Problem set 1

1. Microscopy and resolution.

A. What is the definition of resolution?

B. What is the formula for resolution.

C. Explain, in words, not formulas, how refractive indices, theta, and wave-length affect resolving power?

D. What is the maximal resolving power of a microscope with orange light (600 nm) and a numerical aperture of 0.75?

E. What is the maximal resolving power of a scope with wave-length of 500 nm, theta =75 and oil with an n=1.2

 

 

2. Many biological polymers are formed through dehydration reactions. Draw out these reactions using structural formulas. Highlight the names of the new chemical bonds formed (e.g. ester linkage, peptide bond etc.).

A. Two monosaccharides to a disaccharide.

B. Two amino acids to a dipeptide.

C. Three fatty acids and one glycerol to a triglyceride.

 

 

3. Molecules are often classified as hydrophobic, hydrophilic or amphipathic.

A. How would each class of molecule behave in water?

B. What are the properties of a molecule which make it hydrophobic or hydrophilic?

 

 

4. Given that the chemical formula for ribose is C5H10O5, what is the chemical formula of deoxyribose? (You should not have to refer to your text or notes to answer this question, the names tell you all you need to know).

 

5. Relatively speaking, would it take more energy to separate the strands of a DNA molecule with a 60% AT content or a 40% AT content? WHY?

Problem set 2

1. Peptidoglycan contains a polysaccharide of alternating NAM and NAG moieties. Only the NAM moieties, are attached to the tetrapeptides.

A. What type of bond is found between NAM and the tetrapeptide?

B. What structure is found exclusively in NAM which allows it to form this bond?

 

 

2. The antibiotic penicillin inhibits the cross-linking of the peptidoglycan tetrapeptides. Spheroplasts are bacteria which have had their cell walls mechanically removed. Both spheroplasts and ampicillin treated cells are killed in the mildly hypotonic solution in which most untreated or intact cells thrive. Both spheroplasts and ampicillin treated cells, however, remain viable in isotonic solutions. Explain these phenomena?

 

3. Both dessication and extremely hypertonic solutions kill bacteria via the same mechanism. Explain this mechanism?

 

4. Draw the chemical structure of a phospholipid. Using your diagram, explain why phospholipids are ideal molecules for membranes.

 

5. By comparing and contrasting the cell walls of Gram positive and Gram negative bacteria, explain the differential staining results obtained with a Gram stain?

Problem set 3

1. Oxygen:

A. Diagram the growth one would expect for a facultative anaerobe, an obligate aerobe, an obligate anaerobe and an aerotolerant anaerobe in deep culture slants?

B. What enzyme would you expect to be present in facultative anaerobes, obligate aerobes and aerotolerant anaerobes which would not be found in obligate anaerobes? What reaction does this enzyme catalyze and why does it confer viability in the presence of O2.

2. Using the data given below, determine the nutritional requirements of organism.

Nutritional content of media	Growth
minimal media	-
minimal media + proline	-
minimal media + tryptophan	-
minimal media + vitamin B6	-
minimal media + vitamin B6 + proline	-
minimal media + vitamin B6 + tryptophan	+
minimal media + proline + tryptophan	-
minimal media + vitamin B6 + tryptophan + proline	+

3. Using the data given below, determine the nutritional requirements of organism.

Nutritional content of media	Growth
Minimal media	-
Minimal media + all amino acids	+

Based only on the limited data above, can you determine the precise amino acids which this bacteria requires for growth? Why? How does the data presented below change your conclusion?

Nutritional content of media	Growth
Minimal media + all amino acids but tyrosine	-
Minimal media + all amino acids but phenylalanine	-
Minimal media + all amino acids but glutamine	+
Minimal media + tyrosine	-
Minimal media + phenylalanine	-
Minimal media + tyrosine and phenylalanine	+

The strain tested above can also be grown on minimal media containing only the compound prephenate. Explain this phenomenon. Hint: Look up the structures of tyrosine, phenylalanine and prephenate in a biochemstry textbook.

4. Using the data given below, determine the nutritional requirements of organism.

Nutritional content of media	Growth
minimal media	-
minimal media + tryptophan	+
minimal media + anthranilate	+
minimal media + chorismate	-
minimal media + tryptophan + anthranilate	+
minimal media + chorismate + anthranilate	+
minimal media + tryptophan + chorismate	+
minimal media + tryptophan + anthranilate + chorismate	+

Below is an abridged version of the biosynthetic pathway of the amino acid tryptophan. How does this pathway help explain the above data? Which enzyme is the bacteria lacking? Would you expect the bacteria to grow on minimal media + Intermediate #3?

chorismate ----enzyme #1----> anthranilate ----enzyme#2----> Intermediate #2

--enzyme#3--> Intermediate #3 ----enzyme #4----> Intermediate #4----enzyme#5----> tryptophan

Problem set 4

1. Using the data below, draw a growth curve for the bacteria at its optimal temperature. Start with 1.0 10e6 cells. Lag phase takes one hour. Exponential growth lasts for nine generations.

2. Using the data below, determine the growth rate and generation time for the bacteria. Do it both mathematically and graphically.

Problem set 5

1. Draw a death curve which satisfies the following conditions.

A. The decimal reduction time is 10 min.

B. The thermal death time is 40 minutes.

 

 

2. How does changing the following parameters affect both the decimal reduction time and the thermal death time.

A. Increasing the concentration of the bacterial culture.

B. Increasing the temperature of incubation.

 

 

3. What is the primary mechanism by which the following agents kill microorganisms.

A. Radiation.

B. Moist heat.

C. Detergents

D. Halogens

 

Problem set 6

1. Explain how deltaG°, Keq, endergonic and exergonic reactions are related.

 

2. Describe how enzymes function. What effect do they have on the free energy of the reactants, of the products and activation energy?

 

3. Define Km and Vmax. Describe how these values are determined.

 

4. In respiration, the total catabolism of glucose (C6H1206) will result in the liberation of 6 molecules of CO2. What happens to the carbon atoms of the glucose?

 

5. Fill in the following chart for the aerobic dissimulation of one molecule of glucose:

 

	ATP's consumed	ATP's or GTP's generated by substrate level phosphorylation	NADH2 's and FADH2's generated	ATP's generated by oxidative phosphorylation	Net ATP and GTP production
Glycolytic pathway
pyruvate -> acetylCoA
TCA cycle

6. Explain how uncouplers work. In your answer explain their effect on the electron transport system and the proton-motive force.

7. Micro-organisms can catabolize the disaccharide sucrose. First, they hydrolyze the molecule to generate one glucose molecule and one fructose molecule. What would be the net ATP equivalents synthesized from the complete aerobic oxidation of sucrose? The anaerobic oxidation (fermentation) of sucrose?

8. Facultative anaerobes grow more quickly in the presence of 02 than in the absence of 02. Why? Relate your answer to production of ATP? What processes are used to oxidize NADH2? What type of molecules serve as the terminal electron acceptor in these processes?

9. The amino acid isoleucine can be catabolized by many micro-organisms. It is converted into one molecule of acetyl-CoA and one molecule of succinyl-CoA. This conversion generates 3 NADH2 's and consumes one ATP. What would be the net production of ATP equivalents synthesized during respiration?

10. You have a suspension of E. coli cells in a non nutrient solution. The cells cannot generate ATP because there are absolutely no nutrients. The pH of the non nutrient solution is 7.0. The pH inside the cells is also 7.0. You quickly change the pH of the solution to 4.0 by adding hydrochloric acid. What would happen to the level of ATP in the cells? Would the effect be transitory or permanent? Explain your answer.

11. If a bacterial cell is growing on glucose as its carbon source, why is it important that both the glycolytic and pentose phosphate pathway operate?

Problem set 7

1. Using chemical formulae diagram how CO2 fixation occurs in the Calvin cycle. If a microorganism is not a CO2 autotroph, what alternative mechanisms does it have to for CO2 fixation? Using chemical formulae, diagram on such reaction.

2. What are the mechanisms of nitrogen assimilation using ammonia as a the nitrogen source? What is the difference between the nitrogen atom in ammonia and the nitrogen atom in nitrate. What must occur to the nitrogen atom in nitrate before it can be it can be incorporated into the amino acids glutamate or glutamine?

3. Diagram using chemical formulae the assimilatory sulfate reduction reactions.

4. Give a detailed example of a reductive amination and a transamination reaction as they relate to the biosynthesis of amino acids. To practice writing the structures of glutamate, alpha-keto glutarate and pyruvate use these in your examples.

5. A microorganism is growing aerobically in a media where its sole carbon source is the amino acid glutamate.

A. Glutamate will be deaminated and enter the TCA cycle. What molecule results from the deamination of glutamate? Draw this molecule's structure. What would be the theoretical yield of ATP (and ATP equivalents)?

B. This microorganism will still need to synthesize carbohydrates such as glucose and ribose. Why? What biosynthetic pathways will be utilized to generate glucose and ribose?

6. How do microorganism ensure that they do not synthesize amino acids which they do not require? How does this process work?

7. Oxaloacetate is converted to the amino acid aspartate via a trans amination reaction. Diagram this reaction, include all structures and the names of the molecules involved. (Remember in a trans amination reaction, there must be both an amine acceptor and an amine donor).

8. Peptidoglycan biosynthesis.

A. What molecules in peptidoglycan are derived from glucose?

B. How does the enzyme transpeptidase energetically couple reactions in forming the amino acid cross-links of the peptidoglycan?

9. Theoretically, the net ATP production from the complete dissimulation of one glucose molecule is 38. For a microorganism growing in a nutritionally poor environment, why would the net production of ATP be much lower?

10. Describe the enzymatic processes involved in DNA replication, RNA synthesis and protein synthesis, use chemical formulae when applicable.

11. There are several mechanisms used to control the synthesis of biological macromolecules. Some of the mechanisms directly affect the activity of an enzyme such as allosteric regulation, protein phosphorylation, and feed back inhibition. Define these modes of regulations.

12. The synthesis of biological macromolecules can also be regulated at the transcriptional level. Explain these mechanisms.

1. Describe how the experiments of Griffith; Avery et al., an Hershey and Chase established that DNA was genetic material.

 

2. Explain how different mutant genotypes can result in the same mutant phenotype.

 

3. Why do some mutations change genotype but confer no changes in phenotype?

 

4. Which genetic elements are active on the level of transcription? On the level of translation? What are the consequences of mutations in these genetic elements?

 

5. What types of mutations will lead to the production of an altered protein? Describe these altered proteins?

 

6. Describe a protocol for the isolation of a mutant which has loss the ability to synthesize the amino acid tryptophan. Describe a protocol for the isolation of a mutant which has loss the ability to synthesize all aromatic amino acids. Describe a protocol to isolate a mutant which is resistant to the antibiotic tetracycline.

 

Problem set 9

 

1. Describe a typical viral growth curve and the events of the viral life-cycle that are occurring during each stage of the curve.

 

2. Describe the general architecture of an icosahedral virion?

 

3. How does polarity influence the timing of viral protein synthesis and nucleic acid replication, and the enzymes that must be present in the infecting virion.

 

A. +RNA viral infections

B. -RNA viral infections

C. +DNA viral infections

D. -DNA viral infections

 

4. Describe the general life-cycles of naked and enveloped animal viruses and bacteriophage?

 

5. Describe and explain how ecological factors and sociological factors (at least two of each) favor the emergence of new viruses or the reemergence of old viruses?

 

6. Describe the mechanisms by which retroviruses and DNA tumor viruses cause cancer?

Problem set 10

1. How do the following factors contribute to microbial pathogenesis:

A. capsules and slime layers?

B. fimbriae?

C. coagullase?

D. collagenase

E. hemolysins

 

 

2. Describe how do the following factors inhibit the growth of microbial pathogens:

A. the normal flora?

B. inflammation?

C. fever?

D.  lysozyme?

 

 

3. Describe the mechanism by which interferon inhibits viral infections?

 

4. Compare and contrast endotoxins and exotoxins?

 

5. Describe the mechanism by which exotoxins enter host cells?

 

6. How does the health of a germ-free animal differ from that of a normal animal? What does this reveal about the advantages of the normal flora?

 

7. Describe phagocytosis? What is the significance of the respiratory burst?

Problem set 11

1. Specific vs. non specific immunity

A. What is the primary difference between specific and nonspecific immunity?

 

B. Define and give an example of a) naturally acquired active immunity, b) naturally acquired passive immunity, c) artificially acquired passive immunity and d) artificially acquired active immunity?

 

 

2. Draw the structure of an antibody. Label light chains, heavy chains, Fc, and Fab regions, and constant and variable regions.

 

3. Thoroughly describe a T-dependent antigen humoral response? Indicate at which steps clonal selection occurs. Include all chemical mediators secreted by cells and their effects. Include which antibodies are synthesized and when.

 

4. Contrast the differences between a T-dependent and a T-independent response?

 

5. Describe the cytotoxic T-cell response?

 

6. Describe the NK cell response and its role in immune surveillance?

 

7. Compare and contrast the classical and alternative complement fixation system?

 

8. Antibody diversity

A. Describe the events which occur within an antibody gene in a T-dependent response?

 

B. How does the structure of an antibody gene contribute to the multitude of antibodies that can be produced during the life-time of an individual?