Last revised: Wednesday, March 26, 2003
Topics: Viruses. Gene Transfer Mechanisms.
Text Reading: Chapter 14 and 15.
Overview:
- Chapter 14 covers viruses, both bacterial (phages) and animal, along with general principles. Chapter 15 covers plasmids and various mechanisms by which genes can be exchanged between prokaryotes (and in some cases across domains). This topic is broadly characterized as "Horizontal Gene Transfer", and is a subject of great interest in current literature.
Chapter 14 and lecture notes.
- What
do the following terms mean? Think of a viral example to which each term could
usefully apply.
virion
phage
capsid
virus plaque
icosahedron
eclipse
late genes
early genes
lytic cycle
lysogeny
temperate virus
virulent virus
RNA replicase
reverse transcriptase
"+" RNA
"–" RNA
acute virus infection
persistent virus infection
latent virus infection
viroid
prion
spongiform encephalopathy - How are viruses classified?
- What traits are used to classify viruses? Are viruses classified by genus and species? Are virus names italicized?
- You should be familiar with the following viruses: Phage T4, influenza virus, Phage Lambda, HIV. In each case, know the virion structure (type of coat, type of nucleic acid, etc.), and be familiar with the life cycle.
- What are the stages in a typical lytic life cycle?
- What are the stages by which a lysogenic virus such as lambda can enter into the prophage state? What special viral genes are required for this process to occur?
- What mechanisms do bacterial cells have that protect them from virus attack? Be able to distinguish the differences between: endonucleases, exonucleases, restriction enzymes, modification enzymes.
- What are the stages of animal virus infection? Arrange the following terms in correct temporal sequence: budding, uncoating, attachment, replication.
- What mechanisms do animal cells have that protect them from virus attack? What is the interferon system, and what does it accomplish?
- What is the function of influenza virus hemaglutinin? Neuraminidase?
- Where in the host cell does influenza virus replication occur? What enzyme is needed for this process? Where does the enzyme come from?
- How does influenza virus ensure that its + strand RNA molecules can be successfully decoded by ribosomes? (Hint: how does it “cap” these RNAs?)
- How many pieces of RNA make up the influenza virus genome? How does this compare to other viruses?
- Are antibiotics effective against influenza virus? Why or why not? What other drugs (if any) are effective? How do they work?
- Influenza virus type A undergoes major antigenic changes every few years. How is this thought to occur? What is its significance?
- What is unique about retroviruses? Why is HIV so much more dangerous than other retroviruses?
- Why are viral infections of humans more difficult to treat than bacterial infections?
- How does "horizontal gene transfer" differ from "vertical gene transfer"? Give an example of each situation.
- Is horizontal gene transfer a rare occurrence? Does it have any impact on microbial evolution?
- What happens during bacterial "transformation"? How does "natural transformation" differ from "artificial transformation"? Give an example of a bacterium that is naturally transformable. Are most pathogens naturally transformable? What is meant by "competence"?
- What happens during "generalized transduction"?
- What is a plasmid?
- How might you demonstrate the presence of a plasmid in a bacterial cell?
- What types of genes are carried on plasmids?
- What is meant by each of the following
terms?
- multiple copy plasmid
- single copy plasmid
- copy number
- “curing” a plasmid
- incompatible plasmids
- virulence plasmids
- metabolic plasmids
- plasmid toxin
- R factor
- conjugative plasmid
- pilus
- rolling circle replication
- multiple copy plasmid
- Almost all bacterial cells isolated from nature contain one or more plasmids. In laboratory culture plasmids are frequently lost. Are plasmids necessary? Explain.
- What happens during conjugation? Can all plasmids direct this process, or only certain ones?
- How does a "mobilizable plasmid" differ from a "self-transmissible plasmid"?
- What is "retrotransfer", and how does it differ from transfer of a single mobilizable plasmid?
- What is a "transposon"? What are "conjugative transposons"? How do they differ from conjugative plasmids?
- What is an "insertion sequence"? What is a "transposon?" How do the two differ?
- What is an "integron"? What does the "integrase" enzyme do? How many promoters are present in an integron? Note that most integrons studied to date involve multiple antibiotic resistance.
- Bacterial gene transfer is widely used in research laboratories as a way of creating very specific mutations involving DNA insertions (rather than the more common, but random, technique, of using chemicals or radiation to induce non-specific DNA changes at random, with the hope that a certain mutated gene can be detected later). What is meant by a "gene disruption"? How can this be done? Why does this technique usually involve loss of function of a gene? (Hint: think of the mRNA and polypeptide sequence produced by such a situation).
- What is transposon mutagenesis? How can you select for such mutants?
- Are transposable elements found in any organisms other than bacteria? Is there any evidence that such elements provide mechanisms for horizontal gene transfers between eukaryotic organisms?