Cancer cell growth and telomerase knockdown (Li et al. 2004 paper). Understand the techniques and biology of this paper.

DNA sequencing chemistry:
Sanger and "next generation" (454 pyrosequencing and illumina/solexa "bridge" sequencing.

Expression microarray technologies:  

• How they work and how they’re useful. 
• Data handling and analysis
• Research: Andreasen et al. (2006) microarray paper.

Transgenic and knockout mouse methods.