Study Guide for Exam 3
Study Guide- Exam 3
(covers Classes 3.1 through 3.7)
Class 3.1---03/08/07: DNA Recombination
Know the following terms:
Homologous recombination, bivalents, cross over, chiasmata, recombination joint, branch
migration, patch recombinant, splice recombinant, Holiday structure, D loop, synaptonemal
complex, synapsis, axial elements, lateral elements, central element, cohesions, zip proteins, Hop
proteins, Spo11 protein, RecA, RecBCD complex, chi sequence, Topoisomerase I,
Topoisomerase II, gyrase, integrase, Cre/LOX, intasome, attP sites, attB sites, attL sites, attR
sties, IHF host factors, intasome.
Understand the Following Concepts:
1. Know the structure of the homologous chromosomes as they pair during meiosis. Know that
each chromosome contains 2 sister-chromatids (replicated DNA).
2. Be able to describe the major points of the single-stranded break model of homologous
3. Be able to distinguish between a patch recombinant and a splice recombinant.
4. Understand how a Holiday junction explains alternative resolutions during recombination.
5. Be able to reproduce the double-stranded break model of homologous recombination. Know
that it is a more realistic model of recombination.
6. Know the structure of the synaptonemal complex, and how the major proteins (cohesions,
zip proteins, hop proteins) are used to organize the structure.
7. Know how double-stranded breaks are generated during homologous recombination.
8. Know the role of RecBCD and RecA proteins during recombination in prokaryotes.
9. Know the role of the Ruv proteins in resolving Holiday junctions during recombination.
10. Know how Topoisomerases work, and know the difference between Type I and Type II
topoisomerases in terms of moving strands of DNA.
11. Understand the role of gyrases and topoisomerases in producing or relaxing supercoils in
12. Know the major differences between homologous recombination and site-specific
13. Know the difference between recombinases and integrases.
14. Know how phage lambda integrates and excises into a bacterial host chromosome.
15. Understand the similarities and differences between integrase and topoisomerase I
mechanisms of action.
Class 3.2---03/20/07: DNA Repair
Base excision repair, nucleotide excision, mismatch repair, Thymidine (pyrimidine) dimer, bulky
adducts, UvrAB, UrvA, UrvC, UrvBC, UvrD, base flipping, Alklyadenine DNA glycosylase