BIOL 238 Review 2009

This page provides review questions for BIOL 238 (Spring 2010). Answers may be posted by students.

Chapter 7

1. What are the relative advantages and limitations of bidirectional replication versus rolling circle replication? What kind of genetic entities are likely to favor one over the other?

2. What kinds of mutant phenotypes reveal aspect of the mechanism of DNA replication and cell division? Explain two specific examples.

3. Explain how it's possible for the replisome to replicate the leading and lagging strands simultaneously.

4. During resolution of a catenane, how might a major mutation occur affecting the entire genome? How do you think this mutation is prevented?

5. During rapid growth, why would a bacterial cell die if the antibiotic drug “forms a physical barrier in front of the DNA replication complex.”?

6. What are the relative advantages and limitations of bidirectional versus rolling-circle replication of DNA? Explain in terms of different genome sizes, types, and cell situation when replication occurs.

7. When you sequence a genome, how do you know where the base pairs in the genome are located since the DNA used to sequence the genome is in fragments?

Chapter 8

1. Explain how a biochemical experiment can demonstrate the specific protein targeted by a new antibiotic that impairs transcription.

2. If Mycoplasma genitalium cannot synthesize its own amino acids, does it have extensive/multiple protein channels (ABC pumps) to let amino acids pass its membrane? If proteins are made of amino acids, though, how did the first M. genitalium’s protein channels come into existence?

3. In tRNA, there are "unusual" bases not found in mRNA How are these bases generated? Do you think they arise from a recently-evolved aspect of tRNA, or do you think they are an ancient phenomenon of the original RNA world? Explain.

4. What kinds of pharmaceutical agents could you design to act on gene promoters? Explain using protein and/or RNA molecules.

5. Why do you think bacterial cells absorb protein and nucleic acids that are exported by other bacteria?

6. How could you sequence the genome of an unculturable microbe?

7. What are the different ways of starting or stopping transcription of a gene?

8. As a peptide is synthesized, what problems may need to be solved in order to complete a protein and enable its function?

Chapter 9 and 10

1. In the process of conjugation, how are genes moved? Are genes moved individually or in groups? Could part of a gene be moved?

2. How are microbial species defined? What is the role of vertical phylogeny; and the role of horizontal gene exchange? Explain why species definition is a problem.

3. Why is competence factor exported out of the cell to bind to ComD externally in transformation of Streptococcus? Why doesn't the molecule bind internally? Doesn't exporting CF waste energy?

4. If a spontaneous mutation occurs to form an apurinic site, transcription and replication are hindered, but what actually happens when the replisome gets to the hole where the base should be?

5. Explain how a DNA sequence inverts during phase variation. Would you expect it to revert at the same rate? Why or why not?

6. Explain the different propagation strategies available to a replicative transposon. What are various ways the transposon could spread within a cell? Among organisms?

7. Explain how the ara operon works, and how it differs from the lac operon.

8. Explain how different mechanisms acting at different levels on DNA and RNA can modulate gene expression over a range of time scales, from multiple generations to within a few seconds.

9. Explain the roles of thermodynamic and kinetic effects in attenuation control of the trp operon.

Ma et al. paper

1. What do bacterial biofilms have in common with multicellular organisms? How do they differ?

2. What are the advantages to bacteria of biofilm formation? What properties do biofilms confer?

3. Where in the body do biofilms form infections? Why?

5. How does the ara promoter work (pBAD)? How was pBAD used to test the role of the psl operon in bioflim development?

6. How was it proved that psl encodes PSL polysaccharide? How does PSL compare in structure with alginate?