Biology 180 - Molecular Biology

Thought Questions for Exam 1

Hao Nguyen


1.   Describe the difference(s) between the folding of DNA in a prokaryotic cell and a eukaryotic cell.  Name all the molecules that are responsible for DNA folding.  What form of chromatin exists during the interphase of the cell cycle of a eukaryotic cell?  What form of chromatin exists during the cell division phase of the cell cycle of a eukaryotic cell?


2.   Structurally, what is involved in the denaturation of a double-stranded DNA?  Describe the different methods of DNA denaturation.  What does “melting a double-stranded DNA” involve?


3.   The histone octamer is composed of two of each of the following subunits:  H2A, H2B, H3, and H4.  To complete the 10-nm structure of DNA, another histone subunit            (H1) is also required.  The 30-nm Solenoid structure is spontaneously formed as the

      10-nm structure is established.


a.       Let’s say there is a mutation in the gene that expresses the H3 subunit which causes the gene product (protein) to have an altered configuration.  Do you think that the 30-nm Solenoid structure can still be formed?  Do you think that the DNA molecule can still be used as a template to carry out replication and transcription?  Would the mutation on the H3 gene have any affect on the denaturation of the DNA molecule?  Why or why not for all of the above questions?


b.       Do you think that you can denature the DNA molecule without affecting the histone octamers?  If so, how?  If not, why not?


      c.   Do you think that you can denature the histone octamers without affecting the DNA molecule?  If so, how?  If not, why not?


4.   What are the functions of Histone Acetyltransferase and Histone Deacetylase?  How are they involved in the folding of DNA and chromatin?


5.   What are the roles of the RAP 1 and SIR 3 & 4 in DNA folding/condensation?


6.   Describe the difference between euchromatin and heterochromatin.


7.   What are transposons and how are they formed?  What is a satellite DNA and how is it used by researchers?


8.   What is the role of DNA ligase?  What would happen to DNA replication if a cell is incapable of synthesizing this enzyme?


9.   What is the common function of all DNA polymerases discussed in class?  Why are there so many?  Can a cell survive and function properly without one of these DNA polymerases?  If so, how?  If not, why not?


10.  How is DNA replication initiated?  Describe Elongation and Termination of DNA replication.  Name and describe the function all molecules, complexes, and structures involved.


      a.   Direction of DNA synthesis.

      b.   Okazaki fragments and their function.

      c.   Continuous versus Discontinuous replication.


11.  Name and describe all the different types of DNA mutations discussed in class.  What caused the formation of these mutations?  What would happen to cellular     functions if these mutations were left unrepaired?


12.  What is/are the function of the MRE11/RAD50/XRS2 complex?


13.  Name and describe the function(s) of all types of repair system discussed in class.  Name and describe the function(s) of proteins/enzymes/molecules that are involved in each repair system.  What would happen to the particular DNA repair system if one of these proteins/enzymes/molecules were absent?


14.  Why are there so many different types of repair system within a cell?  What would happen to cellular functions if one or more DNA repair systems were nonfunctional?  Why do repair systems sometimes induce additional DNA mutations?  Is this intentional or inadvertent? 


15.  What are response elements?  What are consensus sequences?  Where are they located?  What are their functions?  What are transcription factors?  What are their functions?