Science Practice Challenge Questions
22.1 Prokaryotic Diversity
Cyanobacteria are single-celled organisms with the capacity to fix nitrogen, N2. Some cyanobacteria cooperatively aggregate as filaments, and heterocysts may form at intervals along the filament between a pair of vegetative (actively growing) cells. Heterocysts are specialized cells that express certain genes when nitrogen becomes limiting. The nitrogenase complex converts the nitrogen in N2 into NH3 (ammonia). This enzyme functions only under anaerobic conditions that are, in part, enforced by an O2 barrier surrounding the cytoplasm of the heterocyst, as shown below.
A. Other modifications displayed in the diagram maintain an anaerobic state and synthesize ammonia from N2. Identify four modifications of vegetative cells, either by their addition to or omission from the heterocyst. Refine the representation by drawing a line between each of the three numbered circles and the feature.
B. Further refine the representation by providing a brief description of the role of each modification in either regulating oxygen or synthesizing ammonia.
The Krebs cycle in prokaryotes and eukaryotes differs. In prokaryotes, the Krebs cycle occurs in the cytoplasm and the intermediate 2-oxoglutarate (α-ketoglutarate) is absent.
C. Construct a representation of the regulation of genes encoding the nitrogen fixation system using the elements below. The irregular shapes are either metabolites or transcription factors, NtcA, HetR, and PatS. In your representation, label each shape using the names on the left in the figure below. Your representation must account for these observations:
- when nitrogen is limiting, 2-oxoglutarate concentration in the cytoplasm increases
- HetR is transcribed when 2-oxoglutarate concentrations are low
- PatS is transcribed when 2-oxoglutarate concentrations are low
- nitrogenase is transcribed when HetR concentrations are high and PatS concentrations are low
- when PatS concentrations are high, nifX genes are not transcribed
D. Heterocysts form along the filament separated by a fixed number of vegetative cells. Based on your model of the regulation of heterocyst development, make and support a claim that accounts for this pattern.
22.2 Structure of Prokaryotes
Gram-negative bacteria have an inner cytoplasmic membrane separated by a peptidoglycan layer from a second outer membrane. In addition, transport proteins called efflux pumps span this double membrane and actively eliminate chemicals such as antibiotics that pass through porins on the outer membrane. These efflux pumps can confer multi-drug resistance, a situation that is threatening human health.
A. Explain how combining a drug that disrupts ATP synthesis in bacteria with antibiotics is a possible strategy for the treatment of bacterial infections caused by antibiotic-resistant gram-negative bacteria.
ATP synthesis in prokaryotes is accomplished by a protein that connects the extracellular space to the cytoplasm. In gram-negative bacteria, the proton gradient that supplies the free energy to convert ADP into ATP is established across the inner membrane.
B. Predict differences in the interactions of eukaryotic and prokaryotic cells with a drug molecule that successfully targets ATP synthesis and provide reasoning for your predictions.
In gram-positive bacteria, ATP synthesis is accomplished by a protein that spans the single membrane and the outer cell wall. During the production of yogurt and wine, which rely on gram-positive bacteria, the pH is controlled. Sodium bicarbonate secretions from the pancreas maintain the pH of the human intestine, where many beneficial methanogens are gram-positive bacteria.
C. Explain why homeostasis for gram-positive bacteria requires control of extracellular pH.
22.3 Prokaryotic Metabolism
That the uniformity of cell size in prokaryotes is independent of the conditions of cell growth has long been a puzzle. Suppose that cells grew for a random period of time and then divided. The largest and smallest, by sometimes dividing to make even larger or smaller cells, would be expected to broaden the distribution of cell sizes, as shown in the diagram on the left for a time, t2, after a time t1. Competing claims are made to explain the fact, however, that the distribution does not broaden: 1) There is a “timer” that initiates cell division, and 2) there is a volume threshold that, when reached, initiates cell division. Recently (Amir, Phys. Rev. Lett, 2014), a third model was suggested: From the end of the last cell division to the next, the cell volume increases by a constant value.
A. Justify the claim of the third model by i) rejecting the two alternative claims, using the fact that growth rate depends on the availability of resources and considering that regulation of expression at a critical volume would require measurement of total volume by the cell, and ii) arguing that adding a constant volume before each cell division would narrow the cell size distribution.
B. Design a plan to test both the most recent model and the timer model.
22.4 Bacterial Diseases in Humans
Escherichia coli Strain A is able to grow in a minimal medium only when supplemented with methionine and biotin. Strain B is able to grow in a minimal medium only when supplemented with threonine, leucine, and thiamine. The two strains are incubated together in a medium containing each supplement. They are then transferred to a minimal medium with no supplements, and each strain is able to grow under these conditions.
A. Describe the evidence that supports information exchange between Strain A and Strain B, and the mechanisms that can account for this behavior demonstrated by Lederberg and Tatum (Nature, 1946).
Colistin is regarded as a last-resort antibiotic in the treatment of multi-drug-resistant, gram-negative bacteria. The MCR-1 gene that confers colistin resistance was recently detected in a plasmid found in E. coli from the intestines of human patients (Liu et al, Lancet Infect. Dis., 2016). Colistin is cheap to produce, is often used as a feed supplement for domesticated animals (12,000 metric tons per year in 2015), and its use is increasing. Colistin is also unstable in water (Healan et al., Antimicrob. Agents Chemother, 2012).
B. Describe the possible biological consequences of an immediate ban on the use of colistin in agriculture.
Life on Earth is sustained by four processes that are unique to prokaryotes: 1) methanogens reduce hydrogen or carbon atoms to produce methane; 2) methanotrophs combine methane with oxygen to form formaldehyde; 3) nitrogen fixation converts N2 into ammonia; and 4) nitrification converts ammonia into nitrates. These processes recycle matter, maintaining the carbon (1 and 2) and nitrogen (3 and 4) cycles.
Methanogens are strictly anaerobic. Estimates of global fluxes of methane from major sources (Kirschke, Nature Geoscience, 2013, in units of 1012 g C/year) are shown in the figure below. Agricultural sources are predominately the microbiomes of ruminants (cows, goats, etc.) and rice cultivated in shallow ponds where anoxic compost and crop residues promote methanogen growth on roots. Other major human activities that contribute to atmospheric methane levels are landfills and natural gas drilling.
The fate of this methane is also shown. Most reacts with OH in the lower atmosphere to make formic acid, which then decomposes into carbon dioxide and water. Methanotrophs consume the remaining methane.
Methane is a component of the carbon cycle, but it is much less significant than carbon dioxide, whose major fluxes are shown in units of 1015 g C/year (NASA, 2015). Oceanic uptake and loss of CO2 are primarily abiotic. Prokaryotic marine organisms account for approximately 50% of the biotic exchanges.
A. Compare quantitatively the rates of carbon cycling as methane between the biosphere and atmosphere. Calculate the percentage of methane production that is anthropocentric (due to human actions).
B. Assuming that the rates of carbon dioxide exchange shown in the diagram are accurate, analyze these data to identify a missing contribution to the carbon budget.
Recently, it was discovered that ruminants fed nitrooxypropanoic acid reduced their methane release from digestion by approximately 50% and increased the rate of meat production by as much as 80% (E. Duin et al., Proc. Natl. Acad. Sci, 2016).
C. Since methane is a greenhouse gas, its release into the atmosphere further increases global temperatures. It has been claimed that a feed supplement program will reduce the effects of climate change. Predict the consequences of such a program and provide reasoning for your prediction.
A vertical profile of methane and oxygen below the surface of a rice paddy are shown in the graph below (Lee et al., Front. Microbiol, 25, 2015). Also shown are estimates of the relative abundance of all genera of methanotrophs (red line) and methanogens (blue line) as a function of depth. Rice paddies are the largest contributor to agricultural methane production. The estimates were based on extraction and analysis of ribosomal RNA from the soil.
D. Justify the selection of these measurements of the concentrations of two types of microbes and the gases that are consumed or produced to the development of a quantitative understanding of the habitat range of both groups and the control of methane release from rice fields.
22.5 Beneficial Prokaryotes
The human gut provides a habitat for approximately 100 trillion bacteria. Some sources claim that the surface area of the cells lining the small and large intestines is between 150 and 300 square meters and compare this area to that of a tennis court. Recent measurements, however, show that the surface area of the gut is closer to that of a studio apartment (Helander and Fandriks, Jour. Gastro, 2014) and is roughly 50 square meters.
A. Calculate the cellular surface area of the 100 trillion (1014) microbes in the typical human gut, assuming that the cells are spherical with an average radius of 0.001 mm. Use this calculated surface area to predict the relative rates of procurement of nutrients by both microbes and the host cells lining the large and small intestines.
Humans compete with microbes for nutrients, but the relationship is mutually beneficial. Between 10 and 30% of ingested food remains undigested before reaching the large intestine. Some microbial waste products, particularly H2 and CH4, are not resources for the host. But short-chain fatty acids like acetic, propionic, and butyric acids are resources that microbes extract from the undigested fraction. The large intestine of the adult human has a length of approximately 1.5 meters with a volume between 6 and 7 liters. The total volume of gut microbes is just a few hundred milliliters.
B. Predict the length of a large intestine with equivalent recovery of resources and the same transit times through the bowel if, rather than 100 trillion organisms with a total volume of 1 L, there were 100 billion (1011) organisms, each with a volume of 10-8 mL (the approximate volume of the epithelial cells lining the intestine).
The relationship between gut microbes and their host is more complex than simple resource recovery, as shown in the figure of the microbiome below. PYY is a hormone that works with the enteric nervous system lining the intestinal wall to cause changes in the period of contractions of muscles (motility) that push material through the intestine.
C. Based on the diagram, summarize the regulation of appetite by the microbiome and the elimination of waste by the host in terms of feedback loops and chemical signaling.
The microbial population of the intestine is referred to as the microbiome. Undernutrition and obesity are both symptoms of malnutrition, and populations of the microbiome vary with the type of malnutrition (Brown et al., Nutr Clin Pract, 2012). The microbiome of humans can be transplanted into germ-free (GF) mice to observe the effects of diet in a controlled experiment of relatively short duration. The microbiomes of healthy and undernourished 6-month-old children were transplanted into GF mice whose growth is graphed below. Growth in both length and weight were reduced when the source of the microbiome was the undernourished child (after Blanton et al., Science, 2016). Both groups of mice were provided with the same nutritional resources.
D. Pose two scientific questions that, when investigated, could lead to a solution for the stunting of growth caused by undernourishment in early infancy that affects millions of children.
Human growth hormone stimulates the release of insulin-like growth factor 1 (IGF-1). IGF-1 is a messenger that activates the production of bone cells called osteocytes. The data (after Schwarzer et al., Science, 2016) show concentrations of this growth factor in mice with no microbiome (GF), wild-type mice whose microbiome and growth provide a control (WT), and mice whose microbiome population is composed entirely of Lactobacillus plantarum (two strains labeled L1 and L2). Lactobacillus is one of many hundred genera of microbial inhabitants of a healthy human intestine.
E. Analyze these data in terms of the potential for disruption of human bone growth due to loss or reduction in diversity of the microbiome.