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Microbiology 52, Spring 2010 Pool of mid-term exam questions Chapter 1 1.

Microbiology 52, Spring 2010
Pool of mid-term exam questions
Chapter 1
1. A) Describe, and/or diagram, in detail the experiments performed by Francesco Redi and Louis Pasteur that helped to disprove the principle of spontaneous generation. B) There are several species of bacteria that, had they been present in Pasteur's swan-neck flask cultures, might have potentially grown after his heat treatment of the broth in the swan-nech flasks. Give at least one example of what bacteria these could have been, and why they would have grown after Pasteur's heat treatment of the cultures?
2. What was Antony van Leeuwenhoek's contribution to microbiology?
3. List three "new" or emerging infectious diseases of humans that first appeared in the United States (see Figure 1.4, Chapter 1). Why are so many of the "new" diseases identified in the United States?
4. Explain why viruses are not included among the three-domain divisions of living microorganisms.
5. As a microbiologist examining an unknown microbial specimen isolated from the environment – what is one component you would test for the presence of that would allow you to determine if the unknown specimen was from the Bacteria or Archaea domain? If you knew the unknow specimen was collected in an extreme environment, what would be your guess, prior to performing any experiment, as to the domain the speimen belongs?
6. List the three major groups of microorganisms in the domain Eucarya that have unicellular members. List one or more important properties that characterize members from each of these three groups.
7. Describe two vital contributions microorganisms make to the environment - without which life as we know it would not be possible. Briefly explain each of your contributions and why each is vital to life as we know it.
8. Take the following list of eight cells, or components of cells, and: (a) list them in order from largest to smallest; (b) say whether each is best viewed with the naked eye, light microscope, electron microscope, or atomic force microscope; (c) give an approximate size with the appropriate units (micometers, nanometers, etc.). Here is the list: E. coli, amino acid alanine, ribosome, yeast, red blood cell, ligase enzyme, virus.
9. List three examples of the influence of microorganisms on human hygiene and/or culture depicted in this painting.
10. List the following items in order from smallest to largest: E. coli, proton, ABC transporter, carbon atom, virus, yeast, molecule of glucose, ribosome. Which two items in the list could you see using a standard light microscope?
11. List four beneficial applications or contributions of bacteria.
12. A colleague of yours sends you a pure sample of a viroid and a pure sample of a virus. Unfortunately, in the mail the labels fall off both the tubes. However, you are pretty sure you can tell which sample is which by testing for the presence of a basic biological component. What component would you test for, and why would this allow you to distinguish between the two samples?
13. Based on the figure presented in the first lecture, how many bacteria (~4 m in diameter) would line up across the diameter of a dime?

Chapter 3
1- A) Define the following four terms associated with light microscopy: refraction, refractive index, resolution and numerical aperture. B) Does the resolution of a microscope depend on the wavelength of light used to observe the sample preparation? What wavelength of visible light would you want to use for the best resolution?
2- List three important differences between light microscopy and electron microscopy.
3- Why is it necessary to stain a sample of bacteria before observing the sample with a microscope? List the staining reagents used in a Gram stain, and what the role of each reagent is. Describe an error one might make when performing a Gram stain that would cause a Gram positive bacteria the be mis-identified as Gram negative.
4- Draw the cell groupings of a typical species of Streptococcus and a typical species of Staphylococcus bacteria. Would a typical Gram stain allow you to differentiate between samples of Staphylococcus aureus and Staphylococcus epidermidis? Why or why not?
5- A) List two essential functions of the cell envelope. B) Label figure one (see figures at the end of this document). C) How do peptidoglycan crosslinks differ between Gram-positive and Gram-negative cell walls?
6- Label figure two (see figures at the end of this document). Name two species of microorganism where this structure would be found.
7- Describe three structures a bacterium might use when attaching to a surface. Why might bacteria need to have mechanisms to ensure their attachment to various surfaces?
8- What are the two major components that make up peptidoglycan? Draw a few layers of peptidoglycan cell wall and describe how they are cross-linked.
9- Label figure three. What is going on at the label numbered "five"?
10- Draw and label a diagram of a typical lipid polysaccharide (LPS) molecule. Where would this LPS molecular be found under normal circumstances? How are the O-side chains related to infection? What is the role of the lipid A component in some infections?
11- Draw and label a typical lipid bilayer. What does the term amphipathic mean?
12- A) Describe bacterial chemotaxis and the role flagella contribute to chemotaxis. In your answer make sure you include the role of attractants, repellents, chemoreceptors and the structural components of the flagella. B) Describe and draw one type of experiment you could use to determine whether a certain chemical acts as an attractant or repellent for E. coli.
13- Define the following three terms: capsule, slime layer, and glycocalyx. How are they related?
14- What conditions might trigger a bacterium to begin forming an endosopre? What is the significance of endospore formation? List two genera of endospore forming bacteria.
15- Why are endospore forming bacteria of special concern to the food industry?
16- On what component of the bacterial envelope do the antimicrobail agents lysozyme and penicillin act? Why are both these agents more effective against Gram positive bacteria than on Gram negative bacteria? Explain why lysozyme can have its effect on bacteria at any stage of cell growth, while penicillin is effective only on actively growing the dividing bacteria.
17- List the functions of six of the prokaryotic structures lsited here: plasma membrane, ribosome, cell wall, capsule, flagella, fimbriae, and nucleoid material.
18- Water will flow into a cell when the environment inside the cell is _________ relative to the outside environment. Water will flow out of a cell when the environment inside the cell is __________ relative to the outside environemnt. A bacterium isolated from pond water and then transferred to sea water is likely to experience the movement of water into or out of the cell? If the sea water is exceptionally salty, what process may act on the bacterium isolated from pond water that would lead to its death?
19- Describe passive diffusion, facilitated diffusion, active transport, and group translocation in terms of their distinctive mechanisms and characteristics. Use specific examples where possible. Include in your answer how chemical gradients can be used to provide energy for transport of nutrients into a cell (or wastes/toxins out of a cell).
20- What is the relationship between permeases/transporters and selectively permeable membranes?
21- Based on Table 3.7, provide five significant differences between prokaryotes and eukaryotes.
22- What property of lens oil allows it to improve the quality of an image when using a 100x oil-immersion lens?
23- In what environmental habitat would you expect to find the greateast diversity of bacterial shapes? Explain why.
24- List three molecules that can pass freely through the cytoplasmic membrane by simple diffusion. List two molecules that require some form of transporter to cross the cytoplasmic membrane.
25- Species of what bacteria lack a cell wall? Are the antibacterial agents lysozyme or penicillin active against these species? Explain your answer.
26- What is a biofilm? Name one type of biofilm commonly found in/on your body.
27- What theory explains how the eukaryotic organelles, mitochondria and chloroplasts, evolved from bacteria? Provide two lines of evidence that support this theory.

Chapter 4
1- Define the important characteristic features of the following nutritional types of microorganisms: autotrophs, heterotrophs, phototrophs, chemoorganotrophs, and chemolithotrophs. Into which of these nutritional types do most human pathogens fall?
2- List eight macroelements required by microorganisms. What is a trace element?
3- Define the following terms: synthetic (or chemically defined) media, complex media, selective media, and differential media. Which type of media would you use if you wanted to quantitate the growth of a microorganism using disaccharides as the sole carbon source?
4- List two properties of the solidifying agent agar that make it ideal for use in bacteriological media.
5- List four methods you could use to measure cell growth (see Table 4.7). What is the difference between a direct and a viable cell count?
6- Describe a biofilm. Give three examples of problems caused by biofilms and one explanation for why they are difficult to treat.
7- Draw and label a diagram depicting binary fission in bacteria.
8- A) Describe the four phases of a growth curve from a batch culture of E. coli. Discuss the cause for each of the phases. B) Explain how the generation time for a microorganism can be calculated from the growth curve. C) Describe two methods you could use to determine the number of cells per ml in the culture at any time point.
9- List four environmental properties that influence the growth of bacteria.
10- Describe the environmental conditions under which the following types of microorganisms would be expected to grow: halophile, alkalophile, psychrophile, mesophile and thermophile.
11- A) You inoculate tubes of thioglycollate agar with a species of bacteria. There is no oxygen available in the bottom on the tube, while there is exposure to atmospheric concentrations of oxygen (~20%) at the very top of the tube. Describe, or draw, where in the tube you would expect the following types of microorganisms to grow: aerotolerant anaerobe, microaerophile, strict anaerobe, obligate aerobe and facultative anaerobe. B) Describe the function of the catalase and superoxide dismutase (SOD) enzymes. Which of the types of microorganisms listed in part A are most likely to have both catalase and SOD enzymes, and which is most likely to lack both catalase and SOD enzymes?
12- What is quorum sensing? Describe how it occurs and discuss its importance to microorganisms (use specific examples).
13- Explain why microorganisms often contaminate and spoil foods like milk and bread, but not honey or chocolate. If three E. coli contaminate a salad and grow with a generation time of 40 minutes, how many bacteria will be present after 5 hours and 20 minutes? What are two ingredients you might add to a salad that would slow or prevent the growth of some species of bacteria?
14- Explain why bacteria are likely to be more susceptible to antibiotics during the first 3/4 of log phase, as opposed to late log phase and stationary phase.
15- How does the synthesis of small organic compounds, such as proline, allow a species of bacteria to live in a high salt environment?
16- Explain the reason(s) why a direct microscopic count of a sample of bacteria in seawater yield a higher number than a pour plate made from the same volume of identical seawater.

Chapter 5
1. Describe three different methods you could use to sterilize 1 litre of water.
2. In general, how do chemical agents control or kill microorganisms? Describe the difference between an antibiotic and a bactericide like phenol.
3. What is the difference between a bactericidal chemical and a bacteriostatic one?
4. What is the difference between sterilization, disinfection and pasteurization?
5. List five classes of chemicals used in disinfection and sterilization (see Table 5.2). If you suspected a knife in your kitchen was contaminated with bacteria - what class of chemical disinfectant would you most likey use? What three exmaples of classes of chemical disinfectants might you typically find in a household medicine cabinet?
6. How does gamma irradiation destroy microorganisms? Although approved by the FDA and WHO, what misonception might lead consumers to be hesitant to buy irradiated food? List two other forms of electromagnetic radiation that can be used to kill microorganisms. Which of these forms of radiation can only kill microorganisms indirectly?
7. How do salting, sugaring or drying foods help lengthen their useful storage times?
8. Describe Joseph Lister’s contribution to medicine.
9. Explain how ultraviolet light kills microorganisms.

Chapter 6
1. A) How is the change in standard free energy (G') related to the equilibrium constant (keq) for a reaction? B) What are exergonic and endergonic reactions?
2. What serves as the energy "currency" for microbial systems? Using microbial organisms as a source, give examples of chemical work, transport work and mechanical work.
3. A) Define reductant, oxidant and standard reduction potential (E'0). B) Write a generalized equation for a redox reaction.
4. Substrates A and B undergo a chemical reaction to form product C. The G ' for this reaction is negative. A) Draw a graph illustrating this reaction, with the progress of the reaction on the X-axis and the free energy on the Y-axis. Include on your graph the initial substrates, the product, the transition state complex, the activation energy and the G'. B) Enzyme E catalyzes this reaction, describe how enzyme E speeds up the production of product C.
5. Explain how an allosteric enzyme can be regulated.
6. Describe the mechanism of feedback inhibition. Use a diagram in your answer.
7. What is the differnce between competitive and non-competitive enzyme inhibition? Use a diagram to illustrate your answer.
8. Explain why fermentation releases less energy than respiration?
9. List three precursor metabolites associated with the glycolytic pathway, two associated with the pentose phosphate pathway, and two associated with the TCA cycle (see Table 6.2). For each precursor metabolite listed, give a biosynthetic role (or end product).
10. Provide an example of the terminal electron acceptor(s) and total ATP gnerated from aerobic respiration, anaerobic respiration and fermentation.
11. Describe the chemiosmotic hypothesis and its role in the electron transport chain.
12. There are several common microbial fermentation pathways that use pyruvate as a starting material. Name three of the common pathways, their end products, any characteristic intermediate products, and an example of a microbial species that can use this fermentation pathway.
13. A) What are the two major functions of the trycarboxylic acid (TCA) pathway? B) How many GTP, NADH and FADH2 are generated from passing one pyruvate through the TCA cycle? C) In what eukaryotic organelle is the TCA pathway located? D) Where is the cycle located in prokaryotes?
14. A) Describe the role of the mitochondrial electron transport chain (ETC) in the generation of a proton motive force (PMF) from the electrons donated by NADH. B) In general terms, describe the structure and function of the ATP synthase and how the PMF generated by the ETC is used. C) How does the ETC of prokaryotic E. coli differ from that of the mitochondria (make sure you mention differences that relate to location, structure and efficiency)?
15. How does the fate of electrons carried by NADPH differ from those carried by NADH?
16. What is a coenzyme? List three coenzymes and provide an example for the use of each.
17. Explain how sulfa drugs, such as sulfanilamide, inhibit bacterial growth without harming the human host.
18. What vitamin is produced by bacteria in the human intestinal tract? What is it needed for in humans, and what is it used for in the bacteria?
19. What is an amphibolic pathway? Give two examples of central metabolic pathways that are amphibolic pathways?
20. Carbohydrates, lipids and proteins contain a good deal of stored energy that can be used by various microorganisms. In general terms, briefly describe how the energy stored in these complex molecules is accessed by microorganisms.
21. The process of fermentation is sometimes used to preserve foods. What occurs in the foods during the fermentation process that would slow the rate of spoilage?
22. List three food products produced with the aid of microorganisms.
23. In general terms, briefly describe how light energy from the sun is converted into ATP and oxygen during the light reactions of photosynthesis. How does this process differ between photosynthesizing organisms that function oxygenically and anoxygenically?
24. How do substrate level phosphorylation and oxidative phosphorylation differ from one another?

Chapter 7
1. Describe Fred Griffith's transformation experiments and his introduction of the transformation principle. Describe how experiments conducted by Avery, MacLeod and McCarty later suggested that the transformation principle was made up of DNA.
2. Describe the important differences in the structure and organization between prokaryotic and eukaryotic chromosomes.
3. Define the following terms or give the function if it is an enzyme: replication, transcription, replication fork, DNA polymerase I, DNA polymerase III, DNA gyrase, single-stranded DNA binding protein, leading strand and lagging strand.
4. How does the 5' end of DNA differ from the 3' end?
5. Define the following terms: codon, reading frame, gene, stop codon, and code degeneracy.
6. Describe the structure and function of a bacterial promoter region.
7. How does the 5' end of DNA differ from the 3' end? What type of bonds are formed between the base pairs of DNA?
8. How do Sigma factors help bacteria respond to environmental changes (give an example)?
9. Why is it so important that the translation macinery recognize the correct reading frame?
10. List three significant differences between prokaryotic and eukaryotic transcription and/or translation.
11. Define the following terms associated with mRNA transcription: promoter, template strand, RNA polymerase, sigma factor, initiation, elongation and termination.
12. Why is short-lived RNA important in cell control mechanisms?
13. What is polycistronic mRNA? Give an example of a microorganism where you would expect to find polycistronic mRNA.
14. Could two mRNA molecules have different nucleotide sequences and yet code for the same protein? Explain your answer.
15. What is a ribozyme? What molecule is thought to have existed first (billions of years ago), DNA, RNA or proteins?
16. Describe the function of tRNA molecules, and draw and label the structure of a tRNA molecule. In your description make sure to describe the process of amino acid activation and the enzymes involved.
17. What happens to a polypeptide that has a signal sequence?
18. Make a diagram of the ribosome that includes the A, E and P sites of the ribsome. Be sure to include the mRNA, the growing peptide chain, amino acids and tRNA molecules. Describe the three stages of protein synthesis at the ribosome. Is protein synthesis a highly regulated process? If yes, why is that so, and if no, why not?
19. What are molecular chaperones and heat-shock proteins? Describe their function.
20. Describe the function of the three genes that make up the lac operon and. Describe in detail how the lac operon is regulated by lactose and cAMP.
21. What is the difference between a constitutive enzyme and an inducible enzyme?
22. Explain the mechanism by which some species of bacteria are able to determine their density in a local environment.
23. You are a microbiologist working for a biotech company. Your boss as given you the project of isolating the gene from a species of Pseudomonas that degrades trinitrotoluene (TNT; an environmental pollutant). You quickly find that the bacteria do not produce the enzyme when grown in nutrient broth, and this makes it difficult to isolate the mRNA you need to identify the gene. What can you try that has a good chance of increasing the amount of the desired enzyme expressed by the bacteria?

Chapter 8
1. What features distinguish a bacterial plasmid from the bacterial chromosome? In your answer describe episome, conjugative plasmid, and R factors (R plasmids).
2. Define the terms genotype and phenotype. Which of the two is most likely to change in response to changes in the environment?
3. List at least two important effects insertion of a transposable element can have on a bacterium. In your answer describe the movement of a transposon, and list the minimally required structural elements of any transposon.
4. Distinguish between F+, F-, Hfr, and F' strains of E. coli with respect to their differing mechanisms, or roles, in bacterial conjugation.
5. What is a plasmid? List at least four useful traits that can be coded for within genes (or operons) found on a bacterial plasmid
6. Describe the process of nonreciprocal general recombination that takes place in bacteria. How is it different from reciprocal general recombination associated within a eukaryotic cell?
7. What type of DNA mutation is associated UV readiation exposure? What are the two repair mechanisms used by cells to repair this type of mutation? Which repair mechanism requires only one primary enzyme? What enzymes activitites are required for the more complex repair mechanism (there are at least three major enzyme activities required)?
8. List two classes of chemical agents that act as mutagens and can lead to mutations. What type of mutation is generally more more damaging, a point mutation, or a frame shift mutation? What is the difference between a missense mutation and a nonsense mutation?
9. The growth of E. coli is normally unaffected by compound XX because wild type E. coli have enzymes that inactivate the toxicity of compound XX. You want to isolate a clone of E. coli that does not grow in the presence of compound XX. Descibe the process you would use to isolate this clone, and use a diagram if necessary. What type of gene would you guess might be mutated in this clone of E. coli? Describe how you would identify a revertant of this clone that was able to grow in the presence of XX.
10. List the similarities and differences between conjugation, transformation, and transduction. Which one of these processes is sensitive to DNase addition?
11. Explain how dead bacteria might confer virulence to avirulent living bacteria.
12. What is a restriction enzyme? Why do bacteria often code for one or more restriction enzymes? How does a species of bacteria prevent restriction enzymes from acting on its own genome?
13. What is the simplest type of transposon? What two features are required by all transposons?
14. You are a student working in a research lab. You isolate a multidrug reistant strain of bacteria from a hospital’s intensive care unit. Your multidrug resistant strain can grow in the presence of penicillin, streptomycin and chloramphenicol. When you mix your multidrug resistant strain with bacteria sensitive to the three antibiotics, you notice that the previously sensitive strain is now resistant to penicillin and chloramphenicol, but not streptomycin. How can you explain these results?

New Questions Fall 2006-10-16
What is the term used to describe an infection acquired in a hospital? Give three reasons for why patients are more at risk for acquiring an infection while being hospitalized. What is an important, but often neglected practice, that physicians and nurses could easily employ to reduce the spread of infections to their patients?
Explain how differences in resident gut microflora between two individuals could help to explain why one individual is overweight, while the other, who has the same diet and exercise pattern, remains thin. What was the surprising finding, in regards to diet and weight, noted by researchers studying germ-free mice in the lab?
What microorganism is responsible for the recent food poisoning associated with fresh spinach (be as specific as possible)? From what source did this contaminant likely come from, and how did it get on the spinach? The same pathogen has also been associated with beef – but why is the contaminantion of beef less likely to harm as many people as fresh spinach?































































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