MBioS 303 Section II, Dr. Farmerie
Study guide #1: Nucleotides and Nucleic Acid Chemistry
Chapter 8 in Lehninger, Lecture notes 1 and 2.
Study Questions
1.
Describe the classical experiment that demonstrated that DNA is the genetic material.
2.
What is the general composition of a nucleotide? A nucleoside? List 5 nucleotides and indicate
if they are purines or pyrimidines.
3.
What are the structural differences between DNA and RNA?
4.
Draw a triphosphate nucleotide for DNA with a purine base. Draw a RNA nucleotide with a
pyrimidine base. Label:
a. Number the base and the sugar
b. Name the base.
c. Indicate if the sugar is ribose or deoxyribose.
d. Label the , , and  phosphoryl groups
e. Indicate the -N-glycosidic bond, anhydride bond, and ester bond.
f. Show which hydroxyl groups are used to link nucleotides together.
5. What is a phosphodiester linkage? Where does the energy come from that drives the
formation of the linkage?
6. In what direction do you read a DNA or RNA sequence?
7. Describe Chargaff’s rules. What is the premise behind the equalities?
8. Describe the “Central Dogma” as proposed by Crick. Was he completely right?
9. Describe the structure of B-form DNA. How does A and Z DNA differ?
10. Define Tm. What contributes to the Tm of a DNA molecule?
11. Why can we monitor the melting of DNA by absorbance of 260 nm light? Describe in terms
of extinction coefficient differences of single and double stranded DNA.
12. What contributes the RNA’s ability to form complex structures?
13. What is alkaline hydrolysis? Why is DNA resitant to alkaline hydrolysis?
14. DNA can form higher order structures in bacteria. What are these higher order structures
called? How are they introduced (i.e. what enzymes are involved)?
15. Define/describe Linking numer, twist and writhe. What are their relationships?
16. How do Topo I and Topo II influence the linking number? Describe in detail.
17. How is DNA organized in higher order structures in eukaryotes? How does this influence
linking number?
18. Describe the 30 nm fiber, and higher order structures in eukaryotic DNA compaction into
mitotic chromosomes.
19. Compare and contrast cohesins and condensins.