1. It is convenient to classify elements into 3 categories: macronutrients (6 elements), micronutrients (4 elements) and trace elements (the other required elements). Which elements belong to these 3 categories?
2. The terms autotroph and hetetotroph refer to C-source. What is the C-source for each?
3. The terms prototroph and auxotroph refer to synthetic abilities for specific nutrients. How do they differ?
4. The terms phototroph, chemotroph, lithotroph, and organotroph refer to energy source (sometimes the same as C-source, but often different). To what do these terms refer? These terms will seem useless at first, but just wait. As we learn more about specific microbes, they will become indispensable.
5. In practice, microbes are defined in terms of both their C-source and their Energy source together; thus terms such as “Chemolithotophic autotroph”, “Photoorganotrophic heterotroph”, “Photolithotophic autotroph”, “Chemoorganotrophic heterotroph” are common. For each such description, be able to identify how the organism obtains its C and its energy.
6. But wait, it gets even more confusing! Some organisms are mixotrophs! What is their claim to fame?
7. We’ll come back later to how organisms acquire S, P, and N. skim this section on p. 100.
8. Skim the section on growth factors and vitamins (pp. 100-101)
9. What is the difference between passive diffusion, facilitated diffusion, and active transport? Note that, although facilitated diffusion is common inside the animal body, it is not common in procaryotes. Considering that bacteria are unicellular and have little control of their environment, suggest a reason why active transport mechanisms are preferred.
10. When “active transport” is mentioned, most biology students think only of ATP-pumps in which transport is linked to ATP hydrolysis. Many bacteria use ion gradients to power active transport with a number of carriers. Ion gradients can be coupled either in symport or antiport fashion. What is the difference?
11. Yet another way of powering active transport is group translocation. Instead of ATP or ion gradients, a different molecule with high-energy phosphate provides initial activation energy that is ultimately coupled to entry of substrate with accompanying phosphorylation. The PTS system in E. coli is a common example, though by no means an isolated one. Examine Fig. 5.4 and note the stages of PTS. Be able to recognize and distinguish this type of transport from those mentioned above.
12. Iron poses a special problem. Iron occurs in two ionic forms: Fe⁺⁺ (ferrous iron) and Fe⁺⁺⁺ (ferric iron). At pH 7, Fe⁺⁺⁺ reacts with water to form an insoluble precipitate, Fe(OH)₃, more commonly known as “rust”. This removes iron from availability, so what is a poor microbe to do? The answer is “siderophores” – what are they? Look at Fig. 5.5 and be able to recognize typical siderophores by name.
13. The remainder of Ch. 5 discusses culture media, a topic also explored in lab. This is important practical information in order to appreciate why different media are used for different purposes. Be familiar with the following terms: defined medium, complex medium, agar, selective medium, differential medium.
14. The discussion of pure culture isolation on streak plates and pour plates should be familiar from your lab experience. Skim this section (pp. 107-111)

Ch. 6. Microbial Growth

1. Examine Fig. 6.1 and note the location of lag, log, stationary, and death phase. What factors determine which phase occurs?
2. For now, skip the "mathematics of growth" (pp. 115-116). We’ll cover relevant details in class.
3. What is generation time? In Table 6.2, what organism has the fastest generation time? The slowest? Are procaryotes faster than eucaryotes?
4. What does a Petroff-Hauser counter do? How does the cell number reported by a P-H counter differ from a viable count?
5. What is a C.F.U., and how does it differ from # of microbes/ml?
6. Be able to calculate C.F.U. from assays of a dilution series. For example, if you measure 25 colonies when plating 1 ml. of a 10^-6 dilution, what is the C.F.U. of the undiluted mixture? How would your answer change if you had sampled 0.5 ml of a 10^-6 dilution and found 25 colonies?
7. What is the simplest and most sensitive technique for measuring bacterial mass?
8. Skim "Growth yields ..." on pp. 120-121.
9. What is the difference between batch and continuous culture systems?
10. How does a chemostat work (examine Fig. 6.11)? How does it differ from a turbidostat?
11. Skim "Balanced and unbalanced growth" on pp. 112-123.
12. The section "Influence of Environmental Factors on Growth" is important and should be read with care. There are any terms that microbiologists use regularly to describe an organism's environmental preferences. What do each of the following mean? Extremophile, osmotolerant, halophile, acidophile, neutrophile, alkalophile, stenothermal, eurythermal, psychrophile, psychrotroph, facultative psychrophile, mesophile, thermophile, hyperthermophile, obligate aerobe, obligate anaerobe, facultative anaerobe, aerotolerant anaerobe, microaerophile, barotolerant, barophile?
13. What is a compatible solute? Give two examples of such solutes used by bacteria, and two different examples of such solutes used by fungi.
14. What is water activity? How is it related humidity? Comparing bacteria and fungi as a group, which group can tolerate lower a_w environments? What metabolic trick do halophilic bacteria use to survive in high salt environments?
15. How do bacteria and fungi differ in their optimal pH for growth, as a rule?
16. What is the internal pH of a bacterium that grows at pH 1?
17. When E. coli is placed in an acidic environment (below pH 5.5), does it adjust, and if so how?
18. What do the cardinal temperatures measure?
19. What adaptations allow psychrophiles to grow at temperature where other bacteria won't grow at all? What adaptations allow thermophiles to grow at temperature where other bacteria won't grow at all?
20. What is it about oxygen that anaerobes can't stand? I.e., what specific mechanisms differentiate aerobes from anaerobes? (Hint: think enzymes).
21. What types of damage does ionizing radiation produce in cells? What damage is caused by UV light? Does ordinary visible light cause any problems for bacteria? How do bacteria that are airborne, and thus often exposed to light, cope with potential damage?