Bring on the tough stuff
Free Response Questions
1. What are some reasons why it might be difficult to apply Koch’s postulates to syphilis?
2. Why is better for sterilizing surgical equipment: autoclaves or antiseptics? Why?
3. When is sporulation a bad road to go down?
4. In bacterial conjugation, why do you think harmful genes could survive and be transferred?
5. You’ve collected plant samples to study their DNA. You’re pretty sure you’ve cleaned them well, removing any contaminants, but you’re getting traces of bacterial DNA all the same. Are your samples dirty, or might there be another explanation? What is it?
6. You want to express a gene but it appears to be toxic to E. coli. What are two ways you might get around this problem?
7. Do thermophiles necessarily have different proteins because of the higher G/C content of their DNA?
8. Why does crop rotation make for more fertile soil?
9. Are the bacteria in our gut commensal or mutualistic?
10. There are no known opportunistic pathogenic archaea. Does that make sense?
11. It is actually very challenging to apply Koch’s postulates to syphilis. The most obvious reason is that willfully infecting humans with a potential infectious microbe is not high on the list of ethical behaviors. Syphilis is also extremely difficult to cultivate, so getting a pure culture of it is nearly impossible.
12. Autoclaving is preferred. Antiseptics walk a balance between not hurting human cells and killing bacterial ones. Accordingly, they might not kill all microbes on the equipment. Alternatively, antiseptic residues might irritate the patient.
13. Sporulation turns out to be a bad choice if conditions rapidly improve. Sporulation is an energy intensive process that takes a bacterial cell out of the pool of growing bacteria for a while. A cell that didn’t choose to sporulate can grow and divide many times while the spore just remains one spore.
14. Harmful genes survive and are transferred to other organisms if the recipient lives long enough to pass those genes on to other organisms. If you think about it, it’s kind of like getting a cold. When you get a cold that’s caused by a virus, your body takes up some viral genes, reproduces that virus, and passes it on to other people. If that virus killed you on contact, that virus would stop at you, but as long as you’re alive and making virus, it can spread.
15. Since chloroplasts are descended from ancient cyanobacterium-like organisms, the DNA in chloroplasts has some similarity with cyanobacterium DNA. It’s possible that your samples are clean, and you’re confusing chloroplast DNA with bacterial DNA.
16. One way is to express the gene in another organism. E. coli is an Gram-negative strain and so antibiotics that work against Gram-negative bacteria would be toxic in E. coli. They would be better expressed in a Gram-positive or fungal host. A second option is to mutate the E. coli and select for E. coli mutants that are able to grow while expressing the gene.
17. No. Thermophiles do have different proteins with stronger intramolecular bonds, but this is not a necessary outcome of a preference for G/C-heavy DNA. The redundancy of the genetic code means that the DNA sequence can be altered without affecting the amino acid sequences of proteins. For example, valine can be coded by GTG, GTC, GTA, OR GTT. Thermophiles preferentially use GTG and GTC to code for valine as these sequences have a higher G/C ratio than GTA and GTT do.
18. Growing plants that form root nodules will increase the nitrogen levels in the soil. These nitrogen compounds include those that are released during plant and microbe growth as well as those that are released when the plants are composted.
19. This is a tricky question. The bacteria that live on and in us have traditionally been considered commensal. This is still mostly the case for skin bacteria. These bacteria consume compounds we release in sweat, for example, but don’t do much for us aside from prevent pathogenic strains from residing there. Gut bacteria are a little more complicated. As we learn more about the various vitamins they produce for us while living in our large intestines, scientists increasingly consider these bacterial mutualistic.
20. There is no right answer to this question. We, as well as a number of scientists, are surprised by this. Even if straight-out pathogenic archaea don’t exist, you would think that archaea would be tempted to do something naughty if you gave them access to our body through a wound of some kind. It’s possible that some known diseases are caused by archaea, but we just haven’t realized it yet.