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Name ______________________________________________________ First Last

(Please Print) PID Number __________-__________

FINAL EXAMINATION

BIOLOGY 422

FALL, 2009 In the spirit of the honor code, I pledge that I have neither given nor received help on this exam. ______________________________ Signature 1________ 2_________ 3_________ 4_________ 5_________ 6_________ 7_________ 8________ 9________ 10 _______ 11________ 12________ 13________ 14______

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NOTE: For all short essays on the exam you will be graded on both the content of your answer (most of the points) and on its organization (a few of the points). Please take the time to write out a practice answer using the back side of the paper and then write you answer in the box provided.

1. (11 points) Fill in the following table describing the effects of various mutations in bacteria and Archaea. Mutant Phenotype (fill in the appropriate box for each mutant)

None observable

Dead under all conditions

Could grow if medium is supplemented with ____

Other Describe the phenotype in a very few words

E. coli which cannot make peptidoglycan

E. coli which cannot make lipids

E. coli which cannot make proline

E. coli which cannot make teichoic acids

E. coli which cannot make cytochromes

Cyanobacteria which cannot take up Mo

Cyanobacteria which cannot make cytochromes

Streptococcus which cannot make a capsule

Bacillus which cannot make lipopolysaccharide

Bacillus which cannot make spores

Archaea which cannot make peptidoglycan

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2. (8 points) Fill in the following table with respect to symbiotic nitrogen fixation by rhizobia. Note that Rhizobium leguminosarum makes nodules on peas and R. meliloti makes nodules on alfalfa. Bacterial genotype Plant genotype Nodules formed

(yes or no) Nitrogen fixation (yes or no)

Wild type R. leguminosarum

Wild type peas

Wild type R. meliloti

Wild type peas

R. leguminosarum lacking the histidine which is phosphorylated in the sensor of the two component system which regulates the nod genes (mutant 1)

Wild type peas

R. leguminosarum in which the response regulator of the two component which regulates the nod genes has an altered configuration so that it always appears phosphorylated

Wild type peas

Wild type R. leguminosarum Peas which fail to make legume hemoglobin

Wild type R. leguminosarum Peas which fail to make flavenoids

R. leguminosarum nifHG—

Wild type peas

R. leguminosarum nifHG—and mutant 1

Wild type peas

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3. ( 15 points) A. Which of the following can provide energy to bacteria? (circle the correct answers; graded as correct minus incorrect)

CH4 CH3OH CO CO2 NO2

- NH3

N2 H2S SO4— H2 H2O

acetate ethanol benzene hexachlorobenzene nylon cellulose octane Fe+2 Fe+3 B. Which of the following can serve as an electron acceptor in anaerobic respiration? (circle the correct answers; graded as correct minus incorrect) CH4 CH3OH CO CO2 NO2

- NH3

N2 H2S SO4— H2 H2O

acetate ethanol benzene hexachlorobenzene nylon cellulose octane Fe+2 Fe+3 C. Which of the following processes generate energy? (circle the correct answers; graded as correct minus incorrect) aerobic respiration anaerobic respiration fermentation nitrogen fixation photosystem 1 cyclic photophosphorylation the TCA cycle methanogenesis CO2 fixation aerobic photosynthesis amino acid biosynthesis .

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4. (7 points) Use the word bank below to answer the following questions. Primary Cytokines Initial response Dendritic cell Innate IgG Allergic response Plasma cell Secondary IgD B cells Memory cell Adaptive IgE T cells Platelet Toxins IgM Hospital microbes Macrophages Beta-blocker IgA You’ve been hired as a consultant for a company that makes animations for microbiology textbook. Your first assignment is to help them illustrate the process of antibody production. You instruct them that this process is classified as part of the _______ Immune Response. Next, you ask them to show the antigen presented to a ____________, which produces peptides of this antigen, and then presents these to a ________________. The cytokines subsequently produced, trigger the development and multiplication of __________________. The primary antibody response that results produces mainly _______antibody. You want to illustrate the important event that happens when the same antigen is presented again, so you emphasize that there should be no T cell to activate the ____________ during this response. This secondary response is mostly _______antibody. 5. (6 points) A plant breeder asks your advice about resistance to two newly described corn diseases. Both are caused by an RNA virus. One is like TYMO viruses and the other, like brome mosaic virus, has a segmented genome. The TYMO-like virus is restricted to corn as a host. The other virus has many hosts among the grasses and there is a related virus known which infects wheat (also a grass). The breeder wants to know whether this information is sufficient for you to make a prediction as to which virus is likely to evolve faster and how the evolution is likely to progress so that he can how to breed plants for resistance to the viruses. You do make a prediction for him and give him the rationale for your prediction. What is your prediction and what are the reasons behind it?

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6. (12 points) Fill in the following table. Note that “rhodo” means purple. Organism and conditions

Energy source Original electron donor

Final electron acceptor

Carbon source

E. coli, minimal medium, glucose, aerobic, light

E. coli, minimal medium, lactose, anaerobic, light

E. coli, minimal medium, anaerobic, CO2,

NO3-,

Rhodosprillum rubrum, minimal medium, organic acids, H2S, anaerobic, light

Cyanobacterium, minimal medium without combined nitrogen, aerobic, light

Halobacterium, aerobic, minimal medium, organic carbon, light, 4 M NaCl

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7. (12 points) You are a microbiologist studying the biosynthetic pathway of cytosine. The genes for the enzymes that manufacture cytosine all lie on an operon. You have noticed two main categories of mutants: those which fail to produce, and those which overproduce. a.) Name (3) possible DIFFERENT causes of a failure to produce cytosine and indicate whether the mutant could be complemented by genes carried on a plasmid and if so, which genes would be required. Mutation How could you complement this mutation (if it

cannot be complemented write “not possible”) 1.

2.

3.

b.) Name (3) possible DIFFERENT causes of overproduction and corresponding ways to complement these mutations. Mutation How could you complement this mutation (if it

cannot be complemented write “not possible”) 1.

2.

3.

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8. (12 points) Fill in the following table with respect to plaques caused by λ phage (indicate clear, cloudy, or none) and answer the thought question.

phage genotype E. coli K12 (-) E. coli K12 (λ) -

wild type λ λ CI- λ PR replaced by Parg all cultures grown on minimal medium with glucose

λ PR replaced by Parg all cultures grown on minimal medium with glycerol* and lactose

λ PR replaced by Parg all cultures grown on complex medium

λ PR replaced by PvirG from Agrobacterium (VirG is the response regulator of a two component system) all cultures grown on complex medium

* glycerol can serve as a carbon source for E. coli but does not participate in the regulation of gene expression by carbon source Lactose (lac) is a sugar, arg is an amino acid. You isolate a new strain of E. coli (N) and discover that it cannot be infected by wild type λ phage. DNA hybridization shows that E. coli N does not contain any DNA homologous to λ DNA. Give two possible mechanisms for the resistance of N to λ phage. 1. ___________________________________________________________________ 2. ____________________________________________________________________

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9. (4 points) While working as a family medicine physician, you’re presented with a patient complaining of sore throat and fever. The fever began yesterday and today your patient noticed a red and rough textured rash on her chest and armpits. Upon examination of her throat you notice that her tongue seems abnormally bright red, although she has no recollection of ingesting something with strong food coloring. What organism is most likely causing these symptoms? ___________________ What is the principle virulence factor used by this organism?_____________________ Should the patient receive antibiotics? Yes/no:__________________ If so what would you prescribe? (antibiotic name or N/A)______________________ 10. (8 points) A farmer wants to add fungicide to the soil in his field to protect his wheat from disease. Which types of fungicide are likely to be degraded and how rapidly? Type of fungicide Probable rate of degradation (check one box only)

Fast Slow Not degraded 1. Derived from a bacterium which kills fungus

2. A small ionic phenolic molecule made in the lab

3. A large uncharged repeating polymer made in the lab

The fungicide he chooses to use belongs to group 2 above. However, he finds that it is degraded faster than he would like. He asks you to identify the organism responsible for its degradation. Assuming the responsible agent(s) can be grown in the laboratory, what do you do? You have medium, fungi, the fungicide, soil samples and other necessary reagents available. Approximately what percentage of bacteria found in nature can be grown in the lab? (Circle one) 90% 10% 1% 0.1%

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11. (9 points) Name three prokaryotic organisms we have studied in this course that exhibit co-evolution, the organisms they have evolved with, and the indicated adaptations of each partner Prokaryote Eukaryote

with which it has evolved

Adaptation of prokaryote

Adaptation of eukaryote

Morphological or cytological

Biochemical or physiological

12. (4 points) The Mars Rover has found a number of feathery red objects that increase in size when in the presence of static electricity. Once they reach about the size of a basketball, the tips of a number of branches break off and are able to follow the same process involving static electricity. a.) What are two other characteristics you would want to look into to determine if they were living organisms? 1. _______________________________________________________ 2. _________________________________________________________ b.) Name one reason why a virus is not considered living ______________________________ 13. (3 points) some beginning biology textbooks state that all living things are ultimately dependent on sunlight for their energy. Is this statement correct? Yes or no (circle one) Why or why not? ____________________________________________________

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14. (9 points) Fill in the following table. Be sure to fill in each box. If the group does not have the item in question write no or none. Property Bacteria Archaea Eukaryote nucleus

and cytoplasm (not mitochondria and chloroplasts)

Composition of the plasma membrane

Composition of the cell wall

Some members can get energy from light

Some members can fix N2

Some members can generate CH4

Some members can use CH4 to grow

Initiator amino acid for protein synthesis

An inhibitor of protein synthesis

Many genes contain introns

We have enjoyed teaching you this semester. We wish you a good holiday.