Exam #1 MOLB / MICR 2021February 10, 2009Name:_________KEY___________TA’s name:______________________________

Answer the first 25 questions on the computer-graded answer sheet by filling in

the proper bubble with a No. 2 pencil. If you change an answer, erase the

undesired mark thoroughly. Mark only the best answer to each question. Each

question is worth 2 points.

Be sure to fill in the boxes for your name, then fill in the corresponding

bubbles beneath them correctly. Please also write your TAs name

somewhere on the scantron!

Questions 26 through 32 are each worth 10 points. Please answer question #26

and then choose to answer four of the six questions numbered 27 through 32.

Circle the questions that you choose.

This exam has 17 pages. Please check to make sure that you have them all. The

last page is a table of amino acids that might be helpful. The exam is worth 100

points.

Important equations / constants:

Nt = No * 2n

*If you feel that you really need to explain one of your answers to a multiple

choice question, please do so on the lines below. I will award credit or

partial credit for good justifications of missed questions.

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1. Antoni van Leeuwenhoek

a. wrote the following passage in a letter to the Royal Society of London, “These animacules had diverse colours, some being whitish and transparent; others with green and very glittering little scales....”b. challenged the notion of spontaneous generation by showing that maggots developed only on meat that was left uncovered and accessible to flies. c. showed that microorganisms live in air and that air itself does not contain some ‘vital force’ that allows for spontaneous generation.d. discovered the existence of heat-resistant bacterial endospores.

2. Which one of the following could be best shown using Koch’s Postulates?

a. That different types of media require different boiling times to be sterile.

b. That all life arises from other living things of the same kind.

c. That air does not contain a “vital force” allowing for spontaneous

generation.

d. That Vibrio cholerae causes cholera.

3. Following is an excerpt from an abstract in the Journal of Applied

Microbiology:

Four species of Pseudomonas, namely Ps. alcaligenes, Ps. mendocina, Ps. putida biovar B and Ps. stutzeri, were isolated from cattle dung enrichments and the soil samples in the premises of the factory manufacturing methyl violet, nearby Pune.All the four species of Pseudomonas were able to remove phenol and methyl violet with simultaneous reduction in chemical oxygen demand (COD), total organic carbon (TOC) and ammoniacal nitrogen from the waste effluent and the removal was found to be optimum at the original alkaline pH (range 7.45–10.6) of the waste effluent, at ambient temperature (28 ± 2°C under aerated culture condition, at inoculum density of 1.5 X 108 cells /ml of the waste effluent and incubation period of 24–48 h.

What process is being described by this abstract?

a. Genetic engineering

b. Bioremediation

c. Spontaneous generation

d. N2 fixation

e. Antibiotic production

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The following picture shows a fragment of the flagellin protein that makes up

procaryotic flagella. It is called the F41 fragment. Use this picture to help you

answer questions 4 through 6.

4. Which statement regarding the F41 flagellin fragment is FALSE?

a. This fragment contains peptide bonds.

b. This fragment is composed primarily of the !-helical secondary structure

element.

c. This fragment is composed of subunits that contain a central carbon, an R group, a carboxyl group and an amino group. d. The subunits of this fragment are linked by 3’-5’ phosphodiester bonds.e. all of the above

5. Notice that three regions have been labeled on the F41 flagellin fragment. Region A refers to the side of the !-helix that faces the aqueous exterior. Region B is the side of the helix that faces the protein interior. Region C is an exposed "-turn. Whereas the amino acids _________ might be found in Region B, they would be very unlikely to be found in Region A.

a. V, L and Fb. H, E and Dc. P, K and Rd. S, D and T

6. The amino acid proline (P) would be most likely found in a. Region Ab. Region Bc. Region Cd. none of the above

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7. The following molecule

a. is a nucleotide.b. is the building block of RNA.c. contains a glycosidic linkage.d. is amphipathic.e. is a triacylglycerol (TAG)

8. Which one of the following would be least likely to be found in the cytoplasmic membrane of a procaryotic cell?

a. phospholipidsb. polysaccharidesc. peptide bondsd. 3’-5’-phosphodiester bonds

e. hopanoids

9. During the second half of the semester we will talk about the archaeon

Archaeoglobus. This thermophilic procaryote generates hydrogen sulfide as a

byproduct of its metabolism and thus often gets a “bad rap” because this

byproduct reacts with the metals in oil refineries and causes corrosion. This

archaeon is characterized by which one of the following?

a. peptidoglycan-containing cell walls

b. mitochondria

c. 70 S ribosomes

d. chloroplasts

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10. Which microorganism would have the components of the electron transport chain across its membrane?

a. Lactococcus lactis (a strictly fermentative lactic acid bacteria that is incapable of any type of respiration)b. Bordetella pertussis (a bacterial pathogen that uses only aerobic respiration).c. Aspergillus niger (a fungus)d. Paramecium bursaria (a protists)

11. The following passage is an excerpt from a summary of an article from the

Canadian Journal of Microbiology:

Natural enrichments of magnetotactic bacteria were used to study the

sites where heavy metals accumulate in uncultured bacteria. Most

bacteria obtained by magnetic concentration from these enrichments

contained, in addition to the magnetosomes, large phosphorus-rich

granules in the cytoplasm.

Clearly the bacteria from these enrichments contain both magnetosomes and

polyphosphate granules. Both of these structures

a. also play a role in cell buoyancy.

b. store polysaccharides.

c. are inclusion bodies.

d. store Asp and Arg.

e. all of the above

12. Which one of the following bacteria most likely contains (a) plasmid/s?

a. An Escherichia coli cell that is capable of replication by binary fission.

b. A Salmonella strain that can live in the presence of the toxic heavy

metals, cadmium and mercury.

c. A Staphylococcus epidermidis strain that produces lipoteichoic acid.

d. An aquatic, photosynthetic bacterium that contains gas vacuoles.

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13. Which statement regarding peptidoglycan is FALSE?a. Although different in overall thickness, the peptidoglycan of Gram-positive and Gram-negative bacteria is the same in structure.b. Although yeast have a cell wall, this wall would not contain peptidoglycan.c. Peptidoglycan is targeted by the antibiotic penicillin.d. The Gram-positive bacterium Staphylococcus aureus would have a thick and exposed layer of peptidoglycan.e. Peptidoglycan contains both sugar derivatives that form glycan chains and unusual amino acids that form tetrapeptide chains.

14. The core polysaccharide region of the lipopolysaccharide (LPS) moleculea. joins the outer membrane of Gram-negative bacteria to the thin peptidoglycan layer.b. is present only in Gram-positive cells. c. allows the LPS molecule to act as an endotoxin. d. contributes to the overall negative charge on the surface of a Gram-negative cell.e. is a narrow channel that allows passage of molecules smaller than about 600 to 700 daltons.

15. I have recently been listening to a book on tape called Salt: A World History. In this book, the author speaks about the use of salt to cure meat. Which one of the following best explains why salt can be used to preserve meat?

a. When salt is placed on meat it creates a hypertonic environment. Microorganisms that might contaminate and spoil the meat are killed when water rushes out of their cytoplasmic membrane and the cell undergoes plasmolysis.b. When salt is placed on meat it creates a hypotonic environment. Microorganisms that might contaminate and spoil the meat are killed when water rushes into their cytoplasm and the cell bursts.c. When salt is placed on meat it creates a hypotonic environment. Microorganisms that might contaminate and spoil the meat are killed when water rushes out of their cytoplasmic membrane and the cell undergoes plasmolysis.d. When salt is placed on meat it creates a hypertonic environment. Microorganisms that might contaminate and spoil the meat are killed when water rushes into their cytoplasm and the cell bursts.

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16. Todar’s Online Textbook of Bacteriology describes certain bacteria as having an external layer, “composed of a single protein or glycoprotein... exhibiting either oblique, square or hexagonal lattice symmetry.” These bacteria are surrounded by a / an

a. capsuleb. slime layerc. sheathd. fimbriaee. S-layer

17. During the second half of the semester, we will work with the swarmingly motile bacterium Proteus mirabilis. Which statement/s regarding this bacterium is/are TRUE? [Assume that the picture below represents the current state of the bacterium.]

a. The direction of rotation of the flagella is currently clockwise.b. The bacterium is currently performing a tumble.c. Proteus mirabilis has chemoreceptors on the surface of its cytoplasmic membrane.d. a and be. a and c

18. Aurora is working in the lab with the bacterium Yersinia pestis 91001. In order to be certain that she is organized, she makes the following table entry in her lab book:

pestis91001Yersinia

Strain designationSpeciesGenus

Although Aurora’s entry is almost perfect, she did make one mistake. What is it?

a. 91001 should be italicized or underlined.b. Yersinia is the species and not the genus name.c. pestis is the species name and not the strain designation.d. Yersinia should not be spelled out the first time it is used.e. all of the above

*Note-Y. pestis is the bacterium that causes the bubonic plague.

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19. ______________ are components of the eucaryotic cytoskeleton. They also play an important role in the nucleus where there provide support to the nuclear envelope.

a. Microtubulesb. Microfilamentsc. Intermediate filamentsd. Heterochromatin

20. Which statement regarding the eucaryotic nucleus is FALSE?a. Within the eucaryotic nucleus, nucleosomes form the core packaging unit of DNA and proteins. b. Like the cytoplasmic membrane, the nuclear membrane is very selectively permeable and only allows free passage of low molecular weight molecules such as O2.c. Within the eucaryotic nucleus, histone proteins assist in the packaging of DNA.d. The nucleolus is a distinct, but not membrane-bound region within the eucaryotic nucleus. It is the site of rRNA synthesis.

21. Which statement is FALSE?a. In eucaryotic cells, integral membrane transport proteins are synthesized in the rough endoplasmic reticulum.b. Large, flattened membranous sacs called cisternae characterize both the rough endoplasmic reticulum and the golgi apparatus.c. In the Golgi apparatus, both the cis (forming) face and the trans (maturing) face are equivalent in terms of enzyme content and degree of vesicle formation.d. In chloroplasts, the thylakoid membrane is the site of the electron transport chain.e. The endosymbiont theory states that mitochondria and chloroplasts evolved from bacterial ancestors.

22. The influenza virus binds to specific receptors on the surface of host respiratory cells. This triggers receptor mediated endocytosis and the virus enters. Which event occurs as the virus exploits the host cell and enters?

a. Pseudopods form and surround the virus.b. A phagolysosome forms.c. A clathrin-coated pit forms.d. Caveolae form.

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23. Spanning the cytoplasmic membrane of E. coli is a transporter that uses a proton (traveling down its concentration gradient) to power the concomitant influx of the important metabolite succinate. This transporter

a. is a permease through which the molecule succinate is transported via facilitated diffusion.b. is an active transporter that uses PMF as the energy source.c. is a symport.d. is an ABC transporter.e. b and c

24. Group translocationa. involves a series of cytosolic events enabling the modification of a molecule as it is being transported into a cell. b. involves the use of a passive antiport.c. involves an ATP Binding Cassette.d. a and be. b and c

25. Matthew is fascinated by a pink contaminate colony growing on one of the TSA plates. He wants to know exactly how many cells are found in the colony. Rachel tells him that the doubling time of the contaminate is 30 minutes. If the colony has been growing overnight (18 hours), how many cells are in the colony?

a. 6.9 X 101 0 cellsb. 1.1 X 109 cellsc. 7.9 X 106 cellsd. none of the above

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26. Bacterial cell walls (Gram-positive and Gram-negative)

Although the Gram-negative bacillus Escherichia coli is the most common

cause of urinary tract infections (UTIs), the Gram-positive bacterium

Streptococcus agalactiae can also sometimes cause UTIs (Postgrad Med J. 1977

April; 53(618): 216–218).

a. (8 points) In the space below, Draw the cell wall of both E. coli and S. agalactiae. Please label all the layers and components of the walls (please include a label on the cytoplasmic (plasma) membrane). If you indicate cell shape in your picture, please be sure it is the correct cell shape.

For Gram-negative: 1 point each for outer membrane with LPS, periplasm, thin peptidoglycan and cytoplasmic membrane.

For Gram-positive: 1 point for each component

b. What is the overall net charge on the cell walls of E. coli and S. agalactiae? In each case, which molecule/s is/are responsible for imparting charge to the cell surfaces?The overall net charge on both Gram-positive and Gram-negative cell surfaces is negative. In Gram-positive cells this charge is imparted by the phosphate moieties on the teichoic acid. The negative charge on Gram-negative cells is imparted by the central region of LPS.

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Questions 27 through 32 are all worth 10 points. Please choose to answer

four of these questions and circle the questions that you choose.

27. Membranes and transportThe following figure depicts a cytoplasmic membrane

a. (3 point) Label the peripheral and integral membrane proteins (1 point). Which one of these proteins would be the easiest for a researcher to isolate and study? Explain. Peripheral membrane proteins are easier to isolate and study because they do not span the entire membrane. They are simply associated with the membrane via electrostatice interactions and do not require the membrane to be disrupted in order to be isolated.

b. (1 point) Label the polar head groups and hydrophobic tails of the phospholipids. (1/2 point for each)

c. (2 points) In what region of the integral membrane protein would one expect to find the amino acids K, E and D? Explain.

The region of the protein exposed to either the aqueous interior or exterior (1 point) would likely be the location of these hydrophilic (water-loving) amino acids (1 point).

d. (2 points) The following passage has two obvious mistakes. Please note

and correct these.

In 1972, S. Jonathan Singer and Garth L. Nicolson developed the

Fluid Mosaic model. This model describes the membrane as an impermeable phospholipid bilayer (the bilayer is semipermeable, not impermeable - small and hydrophobic molecules can pass via simple diffusion) in which proteins and phospholipids are

rigid and tightly tethered (proteins and PLs are free to diffuse laterally and rotate).

*Please note - This question is continued on the next page!!

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Question 27 continued....e. (2 points) One function of integral membrane proteins is in transport. Glycerol can be transported into microbial cells either via facilitated diffusion or active transport. Based on the environment shown in the following picture, is the transporter on the left (a facilitated diffusion transporter) or the transporter on the right (a H+/glycerol symporter) most likely being used? Explain

Because the concentration of glycerol is greater outside of the cell (1 point),

the facilitated diffusion transporter on the left could be used (1 point). The

molecules would be transported passively down their concentration gradient.

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28. Procaryotes (Environment and features)

a. (5 points) Place the letter corresponding to the best match below the numbered

item.A. Primary producers, such as cyanobacteria, that utilize light as

their energy source and CO2 as their carbon source.

B. Bacteria, such as the purple nonsulfur bacteria, that utilize light as an energy source and simple organics as a carbon source.

C. Organisms that cannot multiply if any O2 is present.

D. Bacteria that use organics for both their carbon and energy sources.

E. Organisms that require small amounts of O2 gas for growth.

F. primary producers that utilize inorganic chemicals as their energy source and CO2 as their carbon source.

G. Organisms that require a moderate to high salt concentration in order to grow.

H. Organisms, usually archaea, that have an optimum growth temperature of between 70 and 110ºC.

1. Photoheterotrophs

___B____

2. Photoautotrophs

___A____

3. Halophiles

___G____

4. Microaerophiles

___E____

5. Hyperthermophiles

___H____

b. (5 points) Match the procaryotic cell structure on the left with the most

appropriate term/s on the right.A. Electron transport chain (ETC)

B. endotoxin

C. microtubule

D. endoplasmic reticulum

E. hook and filament

F. hopanoid

G. inclusion body

H. glycocalyx

1. Flagella

____E___

2. Capsule

___H____

3. Lipopolysaccharide (LPS)

___B____

4. Magnetosome

___G____

5. Proton motive force (PMF)

___A____

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29. Eucaryotes

Eucaryotic cells are characterized by membrane-bound organelles. This

question reflects on several of these organelles.

a. (4 points) Mitochondria and chloroplasts are thought to have originated

from bacterial ancestors. List two features of these organelles and explain why

these features give credence to this endosymbiont theory.

Mitochondria and chloroplasts contain their own circular chromosomes

as well as 70S ribosomes. They are also roughly the same size as bacterial

cells and reproduce by binary fission. (Other answers may be

acceptable).

b. (2 points) The pathogen Chlamydia is a smooth criminal in that it enters

host cells via phagocytosis and then secretes molecules that prevent the

merging of a phagosome with a lysosome. Based on the function of the

lysosome, why does this protect the Chlamydia pathogen?

The lysosome is filled with hydrolytic enzymes that degrade

macromolecules Thus, by inibiting fusion, the bacterium saves itself from

degradation.

c.(4 points) Scherffelia dubia is a small, flagellated protist. It is covered in

proteinaceous scales of two types that together form a cell wall (Peck et al.(1995),

Proceedings of the Second European Congress of Protistaology). Based on this knowledge,

would you expect S. dubia to have a well-developed endoplasmic reticulum

and Golgi apparatus. Why or why not?

Yes , because scale proteins are destined for export and thus are

synthesized in the ER and modified in the Golgi.

Note - the scales that surround the protist are made of exported proteins.

These proteins must be made by the protist itself. Also recal that the

function of the ER and Golgi network is the synthesis and export of

proteins.

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30. Growth in culture

Recall that the growth curve describes growth of organisms in the lab in

closed/batch systems. Under these conditions, nutrients are limited and waste

is not removed.

Removed on key - see original

(10 points) Keep the growth curve in mind to help you complete the missing

fields in the following table. The first entry has been done for you.

Culture survival through a few fitter cells.

Total number of cells continues to decrease but a few fitter cells are still able to multiply.

Total number of culturable cells decreases at a constant rate.

Somewhat in debate (multiple answers will suffice)

Growth stops, total number of viable cells stays constant

Synthesis of secondary metabolites continues as cells focus on maintenence and not growth.

Yes, the cells divide at a constant rate. However, the transition to stationary phase begins and growth may no longer be logrithmic.

The synthesis of secondary metabolites (starvation proteins ) that enable the cells to survive in a culture where nutrients are becoming scarce and waste products are accumulating.

Yes, the cells divide at a constant and logrithmic rate.

The synthesis of primary metabolites (aas, nucleotides, and other macromolecule) in order to increase cell MASS!

No, the total number of cells stays constant during this phase as it is a readying phase prior to growth.

The synthesis of enzymes, ribosomes, nucleic acids etc.. that will be needed for replication.

Is there a change in the number of total culturable cells during this stage? Explain

Primary goal/ objective of cells at this stage

Prolonged decline

Death

Stationary

Late Log

Initial Log

Lag

Growth Phase

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31.Procaryotes vs. Eucaryotes

(10 points) Fill in all pertinent fields in the following table. Three boxes have

been filled in for you.

EucaryarRNA

synthesis,

ribosome

assembly

Procaryotic flagella composed of filament

(flagellin), hook and basal body. They move

like propellers and are external to the cell.

Eucaryotic flagella are composed of 9+2

pattern of microtiubules, they move like

whips and are encased in the cytoplasmic

membrane.

Eucarya,

Bacteria and

Archaea

N / ABacteriaCell wall

structure

N / AEucaryaExported

protein

modification

Bacteria and archaea have 70S ribosomes

Eucarya have 80S ribosomes

Protein

synthesis

N/A (Present in only one domain)

Motility

Nucleolus

Golgi Apparatus

Bacteria, Archaea and Eucarya

Ribosomes

Flagella

N-acetylmuramic acid (NAM)

If present in more than one domain, is the structure the same in each? If not, what are the differences?

Is this component present in Bacteria, Archaea and / or Eucarya?

FunctionCell component

32. Omnivore’s Dilemma

(10 points) On WebCT, we have been discussing chapters 1-3 of The

Omnivore’s Dilemma. If you have participated in the discussion, please circle

this question!!

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