The second section of the course examines how mistakes in your DNA are repaired as well as the molecular mechanisms behind the recombination of DNA molecules.  The readings for each section are outlined below with links to the specific web pages.  There is also a link to the online review page for this exam, practice exam problems and their answers.

Exam II Review

Exam II Practice Problems: Exam II Practice.pdf

Exam II Practice Problem Answers: 

Topic 6 DNA Replication II: Origins and Telomeres

Readings:

• Genomes: Origins and Initiation of Replication
• Molecular Biology of the Cell: Methylation and Bacterial Origins (Figure 5-32)
• Molecular Biology of the Cell: Cdk, Eukaryotic Origins and the ORC (Figure 17-22)
• Genomes: End Replication Problem and Telomeres (Section 13.2.4)

Animations:

• Bacterial DNA Replication Initiation Animation
• End-replication Problem and Telomerase Function
• Telomerase and Cancer with another Telomerase Animation

Topic 7 DNA Repair Pathways

Readings:

• Genomes: DNA Repair Pathways

Animations:

• Direct Repair: Photolyases and Methyl-transferases
• Mismatch Repair
• Nucleotide Excision Repair
• DNA Glycosylase Structure Animation

Further Reading: Xeroderma Pigmentosum, Bloom's Syndrome, Werner Syndrome, and Rothmund-Thomson Syndrome

Topic 8 Molecular Mechanisms of General Recombination

Readings:

• Molecular Biology of the Cell: General Recombination

Animations:

• General Recombination Animation from Richard Losick's Molecular Biology Course at Harvard
• An excellent McGraw Hill Animation of Holliday Junction creation and resolution
• An animation of recombination and resolution

• An animation showing branch resolution

• An animation of branch migration

Topic 9 Molecular Mechanisms of Site Specific Recombination

Readings:

• Molecular Biology of the Cell: Site-Specific Recombination; See Figure 5-79 for Basic DNA Rearrangments; Figure 5-80 for Lambda Integration
• Molecular Cell Biology: Cre and other Site-Specific Recombinases; Figures in this section complement the lecture
• Molecular Cell Biology: Knockout Mouse; This section has good figures that describe the process
• Molecular Cell Biology: Conditional Knockout; See Figure 8-35 for a nice visual depiction of the Cre Recombination event

Animations:

• Dr. Richard Losick at Harvard has created a wonderful animation that pulls together visually the ideas behind integrase mediated site-specific recombination.