L5-Growth-Quiz2

Define binary fission

A form of asexual reproduction in prokaryotes (and select single-celled eukaryotes) where a parent cell replicates its genetic material and divides into two equal, genetically identical daughter cells.

Define Budding

An asexual reproductive process where a new organism develops as an outgrowth or protrusion ("bud") from the parent cell, eventually detaching as an asymmetrical daughter cell.

Define minimal medium

a defined medium that has only specific chemical compounds (such as ammonium sulfate for a nitrogen source) required for growth. Example: M9 minimal medium

Define rich/complex medium

has an abundance of nutrients (amino acids, peptides, vitamins) from ingredients such as yeast extract or tryptone; the precise chemical composition is unknown. Examples: TSB, LB

Define Turbidity

The cloudiness of a liquid culture caused by suspended microbial cells, commonly measured using a spectrophotometer (optical density = OD [units]) to estimate biomass density.

Define lag phase

The initial adaptation period following inoculation where cell division has not yet begun; cells actively synthesize enzymes, metabolic machinery, and structural components suited to the new medium. (length of lag depends on age of culture and types of media)

Define log (exponential) phase

The period of rapid growth during which cells divide by binary fission at a constant, maximal rate, doubling the population at fixed time intervals. (during one “generation time” or “doubling time”)

Define Stationary Phase

The plateau phase where the rate of cell division equals the rate of cell death, resulting in a stable population size due to nutrient depletion and toxic metabolic byproduct accumulation.

Define Endospore

A tough, non-reproductive, dormant structure formed inside certain Gram-positive bacteria (e.g., Bacillus and Clostridium species) in response to harsh conditions, granting extreme resistance to heat, radiation, and chemical disinfectants.

Define Quorum Sensing

A density-dependent chemical communication system wherein bacteria release and detect signaling molecules (autoinducers) to coordinate population-wide behaviors like biofilm formation, virulence factor production, or bioluminescence.

Define Biofilm

A surface-attached community of microorganisms enclosed within a self-produced matrix of extracellular polymeric substances (EPS), providing enhanced resistance to antibiotics and immune defenses.

Define Thermophile

An organism that grows best at high temperatures. (50-70 C)

Define Mesophile

An organism that grows best at moderate temperatures. (37 C)

Define Psychrophile

An organism that grows best at cold temperatures. (5 C)

Define Barophile

An organism that grows best under high pressure (faster growth at pressure > 1 atm - some bacteria grow at the bottom of the ocean, at extremely high pressure)

Define Acidophile

An organism that grows best at low pH. {at pH 0.1 - 5.4 (e.g. Lactobacillus acidophilus)]

Define Alkaliphile

An organism that grows best at high pH. {at pH 7.0 - 11.5 (e.g. Vibrio cholera, Alcaligenes faecalis)}

Why are most bacteria on earth non-culturable?

Most bacteria called “non-culturable” are more accurately “not yet cultured”: they may grow in nature, but they do not grow under the laboratory conditions we have tried. A standard plate may lack a nutrient or signal from neighboring microbes, have the wrong oxygen level, temperature, pH, or pressure, or favor fast growers that crowd out slow ones. Some cells may also be dormant when sampled

How can non-culturable bacteria be studied?

16S rRNA gene sequencing identifies bacteria present in an environmental sample.

Metagenomics sequences DNA from the whole community to investigate what genes the bacteria carry. Single-cell sequencing can examine one uncultured cell at a time. Genes suggest possible abilities; they do not, by themselves, prove what a cell is doing. Nature Biotechnology

FISH microscopy uses fluorescent probes to locate and count particular bacteria in a sample. PMC

Fluorescent antibody probes - like FISH, but uses antibodies to recognize proteins that are specific to a group of bacteria

Describe the growth curves of a culture growing at its optimum growth temperature vs. a culture growing at a suboptimal temperature, explain why and how the 2 growth curves differ from each other. Assume all other conditions are the same

The suboptimal culture exhibits a longer lag phase, a shallower log phase slope (slower growth rate), and takes significantly longer to reach stationary phase. 

The optimal culture exhibits a shorter lag phase, a steeper log phase slope (faster growth rate), and takes significantly less time to reach stationary phase.
Reason: The difference occurs because temperature affects Enzyme Kinetics and Thermal Energy, Translation Kinetics and Ribosomal Function.

Describe the growth curves of a culture of E. coli (gram-negative, facultative anaerobic bacterium) vs. a culture of M. tuberculosis (Mycobacterium/waxy layer mycolic acids, obligate aerobic), explain why and how the 2 growth curves differ from each other. Assume all other conditions are the same

Lag Phase:
E.coli has a brief lag phase (under 2 hours). E. coli rapidly senses new nutrients, alters transcription factors, and mobilizes metabolic pathways to prepare for division.
M. Tuberculosis has an extended lag phase lasting several days. The bacterium must re-establish its complex lipid synthesis machinery, and slowly adapt to medium changes.
Log (Exponential) Phase

E. coli is characterized by a steep logarithmic slope. Cells double every 20 minutes, exponentially increasing biomass and rapidly consuming dissolved oxygen and carbon sources.

M. tuberculosis is characterized by a shallow logarithmic slope. Biomass accumulates slowly due to a doubling time of nearly a full day.

Stationary Phase

E. coli enters stationary phase within 12–24 hours as carbon/nitrogen sources deplete and toxic acidic byproducts accumulate.

M. tuberculosis enters stationary phase after 3–5 weeks. Rather than undergoing rapid lysis, it transitions into a physiologically dormant state known as Non-Replicating Persistence (NRP), shutting down active division while maintaining membrane potential and basal metabolic integrity.

Describe the growth curves of a culture in medium with 1x of a limiting nutrient vs. a culture with 2x (twice the amount) of a limiting nutrient, explain why and how the 2 growth curves differ from each other. Assume all other conditions are the same 

The nutrient limits how many cells the culture can ultimately make, but does not limit its growth rate while it is available, the two curves start together and rise at about the same rate. Their lag phases will be the same. However, the culture with 2x (twice the amount) of a limiting nutrient will have a longer log phase than the culture in medium with 1x of a limiting nutrient, but the same steepness. The culture in medium with 1x of a limiting nutrient will start stationary phases sooner than a culture in medium with 1x of a limiting nutrient vs. a culture with 2x (twice the amount) of a limiting nutrient, because they will run out of the limiting nutrient sooner. The culture with 2x (twice the amount) of a limiting nutrient will have twice the amount of ending total CFUs at the stationary phase.

Describe the growth curves of a culture inoculated with cells from a weeks-old, stationary-phase culture vs. a culture inoculated with cells from a fresh, log-phase culture, explain why and how the 2 growth curves differ from each other. Assume all other conditions are the same

When inoculating fresh medium under identical conditions, the primary difference between a culture started from a fresh, log-phase inoculum versus a weeks-old, stationary-phase inoculum is the duration of the lag phase.The culture inoculated with log-phase cells will enter exponential growth almost immediately, whereas the culture inoculated with weeks-old stationary-phase cells will undergo an extended lag phase before commencing division. The weeks-old cells have spent longer with depleted nutrients and accumulated waste. Some may be dormant or damaged, so the culture takes longer to begin dividing. Once both cultures enter the log phase, their exponential growth rates and final stationary cell yields will be identical.

Describe the growth curves of a culture inoculated with 1000 E. coli cells vs. a culture inoculated with 2000 E. coli cells, explain why and how the 2 growth curves differ from each other. Assume all other conditions are the same

Their lag phases will be identical, since both populations require the same adaptation time to synthesize division machinery. Their y-intercepts will be different, the culture inoculated with 2000 E. coli cell will have a higher y-intercept. Their log phases will be the same, because their metabolic rate is not changed by anything. The culture inoculated with 2000 E. coli cells, will reach stationary phases sooner, because there are more cells but the amount of limiting nutrients are the same.

Describe the growth curves of minimal medium inoculated with cells from a minimal medium culture vs. a minimal medium inoculated with cells from a TSB medium culture, explain why and how the 2 growth curves differ from each other. Assume all other conditions are the same

The culture originating from the TSB medium will undergo an extended lag phase, whereas the culture originating from the minimal medium will enter exponential growth almost immediately (with a minimal to brief lag phase). Once adapted, both cultures will grow at the exact same exponential rate during log phase and reach the same final cell yield at stationary phase. The marked difference in lag phase duration is driven by a phenomenon known as nutritional shift-down, where before the cells can divide, they must undergo extensive transcriptional and translational retooling.

Suppose that E. coli has the same growth rate in two different types of media. Would you expect the E. coli cells in both cultures to have the same size and macromolecule composition? Explain why or why not.

Yes, you would expect the E. coli cells in both cultures to have the same average size and macromolecule composition because both properties are fundamentally determined by the growth rate, regardless of the specific chemical composition of the media used to achieve that rate.
Cell size coordination: Classic bacterial physiology laws (such as Schaechter's master studies) demonstrate that cell mass, length, width, and volume scale directly with the growth rate.
Equal rates yield equal sizes: If two different media types yield the exact same mass doubling time (growth rate) for E. coli, the physiological coordination mechanisms will produce cells of equivalent average size and macromolecular density.
RNA and protein levels: The abundance of cellular components like RNA, ribosomes, and total protein content is a direct function of how fast the cell is dividing rather than the external nutrient formulation

What are endospores and why do endospores form? Can all bacteria form endospores?

An endospore is a tough, dormant, and non-reproductive structure built by certain bacteria to survive harsh conditions

Why Do Endospores Form?
Starvation: Bacteria form endospores when key nutrients like carbon or nitrogen run out.
Environmental Stress: Extreme heat, dryness, radiation, and toxic chemicals trigger the process (called sporulation).
Survival: The spore protects the cell’s DNA and core components until the environment becomes safe again

Can all bacteria form endospores?

No, the vast majority of bacteria cannot form endospores. This trait belongs almost exclusively to certain Gram-positive bacteria within the phylum Firmicutes. 

Common examples of spore-forming bacteria include:

Bacillus (B. anthracis, B. cereus, B. subtilis)

Clostridium (C. botulinum, C. tetani, C. perfringens)

How do biofilms form? Why are biofilms important? Where can biofilms be found?

Biofilm – a community of bacterial cells attached to a surface by means of exopolymeric substances.

Biofilm formation is a multi-step process:
Attachment: Free-swimming microbes land on a wet or damp surface and anchor themselves.
Production: The attached cells start making a sticky sugary and protein-rich layer called extracellular polymeric substance (EPS).
Maturation: The community grows thicker, forming a 3D structure with internal channels that circulate nutrients and let cells share genes. (-polymers that form the 3-D extracellular matrix are exopolysaccharides, proteins, and DNA)
Dispersal: Mature parts of the biofilm break off or detach to travel downstream and start new colonies elsewhere

Why are biofilms important?
The matrix helps cells stay attached and can make them harder to remove or kill. Biofilms can contribute to persistent infections and contamination of equipment, but they also have useful roles in ecosystems, such as breaking down waste. 

Where Biofilms Can Be Found
Biofilms form almost anywhere there is a combination of a surface, moisture, and basic nutrients:
In Nature: Slippery coatings on rocks in streams and rivers, hot springs, soil, and deep-sea vents.
At Home: Kitchen sink slime, shower tiles, toilet bowls, and inside air conditioning units or plumbing pipes.
In the Human Body: Dental plaque on teeth, the lining of the gut, or mucosal surfaces in the respiratory tract.
On Man-Made Objects: Medical devices like pacemakers and catheters, contact lenses, industrial pipelines, and ship hulls.

Describe the hypothesis connecting bacterial biofilms with increased risk of heart attacks under stressful conditions.

Stress → Norepinephrine (flight-or-fight response) → Increase in free [Iron] in blood → Dispersal of biofilm in plaque → Rupture of plaque from artery wall → Blood clots (embolism) from to heal rupture → Heart attack or stroke

In Lee et al., 2010, what was the authors’ initial observation about antibiotic resistance of an E. coli population vs. of individual cells?

They initially observed (Figure 1a) that the vast majority of individual E.coli were actually less resistant isolates (LRIs), that is, they are less resistant to the quinolone antibiotic, norfloxacin. Though there are only a few E.coli individuals that were Highly Resistant isolates (HRIs), that is, they are highly resistant to the quinolone antibiotic, norfloxacin. Though the entire population of E.coli (combining LRIs and HRIs), has a high resistance to antibiotics. In summary, individual cells tend to have a lower minimum inhibitory concentration (MIC) than the entire population’s MIC.

In Lee et al., 2010, What is the act of “charity” and who performs it?

C10,12 the Highly Resistant isolates (HRIs) of E.coli carries the act of “charity”, by enduring a fitness cost to produce indole, which protects the more vulnerable cells by inducing various antibiotic-tolerance mechanisms, such as drug efflux pumps (which pump out the antibiotic). The fitness cost for the HRIs is that producing indole is highly  energy-consuming and slows down the growth of the mutant bacteria.  

In Lee et al., 2010, what is the role of indole, and how is indole produced in an E. coli culture that contains norfloxacin?

Indole acts as an intercellular signaling molecule and a stress-response regulator that helps E. coli manage stress and antibiotic tolerance, through upregulating multi-drug efflux pumps. E. coli produces indole when the enzyme tryptophanase (encoded by the tnaA gene) degrades the amino acid tryptophan into indole, pyruvate, and ammonia. Though it is the HRI E.coli that is responsible for producing high concentrations of Indole.

What are two ways in which E. coli can become resistant to antibiotics in this paper (Lee et al., 2010)?

1.)HRI E.coli can become resistant to the antibiotic norfloxacin through mutations. Each resistant isolate carried a mutation in a subunit of a known norfloxacin target, the DNA gyrase encoded by gyrB 22. These mutants also carried a SNP in yciW, which is a widely conserved putative oxidoreductas.

2.) LRI E.coli can become resistant to the antibiotic norfloxacin from receiving indole produced by HRI E.coli during their act of “charity”.

In which growth phase would you expect penicillin to be most effective against bacteria? Why?

Penicillin is most effective against bacteria during the log phase (exponential growth phase) 

Active Division: Bacteria divide quickly and grow at their highest rate during this phase.
Cell Wall Building: Rapid division requires the constant creation of new cell walls.
Targeting Peptidoglycan: Penicillin stops enzymes from cross-linking peptidoglycan, a key part of the cell wall.
Cell Lysis: A weak cell wall cannot handle internal pressure, causing the bacteria to break open and die

In which growth phase would you expect chloramphenicol to be most effective against bacteria? Why?

Chloramphenicol is most effective against bacteria during the Log (Exponential) Phase and the Lag Phase.

Chloramphenicol is a bacteriostatic antibiotic that targets protein synthesis by binding reversibly to the 50S ribosomal subunit and inhibiting peptidyl transferase activity, preventing peptide bond formation during translation elongation.

Log Phase: Halting Rapid Division 

Lag Phase: Preventing Metabolic Adaptation