Molecular Biology Study Guide Exam 1 Spring 2025
1. Be able to discuss the biological roles of nucleotides. Be able to recognize the
bases found in DNA and RNA. Be familiar with the chemical and physical properties
of nucleotides and nucleic acids.
2. Understand RNA structure and physical properties (pp. 324-325). Be able to
discuss how intrastrand base pairing and post-transcriptional modifications might
result in a broad variety of RNAs (p. 390).
3. Know the structure of DNA in detail (pp.183-188). Be familiar with the A-form and
Z-form structural variants, and their biological functions.
4. Be familiar with unusual DNA structures such as H-DNA and G-quadruplexes that
can result from non-standard base pairing and some of the non-standard
pairs/triples, etc. that can occur.
5. Understand how DNA can exist in multiple topological forms. Know the following
terms: overwinding, underwinding, supercoil, linking number. Which type of strain
(overwinding or underwinding) can be relieved by strand separation or the
formation of negative supercoils?
6. Be familiar with chromosomes and chromatin structure. Be able to describe the
structure of a nucleosome. Understand the terms euchromatin and
heterochromatin, and understand the general effect chromatin
condensation/decondensation has on gene expression. (pp. 189-200, p. 204, p. 206-
207, p. 227-228).
7. Be able to discuss how type I and II topoisomerases affect DNA topology (p.269-
271).
8. Be able to calculate the concentration of dsDNA, ssDNA, and RNA from the
absorbance at 260 nm. Understand how the purity of a DNA sample can be
assessed spectrophotometrically using the A 260/A280 ratio.
9. Be able to explain the process of agarose gel electrophoresis of DNA. Know the
relationship between the log length of a DNA molecule and migration distance.
10. Understand DNA denaturation and renaturation. Know how UV absorbance
changes as DNA is denatured, and the physical basis for this observation.
11. Be able to define TM and know how factors such as base composition and ionic
strength affect TM. Be able to calculate T M for a given set of hybridization
conditions.
12. Be familiar with restriction enzymes. Understand the role of these enzymes in
the organisms which produce them. Know how to calculate the number of sites that
will be present in random sequence DNA from the number of nucleotides in the
recognition sequence for a given restriction enzyme.
13. Understand how restriction enzymes and DNA ligase can be used to create
recombinant DNA molecules.
14. Be able to interpret data from a restriction mapping experiment and create a
map of a DNA fragment.
15. Be able to recognize the structures of the 20 amino acids, and know their names
and 3-letter abbreviations. Understand how the amino acids are classified according
to their physical/chemical properties, as well as any specific features of each amino
acid discussed in class (pp.118-119)
16. Be familiar with the formation and structure of peptide bonds (pp. 116-117) Be
able to discuss the levels of protein structure (1 o, 2o. etc.). Be familiar with
secondary structure, including motifs such as the -helix, -sheet, and -turn (pp.
120-141) Be familiar with super secondary structures such as the zinc-finger and
helix-turn-helix DNA binding domains, and the leucine zipper dimerization domain
(examples of protein domains in DNA binding proteins (pp. 404-405)
general DNA replication information/prokaryotes: pp. 253-265)
17. Understand the concept of semiconservative DNA replication and the general
idea of the Meselson-Stahl experiment.
18. Understand the DNA synthesis reaction and the requirements for a nucleoside
triphosphate and 3' OH on the primer.
19. Know the characteristics of a DNA polymerase that contribute to high fidelity
DNA replication (pp. 258-260). Understand processivity and how a sliding clamp
DNA polymerase subunit increases processivity of the polymerase (p.264). Be
familiar with SSBs, single-stranded DNA binding proteins, and their effects on
processivity (p. 263). Understand the roles of helicases (e.g. DNA B protein) and
DNA ligase in replication (pp. 261-262).
20. Be able to explain what is meant by bidirectional replication and understand
why the replication mechanism must differ for the leading and lagging strands.
Understand the overall process of DNA replication in a prokaryote.
