1.When a protein binds to DNA at a site defined by a particular nucleotide sequence, with which parts of the DNA does the protein primarily interact?
A. the phosphate and deoxyribose groups in the DNA backbone
B. the phosphate and deoxyribose groups in the DNA backbone, and hydrophobic interactions with the nucleotide bases
C. nucleotide bases within the major grooves of the DNA
D. nucleotide bases within the major and minor grooves of the DNA
E. none of the above
2. Which of the following proteins binds to DNA with sequence specificity?
A. POI Ill holoenzyme
B. DnaA
C. DnaB
D. Dam methylase
E. Both B and D
3. Which of the following is NOT a functional parallel among all known cellular systems of DNA replication?
A. Replication is initiated at specific sites
B. Replication is continuous on the leading strand and discontinuous on the lagging strand
C. DNA replication is semiconservative
D. Replication forks move away from the origin in one direction
E. Nucleases, polymerases and ligases replace RNA primers with DNA and seal the remaining nick
4. A DNA polymerase cannot synthesize a DNA strand de novo (from the beginning) from a mixture of dNTPs. Which of the following explains the role of the primer in the reaction promoted by this enzyme?
A. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 3 ' end.
B. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 5' end.
C. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 3' end.
D. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 5' end.
E. The primer is a preexisting strand of DNA synthesized by DNA pol I, prior to replicative DNA synthesis by DNA pol Ill.
5. Universal features of DNA polymerases include:
A. 5'-3' exonuclease function.
B. Formation of an 'closed' conformation of the polymerase when the template-nucleotide base pair is correct.
C. Use of a single magnesium ion to orient reacting molecules and assist in dissipation of the negative charge that develops during nucleotidyl transfer.
D. Alignment of conserved residues in the active site for attack of the DNA primer by the 3 'OH on the incoming nucleotide.
E. Continuous unbinding and rebinding of the polymerase to the DNA template as each nucleotide is added.
