MicroBio chapter 4

Why is iron so often a limiting nutrient, when it seems to be so abundant in the environment, and how can organisms overcome this problem?

Iron is usually not free in nature but locked up as Fe(OH)3 which is insoluble and unavailable to cells. Siderophores are molecules produced by some cells that have a very high affinity for soluble ferric iron. These molecules scavenge any small amount of soluble iron and transport it into the cell.

E. coli reprograms during the stationary phase. What are some of the things it does to protect itself?

It decreases its size so that less nutrient is required for maintenance. When it is under stress, it synthesizes various enzymes to protect itself. Some of these handle oxygen radicals, protect DNA and proteins, and increase the amount of crosslinking in peptidoglycan. All of these adaptations result in a stronger, more resistant cell.

When studying the metabolism of an organism, why is it better to grow organisms in a defined synthetic medium instead of a complex medium?

It is difficult to characterize an organism's metabolism when it is growing in a complex medium because the organism is supplied with all of its needs, so it is impossible to determine which metabolic pathways the organism possesses. In a synthetic medium, various substances can be added to determine which ones the organism needs and which ones it can make.

Which of the following is NOT true about the substratebinding protein (SBP) of the ABC transport system?

It is found in the periplasm of Gramnegative cells, It is found tethered in Grampositive cells, It binds to the periplasmic face of the channel and releases the solute, It snags the appropriate solute. ------>It is required for both the uptake and efflux systems.<-------

All of the following are true about the MacConkey medium EXCEPT:

It is selective, It contains bile salts, It is differential, It is both selective and differential. ----->Lactose fermenters appear colorless.<------

Why can't most organisms use the nitrogen gas that is so prevalent in the atmosphere? How do these organisms acquire a usable form of nitrogen?

Nitrogen gas has triple bonds that each hold two atoms together. These triple bonds are very stable and require a large amount of energy to break, and most organisms are unable to break the bonds. Organisms that can't use atmospheric nitrogen as a nitrogen source must rely on other organisms to fix the nitrogen into a usable form. Fixing nitrogen means converting it into ammonium ions that can be used by many types of organisms.

Which of the following is true of all biofilms?

The EPS is secreted by the bacteria.

Which of the following statements is false about the E. coli phosphotransferase system (PTS)?

The Enzyme II complex is specific to the substrates being transported, The substrate is phosphorylated during transport by PTS, making it different from the external substrate; thus, the substrate always travels down its concentration gradient, The phosphate group transferred to the sugar comes from phosphoenolpyruvate., The system has a modular design that accommodates different substrates. ------>The PTS transport requires energy in the form of ATP.<------

How does Anabaena overcome the challenge of performing both photosynthesis and nitrogen fixation?

The autotrophic cyanobacteria Anabaena can generate oxygen by photosynthesis and fix nitrogen to make ammonia. This seems like an impossibility since the nitrogenase required for nitrogen fixation is extremely sensitive to oxygen. The organism overcomes this because every tenth cell converts from a photosynthetic cell to a heterocyst, which no longer fixes carbon dioxide, but rather develops a specialized envelope that limits oxygen access, allowing nitrogen fixation.

The most widely used solidifying agent is __________, which is derived from seaweed.

agar

__________ are responsible for the carbonfixation component of the carbon cycle.

autotrophs

Growth of most microorganisms occurs by:

binary fission

All of Earth's lifeforms are based on:

carbon

Which of the following represents small molecules that fit into specific enzymes and aid in the catalytic process?

cofactors

Which term refers to the condition in which a culture covers the entire plate surface?

confluent

When the population doubles during each given unit of time, the growth is:

exponential

You have isolated a bacterium from the rumen of a cow and wish to know how it transports glucose into the cell. You perform an experiment that shows uptake of radioactively labeled glucose is equal when the organism is grown in media in the presence and absence of inhibitors of energy production. What is the mechanism of glucose transport in this cell?

facilitated diffusion

A microbial population explosion results from the sudden availability of:

food

Microorganisms constantly struggle to survive in natural habitats because of the competition for:

food

The majority of nitrogen in soil and marine environments is fixed by:

free-living bacteria

The time interval required for the formation of two cells from one is called the:

generation time

__________ are specific nutrients that are NOT required by all cells.

growth factors

The time between inoculation and the beginning of growth is usually called the:

lag time

Quorum sensing begins during which growth stage?

late log

A problem with __________ of cell number is that dead cells also scatter light.

optical density measurements

All known microorganisms have a set of genes coding for __________, whose DNA sequences are highly conserved across the phylogenetic tree.

ribosomes

When the intracellular iron concentration is low, ironscavenging molecules called __________ are produced.

siderophores

Which of the following is the best technique for counting only viable cells?

spread plate

Eukaryotic microorganisms enter the __________ phase at much lower cell numbers than bacteria simply because they are bigger than bacteria.

stationary

You are measuring growth in a bacterial culture. The number of viable cells remains constant, and when you check the medium, you find that the carbon source has been used up. What phase of growth is the culture in?

stationary phase

E. coli adjusts to the stationary phase by doing all of the following EXCEPT:

decrease its size, synthesize enzymes to handle oxygen radicals, synthesize proteins to protect DNA and proteins, increase peptidoglycan crosslinking ------->form spores<-------

Metabolism of a microbe is best examined by growing the organism in a:

defined medium

A(n) __________ cell loses membrane integrity and cannot carry out the simple transport functions needed to support life.

depolarized

During which stage of bacterial growth is the culture growing exponentially?

early log

Which form of transport occurs only in eukaryotes?

endocytosis

Some bacteria form environmentally resistant forms called:

endospores

The best method to isolate single colonies is the __________ plate, and the best method to count colonies is the __________ plate.

streak; pour

A(n) __________ is an organism that lives in a close and mutually beneficial association with a second organism.

symbiont

Which of the following proteins represents a coupled transport system where two molecules travel in the same direction?

symport

In which case would the shortest lag period most likely be observed?

transfer from complex medium to fresh complex medium

Which of the following is a micronutrient?

zinc

__________ can consume glucose and, in the absence of oxygen, can break it down into ethanol and carbon dioxide gas.

Yeast

In the laboratory, Escherichia coli can divide into two cells every:

20-30 min

A cafeteria worker who fails to wash his hands thoroughly and fails to wear gloves inoculates a quiche with four E. coli cells when he uses his finger to test whether it is done. By the time you purchase the quiche, there are 128 E. coli cells in it. How many generations did the cells go through?

5

If an organism produces seven offspring per generation, which of the following would express the rate of increase in population, where n corresponds to the number of generations?

7^n

Why does a microbe's growth rate in its natural environment vary greatly from that in the laboratory? Give at least two reasons for this.

A laboratory setting usually affords a very rich medium, and the organism is usually in pure culture and is not competing for nutrients. In the natural environment, nutrient levels are most likely less. Other organisms may be competing more effectively for the nutrients. Also, some organisms may form waste products that are toxic to other organisms.

Siderophore-iron complexes enter cells with the help of:

ABC transporters

Why does binary fission result in an exponential and not a linear growth rate?

Bacteria replicate by binary fission. In this process, one cell grows and divides, producing two daughter cells. Those two will each do the same, and so forth. That means that 1 becomes 2, 2 become 4, and 4 become 8. The relationship then becomes 2 since two daughters are formed from each cell. (A linear relationship would be 1 to 2, 2 to 3, 3 to 4, and so forth.)

Describe the differences between batch culture and growth in a chemostat. What are the advantages of a chemostat?

Batch culture represents growth in a closed system. At some point, one or more essential nutrients will be depleted, or waste products will become insurmountable, both of which, of course, would lead to cessation of growth of the organism and eventually to cell death. Chemostatic growth regulates the flow of nutrients in, and the collection of wastes out, so that growth may be maintained at the exponential stage. For industrial purposes, a chemostat is a plus when one is collecting a cellular product that is produced during exponential growth. It would be desirable to maintain the organism in conditions where it would produce the most product.

What are some specific problems that biofilms can cause in the medical field, and why are they so difficult to prevent and destroy?

Biofilms can grow in medical devices such as catheters and cause infections in patients. They cause damage to equipment such as ventilators. They can grow in lungs of cystic fibrosis patients or on medical transplants. As they grow, they form a thick polysaccharide matrix that increases antibiotic resistance within the biofilms and is difficult to remove with cleaning agents.

Compare and contrast the ABC transporters and group translocation in terms of energy requirements and concentration gradients.

Both forms of transport require energy. The ABC transporters utilize ATP, and group translocation actually begins the process with the expenditure of phosphoenolpyruvate (PEP). ABC transporters bring a solute against the concentration gradient. The same cannot be said about the phosphotransferase system (PTS) because the solute is phosphorylated during the transfer.

How do scientists know of the existence of "unculturable" organisms?

By using molecular biology tools such as PCR and gene sequencing. PCR is used to screen environmental samples for the presence of specific DNA sequences. Comparing DNA sequences of the PCR products with sequences of known organisms reveals insights into the physiology of undiscovered organisms and relationships with known organisms.

If you determined the number of cells in a sample using viable plate counts and optical density measurements, why would the results from the two methods be so different?

Cell numbers from optical density measurements will be much higher than those from viable plate counts. Viable plate counts only count cells that are able to replicate to form colonies on the plates. Some cells won't form colonies due to cell damage or inability to grow on the artificial culture media. Also, organisms that grow in chains or clusters will form a colony from several cells instead of just one. Finally, optical density measurements count both living and dead cells.

Discuss some disadvantages of viable counts of microorganisms.

Colony counting will not reflect the size or growth stage of the cells. The results might also underestimate the number of living cells because some may be damaged and unable to divide, but are still alive. Also, some organisms grow in chains and clusters. If these are not dissociated prior to plating, you will get a false low count.

Compare and contrast complex media, synthetic media, and enriched media.

Complex media contain things such as yeast extract or beef extract, making the exact composition of each chemical unknown. Their composition is thought to mimic the rich environments that some organisms may encounter in their natural environment. Synthetic media is a type of medium that is fully defined. They contain precise amounts of various salts, carbon, nitrogen, and energy sources. Some organisms need special additives to survive in these media. Enriched media contain additional components such as blood that are required for the growth of fastidious organisms.

__________ form the base of the marine food chain.

Cyanobacteria

Explain the difference between electrogenic and electroneutral coupled transport and give an example of each.

Electrogenic coupled transport results in an unequal distribution of charge across the cell membrane. A good example is the lactose symporter, which brings the neutral lactose molecule in along with a proton. Electroneutral coupled transport results in no net charge. An example of this is the sodium ion/proton antiporter.

Which of the following genera does NOT undergo differentiation?

Escherichia

What type of medium and conditions would you need to have in order to select for photoautotrophs?

Phototrophs can generate energy from absorption of light and autotrophs can use CO2 as their sole carbon source, so the medium would not need to contain an energy source or an organic carbon source. The lack of these substances would inhibit the growth of other types of organisms, resulting in a selection for photoautotrophs. The sample would need to be incubated near a light source.

__________ are freeliving organisms that grow and multiply on their own.

Planktonic cells

__________ intercalates between DNA bases, causing dead cells to stain red under a fluorescence scope.

Propidium iodide

Mannitol salt agar (MSA) contains 7.5% NaCl, the carbohydrate mannitol, and the pH indicator phenol red. Some organisms can ferment mannitol, producing acids as a by product. Is this medium likely to be selective and/or differential? Explain.

Since MSA has such a high percentage of salt, it is selective for organisms that are salttolerant and inhibits organisms that can't tolerate it. MSA is also differential for mannitol fermentation. Some organisms ferment mannitol to produce acids, which causes pH to drop. The pH indicator will then turn a different color to indicate that the mannitol has been fermented. Organisms that can't ferment mannitol will not cause the medium to change color.

How do some cyanobacteria fix nitrogen while growing aerobically?

They use special cells called heterocysts that protect the enzyme.

When using the LIVE/DEAD staining procedure, how can you distinguish live versus dead cells, and why do they appear in different colors?

Two fluorescent dyes are used, propidium iodide (PI) and Syto9. Live cells will appear green, and dead cells will appear yellow to red depending on the ratio of the two dyes. The Syto9 labels all cells with green fluorescence, those with intact membranes and those with damaged membranes. The propidium iodide intercalates the DNA bases but can't penetrate the energized membranes of living cells, so only the dead cells will take up this dye. In addition, PI has higher binding affinity to DNA, which can outcompete Syto 9 for bindings to DNA. Hence, Syto9 is excluded from dead/damaged cells.

Define the terms "viable" and "viable but nonculturable." Why are so many environmental organisms believed to be viable but nonculturable?

Viable means that it is possible to grow the organism in a laboratory setting. Viable but nonculturable means that the cells appear to metabolize, but we cannot get them to replicate. It is possible that we just have not figured out how to culture them yet.

What causes an organism to go through the process of sporulation? How can endospores cause problems in the food industry?

When nutrients are not as readily available, the starvation response of some organisms results in the formation of a dormant endospore. If foods are not properly sterilized, endospores could survive in the food, then germinate and cause food spoilage or foodborne illness.

By themselves, heterotrophs would deplete the world of __________ sources and starve to death.

organic carbon

During biofilm formation, as more and more cells bind to the surface, they begin sending signals to each other in a process called:

quorum sensing