Study Guide for Exam 2

Need help on HOW to study?  Consider this:

Test questions that I ask can be thought of as three types that are different by the depth of understanding  that is involved.
1. Perhaps the easiest kind of multiple choice question is one in which you need to recognize the definition of a word. An  example would be AThe word that describes an organism that normally grows at room temperature but can grow slowly in the refrigerator and cause food spoilage is called a, b, c, d, e.@
2. A similar but little more challenging question involves finding an appropriate description for a word: AA psychrotroph a) grows at high temperatures b) can grow at low temperatures but doesn=t prefer it c) use carbon dioxide as a carbon source d) has its optimal growth in a refrigerator@.
3. Reading about a situation and correctly identifying what=s going on shows critical thinking and is the most challenging: AHamburger stored in the refrigerator has a significant number of microbes growing in it. When this hamburger is left at room temperature, the number of microbes increases dramatically. When the bacteria involved are isolated and compared, many of the same bacteria make up most of the population of both the refrigerated hamburger and the hamburger left out at room temperature. How might we classify these bacteria with respect to temperature?@
As you study, think about your depth of understanding so that you would be prepared to answer all 3 types of questions. You may notice, in thinking about the first exam, that most of my multiple choice questions tend to be of the 2^nd type, with a some of the first type thrown in to make the test a little easier, and then a few of the third type to keep you on your toes.

Transport

1. The lipid bilayer of a cell is an excellent barrier to the passage of many types of molecules. Know what molecules can pass through a lipid bilayer and which cannot.

2. Egg white is clear, is it not? The major ingredient (besides water) is protein (egg albumin). When you fry the egg, the protein denatures and turns white because it precipitates out of solution. Guess what? To come OUT of solution it had to be IN SOLUTION. Proteins are soluble in water; the cytoplasm of a cell is mostly dissolved proteins. Putting a protein in water produces a solution, NOT a suspension.

3. Eukaryotes are larger than prokaryotes, have no cell wall, and have an active cytoskeleton involved in creating and moving vesicles in the cytoplasm. They can carry out endocytosis; prokaryotes can not.

4. What is the difference between simple diffusion and facilitated diffusion?

5. When considering ABC transporters, symport and antiport, and group translocation, we talked about as many as THREE different "forms" of energy that can be uses in transport. What are they?

6. In what ways are transport proteins like enzymes? What name do we give them that reflects this similarity?

7. Be able to recognize or describe uniport, symport, and antiport.

Growth and Culturing

8. Bacterial growth occurs when the population increases. Every cell is made of the same materials, so there must be nutrients available to make new cells out of. Living things are carbon based.  What are the 6 most important elements found in cells? What are examples of "macronutrients" that are not in the list of the top 6 elements? What is the definition of trace element? Why do we not have to add these to general purpose culture media?

9. Elements have to be available in the correct chemical form to serve as nutrients. This should help you understand whether a substance can serve as a nutrient source for a bacterium. Some examples are easy: bacteria can't eat diamonds. What about different kinds of sugars? Different forms of N such as nitrogen gas (N₂)?

10. What are growth factors? What does it mean to say that a microbe is fastidious? What are oligotrophs and copiotrophs?

11. What are different ways of classifying culture media? Recognize the difference between complex and defined based on what is in it. Recognize selective and differential media by how it is used. What is enrichment culture, and how can it be used to help isolate a bacterium of a certain metabolic type?

12. What bad things can happen when oxygen interacts with biological molecules? How do bacteria protect themselves from toxic by-products of oxygen? What are two of the most important protective enzymes and what do they do?

13. Be sure you know the terms which describe the relationship of microbes to oxygen. This is often a major factor in trying to differentiate among different types of bacteria in identification.

14. What is the effect of temperature on cells? How do we classify different bacteria based on what temperature range they grow best in? If a bacterium makes a heat resistant endospore, does this necessarily mean that the bacterium is a thermophile (do endospores "grow"?) ?

15. What environmental problem do halotolerant, osmotolerant, and xerotolerant microbes all have to cope with?  What type of microbe does especially well in high salt environments? What type of microbe does well in very sugary environments? or dry environments?

16. Microbes are protected from different types of radiation by blocking or absorbing the radiation before it can affect important molecules, or by efficiency repairing any damage done to the DNA.  What is a barophile?

Self quiz on nutrition

17. What is binary fission? Do bacteria divide by mitosis? What is meant by bacterial "growth"? If you graph bacteria that are in exponential growth (plot cell numbers vs. time), what will the graph look like? What does the graph look like if you graph the log (# of bacteria) vs. time? What does it mean if a graph of actual numbers of bacteria (not log of the #s) vs time is a straight line?

18. What is a bacterial growth curve, and what are the 4 phases of the growth curve? When you make such a graph, what are on the Y and X axes? What is happening during each phase of growth? Do bacteria grow like this usually in nature? Why not?

19. What is the meaning of generation time?  Can you estimate generation time from a graph? Remember that when the population doubles, there are twice as many bacteria; in a log graph, when the population increases from, say, 6 to 7, that means an increase of 10x, not 2x!

20. What are examples of direct counting methods? What is a Petroff-Hausser counting chamber? A Coulter Counter?

21. Is a viable plate count a direct or indirect method of counting? Can you define "viable plate count"? What are two slightly different ways of doing this procedure? What are some advantages and disadvantages to using a spectrophotometer to count cells?  Suppose you were trying to count a bacterium that encases itself it strings of slime so that individual cells would not separate to form colonies or being easily counted with the microscope. How else might you determine whether they were growing or not?

22. What do the terms Vmax and Km mean? What does it mean to say that an enzyme can be saturated? If you boil an enzyme (unless it is from a hyperthermophile) it will stop working. Why? What happens to it?

23. Review Durham fermentation tubes. Why are these examples of differential culture media?  What is normally in them? At what pH does phenol red turn color? What color? Why do we use these to detect fermentation?

24. Be able to do dilution problems whether written out or presented in a diagram.

25. DNA in bacteria is twisted; not just a double helix, but the whole molecule is normally twisted up. What do we call this? Eukaryotes have lots of DNA that doesn't actually code for anything or is not used. Is that the case with bacteria? There are a couple of good arguments for why this must be the case. Try and think of one.

Try this Self Quiz on DNA basics.

26. What is a transposon? What is the difference between and insertion sequence and a transposon? If a bacterium infected you, would you want it to have several transposons? Why or why not? Does a transposon "jump" all by itself? It needs a gene that codes for what?  Be able to list several types of plasmids and briefly describe what they do or what their significance is.

27. Know the difference between sense and antisense, 5' to 3', and what it means for DNA or RNA to be complementary. What are the signals for ending transcription in bacteria? Bacteria have no nucleus and no introns. Explain how this makes the connection between transcription and translation different in bacteria than in eukaryotes and how this helps bacteria flourish.

28. Be able to describe the processes of transformation, transduction, and conjugation. What are they "used" for? What does "competent" mean? What is "homologous recombination"? Which method of gene transfer does NOT require the donor and recipient to be related and why?

29. Biochemical regulation at happens with enzymes, thus "biochemical" instead of "genetic". What is an allosteric site? Describe the process of feedback (endproduct) inhibition. What is the significance of it?

30. What is negative control, positive control, induction, repression? What is an operon? Regulon? Modulon? All this induction and repression and all seems rather complicated. Why don't bacteria just leave these genes on all the time? What word means "gene is on all the time"?

31. The lactose operon is the basic model for bacterial operons. Know the structure of the operon, what turns it on and what prevents it from being turned on. Be able to draw a diagram illustrating diauxic growth and to describe what is happening in the cell.

Self quiz on gene regulation and expression.

32. Modulons are involved in global control, that is, one environmental signal may affect different processes, so different sets of genes are regulated. Be prepared to list several examples and explain one or two. How does an RNA polymerase know which genes need to be transcribed when the environment changes?

DIDN'T MEAN FOR STUFF BELOW HERE TO BE ON THE STUDY GUIDE FOR THIS EXAM!!

33. What is quorum sensing? What is it for, and how do cells accomplish it?

34. What is taxis?  What types of signals do bacteria respond to by moving? Give examples.

35. Bacterial flagella differ from eukaryotic flagella in several ways; explain them. The powering of flagellar movement helps make the point that bacteria can use energy in several forms. Energy in the chemical bonds of nutrients eventually becomes the energy contained in the proton gradient across the membrane, the so-called proton motive force. This energy can be used to operate the flagellar motor OR make ATP (same bit of energy can't be spent twice). To power flagellar movement, the electron transport chain has to be in the cell membrane.

36. What is an axial filament? What type of bacterium produces them? If you stain these bacteria with flagella stain and view them under the microscope, can you see the flagella?

37. What is gliding motility? Can these bacteria swim? Why not? What type of biological polymer seems necessary for gliding motility?

38. What are some changes that a bacterium can undergo to help it when nutrients are low?  When the environment becomes hypertonic?

39.  Make sure you are familiar with the basic structure of DNA (double helix, complementary base pairs, anti-parallel, 5' to 3', etc.),  what transcription and translation are.