Module 1
Consider the case of one E. coli cell undergoing binary division with sufficient nutrients. After three generations of cell division, what proportion of progeny cells will have "ancestral" cell poles (i.e., will possess the same cell wall as was present in the starting parent cell)?
1/4
Consider the following cell fractionation procedure. Place the appropriate labels next to the samples containing the respective cellular "compartments." Note that in each step, the pellet is being resuspended and subjected to a subsequent round of centrifugation.
A. outer membrane B. periplasm C. inner membrane D. inner and outer membranes E. cytoplasm F. spheroplasts and outer membranes
Florence Nightingale's statistical analysis of the leading causes of mortality of British soldiers convinced the British government to do all the following except A. supply soldiers with additional weapons and ammunition.B. improve the quality of water delivered to soldiers.C. improve the ventilation systems in army hospitals and soldiers' living areas.D. improve the standards of army hospitals.
A. supply soldiers with additional weapons and ammunition.
Bacteria exposed to quinolone-type antibiotics rapidly become unable to
B. condense and package their chromosomes. C. replicate their DNA. D. carry out normal gene expression.
Of the reactions that involve reactive oxygen species as shown in the figure below, the one marked -------is the only one not catalyzed by an enzyme.
B; look up
Identify the three domains of life according to the classification system developed by Carl Woese.
Bacteria, Archaea, Eukarya
Which criteria of Koch's postulates would not necessarily be met when trying to link a particular bacterium to a latent infection, such as tuberculosis or Lyme disease?
C. The microbe is found in all cases of the disease but is absent from healthy individuals.D. When the microbe is introduced into a healthy, susceptible host, the same disease occurs.
Label the parts of the microscope in the figure.
E: Eyepiece C: Objectives F: Stage A: Condenser D: Diaphragm B: Light source
Prions are aberrant proteins that cause Creutzfeldt-Jakob disease in humans, mad cow disease from contaminated beef, and scrapie in sheep. Unfortunately, prions have demonstrated the highest resistance to methods of chemical and physical control, including the ability to survive nucleases and UV irradiation. Prions propagate aggregates of prion proteins by altering the normal quaternary conformation of PrPC in the brain. Based on the quaternary structure shown below, which of the following hypotheses could be supported?
the increased presence of beta pleated sheets confers resistance to PrPsc
A bacterial cell is infected by a phage with an RNA genome. The bacteria has not encountered this phage before. Which of the following correctly describes host defense mechanisms that can help protect the bacterial cell?
Neither CRISPR nor restriction endonucleases can provide defense.
The process by which bacteria take up free DNA from the environment is known as ------ . This process has been manipulated in the laboratory and is used routinely the fields of biotechnology and genetic engineering.
transformation
Which of the following would not be included in the formulation of a defined medium?
tryptone
Which of the following best describes how programmed cell death happens in Escherichia coli under low-nutrient conditions?
unstable antitoxin
Good resolution of microscopic objects using electromagnetic radiation (e.g. visible light) requires which of the following?
wavelength smaller than the object contrast magnification
Multiple genes are involved in the cell cycle and polarity of Caulobacter crescentus, which can exist as both a free-swimming, flagellated swarmer cell or a nonmotile stalked cell. A model of this is presented in the figure. Knowing that septation is tightly regulated with DNA replication, what would you expect to see in a divJ- mutant strain of C. crescentus grown in nutrient rich conditions if DivJ is involved in both cell polarity and DNA replication?
No growth, and all cells remain as swarmers.
Rank the following microorganisms from largest to smallest in size.
Pelomxya- Ameba found in soil Spirogyra- Aquatic algae Escherichia coli- bacteria found in the human colon Prochloroccous- photosynthetic marine bacteria varicella- zoster virus- the virus that causes chickenpox
Under what condition would a temperate bacteriophage infecting Staphylococcus aureus (an aerobic bacteria commonly found on the human body) be shifted by environmental cues from lysogeny to a lytic cycle? The temperate phage lambda can undergo two life cycles depending on the environmental cues. During which cycle does phage lambda form a prophage? Temperate bacteriophages can undergo two routes of infection. During ----- the phage DNA is inserted into the bacterial genome and replicated each time the bacterial cell divides.
when phage-infected cells are incubated at 50°C lysogeny lysogeny
In what ways do virions resemble living cells?
Some virions possess genes for tRNA. Their genomes can be larger than some cellular genomes. They possess genes that can direct their own replication.
Why do viable but nonculturable (VBNC) microorganisms, such as Vibrio cholerae and Salmonella typhi, pose a public health risk?
These microorganisms can be pathogenic. Many of these microorganisms are naturally occurring in the environment and therefore cannot be eradicated. Laboratory detection tests can be negative, even in the presence of the organism.
Scientists have used electron microscopy for many years to study structures of microbes. New and improved techniques include cryo-electron microscopy (cryo-EM), which combines flash-freezing with high-intensity electron beams to create high-resolution images. Modern high-intensity electron beams have helped cryo-EM techniques to image the internal ultrastructure of one of the smallest microbes in the ocean, Pelagibacter. What can high-intensity electron beams do that makes them more effective than earlier instruments? How does flash-freezing the samples examined by cryo-EM improve the resolution of the resulting images?
detect smaller structures Flash-freezing retains water in the sample but eliminates ice crystals.
During the process of cell fractionation, isolation of inner and outer membrane components may be accomplished via ultracentrifugation in a sucrose gradient. This technique partitions particles on the basis of -----.
density
You remove old grapes from the refrigerator and notice a white spot on one of them. Because the spot appears fuzzy, you suspect that it is mold. Your ability to view these organisms with the unaided eye is best described as which of the following?
detection
Identify the function(s) of the viral capsid.
determines the shape of the virion protects the viral genome
Consider this image of colonies growing on MacConkey agar and then answer the following questions. MacConkey agar is an example of a medium that is which of the following? MacConkey agar is most suitable for the cultivation of which of the following?
differential based on ability to ferment lactose selective for gram-negative bacteria enteric pathogens (such as Salmonella and Shigella)
Which of the following would have the greatest effect on cell function due to changes in pH?
disrupting protein secondary structure, thus decreasing enzyme activity
When could virions (such as T4 phage particles) be detected within an E. coli cell?
during the end of the lytic cycle
Label the steps and spectra of fluorescence shown in the following figure.
e and g switched
Viruses are most commonly known for infectious diseases such as influenza or measles; however, not all viruses pose harm to the human host, and, in some cases, they can contribute to human survival. Which of the following is an example of the benefits conferred by endogenous viruses?
encoding placental proteins that are essential for early development of human embryos
In this experiment, Escherichia coli cultures were grown at various pH values, and the levels of antiporters were assayed (higher levels indicate upregulation of that antiporter). Also shown is a diagram of the sodium proton antiporter and the putative potassium proton antiporter in the cell, to help you recall whether the protons are being pumped into the cell or out of the cell. Based on which antiporter(s) is/are upregulated, determine which experiment was performed at a pH below optimum (pH 5.5).
experiment a
Which of the following best describes the unusual image alterations that occur when using differential interference contrast microscopy?
false 3d effect
Dark-field microscopy is especially useful for visualizing ------, structures found in some bacteria that are typically not easily detected using light microscopy.
flagella
For an acid-loving microbe (acidophile) living in an acidic environment in the presence of both penicillin and tetracycline, which of the following will end up crossing into the cell and impacting the internal cytoplasmic pH?
form b
Organic farmers use the bacterium Bacillus subtilis to prevent downy mildew in grapes and powdery mildew in greenhouse tomatoes. The farmers are therefore using this bacterium as a ------
fungicide
All of the following organisms can cause some form of pneumonia or walking pneumonia. Some of them are vulnerable to the antibiotic penicillin. Imagine you are conducting an experiment to see which will survive in the presence of penicillin.Choose the graph below that best matches your predicted results. The organisms used in the experiment include the following: 1) the firmicute Streptococcus pneumoniae, 2) the proteobacterium Escherichia coli, 3) the fungus Candida albicans, and 4) Mycoplasma pneumoniae, a bacterium with no cell wall.
graph a
The composition and health effects of the human microbiome are currently topics of extensive interest and research. For example, it is becoming increasingly apparent that the initial development of a robust intestinal microflora is dependent on many factors in a newborn's life, beginning with the mode of delivery (vaginal vs. cesarean section). Other potential influences include premature birth, exposure to antibiotics, and even mode of feeding. Suppose you were interested in the effect of breastfeeding versus formula feeding on the composition of gut flora in newborns. As part of your experiment, stool samples from healthy babies in the study get plated on various agar media. You notice that greater numbers of colonies are recovered when samples are plated on blood agar compared to Luria Bertani (LB) agar. After some diligent subculturing, you isolate several bacterial species capable of slow growth on the blood but not on the LB agar. You correctly surmise that these organisms
have extensive and complex nutritional requirements not met by LB agar.
Evidence suggests that organic carbon released in membrane vesicles by the marine cyanobacterium Prochlorococcus, contributes to their survival by attracting:
heterotrophic bacteria
You have isolated a mutant strain of Bacillus subtilis (which you designate wimP) whose endospores can be killed by boiling water. When you analyze the endospores produced by this strain, you find that compared to endospores produced by the parent (a wild-type strain), the wimP spores have significantly
higher water content
Predicting relatedness of viruses is often very difficult if relying solely on genomic sequences since viruses that share a host can exchange genetic components. This suggests that the ------plays a critical role in the evolution of viruses. Along this vein, examining ------can demonstrate functional relatedness of viruses that can be obscured in genomic sequences due to mutations and continual exchange of genetic information between co-infecting viruses.
host range, proteomics
Which of the following is the best example of an extremophile?
hyperthermophile bacteria Methanopyrus kandleri
Where would extremophiles most likely make up the greatest percentage of microorganisms?
in hydrothermal vents
The presence of hydroxyl radicals indicates that the cell likely has which of the following?
iron
Label the four phases of the bacterial growth curve pictured here by dragging the labels to the correct targets. Suppose the researcher who ran this experiment also measured growth of the culture by taking optical density readings using a spectrophotometer. During which phase would the data be least proportional to that in the above graph (obtained using numbers of viable cells)?
lag, log, stationary, death death phase
Spontaneous generation is the notion that
living organisms arise from nonliving matter.
Despite the wide range of habitats in which they may form, biofilms form in a similar progression of stages. Label the piece of art with the labels that correspond to each stage of biofilm formation by dragging them to the correct targets.
look up
Examine the following illustration of cross-bridge formation during construction of the peptidoglycan cell wall (in this case, from E. coli) and place the labels on the correct targets. Bond hydrolyzed by lysozyme.N-acetylglucosaminePenicillin inactivates the enzyme that generates this bond.This amino acid is not found in proteins.Vancomycin prevents crosslinking by inhibiting this process.N-acetylmuramic acid
look up
Label the steps in which clustered regularly interspaced short palindromic repeats (CRISPR) are used to protect a bacterial cell. Note that the diagram should be labeled clockwise from the phage entry.
look up
The figure shows different methods that a bacterium such as Escherichia coli uses to maintain internal pH as the external pH changes. Label the boxes according to the methods used by dragging the labels on the right to the correct targets.
look up
The following illustration depicts a cell that is synthesizing membrane transporters. Correctly label each of the targets with the corresponding item on the right. Which key enzyme directly involved in the above process is not explicitly shown in the illustration?
look up RNA polymerase
Because iron is an essential nutrient but exists in low usable amounts in the environment, cells will go to great lengths to acquire it. For example, many bacteria produce and secrete iron-binding molecules (of varying structure) known as siderophores. The following diagram illustrates how E. coli can scavenge iron using a specialized siderophore called enterochelin. Label the following piece of art with the labels on the right by dragging them to the correct targets. The FepCGD complex is a type of
look up ABC transport
Pseudomonas aeruginosa represents a well-studied model organism for single-species biofilm formation. This research is also of direct medical significance because of the propensity of these bacteria to form biofilms in the----- of patients with cystic fibrosis. Which of the following early events in biofilm formation by Pseudomonas aeruginosa involves the extension and retraction of a specific pilus? Mature biofilms of Pseudomonas aeruginosa produce flagellated cells for what purpose?
lungs twitching motility to go in search of new places to colonize
The cell envelopes of mycobacteria contain large amounts of these molecules, which make them "acid-fast."
mycolic acids
Most human pathogens are ----
neutrophiles
Certain aquatic bacteria use magnetosomes to direct them to environments with optimal levels of -----.
oxygen
Food chains can be used to describe the relationships among all the organisms in an environment. Food chains describe not only which organisms are consumed by which but also other ways in which organisms depend on each other. In the marine environment, which types of organisms form the base of the food chain? Cyanobacteria do not rely on other organisms for nutrition, but they do depend on other organisms for waste product removal. Which cyanobacterial waste product can be toxic to them?
photoautotrophic oxygen
In the figure, identify which of the shapes are spirochetes viewed through either a light microscope (LM) or a scanning electron microscope (SEM), which shapes are bacilli (either LM or SEM), and which shapes are cocci (either EM or SEM).
pic
Label the cells to correctly depict the endosymbiosis theory proposed by Lynn Margulis.
pic
Label the following figure with the proper associations of light interacting with objects.
pic
Label the steps and spectra of fluorescence shown in the following figure.
pic
The human body harbors a complex bacterial ecosystem within the intestinal tract that we refer to as the gut microbiome. These microbes provide key nutritional benefits to our bodies and are also required for the development and maintenance of a healthy immune system. Imbalances and disruptions in the gut microbiota have been linked to numerous ailments (such as obesity, inflammatory bowel syndrome, and asthma). Obviously there is significant interest in how a healthy gut microbiome is maintained by the host. And given that the intestine can be thought of as a type of culture system, we can design laboratory experiments to test the effects that different variables may have on microbiome stability. The human intestinal tract has been likened to a culture vessel. The most commonly used lab culture systems include batch culture (growth in a test tube or flask) and chemostats. Sort the following list of features into the appropriate categories depending on whether they are characteristic of a batch culture, the gut tract, a chemostat, or gut and chemostat.
pic
Which of the following are characteristic of a vegetative cell, endospore, or both? Which of the following statements is NOT true of sporulation? What is the role of dipicolinic acid in endospore formation?
pic it represents an important form of reproduction for some bacterial species it aids in dehydration of the endospore and enhances heat resistance
Which of the following adaptations helps microbes growing at the bottom of the ocean?
polyunsaturated fats in phospholipids to help increase membrane fluidity
Which of the following is a common compatible solute used by microbes to prevent water loss in a hypertonic medium?
potassium ion
Within the order of viruses called Caudovirales is a/an ----that possesses a thin filamentous tail used to infect Staphylococcus aureus. Since Caudovirales viruses encode virulence factors such as Panton-Valentine leukocidin, which allows bacterial escape from leukocytes, this virus and bacteria have formed a/an ----relationship.
prophage, mutualistic
The "Great Plate Count Anomaly" refers to the discrepancy between the number of microbes that are present in a particular sample and the number that can be grown in the laboratory. In fact, it is estimated that upwards of 99% of prokaryotic species lack a cultured representative. Still, we can both detect these microbes and gain insight into their phylogenetic relatedness, based on the sequences of their ------genes that are acquired from samples using -------.
ribosomal RNA PCA
Many bacteria adapt to adverse environmental conditions by modifying the composition of their cell membranes. For example, the membranes of bacteria subjected to heat stress often contain high levels of which of these compounds?
satturated fatty acids
Tomato mosaic virus (ToMV) causes significant economic losses in agriculture and food crops. ToMV is not only a problem for tomatoes; it can also impact peppers, potatoes, apples, and cherries. Upon infection, the virus causes the plants to yellow and have stunted growth and reduced yield. Fortunately, similar to humans, plants have adapted defenses to survive viral onslaughts. The discovery of ________ in plants has led to a deeper understanding of how cells protect themselves from stress responses and, of course, viral infections.
siRNA for RNA interference
Resolution refers to which of the following?
smallest distance by which two objects can be separated and still be distinguished as separate
Which of the following criteria is not part of the International Committee on Taxonomy of Viruses (ICTV) classification system?
spike proteins
Crop rotation (alternating planting of grains and legumes) has been practiced for thousands of years, long before anyone understood the contribution of to ------enhancing soil fertility.
symbiotic nitrogen fibers
Sterilization indicates
the elimination of all microbes.
Identify the parts of this membrane-associated complex by dragging the labels to the appropriate targets.
A. ATP B. ADP + Pi C. Cytoplasm D. H+ E. Periplasm
Which viral genome is likely to require an RNA-dependent RNA polymerase for transciption upon viral entry?
(-) sense single-stranded RNA
In what ways are wet mount slide preparations disadvantageous when viewing live specimens?
- bacteria appear "hollow" - little contrast with external medium - boils specimen
Analyze the following statements to identify which techniques have similarities to scanning electron microscopy (SEM) for the reason given.
-SEM and transmission electron microscopy use the same illumination source. -SEM and differential interference contrast microscopy both provide a 3D image of the cell surface. -SEM and differential staining both only use one stain.
Drag the correct criteria to the illustration to complete Koch's postulates.
1. the microbe is found in all cases of the disease but is absent from healthy individuals2. the microbe is isolated from the diseased host and grown in pure culture3. when the microbe is introduced into a healthy, susceptible host, the same disease occurs4. the same strain of microbe is isolated from the newly diseased host
Florence Nightingale was the first to use medical statistics to identify and highlight leading causes of mortality. Rank the following items from the most significant cause of death to the least significant in the British army during the Crimean War, according to Nightingale's results.
1. Infectious Disease2. Battle wounds3. All other causes of death
Which of the following is important in determining the focal distance of a magnified object?
1. refractive index of the lens material2. degree of curvature of the parabolic lens
The dilution streaking technique is one of the first things a student learns in microbiology laboratory. It is easy to perform, but there are some common missteps you will want to avoid. Watch the video for a detailed tutorial on how to produce a streak plate while thinking about the importance of each step. After watching the animation, place the nine steps of the dilution streaking technique in the correct order. The dilution streaking technique can take a bit of practice to master. Which of the following represent sources of error that would likely result in failure to obtain isolated colonies? The dilution streaking technique is probably the most common procedure performed by microbiologists on a daily basis. It is not, however, particularly useful for
1. sterilize the loop ( & allow to cool), use it to obtain bacterial inoculum 2. remove sample bacteria from culture flask/plate using sterile loop 3. inoculate section of agar petri dish by sweeping loop back & forth across surface 4. flame loop 2nd time & allow to cool 5. using loop, streak cells from 1st area onto fresh section of agar 6. flame loop 3rd time & allow to cool 7. using loop, draw cells from 2nd area onto another fresh section of agar 8. sterilize loop final time 9. place correct petri dish plate in incubator B. flaming the loop immediately after obtaining the bacterial sample C. forgetting to flame the loop before streaking sequential sections of the plate E. not creating a small section of overlap across sequential sections B. calculating the concentration of viable cells in a culture.
Consider the following experiment involving a log-phase batch culture of E. coli. The objective is to determine the number of viable cells per milliliter. We do this by first serially diluting the culture and then plating a portion of various dilutions on nutrient agar (as shown below). After incubation, we can count the colonies that have grown, and then multiply by the inverse of the corresponding dilution factor to obtain an estimate of the concentration of viable cells in the starting culture. Because we want to express this value as some number per milliliter, we will also need to adjust for the amount that was tranferred to the agar plates (typically 50 to 100 µl). Most colonies will arise from the multiplied division of one individual cell that landed at that particular spot on the agar. However, some species naturally grow as chains or clumps, and therefore one colony does not always equal one cell. This is why instead of "cells" per ml, we refer to counts as "colony-forming units" (or CFU) per ml. When deciding what data to use, plates with less than 30 colonies should be excluded from the analysis because small errors in technique or sampling would become unacceptably amplified. Very crowded plates (that is, with more than 300 colonies) should also be excluded. This is because the potential for two cells to land close together and form a single colony is greater when more concentrated samples are plated. Keep this in mind as you consider the data below. Examine the following illustration. Based on these data, the viable counts in the original culture is estimated to be ------- CFU / ml .
6.05 x 10^7
Examine the following schematic of a bacterial flagellum and correctly label the targets. C
A peptidoglycan B rotor c outer mem d flagellar filament e cell mem f MotAB
Cell biologists studying the mobility of plasma membrane proteins fused mouse and human cells together, creating a heterokaryon. They then examined the localization of mouse and human proteins over time. Initially the mouse and human proteins were restricted to separate halves of the heterokaryon. Over time the mouse and human proteins mixed, with each protein eventually being present over the entire cell surface, consistent with proteins being able to move within the plane of the membrane. What techniques could have been used to examine the locations of the mouse and human membrane proteins?
A.) fluorescence microscopy with fluorophore labeled antibodies E.) fluorescence microscopy with gene fusion reporters
Several mycobacterial species are pathogenic for humans, including Mycobacterium leprae (the causative agent of leprosy) and Mycobacterium tuberculosis. Recent studies have shown that asymmetry during cell division results in subpopulations of either rapidly elongating or slowly elongating cells (termed "accelerators" and "alternators," respectively). Researchers are now interested in how cell polarity and resulting physiological differences may influence the effectiveness of certain antibiotics used to treat mycobacterial diseases. Isoniazid inhibits mycolic acid synthesis and is a first-line antibiotic used to treat tuberculosis. How would you predict accelerators and alternators might vary in their sensitivity to this drug?
Accelerators should be more sensitive than alternators.
Why are elements such as cobalt, copper, manganese, molybdenum, nickel, and zinc referred to as micronutrients?
All cells require these elements in trace amounts.
Which of the following is not a reason why opportunistic pathogens, such as Candida albicans and Staphylococcus aureus, are public health concerns?
All individuals who are exposed to the pathogen will develop an infection.
Which of the following statements is true about all microbes? A. All microbes contain a nucleus.B. All microbes contain a genome.C. All microbes are single cells.D. All microbes cause disease.
B. All microbes contain a genome
A researcher was trying out different chemical compounds as additives to her new formulation for a liquid bandage, something to put on cuts in order to seal them off and help the healing process. She noticed that some of the additives seemed to prevent growth of bacteria on plates, and when she looked at cells subjected to one of the compounds, DK64, after an hour of treatment she saw something like what is seen in the figure below. Based upon these observations, which of the following ideas best describes what is happening with the cells?
DK64 is acting by weakening the cell walls, which likely leads to cells bursting open when subjected to hypotonic conditions.
Match each genome with the first polymerase it uses to initiate viral synthesis.
DNA Polymerase- single stranded DNA- double stranded DNA Host RNA Polymerase- (+) single strand RNA vRNA Polymerase- double stranded RNA- (-) single strand RNA Reverse Transcriptase- double stranded DNA pararetrovirus- (+) RNA retrovirus
Unlike eukaryotes, prokaryotes do not undergo mitosis or meiosis. Instead, most prokaryotes grow by a process known as binary fission, whereby an individual cell produces two identical daughter cells, each with its own chromosome. Watch the following animation on DNA replication during bacterial cell division and then answer the questions below. Order the following events as they occur from beginning to end during DNA replication in a dividing cell. What type of enzyme in the replisome catalyzes addition of nucleotides to the growing DNA strands? Regarding the enzyme in Part 2, ----- of these would be required if a new round of DNA replication began before the first one terminated. Which of the following is true of the newly synthesized daughter chromosomes?
DNA at origin unzips, and two replication forks form Replisomes synthesize daughter chromosomes bidirectionally terminator site is replicated septum forms Daughter cells separate Polymerase 12 Each chromosome contains one parental and one newly synthesized DNA strand.
Gut bacteriophages, or "coliphages," are members of a microbial community that modulates human digestion, the immunesystem, and mental health. Historically, bacteriophages have provided some of the most fundamental insights in molecular biology. In 1952, Alfred Hershey and Martha Chase demonstrated that the transmission of DNA by a bacteriophage to a host cell led to the production of progeny bacteriophages.The discovery by Hershey and Chase confirmed that Another fundamental discovery provided by André Lwoff and Antoinette Gutman demonstrated that a bacteriophage could integrate itself within the bacterial genome. This was the first recognition that _______ could enter or exit a cellular genome.
DNA is the hereditary material of life, genes The avian influenza strain would only infect the lower respiratory tract of humans.
What are the components common to all virions?
DNA or RNA genome and capsid
Scientists are continuously advancing our understanding of the importance of the human gut microbiome in health and disease. Which of the following is not a challenge associated with studying the human microbiome?
Genomic sequencing of the gut microbiome cannot be completed if the microorganisms cannot be cultured in the lab.
The following are all used in applications to obtain estimates of the numbers of cells in a given sample (such as food, culture flask, or soil). Sort the items depending on whether the resulting data would represent direct or indirect counts.
Indirect counts: Protein levels, dry weight, optical density, pour plates, and spread plating Direct counts: Viability stains, Petroff- Hausser chamber, Fluorescence- activated cell sorter (FACS
How does the cell membrane affect osmolarity?
It is semipermeable, allowing water molecules to move across while tending to keep solutes in (or out).
Sort the following fluorophores into their proper categories. DNA/chromosomes vs other components
Label DNA/chromosomes: labeled antibody to helicase, origin sequence tagged with fluorophore, DAPI.Label other components: FM4-64 lipophilic dye, labeled antibody to aquaporin, fusion reporter of GFP and ATP synthase, labeled antibody to B-galactosidase
In response to extreme starvation, some bacterial cells undergo programmed cell death (PCD). In E. coli, PCD is mediated by the toxin-antitoxin pair MazF (the toxin that initiates PCD) and MazE (the antitoxin that keeps MazF in check). PCD lowers the fitness of the bacterial cell, but if the cells in the population are genetically related, then the sacrifice of some cells to keep a subset of the population alive may increase the fitness of that shared genome. There is, however, the risk of mutant "cheaters," cells that do not undergo PCD in response to extreme stress but benefit from the nutrients released from dead cells. Loss of which proteins could result in a cheater cell phenotype?
MazF ClpAP protease
Which of the following describes media and conditions that will be selective for nitrogen-fixing organisms?
Media lack any nitrogen-containing compounds, but N2 is present in the atmosphere.
As an up-and-coming scientist, you decide to create mutant bacteriophages to better examine structural function. Your first mutant lacks a sheath motor protein, so you decide to call this MutS. To determine the loss of function, you add MutS at a multiplicity of infection (MOI) of 1 to Escherichia coli cells and examine the rate of infection. You're very surprised to find that none of the Escherichia coli cells are infected. What happened?
MutS prevented the sheath protein from contracting.
E. coli is a normal inhabitant of the mammalian colon, where it colonizes the mucosal layers. It can also survive quite well outside of the host (in soil, water, produce, and so on), so its presence serves as a convenient indicator of fecal contamination. But the intestine differs substantially from these other habitats with respect to levels of oxygen, nutrients, toxic substances, and so on. To enhance its survival in various niches, E. coli has developed a number of remarkable adaptations. As a member of the Proteobacteria, E. coli possesses a typical Gram-negative cell envelope. In environments outside of the colon, the cells are able to maximize uptake of nutrients by up-regulating expression of What would be the phenotype of an E. coli mutant that constitutively expressed a large-diameter porin (i.e., even in the intestine)?
OmpF D. It would be more sensitive to bile salts and antibiotics such as ampicillin.
What is the effect on species diversity of dumping untreated sewage into a waterway?
Overall negative due to eutrophication, resulting in unrestricted growth of one species able to grow to extreme numbers and outcompete other species.
Classify each of the following groups of organisms as prokaryotes or eukaryotes by dragging the items into the correct category.
Prokaryotes (Archaea, Bacteria)Eukaryotes (Plants, Animals, Protists, Algae, Fungi)
Rhodopseudomonas palustris is a marine microbe with a complex metabolism. It can grow heterotrophically with sufficient nutrients, or it can enter into a state of growth arrest if carbon and nitrogen are in short supply. Even though the cells are not growing and not producing biomass, they still must make repairs to DNA and proteins that are damaged due to environmental factors. How does R. palustris generate sufficient energy to make these repairs without carbon or nitrogen sources? The accompanying graph shows two identical cultures of R. palustris starved for carbon and oxygen. One of the cultures was kept in the dark (open black circles) while the other was exposed to light (closed red circles). Two weeks into the experiment there was a great difference in the number of viable cells in the two cultures. Which statement best summarizes the results of the experiment?
R. palustris switches to photosynthesis to fix CO2, and after this step, cells can generate new components autotrophically. The number of cells in the light exposed culture did not change over the course of one month while the number of cells in the dark culture dropped greatly over the first two weeks and did not recover.
Research by Matthew Sullivan and his colleagues has shown that viruses are very common in marine systems. Why were marine viruses overlooked for so many years? How are Matthew Sullivan and his colleague able to link viruses to the hosts they infect?
Researchers tried to isolate marine viruses using non-marine host cells. They connect virus genome data with viral abundance data.
The relationship between the heterocysts and vegetative cells of Anabeana (a cyanobacterium) is similar to that of
Rhizobium and root nodules of leguminous plants.
Archaea are prokaryotic cells, yet based on the comparative analysis of ------ , archaea are more closely related to eukaryotes than to bacteria.
Ribosomal RNA (rRNA)
Since microbial growth rates in general follow the Arrhenius equation around their optimal growth temperature, what would you expect to happen for mesophilic bacteria shifted from 37°C to 27°C?
The growth rate would be down one-half.
A research lab is using DNA microarrays to examine gene expression in Salmonella enterica during stress. It was noted that when exposed to nutrient limitations, 20 new genes were expressed (as compared to normal laboratory growth conditions); when exposed to oxidative stress, 24 new genes were expressed; and when exposed to low pH, 15 new genes were expressed. The lab then subjected the bacteria to growth in macrophage phagolysosomes, which mimicked the previous three conditions, and noted 59 new genes being expressed. Which of the following would best explain this result?
The result is most likely a coincidence since some of the genes for the different stressors would overlap, some genes wouldn't be expressed under the combined conditions, and some new genes would likely be expressed due to the unrecognized stress of growing in the phagolysosome
Many bacteria and archaea live at the bottom of oceans where the hydrostatic pressure is extreme, and temperatures are low. Scientists are just beginning to learn how these piezophiles are adapted to their environments. E. coli is a barosensitive organism. How does high pressure affect E. coli ribosomes? The cytoplasmic membrane is another cell component that is sensitive to pressure. How does pressure alter cell membranes, and how do barophiles adapt?
The ribosomes dissociate Pressure makes cell membranes less fluid. Barophiles adapt by using high levels of polyunsaturated fatty acids.
Plaque assays are notoriously finicky assays, and whether for a bacteriophage or an animal virus, they will require a soft agar overlay. Which of the following best explains the rationale for this approach?
The soft agar overlay prevents the free diffusion of progeny virions to cells.
Sallie Chisolm and her colleagues have shown that the marine cyanobacterium Prochlorococcus produces large amounts of membrane vesicles and releases them into the open ocean. Which of the statements below best describes the vesicles released by Prochlorococcus? Membrane vesicles produced by some bacteria are made of outer membranes only and contain only periplasmic contents. However, the Prochlorococcus vesicles are made of both inner and outer membranes and contain cytoplasmic contents. What is the best evidence to show that Prochlorococcus vesicles contain cytoplasmic components and not just periplasmic components?
The vesicles are small membrane-bound sacs containing RNA, DNA, and proteins. The vesicles contain nucleic acids.
You have isolated a microorganism from seawater that contains thylakoid membranes, gas vacuoles, and carboxysomes. It is most likely
cyanobacterium
Cell culture methods provide a fruitful avenue to study viral infections in a closed system. This approach, however, is not without limitations. Which of the following is an obstacle to the the propagation of viral strains in cell culture over time?
Virus strains can evolve for tissue culture and no longer be viable for animal research.
Viruses and phage are key players in marine ecosystems with millions of virus-like particles per milliliter of seawater. Two key roles have been identified for marine viruses: driving biodiversity and nutrient cycling. What key feature of marine viruses drives biodiversity in the oceans? Why is the viral shunt so important in marine ecosystems?
Viruses have very limited host ranges. The viral shunt generates dissolved organic and inorganic nutrients that can be used by other organisms.
A pure culture refers to
a culture that contains a single type or strain of microorganism.
Assume you are using a microscope that has the ability to provide specific wavelengths of light. Which of the following provides the best minimum resolution distance?
a system using a wavelength of 400 nm with an angle of the light cone being 72° in air
The ability to move from one place to another is useful. Many bacteria (and archaea) are motile by means of rotary flagella. Watch the video below and answer the following questions. Which of the following scenarios would cause a peritrichously flagellated bacterium (like E. coli) to swim in a forward motion? Upon reorienting after a tumble, an E. coli cell Complete the following sentence by filling in the blanks with one of the word pairs below.Compared to a random walk, a biased random walk has ______________ runs and a _____________ frequency of tumbling.
all flagella turning counterclockwise points itself in a random direction. longer/decreased
Which of the following are associated with X-ray diffraction analysis?
allows visualization at an atomic the level is based on the principle of wave interference requires formation of pure crystals of specimens
Examine the art, then complete the following sentences. This is an example of------ , which uses energy from ------. The blue squares represent the substrate being -------
antiport chemical gradient imported
Water molecules are sufficiently small that they do not require specific transporters to cross biological membranes. But because they are polar, diffusion of these molecules across the phospholipid bilayer is slow. Peter Agre won the 2003 Nobel Prize in Chemistry for his discovery that the rapid movement of water into and out of cells occurs via-----
aquaporins
Permeases, periplasmic nutrient-binding proteins, and membrane-spanning pores (porins) all function to
assist in the uptake of molecules too big or polar to diffuse across lipid bilayers.
Micrococcus tetragenus is one cause of bacterial pneumonia. When observed under the microscope, the cells are grouped as tetrads (as reflected in the species name). This arrangement results from septation that occurs
at right angles.
During a period of time outside the host, a virus may become ----- and lose many factors that are required for infections. These viruses stimulate the immune system with much lower mortality than the fully virulent strains.
attenuated
Below is a graph of growth rate of different kinds of bacteria at different pressures. The red graph line in the figure best represents a ----- microbe.
barotolerant
While not all biofilms are bad, the problems they cause in industrial and medical settings necessitate strategies to discourage their formation. Because of the critical role of quorum sensing in producing biofilms, chemicals that can disrupt this communication network are of particular interest. Suppose you have isolated a compound that alters the quorum signal of Pseudomonas aeruginosa, such that it cannot interact with its normal receptor. Bacterial cells targeted by such a disrupter would most likely
be similar to free-living cells in their sensitivity to antibiotics.
ABC transporters are diverse and numerous. Bacteria often have many different ABC transporters to take advantage of specific nutrients in their environment. Researchers can learn much about a bacterium's lifestyle using genomic approaches to identify ABC transporters and their substrates. Which organisms produce alginate, the substrate for the AguEFG transporter system of the marine microbe Thermotoga maritima? How can purified siderophores from one bacterium be used to inhibit the growth of another bacterium?
brown seaweeds The siderophores from one bacterium can absorb free iron in the media or surrounding environment, thereby depriving the second bacterium of the needed nutrient.
Label the appropriate steps of the Gram stain in the figure below.
ch 2 slides
Label the following illustration of a bacterial cell (plasma) membrane by dragging the items to their respective targets.
ch 3 slides
The phenol ------ is used to compare the maximum effective dilution of a test substance to the maximum effective dilution of phenol to determine the test substance's relative effectiveness in killing microbes.
coefficient