Study Guide for Exam 3            Addendum on Viruses

1. Bacteria respond rapidly to changes in their environments. Ultimately, most of these responses depend on the activation (or repression) of different genes. Some responses involve a single operon: ex. lactose becomes available, so the lac operon is induced. Some changes activate regulons: ex. phosphate starvation triggers synthesis of several proteins coded for by genes scattered around the cell.  Some changes activate modulons, many different genes throughout the chromosome, that respond to a common internal signal such as cAMP: ex. changes in levels of glucose.
    a. What are some other environmental effects that trigger "global" changes in gene expression through the bacterial chromosome?
    b. Second chance: how does the cAMP/CRP system to work?  What is the effect of low glucose or high glucose? Is this an example of positive or negative gene regulation?
    c. What is a Sigma protein?  Remember that as a protein, Sigma is coded for by a gene, and that gene has a promoter, and the protein that reads the specific sequence of that promoter is .....  ?

2. What is quorum sensing? Give an example of why it is helpful for bacteria. What "environmental change" is it a response to? What "components" are needed (an engineering view) to produce a quorum sensing "system"?

3. What is chemotaxis?  What other kinds of taxes are there? What terms do we use to differentiate between signals that attract bacteria vs. signals that repel them?  (these signals are attractants and repellants, respectively)  Understand what runs and tumbles are; be able to describe this process. Where are the proteins that detect the presence of chemicals located? These proteins need to communicate the correct information to the flagellar motors. Where are the motors located?  How are they powered?

4. Spirochetes have internal flagella that run the length of the cell between the inner and outer membranes (Gram negative, obviously). What are these flagella called?  Gliding bacteria move by a different mechanism. If you were to make a wet mount of gliding bacteria in the lab and you saw them moving, where, physically, in the preparation would they be located and why? What type of substance do gliding bacteria need to produce to move?

5. In lab we used a couple of different methods to tell whether bacteria could move or not. What were they? Which was quickest?  In viewing a wet mount, what part of the microscope (aside from the focus knobs) needs to be properly adjusted in order to see the bacteria? If you were looking at colonies on a plate, how might colonies of motile bacteria appear different?

6. How are eukaryotic and prokaryotic flagella different? Be prepared to discuss this.

7. When bacteria start to run out of food, they often either get smaller or long and skinny. Why? What are some other changes that bacteria make when faced with low nutrient conditions?  Can you explain the difference between a low Km and a high Km uptake system? Which would be the most useful to an oligotroph?

8. What is the function of siderophores? Compatible solutes?  Hemolysins? Extracellular proteases? Stress proteins?

9. What are the advantages of forming an endospore? An endospore is not the product of reproduction; explain why.  Natural selection in bacteria typically favors the whole population, not the individual. Why should sporulation require quorum sensing?

10. Competition for the same resource among bacterium seems easy; bacteria attempt to take up and metabolize the same sugar or the same nitrogen source. There are ways that different populations of bacteria cooperate as well. Describe some examples.

11. Various chemicals can be metabolized in an assimilatory or a dissimilatory manner. What is the difference in the purposes of these two types of metabolism, and what is the quantitative difference and why?

12. Review the different chemical and physical factors that affect how well a microbe will grow.  Now give one or more examples of how microbes can alter their environments to match their needs. In a Winogradsky column, a whole lot of altering is going on. Explain the relationship between the bacteria that are turning the mud black and the green and purple bacteria we expect to see soon growing where the light hits the anaerobic zone.

13. Recognize that many bacteria in nature grow attached to surfaces, particles, and each other. What is the advantage for the bacteria to attach to, say, a leaf floating in the water?

14. Biofilms are complicated structures involving communities, not just populations, of microbes. What are one or two practical concerns about problems that biofilms may cause?

15. Understand the principles of enrichment culture, and how by using selective medium or by altering the growth conditions one stands a better chance of isolating a bacterium with a particular characteristic.

16. How much of a Tree of Life could you diagram?  Give it a try.  Recognize a few characteristics that distinguish Archaea from Eubacteria.

17. Great advances in microbiology, especially medical microbiology, were made by getting bacteria to grow in pure cultures and studying them. However, this isn't working particularly well with many bacteria that have yet to be discovered. Why not?  How can we study these bacteria?

18. Be able to recognize/identify several phenotypic and/or molecular techniques that we can use to identify bacteria. If I gave you a pure culture of an organism and asked you to identify it,  what would be a good way to start?

17. Recall the differences between Eukaryotic and Prokaryotic organisms. Which eukaryotes are microbiologists most interested in?

18. Discuss how fungi get their carbon and energy and use appropriate terms. How does this fit with their major role in the biosphere?

19. Unlike the Protists, Fungi have fairly narrow and distinct place in the Tree of Life.  Discuss what they are closely related to and what they are NOT closely related to.

20. Why did there used to be four major groups of fungi instead of 3?  What are the 3? Describe the reproductive structures produced by each group.

21. Know the meaning of fungal terms: hypha, mycelium, dimorphic, spore, conidia, coenocytic, yeast, mold, mycorrhizae, mycosis. Do fungi have cell walls?  What are some of the impacts of fungi on human existence?

22. Recognize the names of several fungi: Saccharomyces, Penicillium, Aspergillus, Candida, Cryptococcus, Pneumocystis, Histoplasma,

23. What's a good adjective to describe the Kingdom Protista? With some general examples, explain what you mean.

24. How do Protozoa get around?  Terminology: cyst, trophozoite, merozoite, schizogony, cytoplasmic streaming, alveoli, apical complex, cilia, plankton, neurotoxin, pseudopodia, paramylon, carageenan,

25. There are 7 major groups of Protists. Name them. This includes naming each of the 4 major groups of Protozoa. The sub-groups of protozoa you should know include:  Apicomplexans (why?), Dinoflagellates (why?), and Euglenoids (explain how this group exemplifies the problem of trying to classify protozoa by calling them plant-like, animal-like, and fungus-like).

26. Be vaguely familiar with the algae; recognize that they are Protists and contribute to your microbiological lab education as well as to your ice cream. ☺

27. Know something about the major role of Phytophthora in human history. Know something about the two varieties of slime molds. Can't help but think that the creates of The Blob (http://www.imdb.com/title/tt0051418/ ) knew something about slime molds.